Repository: chaoyi-wu/RadFM Branch: main Commit: 8d798c554ca0 Files: 60 Total size: 1.4 MB Directory structure: gitextract_uqthi9mp/ ├── LICENSE ├── Quick_demo/ │ ├── Language_files/ │ │ ├── config.json │ │ ├── special_tokens_map.json │ │ ├── tokenizer.model │ │ └── tokenizer_config.json │ ├── MedKEBERT/ │ │ ├── config.json │ │ ├── special_tokens_map.json │ │ ├── tokenizer.json │ │ ├── tokenizer_config.json │ │ └── vocab.txt │ ├── Model/ │ │ └── RadFM/ │ │ ├── __init__.py │ │ ├── blocks.py │ │ ├── helpers.py │ │ ├── multimodality_model.py │ │ ├── my_embedding_layer.py │ │ ├── position_encoding.py │ │ ├── transformer_decoder.py │ │ ├── utils.py │ │ └── vit_3d.py │ └── test.py ├── README.md ├── requirements.txt └── src/ ├── Dataset/ │ ├── dataset/ │ │ ├── MedPix_dataset.py │ │ ├── __init__.py │ │ ├── binary.py │ │ ├── caption_prompt.json │ │ ├── case_report.py │ │ ├── chestxray.py │ │ ├── cls_prompt.json │ │ ├── data_csv/ │ │ │ └── README.md │ │ ├── dicom_to_png_for_VinDR_sampled_using_mammo.py │ │ ├── jpg2nii_data_convert.py │ │ ├── mammo_prompt.json │ │ ├── modality_prompt.json │ │ ├── nii2npy_for_radiopaedio.py │ │ ├── paper_inline.py │ │ ├── pmcoa.py │ │ ├── radiology_feature_prompt.json │ │ ├── radiopaedia.py │ │ ├── report_prompt.json │ │ ├── spinexr_prompt.json │ │ ├── vqa.py │ │ └── yes_no_prompt.json │ ├── multi_dataset.py │ ├── multi_dataset_test.py │ └── multi_dataset_test_for_close.py ├── Model/ │ └── RadFM/ │ ├── __init__.py │ ├── blocks.py │ ├── helpers.py │ ├── multimodality_model.py │ ├── my_embedding_layer.py │ ├── position_encoding.py │ ├── transformer_decoder.py │ ├── utils.py │ └── vit_3d.py ├── My_Trainer/ │ └── trainer.py ├── datasampler.py ├── output_csv_example/ │ └── caption_example.csv ├── test.py └── train.py ================================================ FILE CONTENTS ================================================ ================================================ FILE: LICENSE ================================================ MIT License Copyright (c) 2025 chaoyi-wu Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. ================================================ FILE: Quick_demo/Language_files/config.json ================================================ { "_name_or_path": "/home/cs/leijiayu/wuchaoyi/Finetune_LLAMA/LLAMA_Model/llama-13b-hf", "architectures": [ "LlamaForCausalLM" ], "bos_token_id": 0, "eos_token_id": 1, "hidden_act": "silu", "hidden_size": 5120, "initializer_range": 0.02, "intermediate_size": 13824, "max_sequence_length": 2048, "model_type": "llama", "num_attention_heads": 40, "num_hidden_layers": 40, "pad_token_id": -1, "rms_norm_eps": 1e-06, "tie_word_embeddings": false, "torch_dtype": "float32", "transformers_version": "4.28.0.dev0", "use_cache": true, "vocab_size": 32000 } ================================================ FILE: Quick_demo/Language_files/special_tokens_map.json ================================================ {} ================================================ FILE: Quick_demo/Language_files/tokenizer_config.json ================================================ {"bos_token": "", "eos_token": "", "model_max_length": 1000000000000000019884624838656, "tokenizer_class": "LlamaTokenizer", "unk_token": ""} ================================================ FILE: Quick_demo/MedKEBERT/config.json ================================================ { "_name_or_path": "xmcmic/Med-KEBERT", "architectures": [ "BertModel" ], "attention_probs_dropout_prob": 0.1, "classifier_dropout": null, "gradient_checkpointing": false, "hidden_act": "gelu", "hidden_dropout_prob": 0.1, "hidden_size": 768, "initializer_range": 0.02, "intermediate_size": 3072, "layer_norm_eps": 1e-12, "max_position_embeddings": 512, "model_type": "bert", "num_attention_heads": 12, "num_hidden_layers": 12, "output_hidden_states": true, "pad_token_id": 0, "position_embedding_type": "absolute", "torch_dtype": "float32", "transformers_version": "4.24.0", "type_vocab_size": 2, "use_cache": true, "vocab_size": 30522 } ================================================ FILE: Quick_demo/MedKEBERT/special_tokens_map.json ================================================ { "cls_token": "[CLS]", "mask_token": "[MASK]", "pad_token": "[PAD]", "sep_token": "[SEP]", "unk_token": "[UNK]" } ================================================ FILE: Quick_demo/MedKEBERT/tokenizer.json ================================================ { "version": "1.0", "truncation": null, "padding": null, "added_tokens": [ { "id": 0, "content": "[PAD]", "single_word": false, "lstrip": false, "rstrip": false, "normalized": false, "special": true }, { "id": 1, "content": "[UNK]", "single_word": false, "lstrip": false, "rstrip": false, "normalized": false, "special": true }, { "id": 2, "content": "[CLS]", "single_word": false, "lstrip": false, "rstrip": false, 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28878, "mnc": 28879, "extramedullary": 28880, "rhu": 28881, "tropism": 28882, "hypophosph": 28883, "clarifying": 28884, "judgement": 28885, "jord": 28886, "puzz": 28887, "diplopia": 28888, "deoxynucleotidyl": 28889, "lympho": 28890, "##alogy": 28891, "##6c": 28892, "clothing": 28893, "tph": 28894 } } } ================================================ FILE: Quick_demo/MedKEBERT/tokenizer_config.json ================================================ { "cls_token": "[CLS]", "do_basic_tokenize": true, "do_lower_case": true, "mask_token": "[MASK]", "name_or_path": "xmcmic/Med-KEBERT", "never_split": null, "pad_token": "[PAD]", "sep_token": "[SEP]", "special_tokens_map_file": null, "strip_accents": null, "tokenize_chinese_chars": true, "tokenizer_class": "BertTokenizer", "unk_token": "[UNK]" } ================================================ FILE: Quick_demo/MedKEBERT/vocab.txt ================================================ [PAD] [UNK] [CLS] [SEP] [MASK] ! # $ % & ' ( ) * + , - . / 0 1 2 3 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however tum sm path ma report min sel ##mon ##ery ##ities most ##ences ##adi specific 12 infl ##ectively diagn ##onstr ##ma assess ##ple contr rem ##esis ##ency ep when ##ination our years ##av subs ##idence ##etr ##tern def op mul supp ##ormal acid age ##ren into decre ##ability only ##ange well higher intr ##ograph ##tical ##oph three 19 ##erg ##ork cancer ##iqu ##ently test ##ions ##ited peri ##ology ##ber ##inal pred gener mal human ##echan ##ept induced ##ature ##arg ##ement such ##af mol new ##ible impro observed character import num sec struct mechan ##til ##ord groups ##ix ##ik patient ##ov ##ugh ##rel fir sens demonstr child ##rop occ col ##res ox chang loc ##tid ##ron ##gh rate ##aining blood kn ##lex cases ##ute post related ##use surg process ##cop ##ark tiss micro ##ok ##ured term rat who ##tit fe first ##view ##oma fur suggest valu aff ##uction gene response mem disc addition ##amm ##echn ##ural cal po ##rough neu ##ough ##dro type ##ten ##osph inj those grow ##och development ##osed ##own techn ##round ##ior among sol ##ful respectively ##its ##ulated condition conf ##ines mean care cd ##vention ##ental molec recept ##ucle 15 ##ital ##les month drug factors del through mg ##ains ##arly pop total hyp ps ol ##omen changes il ##fore increase prim cyt bas ##ize correl role invol 00 potential ##di ##ivid obj ##endent prop long prob experim ##ould phys ##ational ##asc ##tained plas subj ##xim fre normal gre ##crib ##urs finding my ##earch medi mus important ##ived stim back adm ##eng lower main ##vers predic ##roph ##omy could simil ##led mechanism 11 ##over ##istic ##ha ii ##ex ##ek within sym hist ##ds ##cin performed ##gan infection so ##air where ##eter ##ody sequ number ##ene comb frequ ##osp lik extr sever hyper therapy 95 review ##ms conclusions prog ##ption ##ps outc less coll ##ider while multi ##ade flu ##cle mm cap each ##ether children requ antib hydro bec 14 treated reported ##iver lim including ##val similar ##ages period poss vir growth tumor do fib some complex aim ##orph ext ##ores ##ock women ##vious ##omes positive ##arge radi pur describ pat reve ##ne 200 13 dna findings ##ric ##otic cy chem factor ##ptom prom did without ##ival ret 30 inhibit ##pha week mo cardi ##ividual mut work ##ples prot ##ground tem er case ##zym four ##iel abs ##tivity mice they ##ily individual ##ues consider dir background 25 ##istr ##abol tissue calc 18 days approach pe av ##ascular ##ativ surf ##ness months previous vit ##ise need curr ##ale ##otyp isol ##oper phosph identified common sing measure ##ically reveal ##ty hem maj ##ake ##iter sev major vis ##oh ##ross beha synth techniqu ##equ organ nucle design caus ##fl ##are presence research ##plet behavi analy second provid mark ##ality differences ##ocyt ##med ##ified further ##uss surv mater vol symptom reduced ##atal small 16 metabol 24 obtained ##ced binding hosp class serum dose ##ning influ ##plications rats ##atis ##crip cult mat ##par initi evidence ##ymph due single early ##ography ##ice und sk day lip expl inform admin ##acy about species ##ety ##lish ##ung ##ties enzym ##ft decreased sl ##ately conditions 05 receptor ##itis bre primary alth ##ension lymph 50 although os subjects ##hip ##esting ##ogn qual diagnosis enh lab ele measured ##ites concentration ##old ##ink ml rati particip ##trib ##int arter ##ins ci ##ressed proteins studied neg ##roscop concentrations fem population ##ectr ##oles ##las pers ##ither ##ests resist improve 100 alpha mr lif rece hep should beta ##ication range ##ateg brain pattern genes developed investigated ##ials ##ych objective samples ##ength ##gf plasma line press lead set phen membr if ec following ##erv interaction revealed ##vir ##emia ##erc ##amic aut ##aging reaction demonstrated ##arget 17 der discuss analyz coun dependent target ##plant anim surgery ang prol ##ening ##onal vs several chron surface ##eptid ##ulin est fam relations ##hy inflamm ##tan ##por ##osure oper ##ind gluc ##ield ##aneous large proper molecular hospital stand ##roduc elect kg adv ##ick les here examined ##asing complet ##cent ##oss survival appear weight prof functional chrom ul effective hear ##ensity evaluated requir information liver unders proced values quan deg again ##tered ##az prac local 201 phase estim polym stress ##cs electr ##tis ##ax determined region ##tions val standard diff ir neur ##ire bone param relationship nec whether rates 01 determine acute ##ause chronic mass body free cle ##arm pain sch sus diab enhanc water occurr either equ before pul life ##ving intervention bacter will 001 characteristic pressure conduc ##onic gu ##omic included greater ur quality ##ian same various ##yr ##ivers ##icient reduction pathw activation structure ##uth provide injur dim ##sp thus ##viron support against many ##plication ##ator ##ulations manag hel ro ratio ##ocytes ##orb contrib ren shown ##lement cir multiple vitro nov ##ification ##iven signal ##tain exposure ##amin symptoms known gly current ##atively direct ##operative sep medical dom ##ules purp psych prec exc nan whereas vi negative genetic production because distrib carb ##andom ##eters ##ission ach fail flow formation 21 fac ##eu sal environ ##rome detected ##amine adj random compound ##ostic ##ellular rele 40 strong ##gram ##ensive ##tric ##ateral ##uted recom ##ists ##ometr possible pub transcrip mort ##itivity ##ude association loss part nm ##up ##emic pap any ##cept reduc compon ##ae ##ct ms ##icity change repres ##ocy ##ynamic ##nal controls membrane success order ##eration confir sex involved muc weeks cent ##otherap six performance muscle responses avail general size ##atus mechanisms ##tif difference oxid ##gn commun mortality particular lo virus ##ablish temper ##ient properties tox hypoth indep five establish strateg assessed cycl models experi lung statis consist ##ann resid ##uk synd differenti ##elial ##istration state increasing overall ##atures behavior ##ision carcin purpose identify men 000 ##ochem 22 sin old 60 ##ward novel management ##olution contin cm regul ##aw heart ##aps ##ised super diet poly presented being analyzed proble amin ##inant scre rap mac ##ologic ##eral neuro magn ct surgical link ##estion contrast ##eutic ##app area like self imaging ##opath death phot foc ##ording intra frequency viv environment ov ##acc eth ##iciency ##iving evaluate volum allow ##reg ##itor active dys outcomes ##ie circ preval ##dr ##active result recent therefore ##otherapy parameters severe outcome ##eric centr peptid stage value vivo very isolated ##elet add ##ographic tra distribution ##ergy short indicate technique decrease ##ust mit enzyme ##oses resistance ##odies ##etes enc ##verage ##lor detection participants morph nit index sw injury experimental renal optim ##tinal ##orts systems male hom induc 23 administration block site cross previously ##ides inhibition stimul accur sensitivity vers diseases ##icular ve ##ogenesis dev characteristics ##ended healthy ##osition ##ably left tested syndrome ##tex ##amp described prepar exhib gas assay therapeutic pregn rapid ##ocial bene ##ule att highly ##asis considered animals ##rh ##tegr glucose ##ancy ##iat ##ull ##oplas artic fat mediated investigate maxim rh benef fil correlation incidence ##inc followed atten available containing 199 ##ours ##eding family ##iological ##ns lesions cere sequence then ##tically ##de status ##ode saf ##ylation tub ##ances better ##ices ##ogenic types kin sample da ##ids ##ouse ##ters improved ##ially ##of prolif ##red hiv relative ##roscopy ##inary caused ##olic ##opt impact 28 ##ops ##ount derived ##ner individuals ##ocard energy breast ##ulf ##ually ##ands surve nor required ##itation her effic ##ces via inflammatory ##otype ##verse insulin cause pharm te release solution ##els integr temperature ##iev cardiac field ##plied hypert ##ygen pc ##ey ##acellular adh secre percent net amino record ##terior bel ultr 35 sites ability dist poor spect mrna ##omp expressed influence approxim combination assessment produced analyses conducted physical prevalence light ##arc ##eline program ##therm ##ves received comparis indicated practi ##itu useful length liter know focus volume ##roc ##line ##oy complications ##ectomy them given elev content refer ##tial skin diabetes ##pr tak ##tine ##monary ##ressive ##ling ##pec monitor abn evaluation sour metast visual ##ortion ##romb ##ibility drugs 26 ver density larg features ##cence adult recover average independent ##ols likely even correlated heter efficacy scale ill valid according hc immune ##ysis synthesis tumors cat continu quantit lig dam impair mar separ compounds diagnostic acet hr ##abil ##enz injection abnormal applied ##ones play question characterized coh often apopt orig ##uble recogn ##izing thir ventr good demonstrate initial cop off ##vent oral ##resp ##order ##go ic cre introduc chall vascular ##cep ##mit social recurr activities medic oste central transcription angi transfer fraction ##orders ##ators ##tanding ##oung might young ##vement spectr 27 ##medi least paper mix 45 made ##mic ##orption failure tissues glyc pa ##otox predict pd util ##ored measures ##tle cellular ##ising carr ##ecting underw enhanced represent cs ##enced 32 measurements receptors ##rees disorders score transplant biological nat female aden areas ##thermore furthermore experiments cri procedure ##ledge ##yro food ##ask ##ta stimulation asp understanding cur epid techniques subsequ literature times regulation successful knowledge ##ales ##art 90 discussed emerg moder strains rna diss adul 80 minim regression 31 observ ##ables ##work combined regions degrees 36 processes ##rob position repe dynamic ##tib ##omal approximately ##lic tests since fin ed oxygen few underwent baseline arr patterns 29 pathway ##ocyte median would culture ##uture ##bers ##igr events ##rogen step affected ##ustr bm proposed ##olar 48 artery air prior thromb nurs progn smok occurred pulmonary resulted ey right collected confirmed limited antibodies fluores ##ont biom coron ess ##iotic suggested ##rosp educ ##opro antibody interactions pcr ##omas ##eness ##erve antigen neurons cogn ##da ##ier ##ochemical achiev epith ##ytic section ax ##ower sensitive methyl electro mid key 33 criter constr ##lying hydrox agg ##iatric ##otor horm ##till suggests ##ru complete pharmac labor network comparison practice versus ##ler lack auth gam refl materials serv inhibited carcinoma ##utr suggesting increases alter recomm structures endoth application established setting trials 70 seen guid additional exerc chemical ##ke place hal vacc history down invas isch catal altern periph cer ##ovascular controlled ##urn 37 malign screening coronary relev across alc iii provides chain lay accum ##10 examination strain corr transp ##ave mir duration adults scores displ electron ##ious disorder bir action prost promo ##ploy depend mouse espec plat iv substr especially hand secondary ##onding future ##ining ##istered ##inetic mel training capac ##ogene seg 75 ##acts corresp selected eight proliferation consum ##rosis ##terol sil defined ##nf rad ##oscop ##oxid ##ethyl ##fusion ##emb ##last agents sum ##bral sle ##ii alcoh ##iratory ##pa inhibitor lat colon peak ##grad detect polymer plac 34 ##utes bar ##ondr et 02 kid recently help toward article still ##set ultras ##aff ##ture desp ##me basis kidne side ##ld ref go ant despite ##orbid cours components ##ying damage glut lit head ##estinal lipid leuk molecules chlor describe structural ##agon suff postoperative clear bil phosphor critical improvement apoptosis ##bry prosp mes fold hip peripheral diffic ##eph cost ##ibr graf ##tre adap criteria distin ##ets metabolic ##agen fer dop kinase ion necess chann ##ancre real ##isting ##yroid signaling exercise ##ochondr chromos populations calcium don peptide bio infected provided daily ##iting depression doc alone nerve differentiation ##ectives aged task strategies ##odes load prevent trial sem ##occ great affect ra series functions ##ergic does therm rang na od ##esth interval ampl fet activated consistent facil point situ ##entially embry concer sn ##anol essential perce ##pre testing 42 eng ##iversity retrosp cou frag sod ##enting elevated moreover ##ints ##50 acids 38 employ resulting cognitive importance reduce plant community hours ##ems top pancre prote absence onset mitochondr cryst glob marked pregnancy simple ##ove myocard medium rare ##ather products linear implant convention degree ##otid ##umin survey ##ptake questionna remains achieved log ##omer transport las lines access reli sci particularly migr seven infections ##bo material ##oint microm natural ##ulate capacity transform sulf ##oids toler lear ##function metabolism ##ca pig cytok ##trans ##arding ##ument diagnosed ##ophil ##ople ##olesterol fract power ##ef ##uter extract procedures older problems ##etry ##ayed ##pri states open markers ##ivery transl transm require ##ogl fluid dig doses appropri ##dom quantitative ##arb delivery ear bacterial ##oster ##12 exposed examine label underst nutr upon ##arr recovery wor ##ics conventional highest magnetic uptake carbon tog stable progression ##utaneous biops undergo variables reproduc together clus pathways ##put ##ortic experience proportion induction ##ched cardiovascular course calculated stro rest ##thr ##imens experiment stem statistically sequences administered ##icians strength gamma maximum cycle ##nas irr ##ogenous origin ##atitis consequ pair ##uff ##se act ##isms component kidney ##itional adverse estimated iss ##encing respond whole host nuclear regarding summ people alcohol ge ##brid cohort polymorph ##icial ##eti respiratory resistant internal bro ##oz antagon pp 65 wall linked ##ession carried tempor public ##gl much 198 prefer lact objectives ventricular include safety inflammation ##inity 43 little needed 03 ##idine 39 mutations domain ##anced wid inhibitors variation ##titution mak ##osa ##istry mamm sleep ##rolog environmental ##ank hypertension special severity best modified ##other fas terms birth ##anning dimension systemic laboratory ##rix distinct specificity protoc ##hydro exhibited ##pling hb animal ped ##acr along motor subsequent ##activity bp taken ##ered var ster relatively endothelial stroke ##roscopic ng identification pt authors const recorded problem fix home pm cholesterol alg ##ceptib monitoring 44 countr evolution ##esized chemotherapy ##encies appar selective conn radiation microb indicating ##ense cys mt ##cler having 55 ##oding ##bp atp susceptib bal randomized ##ulating ##uring spati his dysfunction star ##ea ##ococc ##sh acqu late yield amount macroph degrad reson spe wide incor appropriate hypothesis ##inated limit ##atives traum restric mc ##eff relevant confidence liqu ##io able moderate ##que thick source physiological measurement chromat bacteria bound remov recomb ##onomic platelet ##dl excl ##otypes interventions ##utive causes microscopy treatments ##mediate designed tom composition underlying ##ame ht hs sd ##oral arterial double corresponding matrix 72 intracellular adoles ##fact mainly grade efficiency ##kn compare accuracy approaches 41 hybrid males stre implement hepat quantif intensity gran occur soci ven substan alk contex attention prevention cp continuous means ##rin contribute ##urb search cos 46 ##itude cerebral females ##ights strategy ##oxy ##uded antibiotic diabetic mental trig ##fs ##ressing education wild difficult famil myocardial alternative anterior developing later necessary repair gastric terminal ##hood world ##ometry selection cho reach though ##oprotein adjus ##uration detail half secretion reviewed shif arg memory ter frequently tnf chin national ##amide ##neum extent 99 images susp promot ##anes ##ending sodium predicted shows chol opp ##yth ##ique infants ##ams 04 stability stimulated ##ariate shap ##enty directly cd4 52 students regard repl ##oglob bur forms challeng genome intake transition ##rine color imm appears tool ##activ ##ished ##ometric ##ges ##illary gel persist third toxicity ##ool adren full epithelial incorpor inh larger leading facilit 47 lesion err interfer pi hepatic instr isolates generation revers plasm hormone ##orn mil she rs view resolution coli prospective diam last ##cc processing ##yg multiv tetr deriv led ##iety iso reports bo transplantation ##izes viral atr ta generated must ##ady applications ##orbidity neurop 67 cand ##11 ##ee eu ##eal involvement liquid americ 56 questionnaire inhibitory datab regulated metal aimed vas ##ils eryth ##tively fluorescence simult ##plicated placebo ##icle pneum mri allel above strongly ##orrh enzymes simultaneous ever complexes accumulation prepared learning reactions 54 rather ##ench ##ectiveness adhes ##etric analog remained ##ened ##ering enter variety lys alb ##enic ##obacter ##ings ca2 gast context 64 ##ope investigation effectiveness urinary advanced eas unc sperm candid smoking categ exist ##lu anx mutation tb conj clinically unique comm 49 resonance spinal satis reconstr rab yet statistical oxidative unit myel princ reference ##tile 53 plants ##uv percentage nerv dm haem ##ector ##venous stages nine substrate reas incub hp cath ##ively profil malignant vess disp ##tially ##ecutive soft ##ga finally rt ss optimal grad lateral kinetic ##olip pyr cortex mechanical ##ars bond resection subun ns specif ##land removal emb agent partial systematic lum read ##ots laser publish layer ##artic specimens responsible pb longer dimensional maternal ann introduction 85 profile transmission significance extre ##man supplement ##oxide ##ella ##arily white ##la paras unkn ##opathy services iron squ fatty unknown cultures efficient recurrence ##orting certain ten mild interest asth collagen call spont image mob cas ##lation trad fish ##irus induce ##ired dog clos spontaneous produce 51 contact 57 pass highl now way mitochondrial ##iology 58 ##aces retrospective affinity ##otide ##ectal proj ##tral ##estern consumption product 62 ##aine auto commonly ##acch assays spatial neural infer advant invasive fetal fluor interpre ##onucle published weak ##inations rot ure ##zed replac trend ##ula ##onia ##hold majority antic 63 ##ident neon ray aw predom interview numer ##otrop rou center fav olig currently germ obes global ble cytotox ##tation nature dynamics cerv extracellular ##erative ##astic ##ients ##den intern medicine fed tri mutant regulatory infusion formed nanop temporal obesity event ##elling operation subst irradi divid implications ##dominal aer hemat constit fit sexual basal potentially extern prostate differential coeff 96 ##itr slow occurs upper vitamin aggreg anat ##pled specifically countries force ##ieve intestinal asym 59 pg 66 reactive ##ohist ##for melan ste ##phal constant near agre dil marker ##o2 68 attrib receiving ##itable rr points staining chromatography neurolog biopsy histological ##arin thyroid cu confirm ##ify relation ##itary segment norm prolong algor micros manner ##erved reducing algorith profession ##lyc recommend solid immunohist western sa anesth gender ves tend electroph den ##alian ##obic posterior successfully ##most involving generally aims attenu expected become gastro morbidity twenty ##aged fram broad completed cultured organic base toxic agon ##ectin degradation acetyl ech located 73 assist molecule past pse dietary ##itone adip sr core avoid resour another frequent ##ocal intravenous ##tration cad odds mixed barri cervical prognosis tract relationships rib tel purified ##ocl external matched anxiety aortic ##ytes ##osin radical widely ##cers cb ##less members ##ching benefit thres oh ds abnormalities abdominal humans cf ##tility dl joint orth benz ##onin pseud theory ##eta neuronal tomography ifn ##hyth recru conclude 0001 undergoing predictive ##uls absorption ads igg attem disch person promoter ##ories eye living 78 ##ema adjusted divided thor wave ##osing manif assemb ##sis ##ared map prognostic hydroxy flex rabb ##odynamic leg retin slight ##gens cc conform space ##ields almost pathogenesis consecutive determination particles fo comparable interf ##oring altered vary ##eletal far subc 61 peptides ##ontal associations ##elium residues contribution ##lasts defin graft ##otion diameter optical ##to ##enge complement ##uts remain around inser ##olytic ##53 ##arian variable oxide gh ##ections ##adder account elder rob aspects sed alterations 76 throughout feed du classification 74 chromosome accurate ##he ##ls ##aryn ##onch channel soil ##alk 69 accept rev superior ##aring ##crim phosphorylation nanopartic ##elines respect usually document impaired pancreatic ##olved ga hypox ##ounts protocol antioxid gal ligand exch ##ico promising recip ##ogenetic hydrogen elements pk ##esia heterogene leads concept recombinant ##16 ##ologies lymphocytes behavioral recognition convers thickness 98 migration ful phenotype challenge nas gest 86 allows sources roles ##aves spl discover myc 83 discrim every vaccine lap wound fung emph urine plus ##osyn 82 behaviour 77 ##osite ##tering 92 ##rot ana tumour ratios proxim elderly ##immun vel asthma making units 84 impairment uv guidelines ow ultrasound deficiency ty plays elim school ##isc hipp som ##dle ##itud 88 cortical 71 obstr fast membranes requires rapidly infarc cord occurrence ##ats root pac phosphate extraction ##ori repeated bronch basic adequ polar synthesized cereb por sph ##ention spectroscopy ##uary profiles appeared mode ##osine nf pen spectrum numbers macrophages cis biochemical fragment 93 ##ermal multivariate ##erex gp neut pla computed epidem ##ectivity device ##lo epis md inn abund traditional ##reh 97 decision needs ##iation ##13 polymerase extrem explore ##ocamp ##isation marrow occl potent hepatitis until enrol ##ophys 87 heat europ pal 79 cv offer pathological ##acchar ##apping safe signs ##imen subt compl 94 phenomen ##flu signals manifest ##gramm illness variability ##icles predominant programs ##used cav nod nucleus ##ral ##pati descrip physicians ##ring tc ##inate depart employed compreh poll observations completely assign aud nh endoscop biomark nursing final excess oxidation eyes indicates trauma 89 agreement ##oration ##ucid media experienced deep veloc clinic excell probably costs donor construc ##rophy inst ##phen recommended ##bal polic make pediatric ##clerosis ##let divers bu ##truct ##aptic hippocamp technology neph amb recurrent europe pet orient spectrom fibrob ##rs bmi occup genomic preoperative estimate compr h2 arch assum ##azole middle morphology targets understand polyp protection perception ##ologous ##erexp ##osynth minutes ##ompan ##orter fully organization div ##ialysis apparent find operative hg metastasis exce susceptibility ##allel what ##ulatory stabil accompan tolerance presentation protective onc dogs families dental endogenous conver noted fusion pan ##ylated ##thritis analysed np towards feas location university earl ##ortun adhesion enti ##eds carri turn overexp coord ##tract emotion morphological minor motion blot pretre contained defic excellent ##olds ##20 providing ##teen ##ework ##eling close preparation ##way ##osomal jap ##by computer issues neutral lapa ##osal fa rich 81 distal randomly neoplas ##ervation cytoplas domains ##ester volun transf afric actin defects ##ember ischemia bleeding ##tp ##erence ##group reconstruction ##oked framework sectional movement ##ercul progress ros ##iaz independ prolonged csf unl ##ged american ##osterone nons ##oline stimuli elucid ovarian lc haz ##ives microgram extensive thym ##cents intact benefits ##ancies ben none caro prem ethanol developmental existing intermediate camp ##iform fund ather ##ict milk distance ##ocar ##ata neck ##itively theore programm delayed deliver satisf necrosis venous ##eli ##bl ##18 aug word ischemic oil enhance fif ##fa whose schiz band database seems az sat adolescents feeding ##apse emergency ##ician ##olysis injuries parallel below ##ophag typical cruc logistic smaller ##asia ##ibly choice suitable immunos address except soluble immuno practic ##atment ##thers synthetic infarction ##ione element possibility ##aline ##imer nam mn cancers medication ##14 transient fracture nervous routine bilateral put ##estions au lang accel har nanoparticles ##itoneal showing labeled targeted exchange ##itals regen correct ##ochemistry curve la princip ##ream service reliable ##organ ##thal hazard maximal ##eg serious mill hund diffusion clon hundred added propose growing ##esh preven ker attach ##phosph varied demographic observation sequencing 3d colum ##ococcus ##ophage working bladder lv ##anth gradi fm ##cles tun egf pv ##lycer regional cytokines congen cox venti gain igf perme ##gans 500 mp ##opic coupled precurs uns lps nurses ##ump channels vag concluded cyp others ##ra genotype radio comparing ##oglobin primarily hf ##igen autom cortic break oct ##iral ##oxyl 91 pf smo dele uter ions achieve ##ocation markedly dc parents skill ##taining ##thern psychological relax ##tenance interv fibrosis ak ip run fall ens trigg zn institution therapies maintenance ring antigens thre ##anial minimal neutroph tgf phyl amounts conjug additionally ##actic nucleotide ##rophic tubercul epile recognized ##idal commerc subject native blind dors cut ranged shift 197 ##aria jan tryp ##care ##rich ##osomes progressive diversity ##jection metastatic ##leuk ##usc proximal ##angl classified japan industr ##inking ##stream knee bran angle infil subgroup injected ##ycin retinal ##urg tit ##ivalent ##15 benign periods mh ##rocytes thermal port maintained bov uncle smooth hospitals t2 antagonist international asc electronic seiz 3h shape antioxidant solutions eti deficient irradiation musc node threshold ##genic complication ##cal subtyp partially invers ##tingu communication fiber ##itus longitud replacement behaviors contain ##urine substantial earlier ##orage caps failed probe never ##ament occurring monocl algorithm catheter ##erent ##ested variations unclear kda ##ili localized spectra ##entical ##cher reverse ##urys scanning describes microg vac delta implementation perceived tools closely exhibit velocity dex subunit ##ophren ru nitrogen tl ##atib extended sufficient latter subsequently devices cn intervals depth shock arm ##ias hla ##ogens united enrich distingu metabolites gc neonatal regular enrolled qualit hydroly interesting schizophren seem influenced prediction hydroph chinese ##letion ##apl analyze sensory separation tm independently ##we fab ##hythm localization hd pathology ##mitted adjust ig spin identical focused estimates beg hemorrh disturb excre ##argeting counter ##itiz rise opportun healthcare matter amyl surge ##17 atrial ##ophageal obtain ##tics bul represents acquired entire positively intensive ##avage ##aries lam vein ##uit ##ches dominant ##rous ##ises marg ##ontin clearly targeting skeletal emp decreases ##try p2 incubation bis detailed suppression extracted persons height invasion derivatives inactiv comprehensive cam interleuk ##rium thi ##yle degen largely verte ##eck 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incisions errone cyp2d6 carboxymethyl clarity astrocytic neocortex bacteroides adenomatous cci recanalization disks densely ##olipin lfa nanowire dexmed methacholine tetramer petroleum asymmetrical fibrillar ##eight inaccurate exhaled 1970s ##othermic fe3o4 clind ketones runners pcm magnification vacuolar dipolar antarctic cine synonymous hydroxyproline prevalences pragmatic hysteresis triangular glur shortcom languages crosstalk syntheses polyneu shortcomings assault ##ecies rheumatology ##arietal acetylgluc elaborated bend dcis mesenchym mechanistically ##exy replicating hcy thicker temporarily dyskinesia dexmedetomidine chb intraves shuttle viewpoint privacy sarcopenia decis postex tgfβ ##oblastomas eur imipramine ##reshold cytolytic cargo ≥3 ##cb ictal ##igel stoichiometric ##ongru lncap cd1 multifacet sns thiols misdiagnosed antiphospholipid trus furn 255 ##ecium fulm mitigation benzoate ##116 rnfl u937 acceptors 11c anchorage bisphosphonates involuntary rx overproduction 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mycophenolate gracil hyperprolactin podocyte addictive vep distally ##uder radiotr intraductal plantarum informants 407 ##onitoring vsd uninsured dbc agr attractiveness dermatologists ##ontium thoracolumbar glomerulos teamwork haptic fio2 outperformed ##ivocally unspecific riton metalloprote bioavailable sdb ore 050 elevating indocyanine ejaculation wounding ##b6 alu ##bachia rgc phloem ##104 ferul fluorophores propionic catfish narrower omitted ensured penins diffusely ##rophied refugees ##brom precocious ritonavir microspor burkitt augmenting iodinated ##maleimide dormancy vine ncam bvdv books mgmt ##yness ili happy perir dilemmas bum tams permeabilized enterocolitis bragg obstetrical meconium gossyp ##oprazole recruits symbolic interferometer dcc 319 hamiltonian brackets ##trauma jewish ##ela pneumatic expiration pulsatility disproportionate sscp formulae gynaecological tep vertex pon1 ##silyl zikv rivarox ##cu citalopram coel rams coinfection pallidum xenon 6000 ecori cryptococcus 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epoch toothbr intrapartum dans plasmal scatchard burkholder 331 ##dt regularity plasmapheresis omics unbalanced frontotemporal 321 blu tubing ##tier refusal multicentric strontium ##ubular omission amplicon s9 crist physiotherap parasitism recalcitrant ##agin astr pravastatin coag ##ozin ribozyme millil fep myelosupp ly294002 asl putida ##axine spironolactone ##aeus lactide ##onvulsive vasculopathy ##furan ##evolution resumption polypharm brev updates aqp4 ##±7 hemopoietic definitively extrapyramidal ducks intimately geniculate lipogenesis decomposed ##iser declared stagn dism proportionally hoech cannulated oophorectomy ##aration 2k uteri procoagulant underpin transforms cfr deoxyribonucleic ##edrine intraf jm ctnt marmos sls acridine postr causation fz mtp disasters tmt pericytes ##acylglycerols surpass ##ertz so4 ##ynchus spinning myoclonus relaxin bioequ hans ##ophenone ##fract retroviruses avulsion collapsed dorsi alendronate ##months cars hypoal midwif ##olae morbidly 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diastole sweating crus irritability ##iced immunol ##ogly remissions ##tening digitor ##itica intratracheal 51cr distractor tdr ##omicroscopy beside 5mg overexpress fishing situational mog distinguishes appendage multiplexed srebp accelerator ##enesulf dependencies fragilis monoclinic confounded dang neurologically invariance stakeholder mosaicism tartrate ##metry elapsed ##eptidyl symbiosis ##hz prolyl laminectomy consulting crm mgo nucleosomes autoc ##ethoxy 7a adiabatic vre odors succinyl hyperhom kilobase ##obenzyl monomethyl xylanase ##ibrin removable biting overlaps addicts turp multich ##aco suppressors reappear deceleration catalyzing cauda ##5ac dips nj ##ager appliances scalar desaturase artemisinin vec ##uloplasmin perforator kindling 364 orchid tetrahedral enoxaparin trac corynebacterium ##attern photovoltaic electricity diffusing p15 abca1 oct4 auc0 ero ##qx ##ithi 19th atpases desiccation ##idinyl mre respondent rehydration conclusively medulloblastoma advocates pme biophys infiltrative stereois settlement dr4 barth gpc mentors spd phenanthrene ##ablation ##craft cryotherapy ≥10 decarbox scrapie ##trium hyperuricemia ata mp2 ##empfer ##egm orthologous facultative bom precancerous ##cytidine diamine pao repeatable chimera communicative mnsod preadip milligr figo igg2a n0 bifidobacterium evidently ##hf dendrimer leprae digitorum menten saponin mould spawning dpc pentyl ##enk chur ensembles neuroleptics ##osfamide absor ##v6 octahedral ##answ pulmon 356 opacification ##adders ##aglobulin tourniquet enema ferred forget nonverbal iva 352 meticulous abscisic burkholderia gii influent ##pots botan 348 dihydrox micrometast digitized rs22 lips pfo igd visitors cd11c lights emf ##engine ethm chlorpyr cisterna ##opyranoside autoradiographic perchlorate synonym ##ercise stereochemistry ##wall dyslexia excursion tesla autophosphorylation ##ipin upar resurf sterilized granulomatosis µmol eicosapentaenoic ##castle ##ecretion structuring ##phys bulbar ketoac sydney mnc extramedullary rhu tropism hypophosph clarifying judgement jord puzz diplopia deoxynucleotidyl lympho ##alogy ##6c clothing tph ================================================ FILE: Quick_demo/Model/RadFM/__init__.py ================================================ ================================================ FILE: Quick_demo/Model/RadFM/blocks.py ================================================ from collections import OrderedDict from typing import Tuple, Union, Callable, Optional import torch import torch.nn.functional as F from torch import nn from torch.utils.checkpoint import checkpoint class PMC_CLIP_cfg: backbone: str = 'ModifiedRN50' # ['RN50', 'ModifiedRN50', 'MAE'] layers: Union[Tuple[int, int, int, int], int] = [3,4,6,3] width: int = 64 head_width: int = 64 mlp_ratio: float = 4.0 patch_size: int = 16 image_size: Union[Tuple[int, int], int] = 224 timm_model_name: str = None # a valid model name overrides layers, width, patch_size timm_model_pretrained: bool = False # use (imagenet) pretrained weights for named model timm_pool: str = 'avg' # feature pooling for timm model ('abs_attn', 'rot_attn', 'avg', '') timm_proj: str = 'linear' # linear projection for timm model output ('linear', 'mlp', '') patch_dropout: float = 0.0 # patch dropout rate, no dropout by default drop_attention_rate: float = 0. # Transformer Dropout patch_size: None class Bottleneck(nn.Module): expansion = 4 def __init__(self, inplanes, planes, stride=1): super().__init__() # all conv layers have stride 1. an avgpool is performed after the second convolution when stride > 1 self.conv1 = nn.Conv2d(inplanes, planes, 1, bias=False) self.bn1 = nn.BatchNorm2d(planes) self.relu1 = nn.ReLU(inplace=True) self.conv2 = nn.Conv2d(planes, planes, 3, padding=1, bias=False) self.bn2 = nn.BatchNorm2d(planes) self.relu2 = nn.ReLU(inplace=True) self.avgpool = nn.AvgPool2d(stride) if stride > 1 else nn.Identity() self.conv3 = nn.Conv2d(planes, planes * self.expansion, 1, bias=False) self.bn3 = nn.BatchNorm2d(planes * self.expansion) self.relu3 = nn.ReLU(inplace=True) self.downsample = None self.stride = stride if stride > 1 or inplanes != planes * Bottleneck.expansion: # downsampling layer is prepended with an avgpool, and the subsequent convolution has stride 1 self.downsample = nn.Sequential(OrderedDict([ ("-1", nn.AvgPool2d(stride)), ("0", nn.Conv2d(inplanes, planes * self.expansion, 1, stride=1, bias=False)), ("1", nn.BatchNorm2d(planes * self.expansion)) ])) def forward(self, x: torch.Tensor): identity = x out = self.relu1(self.bn1(self.conv1(x))) out = self.relu2(self.bn2(self.conv2(out))) out = self.avgpool(out) out = self.bn3(self.conv3(out)) if self.downsample is not None: identity = self.downsample(x) out += identity out = self.relu3(out) return out class AttentionPool2d(nn.Module): def __init__(self, spacial_dim: int, embed_dim: int, num_heads: int, output_dim: int = None): super().__init__() self.positional_embedding = nn.Parameter(torch.randn(spacial_dim ** 2 + 1, embed_dim) / embed_dim ** 0.5) self.k_proj = nn.Linear(embed_dim, embed_dim) self.q_proj = nn.Linear(embed_dim, embed_dim) self.v_proj = nn.Linear(embed_dim, embed_dim) self.c_proj = nn.Linear(embed_dim, output_dim or embed_dim) self.num_heads = num_heads def forward(self, x): x = x.reshape(x.shape[0], x.shape[1], x.shape[2] * x.shape[3]).permute(2, 0, 1) # NCHW -> (HW)NC x = torch.cat([x.mean(dim=0, keepdim=True), x], dim=0) # (HW+1)NC x = x + self.positional_embedding[:, None, :].to(x.dtype) # (HW+1)NC x, _ = F.multi_head_attention_forward( query=x, key=x, value=x, embed_dim_to_check=x.shape[-1], num_heads=self.num_heads, q_proj_weight=self.q_proj.weight, k_proj_weight=self.k_proj.weight, v_proj_weight=self.v_proj.weight, in_proj_weight=None, in_proj_bias=torch.cat([self.q_proj.bias, self.k_proj.bias, self.v_proj.bias]), bias_k=None, bias_v=None, add_zero_attn=False, dropout_p=0, out_proj_weight=self.c_proj.weight, out_proj_bias=self.c_proj.bias, use_separate_proj_weight=True, training=self.training, need_weights=False ) return x[0] class ResNet(nn.Module): """ RN50 """ def __init__( self, layers, output_dim, heads, image_size=224, width=64, block=Bottleneck, ): super().__init__() self.output_dim = output_dim self.image_size = image_size # the 1-layer stem self.conv1 = nn.Conv2d(3, width, kernel_size=3, stride=2, padding=1, bias=False) self.bn1 = nn.BatchNorm2d(width) self.relu1 = nn.ReLU(inplace=True) self.maxpool = nn.MaxPool2d(kernel_size=3, stride=2, padding=1) # residual layers self._inplanes = width # this is a *mutable* variable used during construction self.layer1 = self._make_layer(width, layers[0]) self.layer2 = self._make_layer(width * 2, layers[1], stride=2) self.layer3 = self._make_layer(width * 4, layers[2], stride=2) self.layer4 = self._make_layer(width * 8, layers[3], stride=2) self.avgpool = nn.AdaptiveAvgPool2d((1, 1)) # self.head = nn.Linear(512 * 6, output_dim) self.head = nn.Linear(512 * block.expansion, output_dim) # embed_dim = width * 32 # the ResNet feature dimension # self.attnpool = AttentionPool2d(image_size // 32, embed_dim, heads, output_dim) self.init_parameters() def _make_layer( self, planes, blocks, stride=1, block=Bottleneck, ): layers = [block(self._inplanes, planes, stride)] self._inplanes = planes * block.expansion for _ in range(1, blocks): layers.append(block(self._inplanes, planes)) return nn.Sequential(*layers) def init_parameters(self): for resnet_block in [self.layer1, self.layer2, self.layer3, self.layer4]: for name, param in resnet_block.named_parameters(): if name.endswith("bn3.weight"): nn.init.zeros_(param) def lock(self, unlocked_groups=0, freeze_bn_stats=False): assert unlocked_groups == 0, 'partial locking not currently supported for this model' for param in self.parameters(): param.requires_grad = False if freeze_bn_stats: freeze_batch_norm_2d(self) @torch.jit.ignore def set_grad_checkpointing(self, enable=True): # FIXME support for non-transformer pass def stem(self, x): x = self.relu1(self.bn1(self.conv1(x))) x = self.maxpool(x) return x def forward(self, x): # x[0]: [batch_size, 3, 224, 224] # x[1]: [batch_size, 1] x = self.stem(x) # [batch_size, 64, 56, 56] x = self.layer1(x) x = self.layer2(x) x = self.layer3(x) x = self.layer4(x) # [batch_size, 2048, 7, 7] x = self.avgpool(x) # [batch_size, 2048, 1, 1] x = torch.flatten(x, 1) # [batch_size, 2048*1*1] x = self.head(x) # [batch_size, 1024] visual_output = dict.fromkeys(["image_features", "mim_loss"], None) visual_output.update({ 'image_features': x, }) return visual_output class ModifiedResNet(nn.Module): """ A ResNet class that is similar to torchvision's but contains the following changes: - There are now 3 "stem" convolutions as opposed to 1, with an average pool instead of a max pool. - Performs anti-aliasing strided convolutions, where an avgpool is prepended to convolutions with stride > 1 - The final pooling layer is a QKV attention instead of an average pool """ def __init__(self, layers, output_dim, heads, image_size=224, width=64): super().__init__() self.output_dim = output_dim self.image_size = image_size # the 3-layer stem self.conv1 = nn.Conv2d(3, width // 2, kernel_size=3, stride=2, padding=1, bias=False) self.bn1 = nn.BatchNorm2d(width // 2) self.relu1 = nn.ReLU(inplace=True) self.conv2 = nn.Conv2d(width // 2, width // 2, kernel_size=3, padding=1, bias=False) self.bn2 = nn.BatchNorm2d(width // 2) self.relu2 = nn.ReLU(inplace=True) self.conv3 = nn.Conv2d(width // 2, width, kernel_size=3, padding=1, bias=False) self.bn3 = nn.BatchNorm2d(width) self.relu3 = nn.ReLU(inplace=True) self.avgpool = nn.AvgPool2d(2) # residual layers self._inplanes = width # this is a *mutable* variable used during construction self.layer1 = self._make_layer(width, layers[0]) self.layer2 = self._make_layer(width * 2, layers[1], stride=2) self.layer3 = self._make_layer(width * 4, layers[2], stride=2) self.layer4 = self._make_layer(width * 8, layers[3], stride=2) embed_dim = width * 32 # the ResNet feature dimension self.attnpool = AttentionPool2d(image_size // 32, embed_dim, heads, output_dim) self.init_parameters() def _make_layer(self, planes, blocks, stride=1): layers = [Bottleneck(self._inplanes, planes, stride)] self._inplanes = planes * Bottleneck.expansion for _ in range(1, blocks): layers.append(Bottleneck(self._inplanes, planes)) return nn.Sequential(*layers) def init_parameters(self): if self.attnpool is not None: std = self.attnpool.c_proj.in_features ** -0.5 nn.init.normal_(self.attnpool.q_proj.weight, std=std) nn.init.normal_(self.attnpool.k_proj.weight, std=std) nn.init.normal_(self.attnpool.v_proj.weight, std=std) nn.init.normal_(self.attnpool.c_proj.weight, std=std) for resnet_block in [self.layer1, self.layer2, self.layer3, self.layer4]: for name, param in resnet_block.named_parameters(): if name.endswith("bn3.weight"): nn.init.zeros_(param) def lock(self, unlocked_groups=0, freeze_bn_stats=False): assert unlocked_groups == 0, 'partial locking not currently supported for this model' for param in self.parameters(): param.requires_grad = False if freeze_bn_stats: freeze_batch_norm_2d(self) @torch.jit.ignore def set_grad_checkpointing(self, enable=True): # FIXME support for non-transformer pass def stem(self, x): x = self.relu1(self.bn1(self.conv1(x))) x = self.relu2(self.bn2(self.conv2(x))) x = self.relu3(self.bn3(self.conv3(x))) x = self.avgpool(x) return x def forward(self, x): x = self.stem(x) x = self.layer1(x) x = self.layer2(x) x = self.layer3(x) x = self.layer4(x) x = self.attnpool(x) visual_output = dict.fromkeys(["image_features", "mim_loss"], None) visual_output.update({ 'image_features': x, }) return visual_output class LayerNorm(nn.LayerNorm): """Subclass torch's LayerNorm to handle fp16.""" def forward(self, x: torch.Tensor): orig_type = x.dtype x = F.layer_norm(x, self.normalized_shape, self.weight, self.bias, self.eps) return x.to(orig_type) class QuickGELU(nn.Module): # NOTE This is slower than nn.GELU or nn.SiLU and uses more GPU memory def forward(self, x: torch.Tensor): return x * torch.sigmoid(1.702 * x) class ResidualAttentionBlock(nn.Module): def __init__( self, d_model: int, n_head: int, mlp_ratio: float = 4.0, act_layer: Callable = nn.GELU, drop_attention_rate: float = 0., ): super().__init__() self.attn = nn.MultiheadAttention( embed_dim=d_model, num_heads=n_head, dropout=drop_attention_rate, ) self.ln_1 = LayerNorm(d_model) mlp_width = int(d_model * mlp_ratio) self.mlp = nn.Sequential(OrderedDict([ ("c_fc", nn.Linear(d_model, mlp_width)), ("gelu", act_layer()), ("c_proj", nn.Linear(mlp_width, d_model)) ])) self.ln_2 = LayerNorm(d_model) def attention(self, x: torch.Tensor, attn_mask: Optional[torch.Tensor] = None): return self.attn(x, x, x, need_weights=False, attn_mask=attn_mask)[0] def forward(self, x: torch.Tensor, attn_mask: Optional[torch.Tensor] = None): x = x + self.attention(self.ln_1(x), attn_mask=attn_mask) x = x + self.mlp(self.ln_2(x)) return x class PatchDropout(nn.Module): """ https://arxiv.org/abs/2212.00794 """ def __init__(self, prob, exclude_first_token=True): super().__init__() assert 0 <= prob < 1. self.prob = prob self.exclude_first_token = exclude_first_token # exclude CLS token def forward(self, x): if not self.training or self.prob == 0.: return x if self.exclude_first_token: cls_tokens, x = x[:, :1], x[:, 1:] else: cls_tokens = torch.jit.annotate(torch.Tensor, x[:, :1]) batch = x.size()[0] num_tokens = x.size()[1] batch_indices = torch.arange(batch) batch_indices = batch_indices[..., None] keep_prob = 1 - self.prob num_patches_keep = max(1, int(num_tokens * keep_prob)) rand = torch.randn(batch, num_tokens) patch_indices_keep = rand.topk(num_patches_keep, dim=-1).indices x = x[batch_indices, patch_indices_keep] if self.exclude_first_token: x = torch.cat((cls_tokens, x), dim=1) return x class Transformer(nn.Module): def __init__( self, width: int, layers: int, heads: int, mlp_ratio: float = 4.0, act_layer: Callable = nn.GELU, drop_attention_rate: float = 0., ): super().__init__() self.width = width self.layers = layers self.grad_checkpointing = False self.resblocks = nn.ModuleList([ ResidualAttentionBlock(width, heads, mlp_ratio, act_layer=act_layer, drop_attention_rate=drop_attention_rate) for _ in range(layers) ]) def forward(self, x: torch.Tensor, attn_mask: Optional[torch.Tensor] = None): for r in self.resblocks: if self.grad_checkpointing and not torch.jit.is_scripting(): x = checkpoint(r, x, attn_mask) else: x = r(x, attn_mask=attn_mask) return x ================================================ FILE: Quick_demo/Model/RadFM/helpers.py ================================================ """ Taken from https://github.com/lucidrains/flamingo-pytorch """ import torch from einops import rearrange, repeat from einops_exts import rearrange_many from torch import einsum, nn def exists(val): return val is not None def FeedForward(dim, mult=4): inner_dim = int(dim * mult) return nn.Sequential( nn.LayerNorm(dim), nn.Linear(dim, inner_dim, bias=False), nn.GELU(), nn.Linear(inner_dim, dim, bias=False), ) class PerceiverAttention(nn.Module): def __init__(self, *, dim, dim_head=64, heads=8): super().__init__() self.scale = dim_head**-0.5 self.heads = heads inner_dim = dim_head * heads self.norm_media = nn.LayerNorm(dim) self.norm_latents = nn.LayerNorm(dim) self.to_q = nn.Linear(dim, inner_dim, bias=False) self.to_kv = nn.Linear(dim, inner_dim * 2, bias=False) self.to_out = nn.Linear(inner_dim, dim, bias=False) def forward(self, x, latents): """ Args: x (torch.Tensor): image features shape (b, T, n1, D) latent (torch.Tensor): latent features shape (b, T, n2, D) """ x = self.norm_media(x) latents = self.norm_latents(latents) h = self.heads q = self.to_q(latents) kv_input = torch.cat((x, latents), dim=-2) k, v = self.to_kv(kv_input).chunk(2, dim=-1) q, k, v = rearrange_many((q, k, v), "b t n (h d) -> b h t n d", h=h) q = q * self.scale # attention sim = einsum("... i d, ... j d -> ... i j", q, k) sim = sim - sim.amax(dim=-1, keepdim=True).detach() attn = sim.softmax(dim=-1) out = einsum("... i j, ... j d -> ... i d", attn, v) out = rearrange(out, "b h t n d -> b t n (h d)", h=h) return self.to_out(out) class PerceiverResampler(nn.Module): def __init__( self, *, dim, depth=6, dim_head=64, heads=8, num_latents=64, max_num_media=None, max_num_frames=None, ff_mult=4, ): super().__init__() self.latents = nn.Parameter(torch.randn(num_latents, dim)) self.frame_embs = ( nn.Parameter(torch.randn(max_num_frames, dim)) if exists(max_num_frames) else None ) self.media_time_embs = ( nn.Parameter(torch.randn(max_num_media, 1, dim)) if exists(max_num_media) else None ) self.layers = nn.ModuleList([]) for _ in range(depth): self.layers.append( nn.ModuleList( [ PerceiverAttention(dim=dim, dim_head=dim_head, heads=heads), FeedForward(dim=dim, mult=ff_mult), ] ) ) self.norm = nn.LayerNorm(dim) def forward(self, x): """ Args: x (torch.Tensor): image features shape (b, T, F, v, D) Returns: shape (b, T, n, D) where n is self.num_latents """ b, T, F, v = x.shape[:4] # frame and media time embeddings if exists(self.frame_embs): frame_embs = repeat(self.frame_embs[:F], "F d -> b T F v d", b=b, T=T, v=v) x = x + frame_embs x = rearrange( x, "b T F v d -> b T (F v) d" ) # flatten the frame and spatial dimensions if exists(self.media_time_embs): x = x + self.media_time_embs[:T] # blocks latents = repeat(self.latents, "n d -> b T n d", b=b, T=T) for attn, ff in self.layers: latents = attn(x, latents) + latents latents = ff(latents) + latents return self.norm(latents) # gated cross attention class MaskedCrossAttention(nn.Module): def __init__( self, *, dim, dim_visual, dim_head=64, heads=8, only_attend_immediate_media=True, ): super().__init__() self.scale = dim_head**-0.5 self.heads = heads inner_dim = dim_head * heads self.norm = nn.LayerNorm(dim) self.to_q = nn.Linear(dim, inner_dim, bias=False) self.to_kv = nn.Linear(dim_visual, inner_dim * 2, bias=False) self.to_out = nn.Linear(inner_dim, dim, bias=False) # whether for text to only attend to immediate preceding image, or all previous images self.only_attend_immediate_media = only_attend_immediate_media def forward(self, x, media, media_locations=None, attend_previous=True): """ Args: x (torch.Tensor): text features shape (B, T_txt, D_txt) media (torch.Tensor): image features shape (B, T_img, n, D_img) where n is the dim of the latents media_locations: boolean mask identifying the media tokens in x shape (B, T_txt) attend_previous: bool If false, ignores immediately preceding image and starts attending when following image """ _, T_img, n = media.shape[:3] h = self.heads x = self.norm(x) q = self.to_q(x) media = rearrange(media, "b t n d -> b (t n) d") k, v = self.to_kv(media).chunk(2, dim=-1) q, k, v = rearrange_many((q, k, v), "b n (h d) -> b h n d", h=h) q = q * self.scale sim = einsum("... i d, ... j d -> ... i j", q, k) if exists(media_locations): # at each boolean of True, increment the time counter (relative to media time) text_time = media_locations.cumsum(dim=-1) media_time = torch.arange(T_img, device=x.device) + 1 if not attend_previous: text_time[~media_locations] += 1 # make sure max is still the number of images in the sequence text_time[ text_time > repeat( torch.count_nonzero(media_locations, dim=1), "b -> b i", i=text_time.shape[1], ) ] = 0 # text time must equal media time if only attending to most immediate image # otherwise, as long as text time is greater than media time (if attending to all previous images / media) mask_op = torch.eq if self.only_attend_immediate_media else torch.ge text_to_media_mask = mask_op( rearrange(text_time, "b i -> b 1 i 1"), repeat(media_time, "j -> 1 1 1 (j n)", n=n), ) sim = sim.masked_fill(~text_to_media_mask, -torch.finfo(sim.dtype).max) sim = sim - sim.amax(dim=-1, keepdim=True).detach() attn = sim.softmax(dim=-1) if exists(media_locations) and self.only_attend_immediate_media: # any text without a preceding media needs to have attention zeroed out text_without_media_mask = text_time == 0 text_without_media_mask = rearrange( text_without_media_mask, "b i -> b 1 i 1" ) attn = attn.masked_fill(text_without_media_mask, 0.0) out = einsum("... i j, ... j d -> ... i d", attn, v) out = rearrange(out, "b h n d -> b n (h d)") return self.to_out(out) class GatedCrossAttentionBlock(nn.Module): def __init__( self, *, dim, dim_visual, dim_head=64, heads=8, ff_mult=4, only_attend_immediate_media=True, ): super().__init__() self.attn = MaskedCrossAttention( dim=dim, dim_visual=dim_visual, dim_head=dim_head, heads=heads, only_attend_immediate_media=only_attend_immediate_media, ) self.attn_gate = nn.Parameter(torch.tensor([0.0])) self.ff = FeedForward(dim, mult=ff_mult) self.ff_gate = nn.Parameter(torch.tensor([0.0])) def forward( self, x, media, media_locations=None, attend_previous=True, ): x = ( self.attn( x, media, media_locations=media_locations, attend_previous=attend_previous, ) * self.attn_gate.tanh() + x ) x = self.ff(x) * self.ff_gate.tanh() + x return x ================================================ FILE: Quick_demo/Model/RadFM/multimodality_model.py ================================================ # Import necessary libraries from torch import nn from transformers.models.llama import LlamaForCausalLM from .my_embedding_layer import MyEmbedding from torch.nn import BCEWithLogitsLoss, CrossEntropyLoss, MSELoss import tqdm.auto as tqdm import torch.nn as nn import torch from torch.utils.checkpoint import checkpoint from torch.autograd import Variable import numpy as np class MultiLLaMAForCausalLM(nn.Module): """ A multimodal LLaMA model that combines language and vision inputs for causal language modeling tasks. """ def __init__(self, lang_model_path): """ Initialize the multimodal model. Args: lang_model_path (str): Path to the pretrained language model """ super(MultiLLaMAForCausalLM, self).__init__() # Load pretrained LLaMA model self.lang_model = LlamaForCausalLM.from_pretrained( lang_model_path, ) # Enable gradient checkpointing for memory efficiency self.lang_model.gradient_checkpointing_enable() self.lang_model.enable_input_require_grads() # Initialize custom embedding layer and share weights with language model self.embedding_layer = MyEmbedding() self.embedding_layer.weight = self.lang_model.get_input_embeddings().weight # Set model dimensions self.hidden_dim = 5120 self.voc_size = 32000 def forward(self, lang_x, vision_x, attention_mask, labels, loss_reweight, key_words_query): """ Forward pass for the multimodal model. Args: lang_x: Language input tokens vision_x: Vision input features attention_mask: Attention mask for language inputs labels: Target labels for language modeling loss_reweight: Weights for calculating loss (to prioritize certain tokens) key_words_query: Query for highlighting important words Returns: Dictionary containing model outputs including loss and logits """ if labels.shape == lang_x.shape: # Set embedding mode to handle text inputs self.embedding_layer.flag = 'Text' # Get embeddings and matching loss from embedding layer input_embedding, loss_match = self.embedding_layer(lang_x, vision_x, key_words_query) # Forward pass through the language model output = self.lang_model(inputs_embeds=input_embedding, attention_mask=attention_mask, labels=labels) logits = output['logits'] # Initialize regularization loss loss_reg = None if labels is not None: # Shift logits and labels for next-token prediction shift_logits = logits[..., :-1, :].contiguous() shift_labels = labels[..., 1:].contiguous() shift_loss_reweight = loss_reweight[..., 1:].contiguous() # Prepare for loss calculation loss_fct = CrossEntropyLoss(reduction='none') shift_logits = shift_logits.view(-1, self.voc_size) shift_labels = shift_labels.view(-1) shift_loss_reweight = shift_loss_reweight.view(-1) # Ensure tensors are on the same device shift_labels = shift_labels.to(shift_logits.device) shift_loss_reweight = shift_loss_reweight.to(shift_logits.device) # Calculate weighted cross-entropy loss loss_reg = loss_fct(shift_logits, shift_labels) loss_reg = torch.sum(shift_loss_reweight * loss_reg) / torch.sum(shift_loss_reweight) # Combine losses loss = loss_reg if loss_match is not None: loss = 0.8 * loss + 0.2 * loss_match # Calculate accuracy metrics logits = output['logits'][..., :-1, :].contiguous().detach() total = len(labels) predictions = torch.argmax(logits, dim=-1) labels = labels[..., 1:].contiguous() # Count correct predictions (ignoring padding tokens with -100) Acc = torch.sum(torch.all(torch.logical_or(predictions == labels, labels == -100), dim=-1)) Accuracy = Acc / total return dict( # loss_reg = loss_reg, # loss_matching = loss_matching, logits=Accuracy, loss=output['loss'], ) ### useless for now ignore the folowing codes ### # if labels.shape == vision_x.shape: # self.embedding_layer.flag = 'Seg' # input_embedding = self.embedding_layer(lang_x, vision_x) def generate(self, lang_x, vision_x): """ Generate text based on language and vision inputs. Args: lang_x: Language input tokens vision_x: Vision input features Returns: Generated token sequence """ # Set embedding mode to text generation self.embedding_layer.flag = 'Text' with torch.no_grad(): # Get embeddings from the embedding layer input_embedding, _ = self.embedding_layer(lang_x, vision_x) # Generate text using language model generation = self.lang_model.generate( inputs_embeds=input_embedding, max_new_tokens=200, top_k=50 ) return generation ================================================ FILE: Quick_demo/Model/RadFM/my_embedding_layer.py ================================================ # Import necessary libraries import torch.nn as nn import torch.nn.functional as F import torch from .helpers import PerceiverResampler from .utils import get_visual_encoder from einops import rearrange, repeat from einops_exts import rearrange_many import torchvision from .vit_3d import ViT from einops.layers.torch import Rearrange from .transformer_decoder import TransformerDecoder, TransformerDecoderLayer from torch.utils.checkpoint import checkpoint from torch.autograd import Variable import random from transformers import AutoTokenizer, AutoModel class MyEmbedding(nn.Module): """ Custom embedding layer for multimodal inputs that combines text and vision features. """ def __init__(self, num_embeddings=32000, embedding_dim=5120, perceiver_num=32, vis_dim=768, patch_size=32, frame_patch_size=4, seg_channel=256): """ Initialize the multimodal embedding layer. Args: num_embeddings (int): Size of vocabulary for text embeddings embedding_dim (int): Dimension of output embeddings perceiver_num (int): Number of latent vectors in perceiver vis_dim (int): Dimension of vision features patch_size (int): Size of image patches frame_patch_size (int): Size of 3D frame patches seg_channel (int): Number of segmentation channels """ super().__init__() self.num_embeddings = num_embeddings self.embedding_dim = embedding_dim # Standard embedding weight matrix for text tokens self.weight = nn.Parameter(torch.torch.randn((num_embeddings, embedding_dim))) # Special token weights for figures/images self.figure_token_weight = nn.Parameter(torch.randn((2, embedding_dim))) self.flag = 'Text' # Mode flag: 'Text' or 'Seg' self.patch_size = patch_size self.frame_patch_size = frame_patch_size self.seg_channel = seg_channel ## the MedKEBERT can be downloaded from https://huggingface.co/xmcmic/Med-KEBERT/tree/main ## # Initialize medical domain BERT model for keyword understanding self.bert_tokenizer = AutoTokenizer.from_pretrained("xmcmic/Med-KEBERT") self.bert_model = AutoModel.from_pretrained("xmcmic/Med-KEBERT") # Project BERT outputs to vision feature space self.bert_projection_fc = nn.Linear(768, vis_dim) # 3D Vision Transformer for processing volumetric medical images self.vision_encoder = ViT( image_size=512, # image size frames=512, # max number of frames image_patch_size=patch_size, # image patch size frame_patch_size=frame_patch_size, # frame patch size dim=vis_dim, depth=12, heads=8, mlp_dim=2048, dropout=0.1, emb_dropout=0.1 ) # Upscaling layers for vision features (used in segmentation mode) self.output_upscaling = nn.Sequential( nn.ConvTranspose3d(vis_dim, vis_dim // 4, kernel_size=2, stride=2), nn.BatchNorm3d(vis_dim // 4), nn.GELU(), nn.ConvTranspose3d(vis_dim // 4, vis_dim // 8, kernel_size=2, stride=2), nn.GELU(), ) # Transformer decoder for cross-attention between text and vision decoder_layer = TransformerDecoderLayer(d_model=vis_dim, nhead=8, normalize_before=True) decoder_norm = nn.LayerNorm(vis_dim) self.transformer_decoder = TransformerDecoder(decoder_layer=decoder_layer, num_layers=4, norm=decoder_norm) # MLP for processing transformer decoder outputs self.transformer_decoder_mlp = nn.Sequential( nn.Linear(vis_dim, vis_dim // 4), nn.GELU(), nn.Linear(vis_dim // 4, vis_dim // 8), nn.GELU(), ) self.vis_dim = vis_dim # Perceiver resampler to reduce sequence length of vision features self.perceiver = PerceiverResampler(dim=self.vis_dim, num_latents=perceiver_num) # Final projection to embedding dimension self.fc = nn.Linear(self.vis_dim, self.embedding_dim) # Classification head for matching keywords self.cls_head = nn.Linear(self.vis_dim // 8, 1) def forward(self, text_input, vision_x, key_words_query=None): """ Forward pass for the embedding layer. Args: text_input: Text token indices [B, L] vision_x: Visual input features [B, S, C, H, W, D] key_words_query: Optional list of key words for contrastive learning Returns: tuple: (output_embeddings, loss_matching) - output_embeddings: Combined embeddings for text and vision - loss_matching: Contrastive loss for keyword matching (or None) """ if self.flag == 'Text': # Process in text mode B, S, C, H, W, D = vision_x.shape # Reshape for batch processing vision_x = rearrange(vision_x, "b S c h w d-> (b S) c h w d") # Process through vision encoder vision_x, pos_embedding = self.vision_encoder(vision_x) # Reshape back to batch format vision_x = rearrange(vision_x, "(b s F) v d -> b s F v d", b=B, s=S, F=1) loss_matching = None if key_words_query is not None: ## we do not use the following parts in final version. ## You can quota the following codes and if so the bert models will be useless. # key_words_query list[list[str]] B, words, each word matches corresponding vision_x embedding # Extract and deduplicate keywords query_words = [item for sublist in key_words_query for item in sublist] query_words = list(set(query_words)) # Limit number of keywords to process if len(query_words) > 16: random.shuffle(query_words) query_words = query_words[0:16] if query_words != []: # Create binary labels for contrastive learning contrastive_labels = torch.zeros(B, len(query_words)) # B Q for i, sublist in enumerate(key_words_query): for j, item in enumerate(query_words): if item in sublist: contrastive_labels[i, j] = 1 contrastive_labels = contrastive_labels.to(vision_x.dtype).to(vision_x.device) # Get BERT embeddings for keywords with torch.no_grad(): query_words_embedding = self.bert_tokenizer( query_words, padding='max_length', truncation=True, max_length=256, return_tensors="pt" ) query_words_embedding = self.bert_model( input_ids=query_words_embedding['input_ids'].to(vision_x.device), attention_mask=query_words_embedding['attention_mask'].to(vision_x.device) )['last_hidden_state'][:, 0, :].to(vision_x.dtype).to(vision_x.device) # Q,D # Project BERT embeddings to vision space query_words_embedding = self.bert_projection_fc(query_words_embedding) query_words_embedding = query_words_embedding.unsqueeze(0).repeat(B, 1, 1) # B,Q,D _, N, _ = query_words_embedding.shape # Pool vision features image_embedding = vision_x.mean(dim=1) # B V D average pooling to remove multimodality image_embedding = rearrange(image_embedding, "b F v d -> b (F v) d") pos_embedding = rearrange(pos_embedding, "(b s) v d -> b s v d", b=B, s=S)[:, 0, :, :] # Prepare inputs for transformer decoder image_embedding = image_embedding.transpose(0, 1) # (H/P W/P D/P) B D pos_embedding = pos_embedding.transpose(0, 1) # (H/P W/P D/P) B D query_words_embedding = query_words_embedding.transpose(0, 1) # N B D # Cross-attention between keywords and image features oo_embedding, _ = self.transformer_decoder( query_words_embedding, image_embedding, pos=pos_embedding ) oo_embedding = oo_embedding.transpose(0, 1) # B Q D oo_embedding = rearrange(oo_embedding, 'b n d -> (b n) d') oo_embedding = self.transformer_decoder_mlp(oo_embedding) oo_embedding = self.cls_head(oo_embedding).mean(dim=-1) oo_embedding = rearrange(oo_embedding, '(b n) -> b n', b=B, n=N) # B Q # Calculate contrastive loss loss_matching = F.binary_cross_entropy_with_logits(oo_embedding, contrastive_labels) # Process vision features through perceiver resampler vision_x = self.perceiver(vision_x) # reshapes to (b, S, n, d) n = vision_x.shape[2] # Project vision features to embedding dimension vision_x = rearrange(vision_x, "b s n d -> (b s n) d") vision_x = self.fc(vision_x) vision_x = rearrange(vision_x, "(b T) d -> b T d", b=B, T=n*S) # Combine text and vision embeddings embedding_weight = torch.cat([self.weight, self.figure_token_weight], dim=0) embedding_weight = embedding_weight.unsqueeze(0).repeat(B, 1, 1) embedding_weight = torch.cat([embedding_weight, vision_x], dim=1) # Convert text indices to one-hot and compute final embeddings text_input = F.one_hot(text_input, embedding_weight.shape[1]).to(vision_x.dtype).to(vision_x.device) out_put = torch.matmul(text_input, embedding_weight) ## useless for now. ignore the folowing code## # if self.flag == 'Seg': # B,C,H,W,D = vision_x.shape # _,N,_ = text_input.shape # latent_embedding, pos_embedding = self.vision_encoder(vision_x) # B (H/P W/P D/P) D # image_embedding = latent_embedding.transpose(0,1) # (H/P W/P D/P) B D # pos_embedding = pos_embedding.transpose(0,1) # (H/P W/P D/P) B D # text_input = text_input.transpose(0,1) # N B D # mask_embedding,_ = self.transformer_decoder(text_input, image_embedding, pos = pos_embedding) # mask_embedding = mask_embedding.transpose(0,1) # B N D # mask_embedding = rearrange(mask_embedding, 'b n d -> (b n) d') # mask_embedding = self.transformer_decoder_mlp(mask_embedding) # mask_embedding = rearrange(mask_embedding, '(b n) d -> b n d', b=B, n=N,d = self.vis_dim // 8) # vision_x = rearrange(latent_embedding,'b (h w d) c -> b c h w d', h = (H // self.patch_size), w = (W // self.patch_size), d = (D // self.frame_patch_size), c=self.vis_dim) # vision_x = self.output_upscaling(vision_x) #B C H/4 W/4 D/4 # out_put = torch.einsum('bchwd,bnc->bnhwd', vision_x, mask_embedding) return out_put, loss_matching # model = MyEmbedding(vision_encoder_path = '') # text_input = torch.randint(low=0, high=3210, size=(4,2048)) # image_input = torch.randn((4,3,3,512,512,4)) # key_words_query = [[],[],[],['consoliation']] # print(model(text_input, image_input, key_words_query)) ================================================ FILE: Quick_demo/Model/RadFM/position_encoding.py ================================================ # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved """ Various positional encodings for the transformer. """ import math import torch from torch import nn from einops.layers.torch import Rearrange from einops import rearrange, repeat class PositionEmbeddingSine(nn.Module): """ This is a more standard version of the position embedding, very similar to the one used by the Attention is all you need paper, generalized to work on images. """ def __init__(self, num_pos_feats=64, temperature=10000, normalize=False, scale=None): super().__init__() self.num_pos_feats = num_pos_feats self.temperature = temperature self.normalize = normalize if scale is not None and normalize is False: raise ValueError("normalize should be True if scale is passed") if scale is None: scale = 2 * math.pi self.scale = scale def forward(self, tensor_list): x = tensor_list.tensors mask = tensor_list.mask assert mask is not None not_mask = ~mask y_embed = not_mask.cumsum(1, dtype=torch.float32) x_embed = not_mask.cumsum(2, dtype=torch.float32) if self.normalize: eps = 1e-6 y_embed = y_embed / (y_embed[:, -1:, :] + eps) * self.scale x_embed = x_embed / (x_embed[:, :, -1:] + eps) * self.scale dim_t = torch.arange(self.num_pos_feats, dtype=torch.float32, device=x.device) dim_t = self.temperature ** (2 * (dim_t // 2) / self.num_pos_feats) pos_x = x_embed[:, :, :, None] / dim_t pos_y = y_embed[:, :, :, None] / dim_t pos_x = torch.stack((pos_x[:, :, :, 0::2].sin(), pos_x[:, :, :, 1::2].cos()), dim=4).flatten(3) pos_y = torch.stack((pos_y[:, :, :, 0::2].sin(), pos_y[:, :, :, 1::2].cos()), dim=4).flatten(3) pos = torch.cat((pos_y, pos_x), dim=3).permute(0, 3, 1, 2) return pos class PositionEmbeddingLearned(nn.Module): """ Absolute pos embedding, learned. """ def __init__(self, num_pos_feats=256): super().__init__() self.row_embed = nn.Embedding(50, num_pos_feats) self.col_embed = nn.Embedding(50, num_pos_feats) self.reset_parameters() def reset_parameters(self): nn.init.uniform_(self.row_embed.weight) nn.init.uniform_(self.col_embed.weight) def forward(self, tensor_list): x = tensor_list.tensors h, w = x.shape[-2:] i = torch.arange(w, device=x.device) j = torch.arange(h, device=x.device) x_emb = self.col_embed(i) y_emb = self.row_embed(j) pos = torch.cat([ x_emb.unsqueeze(0).repeat(h, 1, 1), y_emb.unsqueeze(1).repeat(1, w, 1), ], dim=-1).permute(2, 0, 1).unsqueeze(0).repeat(x.shape[0], 1, 1, 1) return pos class PositionEmbeddingLearned3d(nn.Module): """ Absolute pos embedding, learned. """ def __init__(self, num_pos_feats=256,h_patch_num = 16, w_patch_num = 16,d_patch_num = 64): super().__init__() self.h_patch_num = h_patch_num self.w_patch_num = w_patch_num self.d_patch_num = d_patch_num self.row_embed = nn.Embedding(h_patch_num, num_pos_feats) self.col_embed = nn.Embedding(w_patch_num, num_pos_feats) self.dep_embed = nn.Embedding(d_patch_num, num_pos_feats) self.reset_parameters() def reset_parameters(self): nn.init.uniform_(self.row_embed.weight) nn.init.uniform_(self.col_embed.weight) nn.init.uniform_(self.dep_embed.weight) def forward(self, B, h, w, d,x): i = (torch.arange(h, device=x.device) + 1)* (self.h_patch_num // h) -1 j = (torch.arange(w, device=x.device) + 1)* (self.w_patch_num // w) -1 k = (torch.arange(d, device=x.device) + 1)* (self.d_patch_num // d) -1 x_emb = self.row_embed(i).unsqueeze(1).unsqueeze(2).repeat(1,w,d,1) y_emb = self.col_embed(j).unsqueeze(0).unsqueeze(2).repeat(h,1,d,1) z_emb = self.dep_embed(k).unsqueeze(0).unsqueeze(1).repeat(h,w,1,1) pos = torch.cat([x_emb,y_emb,z_emb,], dim=-1).unsqueeze(0).repeat(B, 1, 1, 1, 1) pos = rearrange(pos,'b h w d c -> b (h w d) c') return pos def build_position_encoding(args): N_steps = args.hidden_dim // 2 if args.position_embedding in ('v2', 'sine'): # TODO find a better way of exposing other arguments position_embedding = PositionEmbeddingSine(N_steps, normalize=True) elif args.position_embedding in ('v3', 'learned'): position_embedding = PositionEmbeddingLearned(N_steps) else: raise ValueError(f"not supported {args.position_embedding}") return position_embedding # Pos = PositionEmbeddingLearned3d() # x = torch.randn((8,3,32,32,1)) # print(Pos(8,16,16,1,x)) ================================================ FILE: Quick_demo/Model/RadFM/transformer_decoder.py ================================================ """ Code modified from DETR tranformer: https://github.com/facebookresearch/detr Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved """ import copy from typing import Optional, List import pickle as cp import torch import torch.nn.functional as F from torch import nn, Tensor class TransformerDecoder(nn.Module): def __init__(self, decoder_layer, num_layers, norm=None, return_intermediate=False): super().__init__() self.layers = _get_clones(decoder_layer, num_layers) self.num_layers = num_layers self.norm = norm self.return_intermediate = return_intermediate def forward(self, tgt, memory, tgt_mask: Optional[Tensor] = None, memory_mask: Optional[Tensor] = None, tgt_key_padding_mask: Optional[Tensor] = None, memory_key_padding_mask: Optional[Tensor] = None, pos: Optional[Tensor] = None, query_pos: Optional[Tensor] = None): output = tgt T,B,C = memory.shape intermediate = [] atten_layers = [] for n,layer in enumerate(self.layers): residual=True output,ws = layer(output, memory, tgt_mask=tgt_mask, memory_mask=memory_mask, tgt_key_padding_mask=tgt_key_padding_mask, memory_key_padding_mask=memory_key_padding_mask, pos=pos, query_pos=query_pos,residual=residual) atten_layers.append(ws) if self.return_intermediate: intermediate.append(self.norm(output)) if self.norm is not None: output = self.norm(output) if self.return_intermediate: intermediate.pop() intermediate.append(output) if self.return_intermediate: return torch.stack(intermediate) return output,atten_layers class TransformerDecoderLayer(nn.Module): def __init__(self, d_model, nhead, dim_feedforward=2048, dropout=0.1, activation="relu", normalize_before=False): super().__init__() self.self_attn = nn.MultiheadAttention(d_model, nhead, dropout=dropout) self.multihead_attn = nn.MultiheadAttention(d_model, nhead, dropout=dropout) # Implementation of Feedforward model self.linear1 = nn.Linear(d_model, dim_feedforward) self.dropout = nn.Dropout(dropout) self.linear2 = nn.Linear(dim_feedforward, d_model) self.norm1 = nn.LayerNorm(d_model) self.norm2 = nn.LayerNorm(d_model) self.norm3 = nn.LayerNorm(d_model) self.dropout1 = nn.Dropout(dropout) self.dropout2 = nn.Dropout(dropout) self.dropout3 = nn.Dropout(dropout) self.activation = _get_activation_fn(activation) self.normalize_before = normalize_before def with_pos_embed(self, tensor, pos: Optional[Tensor]): return tensor if pos is None else tensor + pos def forward_post(self, tgt, memory, tgt_mask: Optional[Tensor] = None, memory_mask: Optional[Tensor] = None, tgt_key_padding_mask: Optional[Tensor] = None, memory_key_padding_mask: Optional[Tensor] = None, pos: Optional[Tensor] = None, query_pos: Optional[Tensor] = None, residual=True): q = k = self.with_pos_embed(tgt, query_pos) tgt2,ws = self.self_attn(q, k, value=tgt, attn_mask=tgt_mask, key_padding_mask=tgt_key_padding_mask) tgt = self.norm1(tgt) tgt2,ws = self.multihead_attn(query=self.with_pos_embed(tgt, query_pos), key=self.with_pos_embed(memory, pos), value=memory, attn_mask=memory_mask, key_padding_mask=memory_key_padding_mask) # attn_weights [B,NUM_Q,T] tgt = tgt + self.dropout2(tgt2) tgt = self.norm2(tgt) tgt2 = self.linear2(self.dropout(self.activation(self.linear1(tgt)))) tgt = tgt + self.dropout3(tgt2) tgt = self.norm3(tgt) return tgt,ws def forward_pre(self, tgt, memory, tgt_mask: Optional[Tensor] = None, memory_mask: Optional[Tensor] = None, tgt_key_padding_mask: Optional[Tensor] = None, memory_key_padding_mask: Optional[Tensor] = None, pos: Optional[Tensor] = None, query_pos: Optional[Tensor] = None): tgt2 = self.norm1(tgt) q = k = self.with_pos_embed(tgt2, query_pos) tgt2,ws = self.self_attn(q, k, value=tgt2, attn_mask=tgt_mask, key_padding_mask=tgt_key_padding_mask) tgt = tgt + self.dropout1(tgt2) tgt2 = self.norm2(tgt) tgt2,attn_weights = self.multihead_attn(query=self.with_pos_embed(tgt2, query_pos), key=self.with_pos_embed(memory, pos), value=memory, attn_mask=memory_mask, key_padding_mask=memory_key_padding_mask) tgt = tgt + self.dropout2(tgt2) tgt2 = self.norm3(tgt) tgt2 = self.linear2(self.dropout(self.activation(self.linear1(tgt2)))) tgt = tgt + self.dropout3(tgt2) return tgt,attn_weights def forward(self, tgt, memory, tgt_mask: Optional[Tensor] = None, memory_mask: Optional[Tensor] = None, tgt_key_padding_mask: Optional[Tensor] = None, memory_key_padding_mask: Optional[Tensor] = None, pos: Optional[Tensor] = None, query_pos: Optional[Tensor] = None, residual=True): if self.normalize_before: return self.forward_pre(tgt, memory, tgt_mask, memory_mask, tgt_key_padding_mask, memory_key_padding_mask, pos, query_pos) return self.forward_post(tgt, memory, tgt_mask, memory_mask, tgt_key_padding_mask, memory_key_padding_mask, pos, query_pos,residual) def _get_clones(module, N): return nn.ModuleList([copy.deepcopy(module) for i in range(N)]) def _get_activation_fn(activation): """Return an activation function given a string""" if activation == "relu": return F.relu if activation == "gelu": return F.gelu if activation == "glu": return F.glu raise RuntimeError(F"activation should be relu/gelu, not {activation}.") ================================================ FILE: Quick_demo/Model/RadFM/utils.py ================================================ from .blocks import ModifiedResNet,PMC_CLIP_cfg import torch from torchvision import transforms from PIL import Image import torch.nn as nn def extend_instance(obj, mixin): """Apply mixins to a class instance after creation""" base_cls = obj.__class__ base_cls_name = obj.__class__.__name__ obj.__class__ = type( base_cls_name, (mixin, base_cls), {} ) # mixin needs to go first for our forward() logic to work def getattr_recursive(obj, att): """ Return nested attribute of obj Example: getattr_recursive(obj, 'a.b.c') is equivalent to obj.a.b.c """ if att == "": return obj i = att.find(".") if i < 0: return getattr(obj, att) else: return getattr_recursive(getattr(obj, att[:i]), att[i + 1 :]) def setattr_recursive(obj, att, val): """ Set nested attribute of obj Example: setattr_recursive(obj, 'a.b.c', val) is equivalent to obj.a.b.c = val """ if "." in att: obj = getattr_recursive(obj, ".".join(att.split(".")[:-1])) setattr(obj, att.split(".")[-1], val) def get_visual_encoder(model_str): """ Args: str (_type_): str_to_model_path Return: vision_model, visual_dim, img_preprocessor """ normalize = transforms.Normalize((0.485, 0.456, 0.406), (0.229, 0.224, 0.225)) img_preprocessor = transforms.Compose([ transforms.Resize((512,512), interpolation=Image.BICUBIC), transforms.ToTensor(), normalize, ]) if 'PMC-CLIP' in model_str: #vision_cfg = json.load(open(model_args.visual_model_config,'r'))['vision_cfg'] vision_cfg = PMC_CLIP_cfg() vision_heads = vision_cfg.width * 32 // vision_cfg.head_width vision_model = ModifiedResNet( layers=vision_cfg.layers, heads=vision_heads, output_dim = 768, image_size=vision_cfg.image_size, width=vision_cfg.width ) vision_model = vision_load_pretrain(vision_model,model_str) vision_model = nn.Sequential(*list(vision_model.children())[:-2]) visual_dim = 1024 return vision_model,visual_dim,img_preprocessor def vision_load_pretrain(resnet,model_path): checkpoint = torch.load(model_path, map_location='cpu') state_dict = checkpoint['state_dict'] state_dict = {k.replace('module.visual.',''): v for k, v in state_dict.items() if '.visual' in k} resnet.load_state_dict(state_dict) return resnet ================================================ FILE: Quick_demo/Model/RadFM/vit_3d.py ================================================ import torch from torch import nn from einops import rearrange, repeat from einops.layers.torch import Rearrange from .position_encoding import PositionEmbeddingLearned3d # helpers def pair(t): return t if isinstance(t, tuple) else (t, t) # classes class PreNorm(nn.Module): def __init__(self, dim, fn): super().__init__() self.norm = nn.LayerNorm(dim) self.fn = fn def forward(self, x, **kwargs): return self.fn(self.norm(x), **kwargs) class FeedForward(nn.Module): def __init__(self, dim, hidden_dim, dropout = 0.): super().__init__() self.net = nn.Sequential( nn.Linear(dim, hidden_dim), nn.GELU(), nn.Dropout(dropout), nn.Linear(hidden_dim, dim), nn.Dropout(dropout) ) def forward(self, x): return self.net(x) class Attention(nn.Module): def __init__(self, dim, heads = 8, dim_head = 64, dropout = 0.): super().__init__() inner_dim = dim_head * heads project_out = not (heads == 1 and dim_head == dim) self.heads = heads self.scale = dim_head ** -0.5 self.attend = nn.Softmax(dim = -1) self.dropout = nn.Dropout(dropout) self.to_qkv = nn.Linear(dim, inner_dim * 3, bias = False) self.to_out = nn.Sequential( nn.Linear(inner_dim, dim), nn.Dropout(dropout) ) if project_out else nn.Identity() def forward(self, x): qkv = self.to_qkv(x).chunk(3, dim = -1) q, k, v = map(lambda t: rearrange(t, 'b n (h d) -> b h n d', h = self.heads), qkv) dots = torch.matmul(q, k.transpose(-1, -2)) * self.scale attn = self.attend(dots) attn = self.dropout(attn) out = torch.matmul(attn, v) out = rearrange(out, 'b h n d -> b n (h d)') return self.to_out(out) class Transformer(nn.Module): def __init__(self, dim, depth, heads, dim_head, mlp_dim, dropout = 0.): super().__init__() self.layers = nn.ModuleList([]) for _ in range(depth): self.layers.append(nn.ModuleList([ PreNorm(dim, Attention(dim, heads = heads, dim_head = dim_head, dropout = dropout)), PreNorm(dim, FeedForward(dim, mlp_dim, dropout = dropout)) ])) def forward(self, x): for attn, ff in self.layers: x = attn(x) + x x = ff(x) + x return x class ViT(nn.Module): def __init__(self, *, image_size, image_patch_size, frames, frame_patch_size, dim, depth, heads, mlp_dim, pool = 'cls', channels = 3, dim_head = 64, dropout = 0., emb_dropout = 0.): super().__init__() image_height, image_width = pair(image_size) patch_height, patch_width = pair(image_patch_size) assert image_height % patch_height == 0 and image_width % patch_width == 0, 'Image dimensions must be divisible by the patch size.' assert frames % frame_patch_size == 0, 'Frames must be divisible by frame patch size' self.patch_height = patch_height self.patch_width = patch_width self.frame_patch_size = frame_patch_size num_patches = (image_height // patch_height) * (image_width // patch_width) * (frames // frame_patch_size) patch_dim = channels * patch_height * patch_width * frame_patch_size assert pool in {'cls', 'mean'}, 'pool type must be either cls (cls token) or mean (mean pooling)' self.to_patch_embedding = nn.Sequential( Rearrange('b c (h p1) (w p2) (f pf) -> b (h w f) (p1 p2 pf c)', p1 = patch_height, p2 = patch_width, pf = frame_patch_size), nn.LayerNorm(patch_dim), nn.Linear(patch_dim, dim), nn.LayerNorm(dim), ) self.pos_embedding = PositionEmbeddingLearned3d(dim // 3,(image_height // patch_height), (image_width // patch_width), (frames // frame_patch_size)) self.dropout = nn.Dropout(emb_dropout) self.transformer = Transformer(dim, depth, heads, dim_head, mlp_dim, dropout) def forward(self, video): B, C, H, W, D = video.shape x = self.to_patch_embedding(video) b, n, _ = x.shape pos = self.pos_embedding(B, H // self.patch_height, W // self.patch_width, D // self.frame_patch_size,x) x += pos x = self.dropout(x) x = self.transformer(x) return x,pos ================================================ FILE: Quick_demo/test.py ================================================ # Import necessary libraries for data processing, model loading, and inference import tqdm.auto as tqdm import torch.nn.functional as F from typing import Optional, Dict, Sequence from typing import List, Optional, Tuple, Union import transformers from dataclasses import dataclass, field from Model.RadFM.multimodality_model import MultiLLaMAForCausalLM import torch from transformers import AutoModelForCausalLM, AutoTokenizer, LlamaTokenizer from torchvision import transforms from PIL import Image def get_tokenizer(tokenizer_path, max_img_size=100, image_num=32): ''' Initialize the tokenizer with special tokens for image handling Args: tokenizer_path: Path to the base tokenizer max_img_size: Maximum number of images supported in a prompt image_num: Number of token embeddings per image Returns: Tuple of (tokenizer, image_padding_tokens) ''' if isinstance(tokenizer_path, str): image_padding_tokens = [] # Load the base tokenizer from the provided path text_tokenizer = LlamaTokenizer.from_pretrained( tokenizer_path, ) # Define initial special tokens for image markup special_token = {"additional_special_tokens": ["", ""]} # Generate unique tokens for each image position and patch for i in range(max_img_size): image_padding_token = "" for j in range(image_num): image_token = "" image_padding_token = image_padding_token + image_token special_token["additional_special_tokens"].append("") # Store the concatenated tokens for each image image_padding_tokens.append(image_padding_token) # Add all special tokens to the tokenizer text_tokenizer.add_special_tokens( special_token ) # Configure standard special tokens for LLaMA models text_tokenizer.pad_token_id = 0 text_tokenizer.bos_token_id = 1 text_tokenizer.eos_token_id = 2 return text_tokenizer, image_padding_tokens def combine_and_preprocess(question, image_list, image_padding_tokens): ''' Combine text and images into a multimodal input format Args: question: Text input or question to process image_list: List of images with their metadata image_padding_tokens: Special tokens for image placeholders Returns: Tuple of (processed_text, processed_images_tensor) ''' # Define image transformation pipeline transform = transforms.Compose([ transforms.RandomResizedCrop([512, 512], scale=(0.8, 1.0), interpolation=transforms.InterpolationMode.BICUBIC), transforms.ToTensor(), ]) images = [] new_qestions = [_ for _ in question] # Convert question string to list of characters padding_index = 0 # Process each image in the list for img in image_list: img_path = img['img_path'] position = img['position'] # Where to insert the image in the text # Load and transform the image image = Image.open(img_path).convert('RGB') image = transform(image) image = image.unsqueeze(0).unsqueeze(-1) # Add batch and depth dimensions (c,w,h,d) # Resize the image to target dimensions target_H = 512 target_W = 512 target_D = 4 # This can be different for 3D and 2D images. For demonstration we here set this as the default sizes for 2D images. images.append(torch.nn.functional.interpolate(image, size=(target_H, target_W, target_D))) # Insert image placeholder token at the specified position in text new_qestions[position] = "" + image_padding_tokens[padding_index] + "" + new_qestions[position] padding_index += 1 # Stack all images into a batch and add batch dimension vision_x = torch.cat(images, dim=1).unsqueeze(0) # Cat tensors and expand the batch_size dim # Join the character list back into a string text = ''.join(new_qestions) return text, vision_x def main(): ''' Main function to demonstrate the RadFM model inference ''' print("Setup tokenizer") # Initialize tokenizer with special image tokens text_tokenizer, image_padding_tokens = get_tokenizer('./Language_files') print("Finish loading tokenizer") ### Initialize a simple case for demo ### print("Setup demo case") # Define a medical question about a chest X-ray question = "Can you identify any visible signs of Cardiomegaly in the image?" # Specify the image path and where to insert it in the question image = [ { 'img_path': './view1_frontal.jpg', 'position': 0, # Insert at the beginning of the question }, # Can add arbitrary number of images ] # Combine text and images into model-ready format text, vision_x = combine_and_preprocess(question, image, image_padding_tokens) print("Finish loading demo case") print("Setup Model") # Initialize the multimodal model model = MultiLLaMAForCausalLM( lang_model_path='./Language_files', # Build up model based on LLaMa-13B config ) # Load pretrained model weights ckpt = torch.load('./pytorch_model.bin', map_location='cpu') # Please download our checkpoint from huggingface and decompress the original zip file first model.load_state_dict(ckpt) print("Finish loading model") # Move model to GPU and set to evaluation mode model = model.to('cuda') model.eval() # Run inference without gradient computation with torch.no_grad(): # Tokenize the combined text with image placeholders lang_x = text_tokenizer( text, max_length=2048, truncation=True, return_tensors="pt" )['input_ids'].to('cuda') # Move image tensor to GPU vision_x = vision_x.to('cuda') # Generate text response generation = model.generate(lang_x, vision_x) # Decode the generated token IDs to text generated_texts = text_tokenizer.batch_decode(generation, skip_special_tokens=True) # Print results print('---------------------------------------------------') print('Input: ', question) print('Output: ', generated_texts[0]) if __name__ == "__main__": main() ================================================ FILE: README.md ================================================ # RadFM The official code for the paper "Towards Generalist Foundation Model for Radiology by Leveraging Web-scale 2D&3D Medical Data" [ArXiv](http://arxiv.org/abs/2308.02463) [Website](https://chaoyi-wu.github.io/RadFM/) [Model checkpoint](https://huggingface.co/chaoyi-wu/RadFM) In this project, we collect a large-scale medical multi-modal dataset, MedMD, with **16M** 2D or **3D** images. We train a new medical multi-modal generative model RadFM on it, enabling both **2D and 3D** scans, multi-image input and visual-language interleaving cases. ## Latest News: All Datasets are released! We have updated the links in [our dataset table](#dataset-links). You can find all our text part data in https://huggingface.co/datasets/chaoyi-wu/RadFM_data_csv. For decompressing the splited compression files in most cases, please check the following code in linux: ``` cat zip.z* > myzip.zip unzip myzip.zip ``` ## Quick Start: For quick start, you can check the `Quick_demo` path. We demonstrate a simple diagnosis case here to show how to inference with our model. Feel free to modify it as you want. - S1. Download [Model checkpoint](https://huggingface.co/chaoyi-wu/RadFM) or form [baiduyun](https://pan.baidu.com/s/1A-K5nXCbvWAVqvb6dLjYJg?pwd=q1eo) (No need for decompressing). - S2. Decompress the original zip file, you can get a `pytorch_model.bin`. - S3. put `pytorch_model.bin` under path `Quick_demo/`. - S4. python `test.py` and you can get a conversation as: > Input: Can you identify any visible signs of Cardiomegaly in the image? > Output: yes By the way, never try to perform this in cpu and gpus are all you need :). ## Pre-train: For re-training a model on our dataset or large-scale testing our pre-train model, you can check ```src```. Simply, ```train.py``` for training and ```test.py``` for testing. * Check the [data_csv](https://huggingface.co/datasets/chaoyi-wu/RadFM_data_csv) to get how different datasets are processed and download them into `src/Dataset/data_csv` * Modify the path as you disire, and check ```src/train.py``` to pre-train or ```src/train.py``` to test. ## A Detailed Code Explanation: In this part we will introduce the ```src``` directory in detail and the `Quick_demo` is similar. ### Dataset In the `Dataset` directory, there are two main Python files: - `multi_dataset.py` - `multi_dataset_test.py` These files are nearly identical in structure and functionality. The primary difference lies in their usage: `multi_dataset.py` is used for **training**, while `multi_dataset_test.py` is used for **testing**. Both files define a key class: `multi_dataset`. This class provides a generative training format that supports multiple datasets. When an instance of this class is called to retrieve a sample, it returns a dictionary with the following structure: ``` { 'vision_x': vision_x, 'lang_x':lang_x, 'attention_mask': attention_mask, 'labels':labels, 'loss_reweight': reweight_tensor, 'key_words_query': emphasize_words } ``` where, each means: - **`vision_x`**: A tensor representing input images, shaped as **3 × H × W × D**, where `3` is the number of channels (RGB). If only 2D images are provided, they are repeated along the depth dimension (`D = 4` by default). - **`lang_x`** and **`attention_mask`**: These represent tokenized text inputs and corresponding attention masks. They may include special image placeholders, which are replaced with image embedding tokens during the model's forward pass. - **`labels`**: Token IDs corresponding to the output text (e.g., answers). As in standard LLM training, a value of `-100` marks tokens that should be ignored in the loss computation. This supports both reconstruction pretraining and instruction tuning (response-only) loss. - **`loss_reweight`**: An optional tensor used to emphasize specific medical-related terms (e.g., USMLE keywords). It is applied to the per-token autoregressive loss to compute a weighted final loss. - **`key_words_query`**: Currently unused. It was part of an earlier experiment involving query-based classification loss. You can safely ignore this field by setting it to an empty list (`[]`). Then in the sub-directory `dataset`, it contains many detailed dataset-wise classes along with our used prompt for organizing them into generative training style, if you want to see how we prompt different dataset you show check the correponding file carefully. For example the chestxray diagnosis dataset listed in our paper are unfiedly preprocess and prompted in `chestxray.py` with the prompt format listed in `yes_no_prompt.json`. ### My_Trainer and datasampler.py `My_trainer` is a customized version of the `trainer.py` module from `transformers==4.28.1`. The main motivation for creating this separate trainer file is that the original `Trainer` class does not support passing a custom `data_sampler` during `DataLoader` initialization. Our goal is to **prevent mixing 2D and 3D data within the same training batch**, which can lead to significant overhead when trying to unify the tensor dimensions. By controlling the sampling strategy, we can avoid unnecessary data expansion and improve training efficiency. The changes in `My_trainer` are clearly marked with the comment tag `### 吴超逸加 ###`, retained in **Chinese** for easier identification and tracking. These modifications can be integrated into any newer version of the `transformers` library as needed. The `data_sampler.py` python file contains a new distributed sampling function implemented to ensure proper batch organization. It samples either **2D** or **3D** data exclusively within a single batch. This design avoids the computational cost of dynamically expanding 2D data to match 3D inputs when they are mixed in a batch. ### train.py and test.py The two python files are easy to understand. `train.py` is used to train the model including pre-training and instruction tuning. `test.py` is used to perform testing on different datset. Please check the [data_csv](https://huggingface.co/datasets/chaoyi-wu/RadFM_data_csv) download the used train/test split csv files into `src/Dataset/data_csv` along with the image sources from different dataset official website and ensure the image path witten in the csv files have been changed to your local path, then you can run the `test.py` successfully. Please ensure you have at least one Nvidia A100 (80GB) to surpport the inference, otherwise it will be quite slow that you can never obtain the results. The output csv file will be like that presented in `src/output_csv_example/caption_example.csv` (an output example for chestxray report generation). You can compare your output format with it to check whether your code is right. Notably, in `test.py`. we adopt inference batch size as one by default to avoid some necessary padding. You can change it to a larger size but please ensure your padding tokens~(shoud be left padding) and the attention mask is set correctly according to the classic LLM batch-wise generation guideline. Otherwise the model cannot output correctly due to take the padding token into foward caculation. ### Model The main python files in the Model path are two, i.e., `RadFM//multimodality_model.py` and `RadFM/my_embedding_layer.py`. In the `multimodality_model.py`, it defines a class `MultiLLaMAForCausalLM`, it is similar to classic `CausalLM` classes. The forward function in this class is response for the LLM-based fusion and decoding process. As shown by the code, it will first call ``` input_embedding,loss_match= self.embedding_layer(lang_x, vision_x,key_words_query) ``` that the `self.embedding_layer` is defined by `RadFM/my_embedding_layer.py`. The `input_embedding` is the visual-text mixed token embedding sequancing. `loss_mathc` is related to `key_words_query` input and samely, is aborted now, that always equals zero. Then the forward functin will take the `input_embedding` into any LLMs to obtain the final textual generation and calculate the auto-regressive loss based on the input labels and loss_reweight In `my_embedding_layer.py`, the vision input is first processed using a **3D Vision Transformer (ViT)** and a **Perceiver** model. This results in a set of image tokens with shape **S × 32 × d**, where: - `S` is the number of images (or scans) in a training sample, - `32` is a fixed token length per image, - `d` is the embedding dimension. These generated image tokens are then appended to the language token embedding layer, resulting in an expanded embedding matrix of shape **(Vocab_size + 32 × S) × d**. This design allows each image token to be referenced using special placeholder token IDs that are defined as vocab_size+n in expanded LLM tokenizer. By structuring the embedding layer in this way, we canperform the standard token embedding lookup mechanism without requiring explicit loops to insert the token embeddings into textual and reorganize the lenthy embedding output again during the forward pass. When the batch size `B` is greater than 1, each sample in the batch may have different image tokens. Therefore, during the forward pass, each training sample must be **matched with its own corresponding expanded embedding layer**, i.e., the expanded matrixs is of size **B × (Vocab_size + 32 × S) × d**to correctly replace the image placeholders with the appropriate image encoding features. ## Case Study: Some cases produced by our final model: ## Dataset-Links: Datasets downloading URL: | Dataset Name | Link | Access | |--------------|------|--------| | Rad3D-series | - | Please mail the Radiopaedia team to obtain access approvement. Then we can share with you. | | MPx-series | - | Download from the official websit. | | PMC-Figures| https://pan.baidu.com/s/1Src_rhXsaOFp8zJ_3zMFsQ?pwd=p3ne | Open Access | | PMC-Inline | https://huggingface.co/datasets/chaoyi-wu/PMC-Inline | Open Access | | PMC-CaseReport | [Original version](https://huggingface.co/datasets/chaoyi-wu/PMC-CaseReport_original), [Filtered version](https://huggingface.co/datasets/chaoyi-wu/PMC-CaseReport) | Open Access | | VinDr-Mammo | https://www.physionet.org/content/vindr-mammo/1.0.0/ | Credentialed Access | | VinDr-SpineXR | https://www.physionet.org/content/vindr-spinexr/1.0.0/ | Credentialed Access | | VinDr-PCXR | https://physionet.org/content/vindr-pcxr/1.0.0/ | Credentialed Access | | PMC-OA | https://huggingface.co/datasets/axiong/pmc_oa_beta | Open Access | | PMC-VQA | https://huggingface.co/datasets/xmcmic/PMC-VQA | Open Access | | VQA-RAD | https://osf.io/89kps/| Open Access | | SLAKE | https://www.med-vqa.com/slake/ | Open Access | | MIMIC-CXR | https://physionet.org/content/mimic-cxr/2.0.0 | Credentialed Access | | VinDr-CXR | https://physionet.org/content/vindr-cxr/1.0.0/ | Credentialed Access | | NIH ChestXray14 | https://nihcc.app.box.com/v/ChestXray-NIHCC/folder/36938765345 | Open Access | | CheXpert | https://aimi.stanford.edu/chexpert-chest-x-rays | Open Access | | Covid-CXR2 | https://www.kaggle.com/datasets/andyczhao/covidx-cxr2 | Open Access | | NLM-TB | [Montgomery](https://openi.nlm.nih.gov/imgs/collections/NLM-MontgomeryCXRSet.zip), [ChinaSet](https://openi.nlm.nih.gov/imgs/collections/ChinaSet_AllFiles.zip) | Open Access | | Object-CXR | https://web.archive.org/web/20201127235812/https://jfhealthcare.github.io/object-CXR/ | Open Access | | OpenI | https://www.kaggle.com/datasets/raddar/chest-xrays-indiana-university | Open Access | | RSNA| https://www.rsna.org/education/ai-resources-and-training/ai-image-challenge/rsna-pneumonia-detection-challenge-2018| Open Access | | SIIM-ACR | https://www.kaggle.com/datasets/jesperdramsch/siim-acr-pneumothorax-segmentation-data| Open Access | The split of each dataset can be found in https://huggingface.co/datasets/chaoyi-wu/RadFM_data_csv you just need to download the image part from each datasets. ## Dataset Codes and Files Linking: Check the following table to see how to process each dataset and how each file in https://huggingface.co/datasets/chaoyi-wu/RadFM_data_csv is linked to each dataset: | Dataset Name | Process Dataset Code | Related Filename | |--------------|------|--------| | Rad3D-series | [jpg2nii Process Code](https://github.com/chaoyi-wu/RadFM/blob/main/src/Dataset/dataset/jpg2nii_data_convert.py), [nii2npy Process Code](https://github.com/chaoyi-wu/RadFM/blob/main/src/Dataset/dataset/nii2npy_for_radiopaedio.py), [Final Datset to Read npy and Related Texts](https://github.com/chaoyi-wu/RadFM/blob/main/src/Dataset/dataset/radiopaedia.py) | radiology_article_npy_train/test.json | | MPx-series | [MedPix Dataset](https://github.com/chaoyi-wu/RadFM/blob/main/src/Dataset/dataset/MedPix_dataset.py) | MedPix_muli_train/test.csv, MedPix_single_train/test.csv| | PMC-Inline | [Paper-inline Dataset](https://github.com/chaoyi-wu/RadFM/blob/main/src/Dataset/dataset/paper_inline.py) | paper_train.csv (This dataset is not used for evaluation) | | PMC-CaseReport | [Case-report Dataset](https://github.com/chaoyi-wu/RadFM/blob/main/src/Dataset/dataset/case_report.py) | filtered_case_report_train/test.csv | | VinDr-Mammo | [Diagnosis Open Format Dataset](https://github.com/chaoyi-wu/RadFM/blob/main/src/Dataset/dataset/chestxray.py), [Diagnosis Close (yes/no) Format Dataset](https://github.com/chaoyi-wu/RadFM/blob/main/src/Dataset/dataset/binary.py) | mammo_balance_train/test.csv | | VinDr-SpineXR | [Diagnosis Open Format Dataset](https://github.com/chaoyi-wu/RadFM/blob/main/src/Dataset/dataset/chestxray.py), [Diagnosis Close (yes/no) Format Dataset](https://github.com/chaoyi-wu/RadFM/blob/main/src/Dataset/dataset/binary.py) | spinexr_balance_train/test.csv | | VinDr-PCXR | [Diagnosis Open Format Dataset](https://github.com/chaoyi-wu/RadFM/blob/main/src/Dataset/dataset/chestxray.py), [Diagnosis Close (yes/no) Format Dataset](https://github.com/chaoyi-wu/RadFM/blob/main/src/Dataset/dataset/binary.py) | pcxr_balance_train/test.csv | | PMC-OA | [Pmcoa Dataset](https://github.com/chaoyi-wu/RadFM/blob/main/src/Dataset/dataset/pmcoa.py) | pmcoa_image_caption_train/test.csv | | PMC-VQA | [vqa Dataset](https://github.com/chaoyi-wu/RadFM/blob/main/src/Dataset/dataset/vqa.py) | pmcvaq_train/test.csv| | VQA-RAD | [vqa Dataset](https://github.com/chaoyi-wu/RadFM/blob/main/src/Dataset/dataset/vqa.py)| vqarad_train/test.csv | | SLAKE | [vqa Dataset](https://github.com/chaoyi-wu/RadFM/blob/main/src/Dataset/dataset/vqa.py) | slakevqa_train/test.csv | | MIMIC-CXR | [CXR Open Captioning Dataset](https://github.com/chaoyi-wu/RadFM/blob/main/src/Dataset/dataset/chestxray.py) | mimic_caption_train/test.csv | | VinDr-CXR | [Diagnosis Open Format Dataset](https://github.com/chaoyi-wu/RadFM/blob/main/src/Dataset/dataset/chestxray.py), [Diagnosis Close (yes/no) Format Dataset](https://github.com/chaoyi-wu/RadFM/blob/main/src/Dataset/dataset/binary.py) | chestxray_balance_train_new.csv, chestxray_balance_test.csv| | NIH ChestXray14 | [Diagnosis Open Format Dataset](https://github.com/chaoyi-wu/RadFM/blob/main/src/Dataset/dataset/chestxray.py), [Diagnosis Close (yes/no) Format Dataset](https://github.com/chaoyi-wu/RadFM/blob/main/src/Dataset/dataset/binary.py) | chestxray_balance_train_new.csv, chestxray_balance_test.csv | | CheXpert | [Diagnosis Open Format Dataset](https://github.com/chaoyi-wu/RadFM/blob/main/src/Dataset/dataset/chestxray.py), [Diagnosis Close (yes/no) Format Dataset](https://github.com/chaoyi-wu/RadFM/blob/main/src/Dataset/dataset/binary.py) | chestxray_balance_train_new.csv, chestxray_balance_test.csv | | Covid-CXR2 | [Diagnosis Open Format Dataset](https://github.com/chaoyi-wu/RadFM/blob/main/src/Dataset/dataset/chestxray.py), [Diagnosis Close (yes/no) Format Dataset](https://github.com/chaoyi-wu/RadFM/blob/main/src/Dataset/dataset/binary.py) | chestxray_balance_train_new.csv, chestxray_balance_test.csv | | NLM-TB | [Diagnosis Open Format Dataset](https://github.com/chaoyi-wu/RadFM/blob/main/src/Dataset/dataset/chestxray.py), [Diagnosis Close (yes/no) Format Dataset](https://github.com/chaoyi-wu/RadFM/blob/main/src/Dataset/dataset/binary.py) | chestxray_balance_train_new.csv, chestxray_balance_test.csv | | Object-CXR | [Diagnosis Open Format Dataset](https://github.com/chaoyi-wu/RadFM/blob/main/src/Dataset/dataset/chestxray.py), [Diagnosis Close (yes/no) Format Dataset](https://github.com/chaoyi-wu/RadFM/blob/main/src/Dataset/dataset/binary.py) | chestxray_balance_train_new.csv, chestxray_balance_test.csv | | OpenI | [Diagnosis Open Format Dataset](https://github.com/chaoyi-wu/RadFM/blob/main/src/Dataset/dataset/chestxray.py), [Diagnosis Close (yes/no) Format Dataset](https://github.com/chaoyi-wu/RadFM/blob/main/src/Dataset/dataset/binary.py) | chestxray_balance_train_new.csv, chestxray_balance_test.csv | | RSNA| [Diagnosis Open Format Dataset](https://github.com/chaoyi-wu/RadFM/blob/main/src/Dataset/dataset/chestxray.py), [Diagnosis Close (yes/no) Format Dataset](https://github.com/chaoyi-wu/RadFM/blob/main/src/Dataset/dataset/binary.py)| chestxray_balance_train_new.csv, chestxray_balance_test.csv | | SIIM-ACR | [Diagnosis Open Format Dataset](https://github.com/chaoyi-wu/RadFM/blob/main/src/Dataset/dataset/chestxray.py), [Diagnosis Close (yes/no) Format Dataset](https://github.com/chaoyi-wu/RadFM/blob/main/src/Dataset/dataset/binary.py) | chestxray_balance_train_new.csv, chestxray_balance_test.csv| ## Acknowledgment: We sincerely thank all the contributors who uploaded the relevant data in our dataset online. We appreciate their willingness to make these valuable cases publicly available. ## Contact If you have any questions, please feel free to contact wtzxxxwcy02@sjtu.edu.cn. ================================================ FILE: requirements.txt ================================================ einops==0.6.1 einops-exts==0.0.4 huggingface-hub==0.16.4 nibabel==5.1.0 nmslib==2.1.1 opencv-python==4.8.0.76 pandas==2.0.3 Pillow==9.4.0 pytz==2023.3 PyYAML==6.0.1 scikit-learn==1.3.0 scipy==1.11.2 scispacy sentencepiece==0.1.99 SimpleITK==2.2.1 spacy==3.6.1 spacy-alignments==0.9.0 spacy-legacy==3.0.12 spacy-loggers==1.0.4 spacy-transformers==1.2.5 tokenizers==0.13.3 torch==2.0.1 torchaudio==2.0.2 torchvision==0.15.2 tqdm==4.66.1 transformers==4.28.1 ================================================ FILE: src/Dataset/dataset/MedPix_dataset.py ================================================ # Import necessary libraries for data processing, image handling, and model integration from torch.utils.data import Dataset import numpy as np import transformers import pandas as pd import copy import random import os import numpy as np import tqdm import torch import json from PIL import Image import torchvision from transformers import AutoModelForCausalLM, AutoTokenizer, LlamaTokenizer from torchvision import transforms from ast import literal_eval import re import math class MedPix_Single_Dataset(Dataset): """ Dataset class for single-image MedPix data. Processes single medical images with various prompts related to modality, plane orientation, and general image captioning. """ def __init__(self, csv_path, img_root="/gpfs/home/cs/leijiayu/data/MedPix/images/", down_sample_ratio=5): """ Initialize the dataset. Args: csv_path: Path to CSV file containing image metadata img_root: Root directory for images down_sample_ratio: Factor to reduce dataset size """ self.case_list = pd.read_csv(csv_path) self.img_root = img_root # Image transformation pipeline self.transform = transforms.Compose([ transforms.RandomResizedCrop([512, 512], scale=(0.8, 1.0), interpolation=transforms.InterpolationMode.BICUBIC), transforms.ToTensor(), # normalize, # Commented out normalization ]) self.down_sample_ratio = down_sample_ratio # Define template prompts for different tasks self.promt = { # Image captioning prompts "caption": [ "Describe this input image.", "Help captioning the image.", "What can be inflected from the scan?", "Can you give a caption for this image?", "Can you provide a brief summary of the radiology image?", "Please write a report about the image?", "Can you provide an analysis of this image?", "Can you explain what is shown in this image?", "What can be indicated from the radiologic scans?", "What can you infer from this photograph?", ], # Modality identification prompts "modality": [ "What is the modality of the image?", "What type of imaging technique was utilized?", "What imaging technology was used?", "Please tell me the modality of the image.", "Describe the modality of the image.", "Tell me the imaging technology used.", "Can you specify the imaging modality used?", "What kind of imaging modality was applied?", "Which imaging technique was used for this image?", "Could you identify the imaging modality of this picture?", "What type of image modality was used here?", "Can you describe the imaging technique used?" ], # Plane orientation prompts "plane": [ "Please distinguish the plane of the image", "Which view does this scan take from?", "Describe the position.", "What angle is this image taken from?", "Can you explain the orientation of this picture?", "From which direction was this shot taken?", "Can you specify the plane of this picture?", "From which standpoint is this image taken?", "Tell me which plane is the image.", "From what angle is this picture captured?", "Can you determine the shot direction of this image?", "Can you describe the plane of this image?", ], # Yes/no prompts for modality "modality_yes_no": [ "Is this image shot in {object}?", "Is this image in {object}?", "Is {object} used fro this image?", "Was this picture taken in {object}?", "Was this photo captured in {object}?", "Did they use {object} for this image?", "Is this picture from {object}?", "Is this scan shot in {object}?" ], # Yes/no prompts for plane orientation "plane_yes_no": [ "Is this image shot from {object} view?", "Is this image in the view of {object}?", "Was this scan in {object} view?", "Is this photo shot in {object} position?", "Was this picture taken from the perspective of {object}?", "Is this image captured from {object} viewpoint?", "Is this photograph from the angle of {object}?", "Is this snapshot from the view of {object}?", ], } # Lists of possible values for modality and plane categories self.sample_list = { 'modality': ['HE - High Power (>200X)', 'MR - FLAIR', 'Mammograph', 'SPECT', 'MR - FLAIR w/Gd', 'UGI - Upper GI', 'OPHTH - Fundoscopy', 'SBFT - Small Bowel', 'Special Stain (specify in caption)', 'EM - Electron Microscopic', 'MR T2* gradient GRE', 'CT - Montage', 'ECG EKG', 'MR - T2 FLAIR w/Contrast', 'CT - noncontrast', 'MR - ADC Map (App Diff Coeff)', 'Interventional Procedure', 'BE - Barium Enema', 'HE - Low Power (<50x)', 'MR - T2 weighted', 'MR - T1W w/Gd (fat suppressed)', 'AN - Angiogram', 'OR - Operative photograph', 'Montage of Images', 'XR - Plain Film', 'MR - T1W - noncontrast', 'BAS - Barium Swallow', 'US - Ultrasound', 'LOGO', 'HE - Med Power (~50-200x)', 'NM - Nuclear Medicine', 'GR - Gross photograph', 'MR - Other Pulse Seq.', 'Dermatology', 'IVP/IVU - Intravenous Urogram/Pyelogram', 'VCUG - Voiding Cystourethrogram', 'CT - GI Contrast', 'MRS - Spectroscopy', 'MR - Montage', 'Photograph', 'MRA - MR Angiography/Venography', 'MR - T1W w/Gadolinium', 'HSG - Hysterosalpingogram', 'MR T2* gradient,GRE,MPGR,SWAN,SWI', 'Histology - Special Stain (specify in caption)', 'Venogram', 'Arthrogram', 'CT - Myelogram', 'US-D - Doppler Ultrasound', 'CT - GI & IV Contrast', 'CP - Clinical photograph', 'Histology (NOS)', 'Not Assigned', 'MR - PDW Proton Density', 'CT w/contrast (IV)', 'OPHTH - Slit-Lamp', 'CTA - CT Angiography', 'AN - Angiogram (Catheter)', 'MR - T1W SPGR', 'Tomography', 'EP - Endoscopy', 'PET-CT Fusion', 'MR - DWI Diffusion Weighted', 'Drawing', 'PET - Positron Emission', 'SPECT - Single Photon', 'RU - Retrograde Urogram', 'Myelogram', 'Fundoscopy', 'Virtual Colonoscopy', 'Photographs', 'Interventional Procedure (specify in caption)', 'MR - STIR', 'MR - FIESTA'], 'plane': ['Other View (see caption)', 'Mammo - CC', 'Sagittal', 'Image Plane', 'Mammo - XCC', 'Lateral', 'Longitudinal', 'Mammo - Mag CC', 'Frontal', 'Mammo - MLO', 'Transverse', 'Gross Pathology', 'Dermatology', '3D Reconstruction', 'Photograph', 'Histology', 'PA', 'Decubitus', 'Multiple or Montage', 'Oblique', 'AP', 'Drawing', 'Axial', 'Coronal'], } def __len__(self): """Return effective length of dataset after downsampling""" return math.ceil(len(self.case_list)/self.down_sample_ratio) def get_image(self, img_path): """ Load and preprocess an image Args: img_path: Path to the image file Returns: Processed image tensor with shape [C, H, W, 1] """ image = Image.open(img_path).convert('RGB') image = self.transform(image) image = image.unsqueeze(-1) # Add depth dimension [C, H, W, 1] return image def __getitem__(self, idx): """ Get a single sample from the dataset Args: idx: Index of the sample to retrieve Returns: Dictionary containing processed sample with image, question, and answer """ # Apply downsampling with random offset idx = (self.down_sample_ratio*idx + random.randint(0, self.down_sample_ratio-1)) % len(self.case_list) sample = self.case_list.iloc[idx] answer = sample['context'] # Handle different question types if sample['type'] == "modality" or sample['type'] == "plane": pp = random.random() if pp > 0.5: # Direct question about modality or plane question = random.sample(self.promt[sample['type']], 1)[0] else: # Yes/no question about modality or plane question = random.sample(self.promt[sample['type']+'_yes_no'], 1)[0] ppp = random.random() if ppp > 0.5: # True case - format question with correct attribute question = question.format(object=answer) answer = 'yes' else: # False case - randomly select a different attribute sample_list = self.sample_list[sample['type']] try: sample_list.remove(answer) except: pass answer = random.sample(sample_list, 1)[0] question = question.format(object=answer) answer = 'no' else: # For other types, just select a random prompt question = random.sample(self.promt[sample['type']], 1)[0] # Randomly decide where to position the image - before or after question p = random.random() images = [] if p > 0.5: try: # Place image after question images.append( { "image": self.get_image(self.img_root+sample['name']), "position": { "question": len(question) } } ) except: pass else: try: # Place image before question images.append( { "image": self.get_image(self.img_root+sample['name']), "position": { "question": 0 } } ) except: pass # Return formatted sample return { "image_dict": images, "question": str(question), "answer": str(answer), } class MedPix_Multi_Dataset(Dataset): """ Dataset class for multi-image MedPix data. Processes cases with multiple medical images and supports various diagnostic and analytical prompts. """ def __init__(self, csv_path, img_root="/gpfs/home/cs/leijiayu/data/MedPix/images/"): """ Initialize the dataset. Args: csv_path: Path to CSV file containing case metadata img_root: Root directory for images """ self.case_list = pd.read_csv(csv_path) self.img_root = img_root # Image transformation pipeline self.transform = transforms.Compose([ transforms.RandomResizedCrop([512, 512], scale=(0.8, 1.0), interpolation=transforms.InterpolationMode.BICUBIC), transforms.ToTensor(), # normalize, # Commented out normalization ]) # Define template prompts for different diagnostic tasks self.promt = { # Treatment and follow-up prompts "txFollowup": [ "What treatment should the patient take?", "Please give me some treatment advise.", "What is the recommended treatment for this condition?", "What kind of treatment is necessary for this patient?", "Can you suggest a suitable treatment for this case?", "What treatment options are available for this patient?", "What is the best course of treatment for this condition?", "How to follow up with the patient?", "What treatment should be administered for this illness?", "What is the most effective treatment for this disease?" ], # Differential diagnosis prompts "ddx": [ "What illness can you diagnose from this images?", "What disease is shown in the scans?", "Please make diagnosis with the input images?", "What health issue can be inferred from these photos?", "What is the diagnosis based on these medical scans?", "Based on these scans, what is the patient suffering from?", "What ailment can be deduced from these medical images?", "Can you determine the illness from these medical photos?", "Can you identify the disease from these scans?", "What is the medical diagnosis based on these images?", ], # Diagnostic method prompts "dxHow": [ "What imaging technology is used for diagnosis?", "What imaging tests are shown in the images?", "What type of imaging technique is used in medical diagnosis?", "What kind of imaging technology is used for medical purposes?", "Which imaging tests are depicted in these pictures?", "Can you identify the imaging tests in these images?", "What kind of imaging technology is used in healthcare?", "What imaging procedures are used for diagnosing diseases?", "Can you name the imaging tests shown in these photographs?", "Please distinguish the imaging type in these images", ], # General diagnosis prompts "diagnosis": [ "What condition can be diagnosed from these pictures?", "Can you interpret the disease from these medical scans?", "What medical condition is depicted in these images?", "Based on these images, what could be the potential diagnosis?", "What health condition can be identified from these scans?", "Can you diagnose the disease from these medical images?", "What is the patient's condition according to these scans?", "What medical issue can be determined from these photos?", "Can you infer the illness from these medical scans?", "What is the probable diagnosis based on these medical images?", "What illness can you diagnose from this images?", "What disease is shown in the scans?", "Please make diagnosis with the input images?", "What health issue can be inferred from these photos?", "What is the diagnosis based on these medical scans?", "Based on these scans, what is the patient suffering from?", "What ailment can be deduced from these medical images?", ], # Findings description prompts "findings": [ "Caption the case.", "Describe your findings for this patient.", "What is shown in the case?", "Please help me write a report about the patient.", "Can you provide a summary of the case?", "What are the key points in this case?", "Could you explain the details of the case?", "What are your observations about the case?", "Can you give an overview of the case?", "How would you interpret this case?", "What is your analysis of the patient?", "Can you provide a brief on the patient?" ], # Exam result prompts "exam": [ "Make a conclusion for this patient.", "What are the exam results for this patient?", "What is the diagnosis for this patient?", "What are the symptoms presented by this patient?", "Please make diagnosis with the input case.", "Is there any abnormality with the presented case?", "What can be reflected from the input images?", "Please provide me with some diagnosis advise.", "Can you provide a summary of the patient's condition?", "Can you provide a detailed analysis of the patient's condition?" ], # Case discussion prompts "discussion": [ "Discuss about the case more.", "Tell more about the patient's illness.", "What image patterns or knowledge can help you make diagnosis?", "Could you provide more details about the situation?", "What additional information can you provide about the issue?", "Can you explain more about the subject matter?", "What other factors should be considered in this scenario?", "Can you provide more context or background information?", "What other relevant details can you share about this case?", "Can you expand on your initial explanation?" , "What other insights can you provide on this matter?" , "Can you delve deeper into the specifics of the situation?", ], } def __len__(self): """Return the total number of cases in the dataset""" return len(self.case_list) def get_image(self, img_path): """ Load and preprocess an image Args: img_path: Path to the image file Returns: Processed image tensor with shape [C, H, W, 1] """ image = Image.open(img_path).convert('RGB') image = self.transform(image) image = image.unsqueeze(-1) # Add depth dimension [C, H, W, 1] return image def __getitem__(self, idx): """ Get a single case from the dataset Args: idx: Index of the case to retrieve Returns: Dictionary containing processed case with images, question, and answer """ sample = self.case_list.iloc[idx] # Clean up answer text by removing bullet points answer = str(sample['context']).replace('• ', '') # Select random prompt for the specific task type question = random.sample(self.promt[sample['type']], 1)[0] # Optionally prepend patient history to the question history = sample['history'] if history is not None: p = random.random() if p > 0.5: try: question = history + ' ' + question except: pass # Process all images associated with this case image_names = sample['name'].split(',') p = random.random() images = [] # Randomly decide whether to put images after or before question if p > 0.5: # Place images after question for pp in image_names: try: images.append( { "image": self.get_image(self.img_root+pp), "position": { "question": len(question) } } ) except: pass else: # Place images before question for pp in image_names: try: images.append( { "image": self.get_image(self.img_root+pp), "position": { "question": 0 } } ) except: pass # For findings, remove measurements which might be distracting if sample['type'] == "findings": pattern = r"\d+(\.\d+)?\s*(mm|cm|x\d+\s*cm)" answer = re.sub(pattern, "", answer) # Limit number of images to prevent memory issues if len(images) > 10: images = random.sample(images, 10) # Return formatted case return { "image_dict": images, "question": str(question), "answer": str(answer), } class MedPix_QA_Dataset(Dataset): """ Dataset class for MedPix question-answer pairs. Processes medical QA pairs with associated images. """ def __init__(self, csv_path, img_root="/gpfs/home/cs/leijiayu/data/MedPix/images/"): """ Initialize the dataset. Args: csv_path: Path to CSV file containing QA pairs img_root: Root directory for images """ self.case_list = pd.read_csv(csv_path) self.img_root = img_root # Image transformation pipeline self.transform = transforms.Compose([ transforms.RandomResizedCrop([512, 512], scale=(0.8, 1.0), interpolation=transforms.InterpolationMode.BICUBIC), transforms.ToTensor(), # normalize, # Commented out normalization ]) def __len__(self): """Return the total number of QA pairs in the dataset""" return len(self.case_list) def get_image(self, img_path): """ Load and preprocess an image Args: img_path: Path to the image file Returns: Processed image tensor with shape [C, H, W, 1] """ image = Image.open(img_path).convert('RGB') image = self.transform(image) image = image.unsqueeze(-1) # Add depth dimension [C, H, W, 1] return image def __getitem__(self, idx): """ Get a single QA pair from the dataset Args: idx: Index of the QA pair to retrieve Returns: Dictionary containing processed QA pair with image, question, and answer """ sample = self.case_list.iloc[idx] # Extract question, answer and explanation answer = sample['answer'] question = sample['question'] explanation = sample['explanation'] # Combine answer with explanation when available try: answer = answer + '. ' + explanation except: pass # Randomly decide whether to place image before or after question p = random.random() images = [] if p > 0.5: # Place image after question try: images.append( { "image": self.get_image(self.img_root+sample['name']), "position": { "question": len(question) } } ) except: pass else: # Place image before question try: images.append( { "image": self.get_image(self.img_root+sample['name']), "position": { "question": 0 } } ) except: pass # Limit number of images to prevent memory issues if len(images) > 10: images = random.sample(images, 10) # Return formatted QA pair return { "image_dict": images, "question": str(question), "answer": str(answer), } # Example usage (commented out) # dataset = MedPix_Single_Dataset(csv_path = '/gpfs/home/cs/leijiayu/data/MedPix/Preprocessor/MedPix_single_train.csv') # for i in tqdm.tqdm(range(len(dataset))): # sample = dataset[i] # print(len(sample['image_dict']), sample['image_dict'][0]["image"].shape, sample['question'], sample['answer']) # input() # dataset = MedPix_Multi_Dataset(csv_path = '/gpfs/home/cs/leijiayu/data/MedPix/Preprocessor/MedPix_multi_train.csv') # for i in tqdm.tqdm(range(len(dataset))): # sample = dataset[i] # print(len(sample['image_dict']), sample['image_dict'][0]["image"].shape, sample['question'], sample['answer']) # input() # dataset = MedPix_QA_Dataset(csv_path = '/gpfs/home/cs/leijiayu/data/MedPix/Preprocessor/MedPix_questions_train.csv') # for i in tqdm.tqdm(range(len(dataset))): # sample = dataset[i] # print(len(sample['image_dict']), sample['image_dict'][0]["image"].shape, sample['question'], sample['answer']) # input() ================================================ FILE: src/Dataset/dataset/__init__.py ================================================ from .radiopaedia import RadioVQA_Dataset,Radio_Modality_Dataset,Radiofeatures_Dataset,RadioCaption_Dataset from .binary import Binary_Dataset from .chestxray import ChestXray_Dataset from .vqa import VQA_Dataset from .pmcoa import PMCOA_Dataset from .paper_inline import Paper_Inline_dataset from .case_report import CaseReport_dataset from .MedPix_dataset import MedPix_Multi_Dataset,MedPix_Single_Dataset,MedPix_QA_Dataset ================================================ FILE: src/Dataset/dataset/binary.py ================================================ import csv import json import logging import os import re import difflib import sys import torch import random from abc import abstractmethod from itertools import islice from typing import TYPE_CHECKING, Any, Callable, Dict, List, Optional, Tuple, Union from collections.abc import Mapping from torch.utils.data import DataLoader import PIL from torch.utils.data import Dataset import numpy as np import pandas as pd from tqdm import tqdm from torchvision import transforms from collections import defaultdict from PIL import Image class Binary_Dataset(Dataset): """_summary_ Args: Dataset (_type_): caption task formulated as vqa task for Chestxray classification dataset csv_path (_type_): path to csv file prompt_json_file (_type_): path to json file containing binary cls prompts, the answer is yes/no Output: Dict: { "image_dict": {"image": image, "position": {"question": 0}}, # image is a tensor of shape [c,w,h,d] [3,512,512,1], position is a dict, random choice of 0 or len(question) "question": question, # random choice of caption prompts "answer":answer, # caption } """ def __init__(self,csv_path,prompt_json_file): data_info = pd.read_csv(csv_path) self.img_path_list = np.asarray(data_info['image_path']) self.disease_list = np.asarray(data_info['disease']) self.answer_list = np.asarray(data_info['label']) self.transform = transforms.Compose([ transforms.RandomResizedCrop([512,512],scale=(0.8, 1.0), interpolation=transforms.InterpolationMode.BICUBIC), transforms.ToTensor(), ]) with open(prompt_json_file, 'r') as f: self.caption_prompts = json.load(f)['caption_prompt'] self.map_answer = {0:'no',1:'yes'} def __len__(self): return len(self.img_path_list) def __getitem__(self, index): img_path = self.img_path_list[index] image = Image.open(img_path).convert('RGB') image = self.transform(image) image = image.unsqueeze(-1) # c,w,h,d answer = self.map_answer[self.answer_list[index]] question = random.choice(self.caption_prompts).replace('disease',self.disease_list[index]) image_dict = [{ "image": image, "position": { "question": len(question) } }] return { "image_dict": image_dict, "question": question, "answer":answer, } ================================================ FILE: src/Dataset/dataset/caption_prompt.json ================================================ { "caption_prompt": [ "Can you provide a caption consists of finding and impression for this medical image?", "Describe the finding and impression of the medical image you see.", "Please caption this medical scan with finding and impression.", "What is the finding and impression of this image?", "Describe this medical scan with finding and impression.", "Please write a caption consists of finding and impression for this image.", "Can you summarize with finding and impression the images presented?", "Please caption this scan with finding and impression.", "Please provide a caption consists of finding and impression for this medical image.", "Can you provide a summary consists of finding and impression of this radiograph?", "What are the findings and impression presented in this medical scan?", "Please write a caption consists of finding and impression for this scan.", "Can you provide a description consists of finding and impression of this medical scan?", "Please caption this medical scan with finding and impression.", "Can you provide a caption consists of finding and impression for this medical scan?" ] } ================================================ FILE: src/Dataset/dataset/case_report.py ================================================ # Import necessary libraries for data processing, image handling, and model integration from torch.utils.data import Dataset import numpy as np import transformers import pandas as pd import copy import random import os import numpy as np import tqdm import torch import json from PIL import Image import torchvision from transformers import AutoModelForCausalLM, AutoTokenizer, LlamaTokenizer from torchvision import transforms from ast import literal_eval class CaseReport_dataset(Dataset): """ Dataset class for medical case reports with associated images. This dataset processes medical case reports containing text and referenced images, formatting them for multimodal medical AI training or inference. """ def __init__(self, csv_path, img_path): """ Initialize the dataset. Args: csv_path: Path to CSV file containing case reports data img_path: Base path to the directory containing images """ self.img_path = img_path # Root directory for images self.question_list = pd.read_csv(csv_path) # Load dataset from CSV # Define image transformation pipeline # normalize = transforms.Normalize((0.485, 0.456, 0.406), (0.229, 0.224, 0.225)) self.transform = transforms.Compose([ # Crop and resize images to 512x512, maintaining 80-100% of original content transforms.RandomResizedCrop([512, 512], scale=(0.8, 1.0), interpolation=transforms.InterpolationMode.BICUBIC), # Convert to tensor with values in [0, 1] transforms.ToTensor(), # normalize, # Commented out normalization ]) def __len__(self): """Return the total number of samples in the dataset""" return len(self.question_list) def __getitem__(self, idx): """ Get a single sample from the dataset Args: idx: Index of the sample to retrieve Returns: Dictionary containing the processed sample with image, question, and answer """ # Get the row from dataframe sample = self.question_list.iloc[idx] # Extract metadata and content PMC_id = sample['PMC_id'] # PubMed Central ID img_ref = literal_eval(sample['img_ref']) # List of image references context = str(sample['context']) # Case context # Truncate long contexts to focus on beginning and end sentences = context.split('.') if len(sentences) > 5: first_sentence = sentences[0] # Keep the first sentence last_sentences = ". ".join(context.split('.')[-4:]) # Keep the last 4 sentences context = first_sentence + '. ' + last_sentences # Format question by combining context and actual question question = str(context) + '\n' + str(sample['question']).replace('Q:', '') # Clean up answer formatting answer = str(sample['answer']).replace('A:', '') # Process each referenced image images = [] for img_id in img_ref: # Construct the full image path img_path = self.img_path + '/' + PMC_id + '_' + img_id + '.jpg' try: # Load and transform the image image = Image.open(img_path).convert('RGB') image = self.transform(image) # Randomly decide where to place the image in the text # Either at the end of question or at the end of context if random.random() > 0.5: images.append({'image': image, "position": {"question": len(question)}}) else: images.append({'image': image, "position": {"question": len(context)}}) except: # Skip images that can't be loaded continue # Return formatted sample return { "image_dict": images, # List of images with position information "question": question, # Formatted question text "answer": answer, # Answer text } # Example usage (commented out) # csv_path = '/gpfs/home/cs/leijiayu/wuchaoyi/multi_modal/Data/GPT_realdata/casa_report_train.csv' # img_path = '/home/cs/leijiayu/data/all_images/figures/' # dataset = CaseReport_dataset(csv_path, img_path) # print(dataset[0]) ================================================ FILE: src/Dataset/dataset/chestxray.py ================================================ import csv import json import logging import os import re import difflib import sys import torch import random from abc import abstractmethod from itertools import islice from typing import TYPE_CHECKING, Any, Callable, Dict, List, Optional, Tuple, Union from collections.abc import Mapping from torch.utils.data import DataLoader import PIL from torch.utils.data import Dataset import numpy as np import pandas as pd from tqdm import tqdm from torchvision import transforms from collections import defaultdict from PIL import Image class ChestXray_Dataset(Dataset): """_summary_ Args: Dataset (_type_): caption task formulated as vqa task for Chestxray classification dataset csv_path (_type_): path to csv file img_root_dir (_type_): path to image root directory prompt_json_file (_type_): path to json file containing caption prompts Output: Dict: { "image_dict": {"image": image, "position": {"question": 0}}, # image is a tensor of shape [c,w,h,d] [3,512,512,1], position is a dict, random choice of 0 or len(question) "question": question, # random choice of caption prompts "answer":answer, # caption } """ def __init__(self,csv_path,prompt_json_file): data_info = pd.read_csv(csv_path) self.img_path_list = np.asarray(data_info['image_path']) self.answer_list = np.asarray(data_info['label']) self.transform = transforms.Compose([ transforms.RandomResizedCrop([512,512],scale=(0.8, 1.0), interpolation=transforms.InterpolationMode.BICUBIC), transforms.ToTensor(), ]) with open(prompt_json_file, 'r') as f: self.caption_prompts = json.load(f)['caption_prompt'] def __len__(self): return len(self.img_path_list) def __getitem__(self, index): img_path = self.img_path_list[index] try: image = Image.open(img_path).convert('RGB') image = self.transform(image) image = image.unsqueeze(-1) # c,w,h,d except: image = np.random.randn(3,512,512,4) answer = self.answer_list[index] question = random.choice(self.caption_prompts) image_dict = [{ "image": image, "position": { "question": len(question) } }] return { "image_dict": image_dict, "question": question, "answer":answer, } if __name__ == "__main__": test_dataset = ChestXray_Dataset(csv_path = '../data_csv/chestxray.csv', prompt_json_file = './cls_prompt.json') for i in range(10): test_data = test_dataset[i] print(test_data['image_dict'][0]['image'].shape) # [3,512,512,1] #需要确保所有的chestxray img_path都有图像 ================================================ FILE: src/Dataset/dataset/cls_prompt.json ================================================ { "caption_prompt": [ "What is the diagnosis for this chest X-ray?", "Based on this X-ray, what type of lung disease is suspected?", "Can you identify any abnormality in this chest X-ray?", "What are the findings in this chest X-ray?", "What pathology is indicated by this chest X-ray?", "What lung disease is likely present in this chest X-ray?", "What are the potential causes of the findings in this chest X-ray?", "What are your conclusions from this chest X-ray?", "What is your interpretation of this chest X-ray?", "What abnormalities are present in this chest X-ray?", "What is the differential diagnosis for the findings in this chest X-ray?" ] } ================================================ FILE: src/Dataset/dataset/data_csv/README.md ================================================ Please check the [data_csv](https://huggingface.co/datasets/chaoyi-wu/RadFM_data_csv) to download the used train/test split csv files and ensure the image path are related to your local path. ================================================ FILE: src/Dataset/dataset/dicom_to_png_for_VinDR_sampled_using_mammo.py ================================================ import os import cv2 import csv import json import imageio import pandas as pd import numpy as np from tqdm import tqdm import matplotlib.pyplot as plt from pydicom import dcmread def dcm_to_png(dcm_path,save_png_path): ds = dcmread(dcm_path) arr = ds.pixel_array img_array = arr.copy() cv2.normalize(arr, img_array, 0, 255, cv2.NORM_MINMAX) img_array = np.array(img_array,dtype='uint8') # img_array = cv2.resize(img_array, (512,512), interpolation = cv2.INTER_LINEAR) imageio.imwrite(save_png_path,img_array) def preprocess_csv(csv_path,data_dir,save_data_dir): data_info = pd.read_csv(csv_path) patient_file_list = data_info.iloc[:,0] img_file_list = data_info.iloc[:,2] for idx in tqdm(range(len(img_file_list))): patient_file = patient_file_list[idx] img_file = img_file_list[idx] img_path = os.path.join(data_dir,str(patient_file),str(img_file)+'.dicom') os.makedirs(os.path.join(save_data_dir,str(patient_file)), exist_ok=True) save_img_path = os.path.join(save_data_dir,str(patient_file),str(img_file)+'.png') dcm_to_png(img_path,save_img_path) csv_path = './DATA/VinDr/VinDr-Mammo/1.0.0/breast-level_annotations.csv' data_dir = './DATA/VinDr/VinDr-Mammo/1.0.0/images' save_data_dir = './DATA/VinDr/VinDr-Mammo/process/images' os.makedirs(save_data_dir, exist_ok=True) preprocess_csv(csv_path,data_dir,save_data_dir) ================================================ FILE: src/Dataset/dataset/jpg2nii_data_convert.py ================================================ #processed cases accoring to case_id_list, and save a csv file, with image path and image caption import os import cv2 import csv import json import subprocess import pandas as pd import numpy as np import SimpleITK as sitk from tqdm import tqdm from collections import defaultdict def get_image(single_image_dir,single_image_filenames): # single_image_filenames single_image_filenames.sort(key=lambda x: int(x.split('.')[0])) image_list = [] for image_filename in single_image_filenames: image_file = os.path.join(single_image_dir, image_filename) #read jpeg to 2D array image_array = cv2.imread(image_file,0) if image_array is not None: image_size = image_array.shape image_array = cv2.resize(image_array,(512,512),interpolation = cv2.INTER_LINEAR) image_list.append(image_array) else: pass image_array = np.array(image_list) #c,w,h if len(image_array.shape) == 3: if image_array.shape[0] < image_array.shape[1]: image_array = image_array.transpose((1, 2, 0)) # image_array = np.transpose(image_array, (2,0,1)) # w,h,c return image_array gray_list = ['CT','MRI','X-ray','Ultrasound','Mammography'] def convert_case(case_id,image_root_dir,json_root_dir,save_case_dict,save_root_dir=None): # save_image_dir case_images_dir = os.path.join(image_root_dir, case_id) case_json_path = os.path.join(json_root_dir, case_id+'.json') with open(case_json_path, 'r') as f: data = json.load(f) image_nums = (len(data.keys())-1)//2 for image_num in range(1,image_nums+1): case_dict = defaultdict(list) image_dir = os.path.join(case_images_dir, str(image_num)) #./images/1/1 image_caption = data[str(image_num) + '详情'] image_modality = data[str(image_num)][0]['modality'] single_image_names = os.listdir(image_dir) single_image_names.sort(key=lambda x: int(x.split('_')[1])) save_image_series = [] for single_image_name in single_image_names: single_image_dir = os.path.join(image_dir, single_image_name) save_npy_dir = os.path.join(save_root_dir,str(case_id),str(image_num)) single_image_filenames = os.listdir(single_image_dir) if len(os.listdir(single_image_dir)) == 1: # 2D image image_file = os.path.join(single_image_dir, single_image_filenames[0]) save_image_array = cv2.imread(image_file) # w,h,c else: save_image_array = get_image(single_image_dir,single_image_filenames) if not os.path.exists(save_npy_dir): os.makedirs(save_npy_dir) # print(save_image_array.shape) if save_image_array is not None: if len(save_image_array.shape) <= 5 and len(save_image_array.shape) >=2: save_nii_path = os.path.join(save_npy_dir,single_image_name+'.nii.gz') out = sitk.GetImageFromArray(save_image_array) sitk.WriteImage(out, save_nii_path) save_image_series.append(save_nii_path) else: save_npy_path = os.path.join(save_npy_dir,single_image_name+'.npy') np.save(save_npy_path,save_image_array) save_image_series.append(save_npy_path) case_dict['image'] = save_image_series case_dict['image_caption'] = image_caption case_dict['image_modality'] = image_modality save_case_dict.append(case_dict) if __name__ == "__main__": # case_id,image_root_dir,json_root_dir import argparse parser = argparse.ArgumentParser() parser.add_argument('--index', default=0, type=int) parser.add_argument('--add_index', default=0, type=int) parser.add_argument('--start_index', default=1, type=int) parser.add_argument('--end_index', default=1000, type=int) args = parser.parse_args() image_root_dir = '/mnt/petrelfs/share_data/zhangxiaoman/DATA/Radio_VQA/processed_file/images' json_root_dir = '/mnt/petrelfs/share_data/zhangxiaoman/DATA/Radio_VQA/processed_file/jsons' save_root_dir = '/mnt/petrelfs/share_data/zhangxiaoman/DATA/Radio_VQA/processed_file/npys' save_case_dict = [] args.start_index = args.index*1000+1 + args.add_index args.end_index = (args.index+1)*1000+1 for case_id in tqdm(range(args.start_index,args.end_index)): case_id = str(case_id) convert_case(case_id,image_root_dir,json_root_dir,save_case_dict,save_root_dir) # CT_0 (200, 630, 630, 3) # save to csv save_json_file = '/mnt/petrelfs/share_data/zhangxiaoman/DATA/Radio_VQA/processed_file/processed_jsons/processed_json_'+str(args.index)+'.json' with open(save_json_file, 'w', encoding='utf-8') as f: json.dump(save_case_dict, f, ensure_ascii=False,indent=4) # B, S, T, W, H, Z # srun --partition=medai --mpi=pmi2 --quotatype=auto --gres=gpu:0 -n1 --ntasks-per-node=1 python data_convert.py --index 2 --add_index 24 # cd /mnt/petrelfs/share_data/zhangxiaoman/DATA/Radio_VQA/jpeg2npy ================================================ FILE: src/Dataset/dataset/mammo_prompt.json ================================================ { "caption_prompt": [ "What is the diagnosis for this mammogram?", "Based on this X-ray, what type of breast disease is suspected?", "Can you identify any abnormality in this mammogram?", "What are the findings in this mammogram?", "What pathology is indicated by this mammogram?", "What lung disease is likely present in this mammogram?", "What are the potential causes of the findings in this mammogram?", "What are your conclusions from this mammogram?", "What is your interpretation of this mammogram?", "What abnormalities are present in this mammogram?", "What is the differential diagnosis for the findings in this mammogram?", "What is the diagnosis for this breast X-ray?", "Can you identify any abnormality in this breast X-ray?", "What are the findings in this breast X-ray?", "What pathology is indicated by this breast X-ray?", "What lung disease is likely present in this breast X-ray?", "What are the potential causes of the findings in this breast X-ray?", "What are your conclusions from this breast X-ray?", "What is your interpretation of this breast X-ray?", "What abnormalities are present in this breast X-ray?", "What is the differential diagnosis for the findings in this breast X-ray?" ] } ================================================ FILE: src/Dataset/dataset/modality_prompt.json ================================================ { "caption_prompt": [ "What modality is used to take this image?", "What type of imaging modality is used to acquire the above image?", "What imaging modality is used?", "What imaging modality was used to take this image?", "What is the imaging modality?" ], "modality_prompt": [ "Is this image a modality scan?", "Is the given image a modality scan?", "Is the given image a modality?" ] } ================================================ FILE: src/Dataset/dataset/nii2npy_for_radiopaedio.py ================================================ import os import cv2 import csv import json import subprocess import pandas as pd import numpy as np import SimpleITK as sitk from tqdm import tqdm from scipy import ndimage from collections import defaultdict def resize_array(array_list, shape_list): if len(array_list) == 0: return None # Get the median value of the c dimension c_values = [shape[3] for shape in shape_list] z = np.median(c_values) # Resize each array to the same size resized_arrays = [] for array in array_list: resized_array = ndimage.zoom(array, (3/array.shape[0],512/array.shape[1], 512/array.shape[2], z/array.shape[3]), order=0) # print(resized_array.shape) if resized_array.shape[3] == z: resized_arrays.append(resized_array) else: if resized_array.shape[3] > z: resized_arrays.append(resized_array[:,:,:,:int(z)]) else: resized_arrays.append(np.pad(resized_array, ((0,0),(0,0),(0,0),(0,int(z-resized_array.shape[3]))), 'constant', constant_values=0)) # Convert the list of arrays to a numpy array resized_array = np.array(resized_arrays) return resized_array def process_image_list(image_path_list): image_shape_list = [] image_array_list = [] for image_path in image_path_list: if os.path.exists(image_path) == False: continue elif image_path.split('.')[-1] == 'npy': image_array = np.load(image_path) #c,w,h,d try: image_array = cv2.resize(image_array,(512,512)) if len(image_array.shape) == 2: image_array = image_array[np.newaxis,:,:,np.newaxis] # 1wh1 to 3wh1 image_array = np.concatenate([image_array,image_array,image_array],axis=0) elif len(image_array.shape) == 3: #whc to cwh image_array = image_array.transpose(2,0,1)[:,:,:,np.newaxis] image_shape_list.append(image_array.shape) image_array_list.append(image_array) except: pass else: itk_image = sitk.ReadImage(image_path) image_array = sitk.GetArrayFromImage(itk_image) #c,w,h,d if image_array.shape[0] != 512: image_array = cv2.resize(image_array,(512,512)) if len(image_array.shape) == 2: image_array = image_array[np.newaxis,:,:,np.newaxis] image_array = np.concatenate([image_array,image_array,image_array],axis=0) elif len(image_array.shape) == 3: image_array = image_array[np.newaxis,:,:,:] image_array = np.concatenate([image_array,image_array,image_array],axis=0) image_shape_list.append(image_array.shape) image_array_list.append(image_array) save_image_array = resize_array(image_array_list, image_shape_list) return save_image_array def process_json_file(json_file,save_json_file,save_root_dir): if not os.path.exists(save_root_dir): os.makedirs(save_root_dir) with open(json_file, 'r') as f: data = json.load(f) data_len = len(data) for i in tqdm(range(data_len)): samples = data[i]['samples'] for sample_i in tqdm(range(len(samples))): if samples[sample_i]['image'] == []: samples.pop(sample_i) else: image_path_list = samples[sample_i]['image'] case_id = image_path_list[0].split('/')[-3] save_image_array = process_image_list(image_path_list) if save_image_array is not None: save_image_path = os.path.join(save_root_dir, str(case_id)+'_'+str(sample_i)+'.npy') np.save(save_image_path,save_image_array) # 如果边处理边传到aws的话可以参考这一段 # save_aws_image_path = save_image_path.replace('/mnt/petrelfs/share_data/zhangxiaoman/DATA/','s3://zhangxiaoman_hdd_new_share/') # os.system(f'aws s3 cp {save_image_path} {save_aws_image_path} --endpoint-url=http://10.140.27.254') # os.remove(save_image_path) # data[i]['npy_path'] = save_aws_image_path data[i]['samples']['npy_path'] = save_image_path data[i]['samples']['image_size'] = save_image_array.shape else: print(i,image_path_list) if len(samples) == 0: data.pop(i) with open(save_json_file, 'w') as f: json.dump(data, f,ensure_ascii=False,indent=4) if __name__ == "__main__": json_file = '../processed_file/processed_jsons/processed_json_2023-11-18.json' save_json_file = '../processed_file/processed_jsons/processed_json_2023-11-18-npy.json' save_root_dir = '../processed_file/processed_images' process_json_file(json_file,save_json_file,save_root_dir) ================================================ FILE: src/Dataset/dataset/paper_inline.py ================================================ # Import necessary libraries for data processing, image handling, and model integration from torch.utils.data import Dataset import numpy as np import transformers import pandas as pd import copy import random import os import numpy as np import tqdm import torch import json from PIL import Image import torchvision from transformers import AutoModelForCausalLM, AutoTokenizer, LlamaTokenizer from torchvision import transforms class Paper_Inline_dataset(Dataset): """ Dataset class for processing scientific papers with inline images. This dataset extracts text and associated images from scientific papers, preparing them for multimodal model training. """ def __init__(self, csv_path, img_path, sample_sentence_length=50, max_img_size=3): """ Initialize the dataset. Args: csv_path: Path to CSV file containing paper metadata img_path: Root directory for paper figures sample_sentence_length: Maximum number of sentences to include in a sample max_img_size: Maximum number of images to include in a sample """ self.max_img_size = max_img_size self.sample_sentence_length = sample_sentence_length self.img_path = img_path # Load paper paths from CSV self.paper_path = np.array(pd.read_csv(csv_path)['PMC_path']) # Define image transformation pipeline # normalize = transforms.Normalize((0.485, 0.456, 0.406), (0.229, 0.224, 0.225)) self.transform = transforms.Compose([ # Crop and resize images to 512x512, maintaining 80-100% of original content transforms.RandomResizedCrop([512, 512], scale=(0.8, 1.0), interpolation=transforms.InterpolationMode.BICUBIC), # Convert to tensor with values in [0, 1] transforms.ToTensor(), # normalize, # Commented out normalization ]) def __len__(self): """Return the total number of papers in the dataset""" return self.paper_path.shape[0] def __getitem__(self, idx): """ Get a single sample from the dataset Args: idx: Index of the paper to retrieve Returns: Dictionary containing the processed sample with images, question, and answer """ # Load the paper JSON file paper_json = self.paper_path[idx] # Extract PMC ID from the file path PMC_name = paper_json.rsplit('/', 2)[-1].split('.')[0] # Load the list of sentences with image references sentences_list = json.load(open(paper_json, 'r')) # Process the paper to extract text and images image_dict, question, answer = self.random_sample_sentence(sentences_list, PMC_name) # Return formatted sample # Note: question is empty since this is for pretraining with full paper text return { "image_dict": image_dict, # List of images with position information "question": question, # Empty string for this dataset "answer": answer, # Full text content } def random_sample_sentence(self, sentences_list, PMC_name): """ Sample a segment of sentences from a paper and process inline images Args: sentences_list: List of sentences with image references PMC_name: PubMed Central ID for the paper Returns: Tuple of (processed_images, question_text, answer_text) """ sentences_length = len(sentences_list) # Select a segment of the paper - either randomly or around image references p = random.random() if p >= 0.5: # Random segment selection if len(sentences_list) > self.sample_sentence_length: start = random.randint(0, sentences_length - self.sample_sentence_length) sentences_list = sentences_list[start:(start + self.sample_sentence_length)] else: # Try to select a segment containing images if len(sentences_list) > self.sample_sentence_length: sample_start = [] # Find sentences with image references for sentence_id in range(len(sentences_list)): if sentences_list[sentence_id]['img_ref'] != []: # Start 10 sentences before the image if possible if sentence_id - 10 < 0: sample_start.append(0) else: if sentence_id - 10 > sentences_length - self.sample_sentence_length: sample_start.append(sentences_length - self.sample_sentence_length) else: sample_start.append(sentence_id - 10) # If no images found, select random segment if sample_start == []: start = random.randint(0, sentences_length - self.sample_sentence_length) sentences_list = sentences_list[start:(start + self.sample_sentence_length)] else: # Select a random segment that contains images start = sample_start[random.randint(0, len(sample_start) - 1)] sentences_list = sentences_list[start:(start + self.sample_sentence_length)] # Process the selected segment text = '' images = [] for ix in sentences_list: sentence = ix if sentence["img_ref"] == []: # Add plain text without images text = text + sentence['text'] else: # Stop if we've reached the maximum number of images if len(images) + len(sentence["img_ref"]) > self.max_img_size: break # Process each image referenced in the sentence for img_id in sentence["img_ref"]: img_path = self.img_path + '/' + PMC_name + '_' + img_id + '.jpg' if os.path.exists(img_path): try: # Load and transform the image image = Image.open(img_path).convert('RGB') image = self.transform(image) # Add image with position information images.append({'image': image, "position": {"answer": len(text)}}) except: # Skip images that can't be loaded continue # Add the text after processing images text = text + sentence['text'] # For this dataset, we don't use a question-answer format # Instead, all text is in the "answer" field question = '' answer = text return images, question, answer # Example usage (commented out) # csv_path = '/home/cs/leijiayu/wuchaoyi/multi_modal/Data/train_paper.csv' # img_path = '/home/cs/leijiayu/data/all_images/figures/' # dataset = multi_paper_dataset(csv_path, img_path) # print(dataset[0]) ================================================ FILE: src/Dataset/dataset/pmcoa.py ================================================ # Import necessary libraries for data processing, image handling, and model interaction import csv import json import logging import os import re import difflib import sys import torch import random from abc import abstractmethod from itertools import islice from typing import TYPE_CHECKING, Any, Callable, Dict, List, Optional, Tuple, Union from collections.abc import Mapping from torch.utils.data import DataLoader import PIL from torch.utils.data import Dataset import numpy as np import pandas as pd from tqdm import tqdm from torchvision import transforms from collections import defaultdict from PIL import Image class PMCOA_Dataset(Dataset): """ Dataset for processing scientific figures and captions from PubMed Central Open Access (PMC-OA). This dataset formulates image captioning as a visual question answering task, where the model is prompted with a question about an image and should respond with an appropriate caption. Args: csv_path: Path to CSV file with columns [PMC_ID, Figure_path, Caption] img_root_dir: Path to image root directory containing figure images prompt_json_file: Path to JSON file containing caption prompts Output: Dict: { "image_dict": [{"image": image, "position": {"question": position}}], # image is a tensor of shape [c,w,h,d] [3,512,512,1] # position is where to insert the image - either at start (0) or end of question "question": question, # randomly selected caption prompt "answer": answer, # original caption from the paper } """ def __init__(self, csv_path, img_root_dir, prompt_json_file): """ Initialize the dataset. Args: csv_path: Path to CSV file with figure metadata img_root_dir: Root directory containing figure images prompt_json_file: JSON file with caption prompts """ self.img_root_dir = img_root_dir # Load metadata from CSV file data_info = pd.read_csv(csv_path) self.img_path_list = np.asarray(data_info['Figure_path']) self.caption_list = np.asarray(data_info['Caption']) # Define image transformation pipeline # normalize = transforms.Normalize((0.485, 0.456, 0.406), (0.229, 0.224, 0.225)) self.transform = transforms.Compose([ # Crop and resize images to 512x512, maintaining 80-100% of original content transforms.RandomResizedCrop([512, 512], scale=(0.8, 1.0), interpolation=transforms.InterpolationMode.BICUBIC), # Convert to tensor with values in [0, 1] transforms.ToTensor(), # normalize, # Commented out normalization ]) # Load caption prompts from JSON file with open(prompt_json_file, 'r') as f: self.caption_prompts = json.load(f)['caption_prompt'] def __len__(self): """Return the total number of samples in the dataset""" return len(self.img_path_list) def __getitem__(self, index): """ Get a single sample from the dataset Args: index: Index of the sample to retrieve Returns: Dictionary containing processed sample with image, question prompt, and caption answer """ # Get the image filename and construct full path file_name = self.img_path_list[index] img_path = os.path.join(self.img_root_dir, file_name) # Load and preprocess the image image = Image.open(img_path).convert('RGB') image = self.transform(image) # normalize to [0,1] image = image.unsqueeze(-1) # add depth dimension [C, H, W, 1] # Get the caption and a random prompt answer = self.caption_list[index] question = random.choice(self.caption_prompts) # Randomly decide whether to place the image before or after the question if random.random() < 0.5: # Place image before the question image_dict = { "image": image, "position": { "question": 0 # At the beginning of question } } else: # Place image after the question image_dict = { "image": image, "position": { "question": len(question) # At the end of question } } # Return formatted sample return { "image_dict": [image_dict], # List containing one image with position info "question": question, # Caption prompt "answer": answer, # Ground truth caption } if __name__ == "__main__": # Example usage for testing the dataset test_dataset = PMCOA_Dataset( csv_path='../data_csv/pmcoa_image_caption_train.csv', img_root_dir='/home/cs/leijiayu/data/PMCVQA/caption_T060_filtered_top4_sep_v0_subfigures', prompt_json_file='./caption_prompt.json' ) # Test the first 10 samples for i in range(10): test_data = test_dataset[i] print(test_data['image_dict'][0]['image'].shape) # Should print [3,512,512,1] ================================================ FILE: src/Dataset/dataset/radiology_feature_prompt.json ================================================ { "caption_prompt": [ "What disease can be diagnosed from these radiological images and what specific features are typically observed on the images?", "Identify the disease that is typically associated with these radiological images and describe the classic radiological presentation.", "Based on the provided images, which disease is most likely to be diagnosed and how does it manifest on radiological examinations?", "Determine the disease that corresponds to the given radiographic images and describe the characteristic radiological features.", "With these radiological images, which disease would you suspect and what specific radiographic patterns are typically seen?", "Analyze the provided images and identify the disease that is commonly associated with such radiological findings. Discuss the characteristic radiographic manifestations.", "From these radiological images, diagnose the disease and explain the typical radiological presentation observed.", "Assess the radiographic images and determine the disease that is commonly linked to these findings. Describe the typical radiological features associated with this disease.", "Examine the provided radiological images and identify the disease that would most likely be diagnosed based on the characteristic radiologic appearance.", "Based on the presented radiographic findings, indicate the disease that is commonly associated with these images and describe the typical radiological patterns observed." ] } ================================================ FILE: src/Dataset/dataset/radiopaedia.py ================================================ import csv import json import logging import os import re import difflib import sys import cv2 import torch import random from abc import abstractmethod from itertools import islice from scipy import ndimage from typing import TYPE_CHECKING, Any, Callable, Dict, List, Optional, Tuple, Union from collections.abc import Mapping from torch.utils.data import DataLoader import PIL import SimpleITK as sitk from torch.utils.data import Dataset import numpy as np import pandas as pd from tqdm import tqdm from torchvision import transforms from collections import defaultdict from PIL import Image import math class Radio_Modality_Dataset(Dataset): """_summary_ Args: Dataset (_type_): _description_: modality asked task formulated as vqa task for Radiopaedia dataset csv_path (_type_): path to csv file prompt_json_file (_type_): path to json file containing caption prompts Output: Dict: { "image_dict": {"image": image, "position": {"question": 0}}, # image is a tensor of shape [s,c,w,h,d] like, [1,3,512,512,1], position is a dict, random choice of 0 or len(question) "question": question, # random choice of caption prompts "answer":answer, # caption } """ def __init__(self,csv_path,prompt_json_file,modality_json_file,down_sample_ratio = 5): data_info = pd.read_csv(csv_path) self.down_sample_ratio = down_sample_ratio self.img_path_list = np.asarray(data_info['image_path']) self.caption_list = np.asarray(data_info['answer']) with open(prompt_json_file, 'r') as f: self.caption_prompts = json.load(f)['caption_prompt'] with open(prompt_json_file, 'r') as f: self.modality_prompts = json.load(f)['modality_prompt'] with open(modality_json_file, 'r') as f: self.modality_sets = json.load(f)['modality'] def resize_image(self, image): if len(image.shape) == 3: if image.shape[0] > image.shape[2]: image = image.transpose(2,0,1) # print('before resize',image.shape) image = cv2.resize(image,(512,512),interpolation = cv2.INTER_LINEAR) # print('after resize',image.shape) image = image[np.newaxis,:,:,:] image = np.concatenate([image,image,image],axis=0) if image.shape[-1] > 64: image = ndimage.zoom(image, (3/image.shape[0],512/image.shape[1],512/image.shape[2],64/image.shape[3]), order=0) else: image = ndimage.zoom(image, (3/image.shape[0],512/image.shape[1],512/image.shape[2],1), order=0) return image def __len__(self): return math.ceil(len(self.img_path_list)/self.down_sample_ratio) def __getitem__(self, index): index = (self.down_sample_ratio*index +random.randint(0,self.down_sample_ratio-1))%len(self.img_path_list) img_path = self.img_path_list[index] try: itk_image = sitk.ReadImage(img_path) image = sitk.GetArrayFromImage(itk_image) image = self.resize_image(image) except: image = np.random.randn(3,512,512,4) # image = np.load(img_path) # c,w,h,d image = (image-image.min())/(image.max()-image.min()) contain_nan = (True in np.isnan(image)) if contain_nan: image = np.random.randn(3,512,512,4) image = torch.from_numpy(image).float() if random.random() < 0.5: #直接回答 answer = self.caption_list[index] question = random.choice(self.caption_prompts) else: modality = self.caption_list[index] if random.random() < 0.5: # 回答为yes question = random.choice(self.modality_prompts).replace('modality',modality) answer = 'yes' else: select_modality = modality while select_modality == modality: select_modality = random.choice(list(self.modality_sets)) question = random.choice(self.modality_prompts).replace('modality',modality) answer = 'no' if random.random() < 0.5: image_dict = { "image": image, "position": { "question": 0 } } else: image_dict = { "image": image, "position": { "question": len(question) } } return { "image_dict": [image_dict], "question": question, "answer":answer, } class RadioVQA_Dataset(Dataset): """_summary_ Args: Dataset (_type_): _description_: caption task formulated as vqa task for Radiopaedia dataset csv_path (_type_): path to csv file prompt_json_file (_type_): path to json file containing caption prompts Output: Dict: { "image_dict": {"image": image, "position": {"question": 0}}, # image is a tensor of shape [s,c,w,h,d] like, [1,3,512,512,1], position is a dict, random choice of 0 or len(question) "question": question, # random choice of caption prompts "answer":answer, # caption } """ def __init__(self,csv_path): data_info = pd.read_csv(csv_path) # npy_path,image_caption,question,answer self.img_path_list = np.asarray(data_info['image_path']) self.question_list = np.asarray(data_info['question']) self.answer_list = np.asarray(data_info['answer']) def __len__(self): return len(self.img_path_list) def __getitem__(self, index): img_path = self.img_path_list[index] image = np.load(img_path) image = (image-image.min())/(image.max()-image.min()) contain_nan = (True in np.isnan(image)) if contain_nan: image = np.random.randn(3,512,512,4) image = torch.from_numpy(image).float() answer = self.answer_list[index] question = self.question_list[index] image_dict = [] for idx in range(image.shape[0]): if random.random() < 0.5: dict_idx = { "image": image[idx], "position": { "question": 0 } } else: dict_idx = { "image": image[idx], "position": { "question": len(question) } } image_dict.append(dict_idx) if len(image_dict) > 10: images = random.sample(image_dict,10) return { "image_dict": image_dict, "question": question, "answer":answer, } class RadioCaption_Dataset(Dataset): def __init__(self,json_path,prompt_json_file): with open(json_path, 'r') as file: self.json_data = json.load(file) with open(prompt_json_file, 'r') as f: self.caption_prompts = json.load(f)['caption_prompt'] def __len__(self): return len(self.json_data) def __getitem__(self, index): data_index = self.json_data[index] patient_pre = data_index['pre'] patient_pat = data_index['pat'] img_path = data_index['npy_path'] finding = data_index['finding'] impression = data_index['impression'] prompt_question = random.choice(self.caption_prompts) question = patient_pat + ' ' + patient_pre + ' ' + prompt_question image = np.load(img_path) image = (image-image.min())/(image.max()-image.min()) contain_nan = (True in np.isnan(image)) if contain_nan: image = np.random.randn(3,512,512,4) image = torch.from_numpy(image).float() answer = 'Finding: ' + str(finding) + 'Impression: ' + str(impression) image_dict = [] for idx in range(image.shape[0]): if random.random() < 0.5: dict_idx = { "image": image[idx], "position": { "question": 0 } } else: dict_idx = { "image": image[idx], "position": { "question": len(question) } } image_dict.append(dict_idx) return { "image_dict": image_dict, "question": question, "answer":answer, } class Radiofeatures_Dataset(Dataset): def __init__(self,json_path,prompt_json_file,disease_prompt_json_file,article_json_file): with open(json_path, 'r') as file: self.json_data = json.load(file) with open(prompt_json_file, 'r') as f: self.caption_prompts = json.load(f)['caption_prompt'] with open(disease_prompt_json_file, 'r') as f: self.disease_prompts = json.load(f)['caption_prompt'] with open(article_json_file, 'r') as f: self.article_sets = json.load(f).keys() def __len__(self): return len(self.json_data) def __getitem__(self, index): data_index = self.json_data[index] patient_pre = data_index['pre'] patient_pat = data_index['pat'] img_path = data_index['npy_path'] radiographic_features = ' '.join(data_index['radiographic_features']) image = np.load(img_path) image = (image-image.min())/(image.max()-image.min()) contain_nan = (True in np.isnan(image)) if contain_nan: image = np.random.randn(3,512,512,4) image = torch.from_numpy(image).float() if random.random() < 0.5: articles = ' '.join(data_index['articles']) prompt_question = random.choice(self.caption_prompts) question = patient_pat + ' ' + patient_pre + ' ' + prompt_question answer = articles + 'The Radiographic features can be summarized as follows.' + radiographic_features else: articles = data_index['title'] if random.random() < 0.5: # 回答为yes question = random.choice(self.disease_prompts).replace('disease',articles) answer = 'yes' else: select_articles = articles while select_articles == articles: select_articles = random.choice(list(self.article_sets)) question = random.choice(self.disease_prompts).replace('disease',select_articles) answer = 'no' image_dict = [] for idx in range(image.shape[0]): if random.random() < 0.5: dict_idx = { "image": image[idx], "position": { "question": 0 } } else: dict_idx = { "image": image[idx], "position": { "question": len(question) } } image_dict.append(dict_idx) return { "image_dict": image_dict, "question": question, "answer":answer, } """ class Radiodisease_Dataset(Dataset): def __init__(self,json_path,prompt_json_file,article_json_file): with open(json_path, 'r') as file: self.json_data = json.load(file) with open(prompt_json_file, 'r') as f: self.caption_prompts = json.load(f)['caption_prompt'] with open(article_json_file, 'r') as f: self.article_sets = json.load(f).keys() def __len__(self): return len(self.json_data) def __getitem__(self, index): data_index = self.json_data[index] patient_pre = data_index['pre'] patient_pat = data_index['pat'] img_path = data_index['npy_path'] articles = data_index['title'] if random.random() < 0.5: # 回答为yes question = random.choice(self.caption_prompts).replace('disease',articles) answer = 'yes' else: select_articles = articles while select_articles == articles: select_articles = random.choice(list(self.article_sets)) question = random.choice(self.caption_prompts).replace('disease',select_articles) answer = 'no' image = np.load(img_path) image = (image-image.min())/(image.max()-image.min()) image = torch.from_numpy(image).float() image_dict = [] for idx in range(image.shape[0]): if random.random() < 0.5: dict_idx = { "image": image[idx], "position": { "question": 0 } } else: dict_idx = { "image": image[idx], "position": { "question": len(question) } } image_dict.append(dict_idx) return { "image_dict": image_dict, "question": question, "answer":answer, } class Radio_modality_binary_Dataset(Dataset): def __init__(self,csv_path,prompt_json_file,modality_json_file): data_info = pd.read_csv(csv_path) self.img_path_list = np.asarray(data_info['image_path']) self.caption_list = np.asarray(data_info['answer']) with open(prompt_json_file, 'r') as f: self.caption_prompts = json.load(f)['modality_prompt'] with open(modality_json_file, 'r') as f: self.modality_sets = json.load(f)['modality'] def resize_image(self, image): if len(image.shape) == 3: if image.shape[0] > image.shape[2]: image = image.transpose(2,0,1) # print('before resize',image.shape) image = cv2.resize(image,(512,512),interpolation = cv2.INTER_LINEAR) # print('after resize',image.shape) image = image[np.newaxis,:,:,:] image = np.concatenate([image,image,image],axis=0) if image.shape[-1] > 64: image = ndimage.zoom(image, (3/image.shape[0],512/image.shape[1],512/image.shape[2],64/image.shape[3]), order=0) else: image = ndimage.zoom(image, (3/image.shape[0],512/image.shape[1],512/image.shape[2],1), order=0) return image def __len__(self): return len(self.img_path_list) def __getitem__(self, index): img_path = self.img_path_list[index] try: itk_image = sitk.ReadImage(img_path) image = sitk.GetArrayFromImage(itk_image) image = self.resize_image(image) except: image = np.random.randn(3,512,512,4) image = (image-image.min())/(image.max()-image.min()) image = torch.from_numpy(image).float() modality = self.caption_list[index] if random.random() < 0.5: # 回答为yes question = random.choice(self.caption_prompts).replace('modality',modality) answer = 'yes' else: select_modality = modality while select_modality == modality: select_modality = random.choice(list(self.modality_sets)) question = random.choice(self.caption_prompts).replace('modality',modality) answer = 'no' if random.random() < 0.5: image_dict = { "image": image, "position": { "question": 0 } } else: image_dict = { "image": image, "position": { "question": len(question) } } return { "image_dict": [image_dict], "question": question, "answer":answer, } """ ================================================ FILE: src/Dataset/dataset/report_prompt.json ================================================ { "caption_prompt": [ "Can you provide a radiology report for this medical image?", "Describe the medical image you see.", "What is depicted in this picture?", "Please report this medical scan.", "What is the medical significance of this image?", "What can you infer from this picture?", "Can you provide a quick summary of this image?", "Describe this medical scan.", "Please write a radiology report for this image.", "Can you summarize the images presented?", "Please generate a radiology report for this scan.", "Describe the regions of interest in this scan.", "Please provide a caption for this medical image.", "Can you provide a brief summary of this radiograph?", "Describe the structures involved in this medical image.", "What are the findings presented in this medical scan?", "Please write a radiology report for this scan.", "Can you provide a description of this medical scan?", "Please caption this medical scan.", "Can you provide a report summary for this medical scan?" ] } ================================================ FILE: src/Dataset/dataset/spinexr_prompt.json ================================================ { "caption_prompt": [ "What is the diagnosis for this spine X-ray?", "Based on this X-ray, what type of spine disease is suspected?", "Can you identify any abnormality in this spine X-ray?", "What are the findings in this spine X-ray?", "What pathology is indicated by this spine X-ray?", "What lung disease is likely present in this spine X-ray?", "What are the potential causes of the findings in this spine X-ray?", "What are your conclusions from this spine X-ray?", "What is your interpretation of this spine X-ray?", "What abnormalities are present in this spine X-ray?", "What is the differential diagnosis for the findings in this spine X-ray?" ] } ================================================ FILE: src/Dataset/dataset/vqa.py ================================================ import csv import json import logging import os import re import difflib import sys import torch import random from abc import abstractmethod from itertools import islice from typing import TYPE_CHECKING, Any, Callable, Dict, List, Optional, Tuple, Union from collections.abc import Mapping from torch.utils.data import DataLoader import PIL from torch.utils.data import Dataset import numpy as np import pandas as pd from tqdm import tqdm from torchvision import transforms from collections import defaultdict from PIL import Image class VQA_Dataset(Dataset): """_summary_ Args: Dataset (_type_): csv_path (_type_): path to csv file Output: Dict: { "image_dict": {"image": image, "position": {"question": 0}}, # image is a tensor of shape [c,w,h,d] [3,512,512,1], position is a dict, random choice of 0 or len(question) "question": question, # random choice of caption prompts "answer":answer, # caption } """ def __init__(self,csv_path): data_info = pd.read_csv(csv_path) self.img_root_dir_list = np.asarray(data_info['img_root_dir']) self.img_path_list = np.asarray(data_info['Figure_path']) self.question_list = np.asarray(data_info['Question']) self.answer_list = np.asarray(data_info['Answer']) # PMC_ID,Figure_path,Question,Answer self.transform = transforms.Compose([ transforms.RandomResizedCrop([512,512],scale=(0.8, 1.0), interpolation=transforms.InterpolationMode.BICUBIC), transforms.ToTensor(), ]) def __len__(self): return len(self.img_path_list) def __getitem__(self, index): file_name = self.img_path_list[index] img_root_dir = self.img_root_dir_list[index] img_path = os.path.join(img_root_dir,file_name) image = Image.open(img_path).convert('RGB') image = self.transform(image) image = image.unsqueeze(-1) answer = self.answer_list[index] question = str(self.question_list[index]) if random.random() < 0.5: image_dict = { "image": image, "position": { "question": 0 } } else: image_dict = { "image": image, "position": { "question": len(question) } } return { "image_dict": [image_dict], "question": question, "answer":answer, } if __name__ == "__main__": test_dataset = PMCVQA_Dataset(csv_path = '../data_csv/pmcvqa_train.csv') for i in range(10): test_data = test_dataset[i] print(test_data['image_dict'][0]['image'].shape) # [3,512,512,1] ================================================ FILE: src/Dataset/dataset/yes_no_prompt.json ================================================ { "caption_prompt": [ "Is the disease visible in the image?", "Does the image show signs of disease?", "Does the image show any disease?", "Is there any disease in the affected area?", "Does the image depict any visible disease?", "Is there an presence of disease in the image?", "Are there any visible signs of disease in the image?", "Does the image exhibit any disease?", "Are there disease visible in the image?", "Does the image show any signs of disease?", "Can you identify any visible signs of disease in the image?", "Is there any indication of disease in the image?", "Does the image show signs of disease?", "Does the image show any visible signs of disease?" ] } ================================================ FILE: src/Dataset/multi_dataset.py ================================================ # Import necessary libraries for data processing and model interaction from torch.utils.data import Dataset import numpy as np import transformers import pandas as pd import copy import random import os import numpy as np import tqdm import torch import json from PIL import Image import math import torchvision from transformers import AutoModelForCausalLM, AutoTokenizer, LlamaTokenizer from .dataset import * import spacy from spacy.tokens import Span from scispacy.abbreviation import AbbreviationDetector from scispacy.umls_linking import UmlsEntityLinker class umls_extractor: """ Extracts medical entities from text using scispacy and UMLS """ def __init__(self): """Initialize the NLP pipeline with medical entity linking capabilities""" nlp = spacy.load("en_core_sci_lg") nlp.add_pipe("abbreviation_detector") nlp.add_pipe("scispacy_linker", config={"resolve_abbreviations": True, "linker_name": "umls"}) self.nlp = nlp def extract(self, text): """ Extract medical entities from text Args: text: Input text to process Returns: Set of extracted entities """ doc = self.nlp(text) ent_set = doc.ents return ent_set def find_position(label, key_embeddings): """ Creates a tensor of weights for loss calculation based on important keywords Args: label: Token IDs tensor for the target sequence key_embeddings: List of token ID tensors for important medical terms Returns: Tensor of weights where important terms get higher weight (3) """ loss_reweight = torch.ones(label.shape) for i in range(len(label)): if label[i] == -100: # Skip padding or ignored tokens loss_reweight[i] = 0 else: for key_embedding in key_embeddings: if torch.equal(label[i:i+len(key_embedding)], key_embedding): loss_reweight[i:i+len(key_embedding)] = 3 # Increase weight for important terms return loss_reweight def stack_images(images): """ Processes and stacks a list of images to create a batch with consistent dimensions Args: images: List of image tensors Returns: Stacked and resized tensor of images """ target_H = 512 target_W = 512 target_D = 4 if len(images) == 0: return torch.zeros((1, 3, target_H, target_W, target_D)) MAX_D = 4 D_list = list(range(4, 65, 4)) # Find maximum depth among all images for ii in images: try: D = ii.shape[3] if D > MAX_D: MAX_D = D except: continue # Select optimal target depth for temp_D in D_list: if abs(temp_D - MAX_D) < abs(target_D - MAX_D): target_D = temp_D # Resize and stack all images stack_images = [] for s in images: if len(s.shape) == 3: stack_images.append(torch.nn.functional.interpolate(s.unsqueeze(0).unsqueeze(-1), size=(target_H, target_W, target_D))) else: stack_images.append(torch.nn.functional.interpolate(s.unsqueeze(0), size=(target_H, target_W, target_D))) images = torch.cat(stack_images, dim=0) return images class multi_dataset(Dataset): """ A dataset class that combines multiple medical imaging datasets for training a multimodal model """ def __init__(self, text_tokenizer, max_seq=2048, max_img_size=100, image_num=32, voc_size=32000): """ Initialize the multimodal dataset Args: text_tokenizer: Tokenizer or path to tokenizer max_seq: Maximum sequence length max_img_size: Maximum number of images to process image_num: Number of image tokens per image voc_size: Vocabulary size for the tokenizer """ self.text_tokenizer = text_tokenizer self.max_img_size = max_img_size self.image_num = image_num self.max_seq = max_seq self.voc_size = voc_size self.H = 512 self.W = 512 self.image_padding_tokens = [] self.words_extract = umls_extractor() # Initialize tokenizer if path is provided if isinstance(self.text_tokenizer, str): self.text_tokenizer = LlamaTokenizer.from_pretrained( self.text_tokenizer, ) # Add special tokens for image references special_token = {"additional_special_tokens": ["", ""]} for i in range(max_img_size): image_padding_token = "" for j in range(image_num): image_token = "" image_padding_token = image_padding_token + image_token special_token["additional_special_tokens"].append("") self.image_padding_tokens.append(image_padding_token) self.text_tokenizer.add_special_tokens( special_token ) self.text_tokenizer.pad_token_id = 0 self.text_tokenizer.bos_token_id = 1 self.text_tokenizer.eos_token_id = 2 # Initialize empty lists for dataset tracking self.data_whole_2D = [] self.data_whole_3D = [] self.dataset_reflect = {} ### 2D datasets ### Pretrain datasets - currently commented out # paper_inline_dataset = Paper_Inline_dataset(csv_path = '/gpfs/home/cs/leijiayu/wuchaoyi/multi_modal/Data/paper_train.csv', # img_path = '/home/cs/leijiayu/data/all_images/figures/') # self.dataset_reflect['paper_inline_dataset'] = paper_inline_dataset # self.data_whole_2D = self.data_whole_2D + [{'paper_inline_dataset':i} for i in range(len(paper_inline_dataset))] # print('paper_inline_dataset loaded') # pmcoa_dataset = PMCOA_Dataset(csv_path = '/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/pmcoa_image_caption_train.csv', # img_root_dir = '/home/cs/leijiayu/data/PMCVQA/caption_T060_filtered_top4_sep_v0_subfigures', # prompt_json_file = '/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/dataset/caption_prompt.json') # self.dataset_reflect['pmcoa_dataset'] = pmcoa_dataset # self.data_whole_2D = self.data_whole_2D + [{'pmcoa_dataset':i} for i in range(len(pmcoa_dataset))] # print('pmcoa_dataset loaded') ### SFT (Supervised Fine-Tuning) datasets ### MedPix datasets medpix_multi_dataset = MedPix_Multi_Dataset(csv_path='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/MedPix_multi_train.csv') self.dataset_reflect['medpix_multi_dataset'] = medpix_multi_dataset self.data_whole_2D = self.data_whole_2D + [{'medpix_multi_dataset': i} for i in range(len(medpix_multi_dataset))] print('medpix_multi_dataset loaded') medpix_single_dataset = MedPix_Single_Dataset(csv_path='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/MedPix_single_train.csv') self.dataset_reflect['medpix_single_dataset'] = medpix_single_dataset self.data_whole_2D = self.data_whole_2D + [{'medpix_single_dataset': i} for i in range(len(medpix_single_dataset))] print('medpix_single_dataset loaded') medpix_qa_dataset = MedPix_QA_Dataset(csv_path='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/MedPix_questions_train.csv') self.dataset_reflect['medpix_qa_dataset'] = medpix_qa_dataset self.data_whole_2D = self.data_whole_2D + [{'medpix_qa_dataset': i} for i in range(len(medpix_qa_dataset))] print('medpix_qa_dataset loaded') ### Chest X-ray datasets ### Caption datasets chestxray_caption_dataset = ChestXray_Dataset( csv_path='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/mimic_caption_train.csv', prompt_json_file='/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/dataset/report_prompt.json' ) self.dataset_reflect['chestxray_caption_dataset'] = chestxray_caption_dataset self.data_whole_2D = self.data_whole_2D + [{'chestxray_caption_dataset': i} for i in range(len(chestxray_caption_dataset))] print('chestxray_caption_dataset loaded') ### Binary classification datasets chestxray_dataset_bn = Binary_Dataset( csv_path='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/chestxray_balance_train_new.csv', prompt_json_file='/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/dataset/yes_no_prompt.json' ) self.dataset_reflect['chestxray_dataset_bn'] = chestxray_dataset_bn self.data_whole_2D = self.data_whole_2D + [{'chestxray_dataset_bn': i} for i in range(len(chestxray_dataset_bn))] print('chestxray_dataset_bn loaded') pcxr_dataset_bn = Binary_Dataset( csv_path='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/pcxr_balance_train.csv', prompt_json_file='/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/dataset/yes_no_prompt.json' ) self.dataset_reflect['pcxr_dataset_bn'] = pcxr_dataset_bn self.data_whole_2D = self.data_whole_2D + [{'pcxr_dataset_bn': i} for i in range(len(pcxr_dataset_bn))] print('pcxr_dataset_bn loaded') mammo_dataset_bn = Binary_Dataset( csv_path='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/mammo_balance_train.csv', prompt_json_file='/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/dataset/yes_no_prompt.json' ) self.dataset_reflect['mammo_dataset_bn'] = mammo_dataset_bn self.data_whole_2D = self.data_whole_2D + [{'mammo_dataset_bn': i} for i in range(len(mammo_dataset_bn))] print('mammo_dataset_bn loaded') spinexr_dataset_bn = Binary_Dataset( csv_path='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/spinexr_balance_train.csv', prompt_json_file='/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/dataset/yes_no_prompt.json' ) self.dataset_reflect['spinexr_dataset_bn'] = spinexr_dataset_bn self.data_whole_2D = self.data_whole_2D + [{'spinexr_dataset_bn': i} for i in range(len(spinexr_dataset_bn))] print('spinexr_dataset_bn loaded') ### Multi-label classification datasets chestxray_dataset = ChestXray_Dataset( csv_path='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/chestxray_new.csv', prompt_json_file='/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/dataset/cls_prompt.json' ) self.dataset_reflect['chestxray_dataset'] = chestxray_dataset self.data_whole_2D = self.data_whole_2D + [{'chestxray_dataset': i} for i in range(len(chestxray_dataset))] print('chestxray_dataset loaded') pcxr_dataset = ChestXray_Dataset( csv_path='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/pcxr_train_new.csv', prompt_json_file='/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/dataset/cls_prompt.json' ) self.dataset_reflect['pcxr_dataset'] = pcxr_dataset self.data_whole_2D = self.data_whole_2D + [{'pcxr_dataset': i} for i in range(len(pcxr_dataset))] print('pcxr_dataset loaded') mammo_dataset = ChestXray_Dataset( csv_path='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/mammo_train_new.csv', prompt_json_file='/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/dataset/mammo_prompt.json' ) self.dataset_reflect['mammo_dataset'] = mammo_dataset self.data_whole_2D = self.data_whole_2D + [{'mammo_dataset': i} for i in range(len(mammo_dataset))] print('mammo_dataset loaded') spinexr_dataset = ChestXray_Dataset( csv_path='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/spinexr_train_new.csv', prompt_json_file='/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/dataset/spinexr_prompt.json' ) self.dataset_reflect['spinexr_dataset'] = spinexr_dataset self.data_whole_2D = self.data_whole_2D + [{'spinexr_dataset': i} for i in range(len(spinexr_dataset))] print('spinexr_dataset loaded') ### VQA (Visual Question Answering) datasets pmcvqa_dataset = VQA_Dataset(csv_path='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/pmcvqa_train.csv') self.dataset_reflect['pmcvqa_dataset'] = pmcvqa_dataset self.data_whole_2D = self.data_whole_2D + [{'pmcvqa_dataset': i} for i in range(len(pmcvqa_dataset))] print('pmcvqa_dataset loaded') casereport_dataset = CaseReport_dataset( csv_path='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/filtered_case_report_train.csv', img_path='/home/cs/leijiayu/data/all_images/figures/' ) self.dataset_reflect['casereport_dataset'] = casereport_dataset self.data_whole_2D = self.data_whole_2D + [{'casereport_dataset': i} for i in range(len(casereport_dataset))] print('casereport_dataset loaded') vqarad_dataset = VQA_Dataset(csv_path='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/vqarad_train.csv') self.dataset_reflect['vqarad_dataset'] = vqarad_dataset self.data_whole_2D = self.data_whole_2D + [{'vqarad_dataset': i} for i in range(len(vqarad_dataset))] print('vqarad_dataset loaded') slake_dataset = VQA_Dataset(csv_path='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/slakevqa_train.csv') self.dataset_reflect['slake_dataset'] = slake_dataset self.data_whole_2D = self.data_whole_2D + [{'slake_dataset': i} for i in range(len(slake_dataset))] print('slake_dataset loaded') ### 3D datasets radiovqa_dataset = RadioVQA_Dataset(csv_path='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/radiology_vqa_train.csv') self.dataset_reflect['radiovqa_dataset'] = radiovqa_dataset self.data_whole_3D = self.data_whole_3D + [{'radiovqa_dataset': i} for i in range(len(radiovqa_dataset))] print('radiovqa_dataset loaded') radiomodality_dataset = Radio_Modality_Dataset( csv_path='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/radio_modality_train.csv', prompt_json_file='/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/dataset/modality_prompt.json', modality_json_file='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/modality_set.json' ) self.dataset_reflect['radiomodality_dataset'] = radiomodality_dataset self.data_whole_3D = self.data_whole_3D + [{'radiomodality_dataset': i} for i in range(len(radiomodality_dataset))] print('radiomodality_dataset loaded') radiocaption_dataset = RadioCaption_Dataset( json_path='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/radiology_article_npy_train.json', prompt_json_file='/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/dataset/caption_prompt.json', ) self.dataset_reflect['radiocaption_dataset'] = radiocaption_dataset self.data_whole_3D = self.data_whole_3D + [{'radiocaption_dataset': i} for i in range(len(radiocaption_dataset))] print('radiocaption_dataset loaded') radiofeatures_dataset = Radiofeatures_Dataset( json_path='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/radiology_article_npy_train.json', prompt_json_file='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/dataset/radiology_feature_prompt.json', disease_prompt_json_file='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/dataset/yes_no_prompt.json', article_json_file='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/articles_resave.json' ) self.dataset_reflect['radiofeatures_dataset'] = radiofeatures_dataset self.data_whole_3D = self.data_whole_3D + [{'radiofeatures_dataset': i} for i in range(len(radiofeatures_dataset))] print('radiofeatures_dataset loaded') # Combine all datasets self.data_whole = self.data_whole_2D + self.data_whole_3D def __len__(self): """Return the total number of samples in the combined dataset""" return len(self.data_whole) def __getitem__(self, idx): """ Get a specific sample from the dataset Args: idx: Index of the sample to retrieve Returns: Dictionary containing processed inputs for model training """ # Get sample from the appropriate dataset sample = list(self.data_whole[idx].items())[0] dataset_index = sample[0] sample = self.dataset_reflect[sample[0]][sample[1]] ''' Dict: { "image_dict": [ {"image": image, # image is a tensor of shape [c,w,h,d], c is channel=3, w is width, h is height, d is depth(1 for chestxray,pmcoa,pmcvqa) "position": {"question": 0}}, position is a dict, random choice of 0 or len(question) ] "question": question, "answer":answer, } ''' images = sample["image_dict"] question = sample["question"] answer = sample["answer"] # Process text and images together images, question, answer = self.text_add_image(images, question, answer) # Stack images into a single tensor try: vision_x = stack_images(images) except: print(self.data_whole[idx].items()) # Tokenize combined question and answer text self.text_tokenizer.padding_side = "right" text_tensor = self.text_tokenizer( question + ' ' + answer, max_length=self.max_seq, truncation=True, padding="max_length", return_tensors="pt" ) lang_x = text_tensor["input_ids"][0] attention_mask = text_tensor["attention_mask"][0] # Add EOS token if necessary try: lang_x[torch.sum(attention_mask)] = self.text_tokenizer.eos_token_id except: pass # Extract important medical terms for loss weighting emphasize_words = [] emphasize_words = [str(_) for _ in self.words_extract.extract(answer)] if emphasize_words != []: emphasize_words_tensor = self.text_tokenizer( emphasize_words, max_length=self.max_seq ) key_embeddings = [torch.tensor(_[1:]) for _ in emphasize_words_tensor['input_ids']] else: key_embeddings = [] # Tokenize question to determine its length question_tensor = self.text_tokenizer( question, max_length=self.max_seq, truncation=True, padding="max_length", return_tensors="pt" ) question_length = torch.sum(question_tensor["attention_mask"][0]) # Create labels for training (ignore question tokens, padding, and special tokens) labels = lang_x.clone() labels[labels == self.text_tokenizer.pad_token_id] = -100 labels[labels >= self.voc_size] = -100 labels[:question_length] = -100 # Apply weights to important medical terms in the labels reweight_tensor = find_position(labels, key_embeddings) # Don't use keyword emphasis for certain datasets if dataset_index == 'paper_inline_dataset': emphasize_words = [] # Return all processed inputs for model training return { 'vision_x': vision_x, 'lang_x': lang_x, 'attention_mask': attention_mask, 'labels': labels, 'loss_reweight': reweight_tensor, 'key_words_query': emphasize_words } def text_add_image(self, images, question, answer): """ Insert image tokens into text at appropriate positions Args: images: List of image tensors question: Question text answer: Answer text Returns: Tuple of (processed_images, question_with_image_tokens, answer_with_image_tokens) """ ref_image = [] question = str(question) answer = str(answer) # Initialize lists to track image insertion positions question_list = [[] for _ in range(len(str(question)))] answer_list = [[] for _ in range(len(str(answer)))] # Process each image and its position for index, image in enumerate(images): ref_image.append(image["image"]) position = image["position"] position = list(position.items())[0] # Store image indices at their insertion positions if position[0] == 'question': insert_loc = position[1] - 1 if insert_loc < 0: insert_loc = 0 question_list[insert_loc].append(index) if position[0] == 'answer': insert_loc = position[1] - 1 if insert_loc < 0: insert_loc = 0 answer_list[insert_loc].append(index) # Build new question text with image tokens new_question = '' new_answer = '' question = str(question) for char_i in range(len(question)): if question_list[char_i] == []: new_question = new_question + question[char_i] if question_list[char_i] != []: for img_index in question_list[char_i]: try: new_question = new_question + '' + self.image_padding_tokens[img_index] + '' except: print("Error: out of max image input size") new_question = new_question + question[char_i] # Build new answer text with image tokens answer = str(answer) for char_i in range(len(str(answer))): if answer_list[char_i] == []: new_answer = new_answer + answer[char_i] if answer_list[char_i] != []: for img_index in answer_list[char_i]: try: new_answer = new_answer + '' + self.image_padding_tokens[img_index] + '' except: print("Error: out of max image input size") new_answer = new_answer + answer[char_i] # Remove bullet points for cleaner text new_answer = new_answer.replace('•', '') return ref_image, new_question, new_answer # torch.set_printoptions(profile="full") # text_tokenizer = '/home/cs/leijiayu/wuchaoyi/Finetune_LLAMA/LLAMA_Model/tokenizer' # dataset = multi_dataset(text_tokenizer = text_tokenizer) # print(len(dataset)) # for i in range(10): # dataset[i] # input() ================================================ FILE: src/Dataset/multi_dataset_test.py ================================================ # Import necessary libraries for data processing, model interaction, and image handling from torch.utils.data import Dataset import numpy as np import transformers import pandas as pd import copy import random import os import numpy as np import tqdm import torch import json from PIL import Image import math import torchvision from transformers import AutoModelForCausalLM, AutoTokenizer, LlamaTokenizer from .dataset import * def stack_images(images): """ Process and stack multiple images to a consistent format Args: images: List of image tensors Returns: Stacked tensor of images with consistent dimensions """ # Set target dimensions target_H = 512 target_W = 512 target_D = 4 # Return empty tensor if no images if len(images) == 0: return torch.zeros((1, 3, target_H, target_W, target_D)) # Find optimal depth for 3D images MAX_D = 4 D_list = list(range(4, 65, 4)) for ii in images: try: D = ii.shape[3] if D > MAX_D: MAX_D = D except: continue # Select closest target depth for temp_D in D_list: if abs(temp_D - MAX_D) < abs(target_D - MAX_D): target_D = temp_D # Process each image to the target dimensions stack_images = [] for s in images: s = torch.tensor(s) if len(s.shape) == 3: # For 2D images, add depth dimension stack_images.append(torch.nn.functional.interpolate(s.unsqueeze(0).unsqueeze(-1), size=(target_H, target_W, target_D))) else: # For 3D images stack_images.append(torch.nn.functional.interpolate(s.unsqueeze(0), size=(target_H, target_W, target_D))) # Concatenate all processed images images = torch.cat(stack_images, dim=0) return images class multi_dataset(Dataset): """ Dataset class for testing multimodal models on different medical imaging tasks """ def __init__(self, text_tokenizer, test_split='close', max_seq=2048, max_img_size=10, image_num=32, voc_size=32000): """ Initialize the test dataset Args: text_tokenizer: Tokenizer or path to tokenizer test_split: Which test split to use ('diagnosis', 'modality', 'vqa', 'caption', 'feature') max_seq: Maximum sequence length max_img_size: Maximum number of images to process image_num: Number of image tokens per image voc_size: Vocabulary size """ self.text_tokenizer = text_tokenizer self.max_img_size = max_img_size self.image_num = image_num self.max_seq = max_seq self.voc_size = voc_size self.H = 512 self.W = 512 self.image_padding_tokens = [] self.test_split = test_split # Initialize tokenizer with special tokens for images if isinstance(self.text_tokenizer, str): self.text_tokenizer = LlamaTokenizer.from_pretrained( self.text_tokenizer, ) special_token = {"additional_special_tokens": ["", ""]} # Create special tokens for each image position and patch for i in range(max_img_size): image_padding_token = "" for j in range(image_num): image_token = "" image_padding_token = image_padding_token + image_token special_token["additional_special_tokens"].append("") self.image_padding_tokens.append(image_padding_token) # Add special tokens to tokenizer self.text_tokenizer.add_special_tokens( special_token ) # Set standard special tokens for LLaMA self.text_tokenizer.pad_token_id = 0 self.text_tokenizer.bos_token_id = 1 self.text_tokenizer.eos_token_id = 2 # Initialize dataset tracking variables self.data_whole_2D = [] self.data_whole_3D = [] self.dataset_reflect = {} ### Load appropriate datasets based on test_split ### # Diagnosis task datasets (binary and multi-class classification) if self.test_split == 'diagnosis': # Binary classification datasets chestxray_dataset_bn = Binary_Dataset( csv_path='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/chestxray_balance_test.csv', prompt_json_file='/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/dataset/yes_no_prompt.json' ) self.dataset_reflect['chestxray_dataset_bn'] = chestxray_dataset_bn self.data_whole_2D = self.data_whole_2D + [{'chestxray_dataset_bn': i} for i in range(len(chestxray_dataset_bn))] print('chestxray_dataset_bn loaded') pcxr_dataset_bn = Binary_Dataset( csv_path='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/pcxr_balance_test.csv', prompt_json_file='/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/dataset/yes_no_prompt.json' ) self.dataset_reflect['pcxr_dataset_bn'] = pcxr_dataset_bn self.data_whole_2D = self.data_whole_2D + [{'pcxr_dataset_bn': i} for i in range(len(pcxr_dataset_bn))] print('pcxr_dataset_bn loaded') mammo_dataset_bn = Binary_Dataset( csv_path='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/mammo_balance_test.csv', prompt_json_file='/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/dataset/yes_no_prompt.json' ) self.dataset_reflect['mammo_dataset_bn'] = mammo_dataset_bn self.data_whole_2D = self.data_whole_2D + [{'mammo_dataset_bn': i} for i in range(len(mammo_dataset_bn))] print('mammo_dataset_bn loaded') spinexr_dataset_bn = Binary_Dataset( csv_path='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/spinexr_balance_test.csv', prompt_json_file='/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/dataset/yes_no_prompt.json' ) self.dataset_reflect['spinexr_dataset_bn'] = spinexr_dataset_bn self.data_whole_2D = self.data_whole_2D + [{'spinexr_dataset_bn': i} for i in range(len(spinexr_dataset_bn))] print('spinexr_dataset_bn loaded') # Multi-label classification datasets chestxray_dataset = ChestXray_Dataset( csv_path='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/chestxray_test.csv', prompt_json_file='/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/dataset/cls_prompt.json' ) self.dataset_reflect['chestxray_dataset'] = chestxray_dataset self.data_whole_2D = self.data_whole_2D + [{'chestxray_dataset': i} for i in range(len(chestxray_dataset))] print('chestxray_dataset loaded') pcxr_dataset = ChestXray_Dataset( csv_path='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/pcxr_test.csv', prompt_json_file='/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/dataset/cls_prompt.json' ) self.dataset_reflect['pcxr_dataset'] = pcxr_dataset self.data_whole_2D = self.data_whole_2D + [{'pcxr_dataset': i} for i in range(len(pcxr_dataset))] print('pcxr_dataset loaded') mammo_dataset = ChestXray_Dataset( csv_path='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/mammo_test.csv', prompt_json_file='/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/dataset/mammo_prompt.json' ) self.dataset_reflect['mammo_dataset'] = mammo_dataset self.data_whole_2D = self.data_whole_2D + [{'mammo_dataset': i} for i in range(len(mammo_dataset))] print('mammo_dataset loaded') spinexr_dataset = ChestXray_Dataset( csv_path='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/spinexr_test.csv', prompt_json_file='/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/dataset/spinexr_prompt.json' ) self.dataset_reflect['spinexr_dataset'] = spinexr_dataset self.data_whole_2D = self.data_whole_2D + [{'spinexr_dataset': i} for i in range(len(spinexr_dataset))] print('spinexr_dataset loaded') # Modality classification datasets if self.test_split == 'modality': radiomodality_dataset = Radio_Modality_Dataset( csv_path='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/radio_modality_test.csv', prompt_json_file='/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/dataset/modality_prompt.json', modality_json_file='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/modality_set.json', down_sample_ratio=1 ) self.dataset_reflect['radiomodality_dataset'] = radiomodality_dataset self.data_whole_3D = self.data_whole_3D + [{'radiomodality_dataset': i} for i in range(len(radiomodality_dataset))] print('radiomodality_dataset loaded') # Visual Question Answering datasets if self.test_split == 'vqa': # Load VQA datasets for 2D images pmcvqa_dataset = VQA_Dataset(csv_path='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/pmcvqa_test.csv') self.dataset_reflect['pmcvqa_dataset'] = pmcvqa_dataset self.data_whole_2D = self.data_whole_2D + [{'pmcvqa_dataset': i} for i in range(len(pmcvqa_dataset))] print('pmcvqa_dataset loaded') casereport_dataset = CaseReport_dataset( csv_path='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/filtered_case_report_test.csv', img_path='/home/cs/leijiayu/data/all_images/figures/' ) self.dataset_reflect['casereport_dataset'] = casereport_dataset self.data_whole_2D = self.data_whole_2D + [{'casereport_dataset': i} for i in range(len(casereport_dataset))] print('casereport_dataset loaded') vqarad_dataset = VQA_Dataset(csv_path='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/vqarad_test.csv') self.dataset_reflect['vqarad_dataset'] = vqarad_dataset self.data_whole_2D = self.data_whole_2D + [{'vqarad_dataset': i} for i in range(len(vqarad_dataset))] print('vqarad_dataset loaded') slake_dataset = VQA_Dataset(csv_path='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/slakevqa_test.csv') self.dataset_reflect['slake_dataset'] = slake_dataset self.data_whole_2D = self.data_whole_2D + [{'slake_dataset': i} for i in range(len(slake_dataset))] print('slake_dataset loaded') # Load VQA dataset for 3D images radiovqa_dataset = RadioVQA_Dataset(csv_path='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/radiology_vqa_test.csv') self.dataset_reflect['radiovqa_dataset'] = radiovqa_dataset self.data_whole_3D = self.data_whole_3D + [{'radiovqa_dataset': i} for i in range(len(radiovqa_dataset))] print('radiovqa_dataset loaded') # Image captioning datasets if self.test_split == 'caption': # Load captioning datasets for 2D images chestxray_caption_dataset = ChestXray_Dataset( csv_path='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/mimic_caption_test.csv', prompt_json_file='/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/dataset/report_prompt.json' ) self.dataset_reflect['chestxray_caption_dataset'] = chestxray_caption_dataset self.data_whole_2D = self.data_whole_2D + [{'chestxray_caption_dataset': i} for i in range(len(chestxray_caption_dataset))] print('chestxray_caption_dataset loaded') # Load captioning dataset for 3D images radiocaption_dataset = RadioCaption_Dataset( json_path='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/radiology_article_npy_test.json', prompt_json_file='/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/dataset/caption_prompt.json' ) self.dataset_reflect['radiocaption_dataset'] = radiocaption_dataset self.data_whole_3D = self.data_whole_3D + [{'radiocaption_dataset': i} for i in range(len(radiocaption_dataset))] print('radiocaption_dataset loaded') # Feature extraction datasets if self.test_split == 'feature': radiofeatures_dataset = Radiofeatures_Dataset( json_path='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/radiology_article_npy_test.json', prompt_json_file='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/dataset/radiology_feature_prompt.json', disease_prompt_json_file='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/dataset/yes_no_prompt.json', article_json_file='/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/articles_resave.json' ) self.dataset_reflect['radiofeatures_dataset'] = radiofeatures_dataset self.data_whole_3D = self.data_whole_3D + [{'radiofeatures_dataset': i} for i in range(len(radiofeatures_dataset))] print('radiofeatures_dataset loaded') # Combine 2D and 3D datasets self.data_whole = self.data_whole_2D + self.data_whole_3D def __len__(self): """Return the total number of samples across all test datasets""" return len(self.data_whole) def __getitem__(self, idx): """ Get a single test sample Args: idx: Index of the sample Returns: Dictionary with processed inputs for model testing """ # Extract dataset name and sample index sample = list(self.data_whole[idx].items())[0] belong_to = sample[0] # Which dataset this sample belongs to sample = self.dataset_reflect[sample[0]][sample[1]] # Get the actual sample ''' Dict: { "image_dict": [ {"image": image, # image is a tensor of shape [c,w,h,d], c is channel=3, w is width, h is height, d is depth(1 for chestxray,pmcoa,pmcvqa) "position": {"question": 0}}, position is a dict, random choice of 0 or len(question) ] "question": question, "answer":answer, } ''' # Extract images and text from sample images = sample["image_dict"] # Limit number of images to prevent memory issues if len(images) > 8: images = random.sample(images, 8) question = str(sample["question"]) answer = str(sample["answer"]) # Combine text and images images, question, answer = self.text_add_image(images, question, answer) # Create stacked image tensor try: vision_x = stack_images(images) except: print(self.data_whole[idx].items()) input() # Return processed sample for testing return { 'vision_x': vision_x, 'question': question, 'answer': answer, 'belong_to': belong_to, } def text_add_image(self, images, question, answer): """ Insert image tokens into the text at appropriate positions Args: images: List of image tensors question: Question text answer: Answer text Returns: Tuple of (processed_images, question_with_image_tokens, answer_with_image_tokens) """ ref_image = [] # Initialize lists to track image insertion positions question_list = [[] for _ in range(len(str(question)))] answer_list = [[] for _ in range(len(str(answer)))] # Process each image and its position for index, image in enumerate(images): ref_image.append(image["image"]) position = image["position"] position = list(position.items())[0] # Record image indices at their insertion positions if position[0] == 'question': insert_loc = position[1] - 1 if insert_loc < 0: insert_loc = 0 question_list[insert_loc].append(index) if position[0] == 'answer': insert_loc = position[1] - 1 if insert_loc < 0: insert_loc = 0 answer_list[insert_loc].append(index) # Build new question text with image tokens new_question = '' new_answer = '' for char_i in range(len(question)): if question_list[char_i] == []: new_question = new_question + question[char_i] if question_list[char_i] != []: for img_index in question_list[char_i]: try: new_question = new_question + '' + self.image_padding_tokens[img_index] + '' except: print("Error: out of max image input size") new_question = new_question + question[char_i] # Build new answer text with image tokens for char_i in range(len(answer)): if answer_list[char_i] == []: new_answer = new_answer + answer[char_i] if answer_list[char_i] != []: for img_index in answer_list[char_i]: try: new_answer = new_answer + '' + self.image_padding_tokens[img_index] + '' except: print("Error: out of max image input size") new_answer = new_answer + answer[char_i] # Clean up text formatting new_answer = new_answer.replace('•', '') return ref_image, new_question, new_answer # torch.set_printoptions(profile="full") # text_tokenizer = '/home/cs/leijiayu/wuchaoyi/Finetune_LLAMA/LLAMA_Model/tokenizer' # dataset = multi_dataset(text_tokenizer = text_tokenizer) # print(len(dataset)) # for i in range(10): # dataset[i] # input() ================================================ FILE: src/Dataset/multi_dataset_test_for_close.py ================================================ from torch.utils.data import Dataset import numpy as np import transformers import pandas as pd import copy import random import os import numpy as np import tqdm import torch import json from PIL import Image import math import torchvision from transformers import AutoModelForCausalLM, AutoTokenizer, LlamaTokenizer from .dataset import * def find_position(label, key_embeddings): loss_reweight = torch.ones(label.shape) for i in range(len(label)): if label[i] == -100: loss_reweight[i] = 0 else: for key_embedding in key_embeddings: if torch.equal(label[i:i+len(key_embedding)], key_embedding): loss_reweight[i:i+len(key_embedding)] = 3 return loss_reweight def stack_images(images): target_H = 512 target_W = 512 target_D = 4 if len(images) == 0: return torch.zeros((1,3,target_H,target_W,target_D)) MAX_D = 4 D_list = list(range(4,65,4)) for ii in images: try: D = ii.shape[3] if D > MAX_D: MAX_D = D except: continue for temp_D in D_list: if abs(temp_D - MAX_D)< abs(target_D - MAX_D): target_D = temp_D stack_images = [] for s in images: if len(s.shape) == 3: #print(s.shape) stack_images.append(torch.nn.functional.interpolate(s.unsqueeze(0).unsqueeze(-1), size = (target_H,target_W,target_D))) else: stack_images.append(torch.nn.functional.interpolate(s.unsqueeze(0), size = (target_H,target_W,target_D))) images = torch.cat(stack_images, dim=0) return images class multi_dataset_close(Dataset): def __init__(self, text_tokenizer, test_split = 'close', max_seq = 2048, max_img_size = 10, image_num=32,voc_size =32000, down_sample_ratio = 100): self.down_sample_ratio = down_sample_ratio self.text_tokenizer = text_tokenizer self.max_img_size = max_img_size self.image_num = image_num self.max_seq = max_seq self.voc_size = voc_size self.H = 512 self.W = 512 self.image_padding_tokens = [] if isinstance(self.text_tokenizer,str): self.text_tokenizer = LlamaTokenizer.from_pretrained( self.text_tokenizer, ) special_token = {"additional_special_tokens": ["",""]} for i in range(max_img_size): image_padding_token = "" for j in range(image_num): image_token = "" image_padding_token = image_padding_token + image_token special_token["additional_special_tokens"].append("") self.image_padding_tokens.append(image_padding_token) self.text_tokenizer.add_special_tokens( special_token ) self.text_tokenizer.pad_token_id = 0 self.text_tokenizer.bos_token_id = 1 self.text_tokenizer.eos_token_id = 2 self.data_whole_2D = [] self.data_whole_3D = [] self.dataset_reflect = {} self.test_split = test_split ### closed ### if self.test_split == 'close': chestxray_dataset_bn = Binary_Dataset(csv_path = '/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/chestxray_balance_test.csv', prompt_json_file = '/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/dataset/yes_no_prompt.json') self.dataset_reflect['chestxray_dataset_bn'] = chestxray_dataset_bn self.data_whole_2D = self.data_whole_2D + [{'chestxray_dataset_bn':i} for i in range(len(chestxray_dataset_bn))] print('chestxray_dataset_bn loaded') pcxr_dataset_bn = Binary_Dataset(csv_path = '/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/pcxr_balance_test.csv', prompt_json_file = '/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/dataset/yes_no_prompt.json') self.dataset_reflect['pcxr_dataset_bn'] = pcxr_dataset_bn self.data_whole_2D = self.data_whole_2D + [{'pcxr_dataset_bn':i} for i in range(len(pcxr_dataset_bn))] print('pcxr_dataset_bn loaded') mammo_dataset_bn = Binary_Dataset(csv_path = '/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/mammo_balance_test.csv', prompt_json_file = '/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/dataset/yes_no_prompt.json') self.dataset_reflect['mammo_dataset_bn'] = mammo_dataset_bn self.data_whole_2D = self.data_whole_2D + [{'mammo_dataset_bn':i} for i in range(len(mammo_dataset_bn))] print('mammo_dataset_bn loaded') spinexr_dataset_bn = Binary_Dataset(csv_path = '/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/spinexr_balance_test.csv', prompt_json_file = '/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/dataset/yes_no_prompt.json') self.dataset_reflect['spinexr_dataset_bn'] = spinexr_dataset_bn self.data_whole_2D = self.data_whole_2D + [{'spinexr_dataset_bn':i} for i in range(len(spinexr_dataset_bn))] print('spinexr_dataset_bn loaded') radiomodality_dataset = Radio_Modality_Dataset(csv_path = '/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/radio_modality_test.csv', prompt_json_file = '/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/dataset/modality_prompt.json', modality_json_file = '/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/modality_set.json') self.dataset_reflect['radiomodality_dataset'] = radiomodality_dataset self.data_whole_3D = self.data_whole_3D + [{'radiomodality_dataset':i} for i in range(len(radiomodality_dataset))] print('radiomodality_dataset loaded') ### multi-label ### chestxray_dataset = ChestXray_Dataset(csv_path = '/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/chestxray_test.csv', prompt_json_file = '/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/dataset/cls_prompt.json') self.dataset_reflect['chestxray_dataset'] = chestxray_dataset self.data_whole_2D = self.data_whole_2D + [{'chestxray_dataset':i} for i in range(len(chestxray_dataset))] print('chestxray_dataset loaded') pcxr_dataset = ChestXray_Dataset(csv_path = '/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/pcxr_test.csv', prompt_json_file = '/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/dataset/cls_prompt.json') self.dataset_reflect['pcxr_dataset'] = pcxr_dataset self.data_whole_2D = self.data_whole_2D + [{'pcxr_dataset':i} for i in range(len(pcxr_dataset))] print('pcxr_dataset loaded') mammo_dataset = ChestXray_Dataset(csv_path = '/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/mammo_test.csv', prompt_json_file = '/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/dataset/mammo_prompt.json') self.dataset_reflect['mammo_dataset'] = mammo_dataset self.data_whole_2D = self.data_whole_2D + [{'mammo_dataset':i} for i in range(len(mammo_dataset))] print('mammo_dataset loaded') spinexr_dataset = ChestXray_Dataset(csv_path = '/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/spinexr_test.csv', prompt_json_file = '/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/dataset/spinexr_prompt.json') self.dataset_reflect['spinexr_dataset'] = spinexr_dataset self.data_whole_2D = self.data_whole_2D + [{'spinexr_dataset':i} for i in range(len(spinexr_dataset))] print('spinexr_dataset loaded') medpix_single_dataset = MedPix_Single_Dataset(csv_path = '/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/MedPix_single_test_close.csv') self.dataset_reflect['medpix_single_dataset'] = medpix_single_dataset self.data_whole_2D = self.data_whole_2D + [{'medpix_single_dataset':i} for i in range(len(medpix_single_dataset))] print('medpix_single_dataset loaded') vqarad_dataset = VQA_Dataset(csv_path = '/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/vqarad_test.csv') self.dataset_reflect['vqarad_dataset'] = vqarad_dataset self.data_whole_2D = self.data_whole_2D + [{'vqarad_dataset':i} for i in range(len(vqarad_dataset))] print('vqarad_dataset loaded') slake_dataset = VQA_Dataset(csv_path = '/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/New_Dataset/data_csv/slakevqa_test.csv') self.dataset_reflect['slake_dataset'] = slake_dataset self.data_whole_2D = self.data_whole_2D + [{'slake_dataset':i} for i in range(len(slake_dataset))] print('slake_dataset loaded') self.data_whole = self.data_whole_2D + self.data_whole_3D random.shuffle(self.data_whole) def __len__(self): return math.ceil(len(self.data_whole)/self.down_sample_ratio) def __getitem__(self, idx): idx = (self.down_sample_ratio*idx +random.randint(0,self.down_sample_ratio-1))%len(self.data_whole) # vision_x, lang_x, attention_mask, labels sample = list(self.data_whole[idx].items())[0] dataset_index = sample[0] #print(sample) sample = self.dataset_reflect[sample[0]][sample[1]] ''' Dict: { "image_dict": [ {"image": image, # image is a tensor of shape [c,w,h,d], c is channel=3, w is width, h is height, d is depth(1 for chestxray,pmcoa,pmcvqa) "position": {"question": 0}}, position is a dict, random choice of 0 or len(question) ] "question": question, "answer":answer, } ''' images = sample["image_dict"] question = str(sample["question"]) answer = str(sample["answer"]) images, question, answer = self.text_add_image(images,question,answer) # print(question,answer) ### make vision_x try: vision_x = stack_images(images) except: print(self.data_whole[idx].items()) #print(vision_x.shape,question,answer) ### make lang_x ### self.text_tokenizer.padding_side = "right" text_tensor = self.text_tokenizer( question + ' ' + answer, max_length=self.max_seq, truncation=True, padding="max_length", return_tensors="pt" ) lang_x = text_tensor["input_ids"][0] attention_mask = text_tensor["attention_mask"][0] try: lang_x[torch.sum(attention_mask)] = self.text_tokenizer.eos_token_id except: pass ### make label ### emphasize_words = [] # emphasize_words = [str(_) for _ in self.words_extract.extract(answer)] if emphasize_words != []: emphasize_words_tensor = self.text_tokenizer( emphasize_words , max_length=self.max_seq ) key_embeddings = [torch.tensor(_[1:]) for _ in emphasize_words_tensor['input_ids']] else: key_embeddings = [] question_tensor = self.text_tokenizer( question, max_length=self.max_seq, truncation=True, padding="max_length", return_tensors="pt" ) question_length = torch.sum(question_tensor["attention_mask"][0]) labels = lang_x.clone() labels[labels == self.text_tokenizer.pad_token_id] = -100 labels[labels >= self.voc_size] = -100 labels[:question_length] = -100 reweight_tensor = find_position(labels, key_embeddings) if dataset_index == 'paper_inline_dataset': emphasize_words = [] # print(labels,key_embeddings,reweight_tensor) return {'vision_x': vision_x,'lang_x':lang_x, 'attention_mask': attention_mask, 'labels':labels, 'loss_reweight': reweight_tensor, 'key_words_query': emphasize_words} def text_add_image(self,images,question,answer): question = str(question) answer = str(answer) ref_image = [] question_list = [[] for _ in range(len(str(question)))] answer_list = [[] for _ in range(len(str(answer)))] for index, image in enumerate(images): ref_image.append(image["image"]) position = image["position"] position = list(position.items())[0] if position[0] == 'question': insert_loc = position[1] -1 if insert_loc < 0: insert_loc = 0 question_list[insert_loc].append(index) if position[0] == 'answer': insert_loc = position[1] -1 if insert_loc < 0: insert_loc = 0 answer_list[insert_loc].append(index) new_question = '' new_answer = '' for char_i in range(len(question)): if question_list[char_i] == []: new_question = new_question + question[char_i] if question_list[char_i] != []: for img_index in question_list[char_i]: try: new_question = new_question + '' + self.image_padding_tokens[img_index] + '' except: print("Error: out of max image input size") new_question = new_question + question[char_i] for char_i in range(len(answer)): if answer_list[char_i] == []: new_answer = new_answer + answer[char_i] if answer_list[char_i] != []: for img_index in answer_list[char_i]: try: new_answer = new_answer + '' + self.image_padding_tokens[img_index] + '' except: print("Error: out of max image input size") new_answer = new_answer + answer[char_i] new_answer = new_answer.replace('•','') return ref_image,new_question,new_answer # torch.set_printoptions(profile="full") # text_tokenizer = '/home/cs/leijiayu/wuchaoyi/Finetune_LLAMA/LLAMA_Model/tokenizer' # dataset = multi_dataset_close(text_tokenizer = text_tokenizer) # print(len(dataset)) # for i in range(10): # dataset[i] # input() ================================================ FILE: src/Model/RadFM/__init__.py ================================================ ================================================ FILE: src/Model/RadFM/blocks.py ================================================ from collections import OrderedDict from typing import Tuple, Union, Callable, Optional import torch import torch.nn.functional as F from torch import nn from torch.utils.checkpoint import checkpoint class PMC_CLIP_cfg: backbone: str = 'ModifiedRN50' # ['RN50', 'ModifiedRN50', 'MAE'] layers: Union[Tuple[int, int, int, int], int] = [3,4,6,3] width: int = 64 head_width: int = 64 mlp_ratio: float = 4.0 patch_size: int = 16 image_size: Union[Tuple[int, int], int] = 224 timm_model_name: str = None # a valid model name overrides layers, width, patch_size timm_model_pretrained: bool = False # use (imagenet) pretrained weights for named model timm_pool: str = 'avg' # feature pooling for timm model ('abs_attn', 'rot_attn', 'avg', '') timm_proj: str = 'linear' # linear projection for timm model output ('linear', 'mlp', '') patch_dropout: float = 0.0 # patch dropout rate, no dropout by default drop_attention_rate: float = 0. # Transformer Dropout patch_size: None class Bottleneck(nn.Module): expansion = 4 def __init__(self, inplanes, planes, stride=1): super().__init__() # all conv layers have stride 1. an avgpool is performed after the second convolution when stride > 1 self.conv1 = nn.Conv2d(inplanes, planes, 1, bias=False) self.bn1 = nn.BatchNorm2d(planes) self.relu1 = nn.ReLU(inplace=True) self.conv2 = nn.Conv2d(planes, planes, 3, padding=1, bias=False) self.bn2 = nn.BatchNorm2d(planes) self.relu2 = nn.ReLU(inplace=True) self.avgpool = nn.AvgPool2d(stride) if stride > 1 else nn.Identity() self.conv3 = nn.Conv2d(planes, planes * self.expansion, 1, bias=False) self.bn3 = nn.BatchNorm2d(planes * self.expansion) self.relu3 = nn.ReLU(inplace=True) self.downsample = None self.stride = stride if stride > 1 or inplanes != planes * Bottleneck.expansion: # downsampling layer is prepended with an avgpool, and the subsequent convolution has stride 1 self.downsample = nn.Sequential(OrderedDict([ ("-1", nn.AvgPool2d(stride)), ("0", nn.Conv2d(inplanes, planes * self.expansion, 1, stride=1, bias=False)), ("1", nn.BatchNorm2d(planes * self.expansion)) ])) def forward(self, x: torch.Tensor): identity = x out = self.relu1(self.bn1(self.conv1(x))) out = self.relu2(self.bn2(self.conv2(out))) out = self.avgpool(out) out = self.bn3(self.conv3(out)) if self.downsample is not None: identity = self.downsample(x) out += identity out = self.relu3(out) return out class AttentionPool2d(nn.Module): def __init__(self, spacial_dim: int, embed_dim: int, num_heads: int, output_dim: int = None): super().__init__() self.positional_embedding = nn.Parameter(torch.randn(spacial_dim ** 2 + 1, embed_dim) / embed_dim ** 0.5) self.k_proj = nn.Linear(embed_dim, embed_dim) self.q_proj = nn.Linear(embed_dim, embed_dim) self.v_proj = nn.Linear(embed_dim, embed_dim) self.c_proj = nn.Linear(embed_dim, output_dim or embed_dim) self.num_heads = num_heads def forward(self, x): x = x.reshape(x.shape[0], x.shape[1], x.shape[2] * x.shape[3]).permute(2, 0, 1) # NCHW -> (HW)NC x = torch.cat([x.mean(dim=0, keepdim=True), x], dim=0) # (HW+1)NC x = x + self.positional_embedding[:, None, :].to(x.dtype) # (HW+1)NC x, _ = F.multi_head_attention_forward( query=x, key=x, value=x, embed_dim_to_check=x.shape[-1], num_heads=self.num_heads, q_proj_weight=self.q_proj.weight, k_proj_weight=self.k_proj.weight, v_proj_weight=self.v_proj.weight, in_proj_weight=None, in_proj_bias=torch.cat([self.q_proj.bias, self.k_proj.bias, self.v_proj.bias]), bias_k=None, bias_v=None, add_zero_attn=False, dropout_p=0, out_proj_weight=self.c_proj.weight, out_proj_bias=self.c_proj.bias, use_separate_proj_weight=True, training=self.training, need_weights=False ) return x[0] class ResNet(nn.Module): """ RN50 """ def __init__( self, layers, output_dim, heads, image_size=224, width=64, block=Bottleneck, ): super().__init__() self.output_dim = output_dim self.image_size = image_size # the 1-layer stem self.conv1 = nn.Conv2d(3, width, kernel_size=3, stride=2, padding=1, bias=False) self.bn1 = nn.BatchNorm2d(width) self.relu1 = nn.ReLU(inplace=True) self.maxpool = nn.MaxPool2d(kernel_size=3, stride=2, padding=1) # residual layers self._inplanes = width # this is a *mutable* variable used during construction self.layer1 = self._make_layer(width, layers[0]) self.layer2 = self._make_layer(width * 2, layers[1], stride=2) self.layer3 = self._make_layer(width * 4, layers[2], stride=2) self.layer4 = self._make_layer(width * 8, layers[3], stride=2) self.avgpool = nn.AdaptiveAvgPool2d((1, 1)) # self.head = nn.Linear(512 * 6, output_dim) self.head = nn.Linear(512 * block.expansion, output_dim) # embed_dim = width * 32 # the ResNet feature dimension # self.attnpool = AttentionPool2d(image_size // 32, embed_dim, heads, output_dim) self.init_parameters() def _make_layer( self, planes, blocks, stride=1, block=Bottleneck, ): layers = [block(self._inplanes, planes, stride)] self._inplanes = planes * block.expansion for _ in range(1, blocks): layers.append(block(self._inplanes, planes)) return nn.Sequential(*layers) def init_parameters(self): for resnet_block in [self.layer1, self.layer2, self.layer3, self.layer4]: for name, param in resnet_block.named_parameters(): if name.endswith("bn3.weight"): nn.init.zeros_(param) def lock(self, unlocked_groups=0, freeze_bn_stats=False): assert unlocked_groups == 0, 'partial locking not currently supported for this model' for param in self.parameters(): param.requires_grad = False if freeze_bn_stats: freeze_batch_norm_2d(self) @torch.jit.ignore def set_grad_checkpointing(self, enable=True): # FIXME support for non-transformer pass def stem(self, x): x = self.relu1(self.bn1(self.conv1(x))) x = self.maxpool(x) return x def forward(self, x): # x[0]: [batch_size, 3, 224, 224] # x[1]: [batch_size, 1] x = self.stem(x) # [batch_size, 64, 56, 56] x = self.layer1(x) x = self.layer2(x) x = self.layer3(x) x = self.layer4(x) # [batch_size, 2048, 7, 7] x = self.avgpool(x) # [batch_size, 2048, 1, 1] x = torch.flatten(x, 1) # [batch_size, 2048*1*1] x = self.head(x) # [batch_size, 1024] visual_output = dict.fromkeys(["image_features", "mim_loss"], None) visual_output.update({ 'image_features': x, }) return visual_output class ModifiedResNet(nn.Module): """ A ResNet class that is similar to torchvision's but contains the following changes: - There are now 3 "stem" convolutions as opposed to 1, with an average pool instead of a max pool. - Performs anti-aliasing strided convolutions, where an avgpool is prepended to convolutions with stride > 1 - The final pooling layer is a QKV attention instead of an average pool """ def __init__(self, layers, output_dim, heads, image_size=224, width=64): super().__init__() self.output_dim = output_dim self.image_size = image_size # the 3-layer stem self.conv1 = nn.Conv2d(3, width // 2, kernel_size=3, stride=2, padding=1, bias=False) self.bn1 = nn.BatchNorm2d(width // 2) self.relu1 = nn.ReLU(inplace=True) self.conv2 = nn.Conv2d(width // 2, width // 2, kernel_size=3, padding=1, bias=False) self.bn2 = nn.BatchNorm2d(width // 2) self.relu2 = nn.ReLU(inplace=True) self.conv3 = nn.Conv2d(width // 2, width, kernel_size=3, padding=1, bias=False) self.bn3 = nn.BatchNorm2d(width) self.relu3 = nn.ReLU(inplace=True) self.avgpool = nn.AvgPool2d(2) # residual layers self._inplanes = width # this is a *mutable* variable used during construction self.layer1 = self._make_layer(width, layers[0]) self.layer2 = self._make_layer(width * 2, layers[1], stride=2) self.layer3 = self._make_layer(width * 4, layers[2], stride=2) self.layer4 = self._make_layer(width * 8, layers[3], stride=2) embed_dim = width * 32 # the ResNet feature dimension self.attnpool = AttentionPool2d(image_size // 32, embed_dim, heads, output_dim) self.init_parameters() def _make_layer(self, planes, blocks, stride=1): layers = [Bottleneck(self._inplanes, planes, stride)] self._inplanes = planes * Bottleneck.expansion for _ in range(1, blocks): layers.append(Bottleneck(self._inplanes, planes)) return nn.Sequential(*layers) def init_parameters(self): if self.attnpool is not None: std = self.attnpool.c_proj.in_features ** -0.5 nn.init.normal_(self.attnpool.q_proj.weight, std=std) nn.init.normal_(self.attnpool.k_proj.weight, std=std) nn.init.normal_(self.attnpool.v_proj.weight, std=std) nn.init.normal_(self.attnpool.c_proj.weight, std=std) for resnet_block in [self.layer1, self.layer2, self.layer3, self.layer4]: for name, param in resnet_block.named_parameters(): if name.endswith("bn3.weight"): nn.init.zeros_(param) def lock(self, unlocked_groups=0, freeze_bn_stats=False): assert unlocked_groups == 0, 'partial locking not currently supported for this model' for param in self.parameters(): param.requires_grad = False if freeze_bn_stats: freeze_batch_norm_2d(self) @torch.jit.ignore def set_grad_checkpointing(self, enable=True): # FIXME support for non-transformer pass def stem(self, x): x = self.relu1(self.bn1(self.conv1(x))) x = self.relu2(self.bn2(self.conv2(x))) x = self.relu3(self.bn3(self.conv3(x))) x = self.avgpool(x) return x def forward(self, x): x = self.stem(x) x = self.layer1(x) x = self.layer2(x) x = self.layer3(x) x = self.layer4(x) x = self.attnpool(x) visual_output = dict.fromkeys(["image_features", "mim_loss"], None) visual_output.update({ 'image_features': x, }) return visual_output class LayerNorm(nn.LayerNorm): """Subclass torch's LayerNorm to handle fp16.""" def forward(self, x: torch.Tensor): orig_type = x.dtype x = F.layer_norm(x, self.normalized_shape, self.weight, self.bias, self.eps) return x.to(orig_type) class QuickGELU(nn.Module): # NOTE This is slower than nn.GELU or nn.SiLU and uses more GPU memory def forward(self, x: torch.Tensor): return x * torch.sigmoid(1.702 * x) class ResidualAttentionBlock(nn.Module): def __init__( self, d_model: int, n_head: int, mlp_ratio: float = 4.0, act_layer: Callable = nn.GELU, drop_attention_rate: float = 0., ): super().__init__() self.attn = nn.MultiheadAttention( embed_dim=d_model, num_heads=n_head, dropout=drop_attention_rate, ) self.ln_1 = LayerNorm(d_model) mlp_width = int(d_model * mlp_ratio) self.mlp = nn.Sequential(OrderedDict([ ("c_fc", nn.Linear(d_model, mlp_width)), ("gelu", act_layer()), ("c_proj", nn.Linear(mlp_width, d_model)) ])) self.ln_2 = LayerNorm(d_model) def attention(self, x: torch.Tensor, attn_mask: Optional[torch.Tensor] = None): return self.attn(x, x, x, need_weights=False, attn_mask=attn_mask)[0] def forward(self, x: torch.Tensor, attn_mask: Optional[torch.Tensor] = None): x = x + self.attention(self.ln_1(x), attn_mask=attn_mask) x = x + self.mlp(self.ln_2(x)) return x class PatchDropout(nn.Module): """ https://arxiv.org/abs/2212.00794 """ def __init__(self, prob, exclude_first_token=True): super().__init__() assert 0 <= prob < 1. self.prob = prob self.exclude_first_token = exclude_first_token # exclude CLS token def forward(self, x): if not self.training or self.prob == 0.: return x if self.exclude_first_token: cls_tokens, x = x[:, :1], x[:, 1:] else: cls_tokens = torch.jit.annotate(torch.Tensor, x[:, :1]) batch = x.size()[0] num_tokens = x.size()[1] batch_indices = torch.arange(batch) batch_indices = batch_indices[..., None] keep_prob = 1 - self.prob num_patches_keep = max(1, int(num_tokens * keep_prob)) rand = torch.randn(batch, num_tokens) patch_indices_keep = rand.topk(num_patches_keep, dim=-1).indices x = x[batch_indices, patch_indices_keep] if self.exclude_first_token: x = torch.cat((cls_tokens, x), dim=1) return x class Transformer(nn.Module): def __init__( self, width: int, layers: int, heads: int, mlp_ratio: float = 4.0, act_layer: Callable = nn.GELU, drop_attention_rate: float = 0., ): super().__init__() self.width = width self.layers = layers self.grad_checkpointing = False self.resblocks = nn.ModuleList([ ResidualAttentionBlock(width, heads, mlp_ratio, act_layer=act_layer, drop_attention_rate=drop_attention_rate) for _ in range(layers) ]) def forward(self, x: torch.Tensor, attn_mask: Optional[torch.Tensor] = None): for r in self.resblocks: if self.grad_checkpointing and not torch.jit.is_scripting(): x = checkpoint(r, x, attn_mask) else: x = r(x, attn_mask=attn_mask) return x ================================================ FILE: src/Model/RadFM/helpers.py ================================================ """ Taken from https://github.com/lucidrains/flamingo-pytorch """ import torch from einops import rearrange, repeat from einops_exts import rearrange_many from torch import einsum, nn def exists(val): return val is not None def FeedForward(dim, mult=4): inner_dim = int(dim * mult) return nn.Sequential( nn.LayerNorm(dim), nn.Linear(dim, inner_dim, bias=False), nn.GELU(), nn.Linear(inner_dim, dim, bias=False), ) class PerceiverAttention(nn.Module): def __init__(self, *, dim, dim_head=64, heads=8): super().__init__() self.scale = dim_head**-0.5 self.heads = heads inner_dim = dim_head * heads self.norm_media = nn.LayerNorm(dim) self.norm_latents = nn.LayerNorm(dim) self.to_q = nn.Linear(dim, inner_dim, bias=False) self.to_kv = nn.Linear(dim, inner_dim * 2, bias=False) self.to_out = nn.Linear(inner_dim, dim, bias=False) def forward(self, x, latents): """ Args: x (torch.Tensor): image features shape (b, T, n1, D) latent (torch.Tensor): latent features shape (b, T, n2, D) """ x = self.norm_media(x) latents = self.norm_latents(latents) h = self.heads q = self.to_q(latents) kv_input = torch.cat((x, latents), dim=-2) k, v = self.to_kv(kv_input).chunk(2, dim=-1) q, k, v = rearrange_many((q, k, v), "b t n (h d) -> b h t n d", h=h) q = q * self.scale # attention sim = einsum("... i d, ... j d -> ... i j", q, k) sim = sim - sim.amax(dim=-1, keepdim=True).detach() attn = sim.softmax(dim=-1) out = einsum("... i j, ... j d -> ... i d", attn, v) out = rearrange(out, "b h t n d -> b t n (h d)", h=h) return self.to_out(out) class PerceiverResampler(nn.Module): def __init__( self, *, dim, depth=6, dim_head=64, heads=8, num_latents=64, max_num_media=None, max_num_frames=None, ff_mult=4, ): super().__init__() self.latents = nn.Parameter(torch.randn(num_latents, dim)) self.frame_embs = ( nn.Parameter(torch.randn(max_num_frames, dim)) if exists(max_num_frames) else None ) self.media_time_embs = ( nn.Parameter(torch.randn(max_num_media, 1, dim)) if exists(max_num_media) else None ) self.layers = nn.ModuleList([]) for _ in range(depth): self.layers.append( nn.ModuleList( [ PerceiverAttention(dim=dim, dim_head=dim_head, heads=heads), FeedForward(dim=dim, mult=ff_mult), ] ) ) self.norm = nn.LayerNorm(dim) def forward(self, x): """ Args: x (torch.Tensor): image features shape (b, T, F, v, D) Returns: shape (b, T, n, D) where n is self.num_latents """ b, T, F, v = x.shape[:4] # frame and media time embeddings if exists(self.frame_embs): frame_embs = repeat(self.frame_embs[:F], "F d -> b T F v d", b=b, T=T, v=v) x = x + frame_embs x = rearrange( x, "b T F v d -> b T (F v) d" ) # flatten the frame and spatial dimensions if exists(self.media_time_embs): x = x + self.media_time_embs[:T] # blocks latents = repeat(self.latents, "n d -> b T n d", b=b, T=T) for attn, ff in self.layers: latents = attn(x, latents) + latents latents = ff(latents) + latents return self.norm(latents) # gated cross attention class MaskedCrossAttention(nn.Module): def __init__( self, *, dim, dim_visual, dim_head=64, heads=8, only_attend_immediate_media=True, ): super().__init__() self.scale = dim_head**-0.5 self.heads = heads inner_dim = dim_head * heads self.norm = nn.LayerNorm(dim) self.to_q = nn.Linear(dim, inner_dim, bias=False) self.to_kv = nn.Linear(dim_visual, inner_dim * 2, bias=False) self.to_out = nn.Linear(inner_dim, dim, bias=False) # whether for text to only attend to immediate preceding image, or all previous images self.only_attend_immediate_media = only_attend_immediate_media def forward(self, x, media, media_locations=None, attend_previous=True): """ Args: x (torch.Tensor): text features shape (B, T_txt, D_txt) media (torch.Tensor): image features shape (B, T_img, n, D_img) where n is the dim of the latents media_locations: boolean mask identifying the media tokens in x shape (B, T_txt) attend_previous: bool If false, ignores immediately preceding image and starts attending when following image """ _, T_img, n = media.shape[:3] h = self.heads x = self.norm(x) q = self.to_q(x) media = rearrange(media, "b t n d -> b (t n) d") k, v = self.to_kv(media).chunk(2, dim=-1) q, k, v = rearrange_many((q, k, v), "b n (h d) -> b h n d", h=h) q = q * self.scale sim = einsum("... i d, ... j d -> ... i j", q, k) if exists(media_locations): # at each boolean of True, increment the time counter (relative to media time) text_time = media_locations.cumsum(dim=-1) media_time = torch.arange(T_img, device=x.device) + 1 if not attend_previous: text_time[~media_locations] += 1 # make sure max is still the number of images in the sequence text_time[ text_time > repeat( torch.count_nonzero(media_locations, dim=1), "b -> b i", i=text_time.shape[1], ) ] = 0 # text time must equal media time if only attending to most immediate image # otherwise, as long as text time is greater than media time (if attending to all previous images / media) mask_op = torch.eq if self.only_attend_immediate_media else torch.ge text_to_media_mask = mask_op( rearrange(text_time, "b i -> b 1 i 1"), repeat(media_time, "j -> 1 1 1 (j n)", n=n), ) sim = sim.masked_fill(~text_to_media_mask, -torch.finfo(sim.dtype).max) sim = sim - sim.amax(dim=-1, keepdim=True).detach() attn = sim.softmax(dim=-1) if exists(media_locations) and self.only_attend_immediate_media: # any text without a preceding media needs to have attention zeroed out text_without_media_mask = text_time == 0 text_without_media_mask = rearrange( text_without_media_mask, "b i -> b 1 i 1" ) attn = attn.masked_fill(text_without_media_mask, 0.0) out = einsum("... i j, ... j d -> ... i d", attn, v) out = rearrange(out, "b h n d -> b n (h d)") return self.to_out(out) class GatedCrossAttentionBlock(nn.Module): def __init__( self, *, dim, dim_visual, dim_head=64, heads=8, ff_mult=4, only_attend_immediate_media=True, ): super().__init__() self.attn = MaskedCrossAttention( dim=dim, dim_visual=dim_visual, dim_head=dim_head, heads=heads, only_attend_immediate_media=only_attend_immediate_media, ) self.attn_gate = nn.Parameter(torch.tensor([0.0])) self.ff = FeedForward(dim, mult=ff_mult) self.ff_gate = nn.Parameter(torch.tensor([0.0])) def forward( self, x, media, media_locations=None, attend_previous=True, ): x = ( self.attn( x, media, media_locations=media_locations, attend_previous=attend_previous, ) * self.attn_gate.tanh() + x ) x = self.ff(x) * self.ff_gate.tanh() + x return x ================================================ FILE: src/Model/RadFM/multimodality_model.py ================================================ # Import necessary libraries from torch import nn from transformers.models.llama import LlamaForCausalLM from .my_embedding_layer import MyEmbedding from torch.nn import BCEWithLogitsLoss, CrossEntropyLoss, MSELoss import tqdm.auto as tqdm import torch.nn as nn import torch from torch.utils.checkpoint import checkpoint from torch.autograd import Variable import numpy as np class MultiLLaMAForCausalLM(nn.Module): """ A multimodal LLaMA model that combines language and vision inputs for causal language modeling tasks. """ def __init__(self, lang_model_path): """ Initialize the multimodal model. Args: lang_model_path (str): Path to the pretrained language model """ super(MultiLLaMAForCausalLM, self).__init__() # Load pretrained LLaMA model self.lang_model = LlamaForCausalLM.from_pretrained( lang_model_path, ) # Enable gradient checkpointing for memory efficiency self.lang_model.gradient_checkpointing_enable() self.lang_model.enable_input_require_grads() # Initialize custom embedding layer and share weights with language model self.embedding_layer = MyEmbedding() self.embedding_layer.weight = self.lang_model.get_input_embeddings().weight # Set model dimensions self.hidden_dim = 5120 self.voc_size = 32000 def forward(self, lang_x, vision_x, attention_mask, labels, loss_reweight, key_words_query): """ Forward pass for the multimodal model. Args: lang_x: Language input tokens vision_x: Vision input features attention_mask: Attention mask for language inputs labels: Target labels for language modeling loss_reweight: Weights for calculating loss (to prioritize certain tokens) key_words_query: Query for highlighting important words Returns: Dictionary containing model outputs including loss and logits """ if labels.shape == lang_x.shape: # Set embedding mode to handle text inputs self.embedding_layer.flag = 'Text' # Get embeddings and matching loss from embedding layer input_embedding, loss_match = self.embedding_layer(lang_x, vision_x, key_words_query) # Forward pass through the language model output = self.lang_model(inputs_embeds=input_embedding, attention_mask=attention_mask, labels=labels) logits = output['logits'] # Initialize regularization loss loss_reg = None if labels is not None: # Shift logits and labels for next-token prediction shift_logits = logits[..., :-1, :].contiguous() shift_labels = labels[..., 1:].contiguous() shift_loss_reweight = loss_reweight[..., 1:].contiguous() # Prepare for loss calculation loss_fct = CrossEntropyLoss(reduction='none') shift_logits = shift_logits.view(-1, self.voc_size) shift_labels = shift_labels.view(-1) shift_loss_reweight = shift_loss_reweight.view(-1) # Ensure tensors are on the same device shift_labels = shift_labels.to(shift_logits.device) shift_loss_reweight = shift_loss_reweight.to(shift_logits.device) # Calculate weighted cross-entropy loss loss_reg = loss_fct(shift_logits, shift_labels) loss_reg = torch.sum(shift_loss_reweight * loss_reg) / torch.sum(shift_loss_reweight) # Combine losses loss = loss_reg if loss_match is not None: loss = 0.8 * loss + 0.2 * loss_match # Calculate accuracy metrics logits = output['logits'][..., :-1, :].contiguous().detach() total = len(labels) predictions = torch.argmax(logits, dim=-1) labels = labels[..., 1:].contiguous() # Count correct predictions (ignoring padding tokens with -100) Acc = torch.sum(torch.all(torch.logical_or(predictions == labels, labels == -100), dim=-1)) Accuracy = Acc / total return dict( # loss_reg = loss_reg, # loss_matching = loss_matching, logits=Accuracy, loss=output['loss'], ) ### useless for now ignore the folowing codes ### # if labels.shape == vision_x.shape: # self.embedding_layer.flag = 'Seg' # input_embedding = self.embedding_layer(lang_x, vision_x) def generate(self, lang_x, vision_x): """ Generate text based on language and vision inputs. Args: lang_x: Language input tokens vision_x: Vision input features Returns: Generated token sequence """ # Set embedding mode to text generation self.embedding_layer.flag = 'Text' with torch.no_grad(): # Get embeddings from the embedding layer input_embedding, _ = self.embedding_layer(lang_x, vision_x) # Generate text using language model generation = self.lang_model.generate( inputs_embeds=input_embedding, max_new_tokens=200, top_k=50 ) return generation ================================================ FILE: src/Model/RadFM/my_embedding_layer.py ================================================ # Import necessary libraries import torch.nn as nn import torch.nn.functional as F import torch from .helpers import PerceiverResampler from .utils import get_visual_encoder from einops import rearrange, repeat from einops_exts import rearrange_many import torchvision from .vit_3d import ViT from einops.layers.torch import Rearrange from .transformer_decoder import TransformerDecoder, TransformerDecoderLayer from torch.utils.checkpoint import checkpoint from torch.autograd import Variable import random from transformers import AutoTokenizer, AutoModel class MyEmbedding(nn.Module): """ Custom embedding layer for multimodal inputs that combines text and vision features. """ def __init__(self, num_embeddings=32000, embedding_dim=5120, perceiver_num=32, vis_dim=768, patch_size=32, frame_patch_size=4, seg_channel=256): """ Initialize the multimodal embedding layer. Args: num_embeddings (int): Size of vocabulary for text embeddings embedding_dim (int): Dimension of output embeddings perceiver_num (int): Number of latent vectors in perceiver vis_dim (int): Dimension of vision features patch_size (int): Size of image patches frame_patch_size (int): Size of 3D frame patches seg_channel (int): Number of segmentation channels """ super().__init__() self.num_embeddings = num_embeddings self.embedding_dim = embedding_dim # Standard embedding weight matrix for text tokens self.weight = nn.Parameter(torch.torch.randn((num_embeddings, embedding_dim))) # Special token weights for figures/images self.figure_token_weight = nn.Parameter(torch.randn((2, embedding_dim))) self.flag = 'Text' # Mode flag: 'Text' or 'Seg' self.patch_size = patch_size self.frame_patch_size = frame_patch_size self.seg_channel = seg_channel ## the MedKEBERT can be downloaded from https://huggingface.co/xmcmic/Med-KEBERT/tree/main ## # Initialize medical domain BERT model for keyword understanding self.bert_tokenizer = AutoTokenizer.from_pretrained("xmcmic/Med-KEBERT") self.bert_model = AutoModel.from_pretrained("xmcmic/Med-KEBERT") # Project BERT outputs to vision feature space self.bert_projection_fc = nn.Linear(768, vis_dim) # 3D Vision Transformer for processing volumetric medical images self.vision_encoder = ViT( image_size=512, # image size frames=512, # max number of frames image_patch_size=patch_size, # image patch size frame_patch_size=frame_patch_size, # frame patch size dim=vis_dim, depth=12, heads=8, mlp_dim=2048, dropout=0.1, emb_dropout=0.1 ) # Upscaling layers for vision features (used in segmentation mode) self.output_upscaling = nn.Sequential( nn.ConvTranspose3d(vis_dim, vis_dim // 4, kernel_size=2, stride=2), nn.BatchNorm3d(vis_dim // 4), nn.GELU(), nn.ConvTranspose3d(vis_dim // 4, vis_dim // 8, kernel_size=2, stride=2), nn.GELU(), ) # Transformer decoder for cross-attention between text and vision decoder_layer = TransformerDecoderLayer(d_model=vis_dim, nhead=8, normalize_before=True) decoder_norm = nn.LayerNorm(vis_dim) self.transformer_decoder = TransformerDecoder(decoder_layer=decoder_layer, num_layers=4, norm=decoder_norm) # MLP for processing transformer decoder outputs self.transformer_decoder_mlp = nn.Sequential( nn.Linear(vis_dim, vis_dim // 4), nn.GELU(), nn.Linear(vis_dim // 4, vis_dim // 8), nn.GELU(), ) self.vis_dim = vis_dim # Perceiver resampler to reduce sequence length of vision features self.perceiver = PerceiverResampler(dim=self.vis_dim, num_latents=perceiver_num) # Final projection to embedding dimension self.fc = nn.Linear(self.vis_dim, self.embedding_dim) # Classification head for matching keywords self.cls_head = nn.Linear(self.vis_dim // 8, 1) def forward(self, text_input, vision_x, key_words_query=None): """ Forward pass for the embedding layer. Args: text_input: Text token indices [B, L] vision_x: Visual input features [B, S, C, H, W, D] key_words_query: Optional list of key words for contrastive learning Returns: tuple: (output_embeddings, loss_matching) - output_embeddings: Combined embeddings for text and vision - loss_matching: Contrastive loss for keyword matching (or None) """ if self.flag == 'Text': # Process in text mode B, S, C, H, W, D = vision_x.shape # Reshape for batch processing vision_x = rearrange(vision_x, "b S c h w d-> (b S) c h w d") # Process through vision encoder vision_x, pos_embedding = self.vision_encoder(vision_x) # Reshape back to batch format vision_x = rearrange(vision_x, "(b s F) v d -> b s F v d", b=B, s=S, F=1) loss_matching = None if key_words_query is not None: ## we do not use the following parts in final version. ## You can quota the following codes and if so the bert models will be useless. # key_words_query list[list[str]] B, words, each word matches corresponding vision_x embedding # Extract and deduplicate keywords query_words = [item for sublist in key_words_query for item in sublist] query_words = list(set(query_words)) # Limit number of keywords to process if len(query_words) > 16: random.shuffle(query_words) query_words = query_words[0:16] if query_words != []: # Create binary labels for contrastive learning contrastive_labels = torch.zeros(B, len(query_words)) # B Q for i, sublist in enumerate(key_words_query): for j, item in enumerate(query_words): if item in sublist: contrastive_labels[i, j] = 1 contrastive_labels = contrastive_labels.to(vision_x.dtype).to(vision_x.device) # Get BERT embeddings for keywords with torch.no_grad(): query_words_embedding = self.bert_tokenizer( query_words, padding='max_length', truncation=True, max_length=256, return_tensors="pt" ) query_words_embedding = self.bert_model( input_ids=query_words_embedding['input_ids'].to(vision_x.device), attention_mask=query_words_embedding['attention_mask'].to(vision_x.device) )['last_hidden_state'][:, 0, :].to(vision_x.dtype).to(vision_x.device) # Q,D # Project BERT embeddings to vision space query_words_embedding = self.bert_projection_fc(query_words_embedding) query_words_embedding = query_words_embedding.unsqueeze(0).repeat(B, 1, 1) # B,Q,D _, N, _ = query_words_embedding.shape # Pool vision features image_embedding = vision_x.mean(dim=1) # B V D average pooling to remove multimodality image_embedding = rearrange(image_embedding, "b F v d -> b (F v) d") pos_embedding = rearrange(pos_embedding, "(b s) v d -> b s v d", b=B, s=S)[:, 0, :, :] # Prepare inputs for transformer decoder image_embedding = image_embedding.transpose(0, 1) # (H/P W/P D/P) B D pos_embedding = pos_embedding.transpose(0, 1) # (H/P W/P D/P) B D query_words_embedding = query_words_embedding.transpose(0, 1) # N B D # Cross-attention between keywords and image features oo_embedding, _ = self.transformer_decoder( query_words_embedding, image_embedding, pos=pos_embedding ) oo_embedding = oo_embedding.transpose(0, 1) # B Q D oo_embedding = rearrange(oo_embedding, 'b n d -> (b n) d') oo_embedding = self.transformer_decoder_mlp(oo_embedding) oo_embedding = self.cls_head(oo_embedding).mean(dim=-1) oo_embedding = rearrange(oo_embedding, '(b n) -> b n', b=B, n=N) # B Q # Calculate contrastive loss loss_matching = F.binary_cross_entropy_with_logits(oo_embedding, contrastive_labels) # Process vision features through perceiver resampler vision_x = self.perceiver(vision_x) # reshapes to (b, S, n, d) n = vision_x.shape[2] # Project vision features to embedding dimension vision_x = rearrange(vision_x, "b s n d -> (b s n) d") vision_x = self.fc(vision_x) vision_x = rearrange(vision_x, "(b T) d -> b T d", b=B, T=n*S) # Combine text and vision embeddings embedding_weight = torch.cat([self.weight, self.figure_token_weight], dim=0) embedding_weight = embedding_weight.unsqueeze(0).repeat(B, 1, 1) embedding_weight = torch.cat([embedding_weight, vision_x], dim=1) # Convert text indices to one-hot and compute final embeddings text_input = F.one_hot(text_input, embedding_weight.shape[1]).to(vision_x.dtype).to(vision_x.device) out_put = torch.matmul(text_input, embedding_weight) ## useless for now. ignore the folowing code## # if self.flag == 'Seg': # B,C,H,W,D = vision_x.shape # _,N,_ = text_input.shape # latent_embedding, pos_embedding = self.vision_encoder(vision_x) # B (H/P W/P D/P) D # image_embedding = latent_embedding.transpose(0,1) # (H/P W/P D/P) B D # pos_embedding = pos_embedding.transpose(0,1) # (H/P W/P D/P) B D # text_input = text_input.transpose(0,1) # N B D # mask_embedding,_ = self.transformer_decoder(text_input, image_embedding, pos = pos_embedding) # mask_embedding = mask_embedding.transpose(0,1) # B N D # mask_embedding = rearrange(mask_embedding, 'b n d -> (b n) d') # mask_embedding = self.transformer_decoder_mlp(mask_embedding) # mask_embedding = rearrange(mask_embedding, '(b n) d -> b n d', b=B, n=N,d = self.vis_dim // 8) # vision_x = rearrange(latent_embedding,'b (h w d) c -> b c h w d', h = (H // self.patch_size), w = (W // self.patch_size), d = (D // self.frame_patch_size), c=self.vis_dim) # vision_x = self.output_upscaling(vision_x) #B C H/4 W/4 D/4 # out_put = torch.einsum('bchwd,bnc->bnhwd', vision_x, mask_embedding) return out_put, loss_matching # model = MyEmbedding(vision_encoder_path = '') # text_input = torch.randint(low=0, high=3210, size=(4,2048)) # image_input = torch.randn((4,3,3,512,512,4)) # key_words_query = [[],[],[],['consoliation']] # print(model(text_input, image_input, key_words_query)) ================================================ FILE: src/Model/RadFM/position_encoding.py ================================================ # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved """ Various positional encodings for the transformer. """ import math import torch from torch import nn from einops.layers.torch import Rearrange from einops import rearrange, repeat class PositionEmbeddingSine(nn.Module): """ This is a more standard version of the position embedding, very similar to the one used by the Attention is all you need paper, generalized to work on images. """ def __init__(self, num_pos_feats=64, temperature=10000, normalize=False, scale=None): super().__init__() self.num_pos_feats = num_pos_feats self.temperature = temperature self.normalize = normalize if scale is not None and normalize is False: raise ValueError("normalize should be True if scale is passed") if scale is None: scale = 2 * math.pi self.scale = scale def forward(self, tensor_list): x = tensor_list.tensors mask = tensor_list.mask assert mask is not None not_mask = ~mask y_embed = not_mask.cumsum(1, dtype=torch.float32) x_embed = not_mask.cumsum(2, dtype=torch.float32) if self.normalize: eps = 1e-6 y_embed = y_embed / (y_embed[:, -1:, :] + eps) * self.scale x_embed = x_embed / (x_embed[:, :, -1:] + eps) * self.scale dim_t = torch.arange(self.num_pos_feats, dtype=torch.float32, device=x.device) dim_t = self.temperature ** (2 * (dim_t // 2) / self.num_pos_feats) pos_x = x_embed[:, :, :, None] / dim_t pos_y = y_embed[:, :, :, None] / dim_t pos_x = torch.stack((pos_x[:, :, :, 0::2].sin(), pos_x[:, :, :, 1::2].cos()), dim=4).flatten(3) pos_y = torch.stack((pos_y[:, :, :, 0::2].sin(), pos_y[:, :, :, 1::2].cos()), dim=4).flatten(3) pos = torch.cat((pos_y, pos_x), dim=3).permute(0, 3, 1, 2) return pos class PositionEmbeddingLearned(nn.Module): """ Absolute pos embedding, learned. """ def __init__(self, num_pos_feats=256): super().__init__() self.row_embed = nn.Embedding(50, num_pos_feats) self.col_embed = nn.Embedding(50, num_pos_feats) self.reset_parameters() def reset_parameters(self): nn.init.uniform_(self.row_embed.weight) nn.init.uniform_(self.col_embed.weight) def forward(self, tensor_list): x = tensor_list.tensors h, w = x.shape[-2:] i = torch.arange(w, device=x.device) j = torch.arange(h, device=x.device) x_emb = self.col_embed(i) y_emb = self.row_embed(j) pos = torch.cat([ x_emb.unsqueeze(0).repeat(h, 1, 1), y_emb.unsqueeze(1).repeat(1, w, 1), ], dim=-1).permute(2, 0, 1).unsqueeze(0).repeat(x.shape[0], 1, 1, 1) return pos class PositionEmbeddingLearned3d(nn.Module): """ Absolute pos embedding, learned. """ def __init__(self, num_pos_feats=256,h_patch_num = 16, w_patch_num = 16,d_patch_num = 64): super().__init__() self.h_patch_num = h_patch_num self.w_patch_num = w_patch_num self.d_patch_num = d_patch_num self.row_embed = nn.Embedding(h_patch_num, num_pos_feats) self.col_embed = nn.Embedding(w_patch_num, num_pos_feats) self.dep_embed = nn.Embedding(d_patch_num, num_pos_feats) self.reset_parameters() def reset_parameters(self): nn.init.uniform_(self.row_embed.weight) nn.init.uniform_(self.col_embed.weight) nn.init.uniform_(self.dep_embed.weight) def forward(self, B, h, w, d,x): i = (torch.arange(h, device=x.device) + 1)* (self.h_patch_num // h) -1 j = (torch.arange(w, device=x.device) + 1)* (self.w_patch_num // w) -1 k = (torch.arange(d, device=x.device) + 1)* (self.d_patch_num // d) -1 x_emb = self.row_embed(i).unsqueeze(1).unsqueeze(2).repeat(1,w,d,1) y_emb = self.col_embed(j).unsqueeze(0).unsqueeze(2).repeat(h,1,d,1) z_emb = self.dep_embed(k).unsqueeze(0).unsqueeze(1).repeat(h,w,1,1) pos = torch.cat([x_emb,y_emb,z_emb,], dim=-1).unsqueeze(0).repeat(B, 1, 1, 1, 1) pos = rearrange(pos,'b h w d c -> b (h w d) c') return pos def build_position_encoding(args): N_steps = args.hidden_dim // 2 if args.position_embedding in ('v2', 'sine'): # TODO find a better way of exposing other arguments position_embedding = PositionEmbeddingSine(N_steps, normalize=True) elif args.position_embedding in ('v3', 'learned'): position_embedding = PositionEmbeddingLearned(N_steps) else: raise ValueError(f"not supported {args.position_embedding}") return position_embedding # Pos = PositionEmbeddingLearned3d() # x = torch.randn((8,3,32,32,1)) # print(Pos(8,16,16,1,x)) ================================================ FILE: src/Model/RadFM/transformer_decoder.py ================================================ """ Code modified from DETR tranformer: https://github.com/facebookresearch/detr Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved """ import copy from typing import Optional, List import pickle as cp import torch import torch.nn.functional as F from torch import nn, Tensor class TransformerDecoder(nn.Module): def __init__(self, decoder_layer, num_layers, norm=None, return_intermediate=False): super().__init__() self.layers = _get_clones(decoder_layer, num_layers) self.num_layers = num_layers self.norm = norm self.return_intermediate = return_intermediate def forward(self, tgt, memory, tgt_mask: Optional[Tensor] = None, memory_mask: Optional[Tensor] = None, tgt_key_padding_mask: Optional[Tensor] = None, memory_key_padding_mask: Optional[Tensor] = None, pos: Optional[Tensor] = None, query_pos: Optional[Tensor] = None): output = tgt T,B,C = memory.shape intermediate = [] atten_layers = [] for n,layer in enumerate(self.layers): residual=True output,ws = layer(output, memory, tgt_mask=tgt_mask, memory_mask=memory_mask, tgt_key_padding_mask=tgt_key_padding_mask, memory_key_padding_mask=memory_key_padding_mask, pos=pos, query_pos=query_pos,residual=residual) atten_layers.append(ws) if self.return_intermediate: intermediate.append(self.norm(output)) if self.norm is not None: output = self.norm(output) if self.return_intermediate: intermediate.pop() intermediate.append(output) if self.return_intermediate: return torch.stack(intermediate) return output,atten_layers class TransformerDecoderLayer(nn.Module): def __init__(self, d_model, nhead, dim_feedforward=2048, dropout=0.1, activation="relu", normalize_before=False): super().__init__() self.self_attn = nn.MultiheadAttention(d_model, nhead, dropout=dropout) self.multihead_attn = nn.MultiheadAttention(d_model, nhead, dropout=dropout) # Implementation of Feedforward model self.linear1 = nn.Linear(d_model, dim_feedforward) self.dropout = nn.Dropout(dropout) self.linear2 = nn.Linear(dim_feedforward, d_model) self.norm1 = nn.LayerNorm(d_model) self.norm2 = nn.LayerNorm(d_model) self.norm3 = nn.LayerNorm(d_model) self.dropout1 = nn.Dropout(dropout) self.dropout2 = nn.Dropout(dropout) self.dropout3 = nn.Dropout(dropout) self.activation = _get_activation_fn(activation) self.normalize_before = normalize_before def with_pos_embed(self, tensor, pos: Optional[Tensor]): return tensor if pos is None else tensor + pos def forward_post(self, tgt, memory, tgt_mask: Optional[Tensor] = None, memory_mask: Optional[Tensor] = None, tgt_key_padding_mask: Optional[Tensor] = None, memory_key_padding_mask: Optional[Tensor] = None, pos: Optional[Tensor] = None, query_pos: Optional[Tensor] = None, residual=True): q = k = self.with_pos_embed(tgt, query_pos) tgt2,ws = self.self_attn(q, k, value=tgt, attn_mask=tgt_mask, key_padding_mask=tgt_key_padding_mask) tgt = self.norm1(tgt) tgt2,ws = self.multihead_attn(query=self.with_pos_embed(tgt, query_pos), key=self.with_pos_embed(memory, pos), value=memory, attn_mask=memory_mask, key_padding_mask=memory_key_padding_mask) # attn_weights [B,NUM_Q,T] tgt = tgt + self.dropout2(tgt2) tgt = self.norm2(tgt) tgt2 = self.linear2(self.dropout(self.activation(self.linear1(tgt)))) tgt = tgt + self.dropout3(tgt2) tgt = self.norm3(tgt) return tgt,ws def forward_pre(self, tgt, memory, tgt_mask: Optional[Tensor] = None, memory_mask: Optional[Tensor] = None, tgt_key_padding_mask: Optional[Tensor] = None, memory_key_padding_mask: Optional[Tensor] = None, pos: Optional[Tensor] = None, query_pos: Optional[Tensor] = None): tgt2 = self.norm1(tgt) q = k = self.with_pos_embed(tgt2, query_pos) tgt2,ws = self.self_attn(q, k, value=tgt2, attn_mask=tgt_mask, key_padding_mask=tgt_key_padding_mask) tgt = tgt + self.dropout1(tgt2) tgt2 = self.norm2(tgt) tgt2,attn_weights = self.multihead_attn(query=self.with_pos_embed(tgt2, query_pos), key=self.with_pos_embed(memory, pos), value=memory, attn_mask=memory_mask, key_padding_mask=memory_key_padding_mask) tgt = tgt + self.dropout2(tgt2) tgt2 = self.norm3(tgt) tgt2 = self.linear2(self.dropout(self.activation(self.linear1(tgt2)))) tgt = tgt + self.dropout3(tgt2) return tgt,attn_weights def forward(self, tgt, memory, tgt_mask: Optional[Tensor] = None, memory_mask: Optional[Tensor] = None, tgt_key_padding_mask: Optional[Tensor] = None, memory_key_padding_mask: Optional[Tensor] = None, pos: Optional[Tensor] = None, query_pos: Optional[Tensor] = None, residual=True): if self.normalize_before: return self.forward_pre(tgt, memory, tgt_mask, memory_mask, tgt_key_padding_mask, memory_key_padding_mask, pos, query_pos) return self.forward_post(tgt, memory, tgt_mask, memory_mask, tgt_key_padding_mask, memory_key_padding_mask, pos, query_pos,residual) def _get_clones(module, N): return nn.ModuleList([copy.deepcopy(module) for i in range(N)]) def _get_activation_fn(activation): """Return an activation function given a string""" if activation == "relu": return F.relu if activation == "gelu": return F.gelu if activation == "glu": return F.glu raise RuntimeError(F"activation should be relu/gelu, not {activation}.") ================================================ FILE: src/Model/RadFM/utils.py ================================================ from .blocks import ModifiedResNet,PMC_CLIP_cfg import torch from torchvision import transforms from PIL import Image import torch.nn as nn def extend_instance(obj, mixin): """Apply mixins to a class instance after creation""" base_cls = obj.__class__ base_cls_name = obj.__class__.__name__ obj.__class__ = type( base_cls_name, (mixin, base_cls), {} ) # mixin needs to go first for our forward() logic to work def getattr_recursive(obj, att): """ Return nested attribute of obj Example: getattr_recursive(obj, 'a.b.c') is equivalent to obj.a.b.c """ if att == "": return obj i = att.find(".") if i < 0: return getattr(obj, att) else: return getattr_recursive(getattr(obj, att[:i]), att[i + 1 :]) def setattr_recursive(obj, att, val): """ Set nested attribute of obj Example: setattr_recursive(obj, 'a.b.c', val) is equivalent to obj.a.b.c = val """ if "." in att: obj = getattr_recursive(obj, ".".join(att.split(".")[:-1])) setattr(obj, att.split(".")[-1], val) def get_visual_encoder(model_str): """ Args: str (_type_): str_to_model_path Return: vision_model, visual_dim, img_preprocessor """ normalize = transforms.Normalize((0.485, 0.456, 0.406), (0.229, 0.224, 0.225)) img_preprocessor = transforms.Compose([ transforms.Resize((512,512), interpolation=Image.BICUBIC), transforms.ToTensor(), normalize, ]) if 'PMC-CLIP' in model_str: #vision_cfg = json.load(open(model_args.visual_model_config,'r'))['vision_cfg'] vision_cfg = PMC_CLIP_cfg() vision_heads = vision_cfg.width * 32 // vision_cfg.head_width vision_model = ModifiedResNet( layers=vision_cfg.layers, heads=vision_heads, output_dim = 768, image_size=vision_cfg.image_size, width=vision_cfg.width ) vision_model = vision_load_pretrain(vision_model,model_str) vision_model = nn.Sequential(*list(vision_model.children())[:-2]) visual_dim = 1024 return vision_model,visual_dim,img_preprocessor def vision_load_pretrain(resnet,model_path): checkpoint = torch.load(model_path, map_location='cpu') state_dict = checkpoint['state_dict'] state_dict = {k.replace('module.visual.',''): v for k, v in state_dict.items() if '.visual' in k} resnet.load_state_dict(state_dict) return resnet ================================================ FILE: src/Model/RadFM/vit_3d.py ================================================ import torch from torch import nn from einops import rearrange, repeat from einops.layers.torch import Rearrange from .position_encoding import PositionEmbeddingLearned3d # helpers def pair(t): return t if isinstance(t, tuple) else (t, t) # classes class PreNorm(nn.Module): def __init__(self, dim, fn): super().__init__() self.norm = nn.LayerNorm(dim) self.fn = fn def forward(self, x, **kwargs): return self.fn(self.norm(x), **kwargs) class FeedForward(nn.Module): def __init__(self, dim, hidden_dim, dropout = 0.): super().__init__() self.net = nn.Sequential( nn.Linear(dim, hidden_dim), nn.GELU(), nn.Dropout(dropout), nn.Linear(hidden_dim, dim), nn.Dropout(dropout) ) def forward(self, x): return self.net(x) class Attention(nn.Module): def __init__(self, dim, heads = 8, dim_head = 64, dropout = 0.): super().__init__() inner_dim = dim_head * heads project_out = not (heads == 1 and dim_head == dim) self.heads = heads self.scale = dim_head ** -0.5 self.attend = nn.Softmax(dim = -1) self.dropout = nn.Dropout(dropout) self.to_qkv = nn.Linear(dim, inner_dim * 3, bias = False) self.to_out = nn.Sequential( nn.Linear(inner_dim, dim), nn.Dropout(dropout) ) if project_out else nn.Identity() def forward(self, x): qkv = self.to_qkv(x).chunk(3, dim = -1) q, k, v = map(lambda t: rearrange(t, 'b n (h d) -> b h n d', h = self.heads), qkv) dots = torch.matmul(q, k.transpose(-1, -2)) * self.scale attn = self.attend(dots) attn = self.dropout(attn) out = torch.matmul(attn, v) out = rearrange(out, 'b h n d -> b n (h d)') return self.to_out(out) class Transformer(nn.Module): def __init__(self, dim, depth, heads, dim_head, mlp_dim, dropout = 0.): super().__init__() self.layers = nn.ModuleList([]) for _ in range(depth): self.layers.append(nn.ModuleList([ PreNorm(dim, Attention(dim, heads = heads, dim_head = dim_head, dropout = dropout)), PreNorm(dim, FeedForward(dim, mlp_dim, dropout = dropout)) ])) def forward(self, x): for attn, ff in self.layers: x = attn(x) + x x = ff(x) + x return x class ViT(nn.Module): def __init__(self, *, image_size, image_patch_size, frames, frame_patch_size, dim, depth, heads, mlp_dim, pool = 'cls', channels = 3, dim_head = 64, dropout = 0., emb_dropout = 0.): super().__init__() image_height, image_width = pair(image_size) patch_height, patch_width = pair(image_patch_size) assert image_height % patch_height == 0 and image_width % patch_width == 0, 'Image dimensions must be divisible by the patch size.' assert frames % frame_patch_size == 0, 'Frames must be divisible by frame patch size' self.patch_height = patch_height self.patch_width = patch_width self.frame_patch_size = frame_patch_size num_patches = (image_height // patch_height) * (image_width // patch_width) * (frames // frame_patch_size) patch_dim = channels * patch_height * patch_width * frame_patch_size assert pool in {'cls', 'mean'}, 'pool type must be either cls (cls token) or mean (mean pooling)' self.to_patch_embedding = nn.Sequential( Rearrange('b c (h p1) (w p2) (f pf) -> b (h w f) (p1 p2 pf c)', p1 = patch_height, p2 = patch_width, pf = frame_patch_size), nn.LayerNorm(patch_dim), nn.Linear(patch_dim, dim), nn.LayerNorm(dim), ) self.pos_embedding = PositionEmbeddingLearned3d(dim // 3,(image_height // patch_height), (image_width // patch_width), (frames // frame_patch_size)) self.dropout = nn.Dropout(emb_dropout) self.transformer = Transformer(dim, depth, heads, dim_head, mlp_dim, dropout) def forward(self, video): B, C, H, W, D = video.shape x = self.to_patch_embedding(video) b, n, _ = x.shape pos = self.pos_embedding(B, H // self.patch_height, W // self.patch_width, D // self.frame_patch_size,x) x += pos x = self.dropout(x) x = self.transformer(x) return x,pos ================================================ FILE: src/My_Trainer/trainer.py ================================================ # coding=utf-8 # Copyright 2020-present the HuggingFace Inc. team. # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. """ The Trainer class, to easily train a 🤗 Transformers from scratch or finetune it on a new task. """ import contextlib import functools import glob import inspect import math import os import random import re import shutil import sys import time import warnings from collections.abc import Mapping from pathlib import Path from typing import TYPE_CHECKING, Any, Callable, Dict, List, Optional, Tuple, Union from tqdm.auto import tqdm # Integrations must be imported before ML frameworks: # isort: off from transformers.integrations import ( default_hp_search_backend, get_reporting_integration_callbacks, hp_params, is_fairscale_available, is_optuna_available, is_ray_tune_available, is_sigopt_available, is_wandb_available, run_hp_search_optuna, run_hp_search_ray, run_hp_search_sigopt, run_hp_search_wandb, ) # isort: on import numpy as np import torch import torch.distributed as dist from huggingface_hub import Repository, create_repo from packaging import version from torch import nn from torch.utils.data import DataLoader, Dataset, RandomSampler, SequentialSampler from torch.utils.data.distributed import DistributedSampler from transformers import __version__ from transformers.configuration_utils import PretrainedConfig from transformers.data.data_collator import DataCollator, DataCollatorWithPadding, default_data_collator from transformers.debug_utils import DebugOption, DebugUnderflowOverflow from transformers.deepspeed import deepspeed_init, is_deepspeed_zero3_enabled from transformers.dependency_versions_check import dep_version_check from transformers.modelcard import TrainingSummary from transformers.modeling_utils import PreTrainedModel, load_sharded_checkpoint, unwrap_model from transformers.models.auto.modeling_auto import MODEL_FOR_CAUSAL_LM_MAPPING_NAMES, MODEL_MAPPING_NAMES from transformers.optimization import Adafactor, get_scheduler from transformers.pytorch_utils import ALL_LAYERNORM_LAYERS, is_torch_greater_or_equal_than_1_10, is_torch_less_than_1_11 from transformers.tokenization_utils_base import PreTrainedTokenizerBase from transformers.trainer_callback import ( CallbackHandler, DefaultFlowCallback, PrinterCallback, ProgressCallback, TrainerCallback, TrainerControl, TrainerState, ) from transformers.trainer_pt_utils import ( DistributedLengthGroupedSampler, DistributedSamplerWithLoop, DistributedTensorGatherer, IterableDatasetShard, LabelSmoother, LengthGroupedSampler, SequentialDistributedSampler, ShardSampler, distributed_broadcast_scalars, distributed_concat, find_batch_size, get_model_param_count, get_module_class_from_name, get_parameter_names, nested_concat, nested_detach, nested_numpify, nested_truncate, nested_xla_mesh_reduce, reissue_pt_warnings, ) from transformers.trainer_utils import ( PREFIX_CHECKPOINT_DIR, BestRun, EvalLoopOutput, EvalPrediction, FSDPOption, HPSearchBackend, HubStrategy, IntervalStrategy, PredictionOutput, RemoveColumnsCollator, ShardedDDPOption, TrainerMemoryTracker, TrainOutput, default_compute_objective, default_hp_space, denumpify_detensorize, enable_full_determinism, find_executable_batch_size, get_last_checkpoint, has_length, number_of_arguments, seed_worker, set_seed, speed_metrics, ) from transformers.training_args import OptimizerNames, ParallelMode, TrainingArguments from transformers.utils import ( CONFIG_NAME, SAFE_WEIGHTS_INDEX_NAME, SAFE_WEIGHTS_NAME, WEIGHTS_INDEX_NAME, WEIGHTS_NAME, can_return_loss, find_labels, get_full_repo_name, is_accelerate_available, is_apex_available, is_datasets_available, is_in_notebook, is_ipex_available, is_safetensors_available, is_sagemaker_dp_enabled, is_sagemaker_mp_enabled, is_torch_compile_available, is_torch_neuroncore_available, is_torch_tpu_available, logging, strtobool, ) from transformers.utils.generic import ContextManagers _is_native_cpu_amp_available = is_torch_greater_or_equal_than_1_10 DEFAULT_CALLBACKS = [DefaultFlowCallback] DEFAULT_PROGRESS_CALLBACK = ProgressCallback if is_in_notebook(): from transformers.utils.notebook import NotebookProgressCallback DEFAULT_PROGRESS_CALLBACK = NotebookProgressCallback if is_apex_available(): from apex import amp if is_datasets_available(): import datasets if is_torch_tpu_available(check_device=False): import torch_xla.core.xla_model as xm import torch_xla.debug.metrics as met import torch_xla.distributed.parallel_loader as pl if is_fairscale_available(): dep_version_check("fairscale") import fairscale from fairscale.nn.data_parallel import FullyShardedDataParallel as FullyShardedDDP from fairscale.nn.data_parallel import ShardedDataParallel as ShardedDDP from fairscale.nn.wrap import auto_wrap from fairscale.optim import OSS from fairscale.optim.grad_scaler import ShardedGradScaler if is_sagemaker_mp_enabled(): import smdistributed.modelparallel.torch as smp from smdistributed.modelparallel import __version__ as SMP_VERSION IS_SAGEMAKER_MP_POST_1_10 = version.parse(SMP_VERSION) >= version.parse("1.10") from transformers.trainer_pt_utils import smp_forward_backward, smp_forward_only, smp_gather, smp_nested_concat else: IS_SAGEMAKER_MP_POST_1_10 = False if is_safetensors_available(): import safetensors.torch skip_first_batches = None if is_accelerate_available(): from accelerate import __version__ as accelerate_version if version.parse(accelerate_version) >= version.parse("0.16"): from accelerate import skip_first_batches if TYPE_CHECKING: import optuna logger = logging.get_logger(__name__) # Name of the files used for checkpointing TRAINING_ARGS_NAME = "training_args.bin" TRAINER_STATE_NAME = "trainer_state.json" OPTIMIZER_NAME = "optimizer.pt" SCHEDULER_NAME = "scheduler.pt" SCALER_NAME = "scaler.pt" class Trainer: """ Trainer is a simple but feature-complete training and eval loop for PyTorch, optimized for 🤗 Transformers. Args: model ([`PreTrainedModel`] or `torch.nn.Module`, *optional*): The model to train, evaluate or use for predictions. If not provided, a `model_init` must be passed. [`Trainer`] is optimized to work with the [`PreTrainedModel`] provided by the library. You can still use your own models defined as `torch.nn.Module` as long as they work the same way as the 🤗 Transformers models. args ([`TrainingArguments`], *optional*): The arguments to tweak for training. Will default to a basic instance of [`TrainingArguments`] with the `output_dir` set to a directory named *tmp_trainer* in the current directory if not provided. data_collator (`DataCollator`, *optional*): The function to use to form a batch from a list of elements of `train_dataset` or `eval_dataset`. Will default to [`default_data_collator`] if no `tokenizer` is provided, an instance of [`DataCollatorWithPadding`] otherwise. train_dataset (`torch.utils.data.Dataset` or `torch.utils.data.IterableDataset`, *optional*): The dataset to use for training. If it is a [`~datasets.Dataset`], columns not accepted by the `model.forward()` method are automatically removed. Note that if it's a `torch.utils.data.IterableDataset` with some randomization and you are training in a distributed fashion, your iterable dataset should either use a internal attribute `generator` that is a `torch.Generator` for the randomization that must be identical on all processes (and the Trainer will manually set the seed of this `generator` at each epoch) or have a `set_epoch()` method that internally sets the seed of the RNGs used. eval_dataset (Union[`torch.utils.data.Dataset`, Dict[str, `torch.utils.data.Dataset`]), *optional*): The dataset to use for evaluation. If it is a [`~datasets.Dataset`], columns not accepted by the `model.forward()` method are automatically removed. If it is a dictionary, it will evaluate on each dataset prepending the dictionary key to the metric name. tokenizer ([`PreTrainedTokenizerBase`], *optional*): The tokenizer used to preprocess the data. If provided, will be used to automatically pad the inputs to the maximum length when batching inputs, and it will be saved along the model to make it easier to rerun an interrupted training or reuse the fine-tuned model. model_init (`Callable[[], PreTrainedModel]`, *optional*): A function that instantiates the model to be used. If provided, each call to [`~Trainer.train`] will start from a new instance of the model as given by this function. The function may have zero argument, or a single one containing the optuna/Ray Tune/SigOpt trial object, to be able to choose different architectures according to hyper parameters (such as layer count, sizes of inner layers, dropout probabilities etc). compute_metrics (`Callable[[EvalPrediction], Dict]`, *optional*): The function that will be used to compute metrics at evaluation. Must take a [`EvalPrediction`] and return a dictionary string to metric values. callbacks (List of [`TrainerCallback`], *optional*): A list of callbacks to customize the training loop. Will add those to the list of default callbacks detailed in [here](callback). If you want to remove one of the default callbacks used, use the [`Trainer.remove_callback`] method. optimizers (`Tuple[torch.optim.Optimizer, torch.optim.lr_scheduler.LambdaLR]`, *optional*): A tuple containing the optimizer and the scheduler to use. Will default to an instance of [`AdamW`] on your model and a scheduler given by [`get_linear_schedule_with_warmup`] controlled by `args`. preprocess_logits_for_metrics (`Callable[[torch.Tensor, torch.Tensor], torch.Tensor]`, *optional*): A function that preprocess the logits right before caching them at each evaluation step. Must take two tensors, the logits and the labels, and return the logits once processed as desired. The modifications made by this function will be reflected in the predictions received by `compute_metrics`. Note that the labels (second parameter) will be `None` if the dataset does not have them. Important attributes: - **model** -- Always points to the core model. If using a transformers model, it will be a [`PreTrainedModel`] subclass. - **model_wrapped** -- Always points to the most external model in case one or more other modules wrap the original model. This is the model that should be used for the forward pass. For example, under `DeepSpeed`, the inner model is wrapped in `DeepSpeed` and then again in `torch.nn.DistributedDataParallel`. If the inner model hasn't been wrapped, then `self.model_wrapped` is the same as `self.model`. - **is_model_parallel** -- Whether or not a model has been switched to a model parallel mode (different from data parallelism, this means some of the model layers are split on different GPUs). - **place_model_on_device** -- Whether or not to automatically place the model on the device - it will be set to `False` if model parallel or deepspeed is used, or if the default `TrainingArguments.place_model_on_device` is overridden to return `False` . - **is_in_train** -- Whether or not a model is currently running `train` (e.g. when `evaluate` is called while in `train`) """ from transformers.trainer_pt_utils import _get_learning_rate, log_metrics, metrics_format, save_metrics, save_state def __init__( self, model: Union[PreTrainedModel, nn.Module] = None, args: TrainingArguments = None, data_collator: Optional[DataCollator] = None, train_dataset: Optional[Dataset] = None, eval_dataset: Optional[Union[Dataset, Dict[str, Dataset]]] = None, tokenizer: Optional[PreTrainedTokenizerBase] = None, model_init: Optional[Callable[[], PreTrainedModel]] = None, compute_metrics: Optional[Callable[[EvalPrediction], Dict]] = None, callbacks: Optional[List[TrainerCallback]] = None, optimizers: Tuple[torch.optim.Optimizer, torch.optim.lr_scheduler.LambdaLR] = (None, None), preprocess_logits_for_metrics: Optional[Callable[[torch.Tensor, torch.Tensor], torch.Tensor]] = None, ): if args is None: output_dir = "tmp_trainer" logger.info(f"No `TrainingArguments` passed, using `output_dir={output_dir}`.") args = TrainingArguments(output_dir=output_dir) self.args = args # Seed must be set before instantiating the model when using model enable_full_determinism(self.args.seed) if self.args.full_determinism else set_seed(self.args.seed) self.hp_name = None self.deepspeed = None self.is_in_train = False # memory metrics - must set up as early as possible self._memory_tracker = TrainerMemoryTracker(self.args.skip_memory_metrics) self._memory_tracker.start() # set the correct log level depending on the node log_level = args.get_process_log_level() logging.set_verbosity(log_level) # force device and distributed setup init explicitly args._setup_devices if model is None: if model_init is not None: self.model_init = model_init model = self.call_model_init() else: raise RuntimeError("`Trainer` requires either a `model` or `model_init` argument") else: if model_init is not None: warnings.warn( "`Trainer` requires either a `model` or `model_init` argument, but not both. `model_init` will" " overwrite your model when calling the `train` method. This will become a fatal error in the next" " release.", FutureWarning, ) self.model_init = model_init if model.__class__.__name__ in MODEL_MAPPING_NAMES: raise ValueError( f"The model you have picked ({model.__class__.__name__}) cannot be used as is for training: it only " "computes hidden states and does not accept any labels. You should choose a model with a head " "suitable for your task like any of the `AutoModelForXxx` listed at " "https://huggingface.co/docs/transformers/model_doc/auto." ) if hasattr(model, "is_parallelizable") and model.is_parallelizable and model.model_parallel: self.is_model_parallel = True else: self.is_model_parallel = False if ( getattr(model, "hf_device_map", None) is not None and len([device for device in set(model.hf_device_map.values()) if device not in ["cpu", "disk"]]) > 1 and not self.is_model_parallel ): self.is_model_parallel = True # warn users logger.info( "You have loaded a model on multiple GPUs. `is_model_parallel` attribute will be force-set" " to `True` to avoid any unexpected behavior such as device placement mismatching." ) # At this stage the model is already loaded if getattr(model, "is_loaded_in_8bit", False): if getattr(model, "_is_int8_training_enabled", False): logger.info( "The model is loaded in 8-bit precision. To train this model you need to add additional modules" " inside the model such as adapters using `peft` library and freeze the model weights. Please" " check " " the examples in https://github.com/huggingface/peft for more details." ) else: raise ValueError( "The model you want to train is loaded in 8-bit precision. if you want to fine-tune an 8-bit" " model, please make sure that you have installed `bitsandbytes>=0.37.0`. " ) # Setup Sharded DDP training self.sharded_ddp = None if len(args.sharded_ddp) > 0: if args.deepspeed: raise ValueError( "Using --sharded_ddp xxx together with --deepspeed is not possible, deactivate one of those flags." ) if len(args.fsdp) > 0: raise ValueError( "Using --sharded_ddp xxx together with --fsdp is not possible, deactivate one of those flags." ) if args.local_rank == -1: raise ValueError("Using sharded DDP only works in distributed training.") elif not is_fairscale_available(): raise ImportError("Sharded DDP training requires fairscale: `pip install fairscale`.") elif ShardedDDPOption.SIMPLE not in args.sharded_ddp and FullyShardedDDP is None: raise ImportError( "Sharded DDP in a mode other than simple training requires fairscale version >= 0.3, found " f"{fairscale.__version__}. Upgrade your fairscale library: `pip install --upgrade fairscale`." ) elif ShardedDDPOption.SIMPLE in args.sharded_ddp: self.sharded_ddp = ShardedDDPOption.SIMPLE elif ShardedDDPOption.ZERO_DP_2 in args.sharded_ddp: self.sharded_ddp = ShardedDDPOption.ZERO_DP_2 elif ShardedDDPOption.ZERO_DP_3 in args.sharded_ddp: self.sharded_ddp = ShardedDDPOption.ZERO_DP_3 self.fsdp = None if len(args.fsdp) > 0: if args.deepspeed: raise ValueError( "Using --fsdp xxx together with --deepspeed is not possible, deactivate one of those flags." ) if not args.fsdp_config["xla"] and args.local_rank == -1: raise ValueError("Using fsdp only works in distributed training.") # dep_version_check("torch>=1.12.0") # Would have to update setup.py with torch>=1.12.0 # which isn't ideally given that it will force people not using FSDP to also use torch>=1.12.0 # below is the current alternative. if version.parse(version.parse(torch.__version__).base_version) < version.parse("1.12.0"): raise ValueError("FSDP requires PyTorch >= 1.12.0") from torch.distributed.fsdp.fully_sharded_data_parallel import BackwardPrefetch, ShardingStrategy if FSDPOption.FULL_SHARD in args.fsdp: self.fsdp = ShardingStrategy.FULL_SHARD elif FSDPOption.SHARD_GRAD_OP in args.fsdp: self.fsdp = ShardingStrategy.SHARD_GRAD_OP elif FSDPOption.NO_SHARD in args.fsdp: self.fsdp = ShardingStrategy.NO_SHARD self.backward_prefetch = BackwardPrefetch.BACKWARD_PRE if "backward_prefetch" in self.args.fsdp_config and "backward_pos" not in self.backward_prefetch: self.backward_prefetch = BackwardPrefetch.BACKWARD_POST self.forward_prefetch = False if self.args.fsdp_config.get("forward_prefect", False): self.forward_prefetch = True self.limit_all_gathers = False if self.args.fsdp_config.get("limit_all_gathers", False): self.limit_all_gathers = True # one place to sort out whether to place the model on device or not # postpone switching model to cuda when: # 1. MP - since we are trying to fit a much bigger than 1 gpu model # 2. fp16-enabled DeepSpeed loads the model in half the size and it doesn't need .to() anyway, # and we only use deepspeed for training at the moment # 3. full bf16 or fp16 eval - since the model needs to be cast to the right dtype first # 4. Sharded DDP - same as MP # 5. FSDP - same as MP self.place_model_on_device = args.place_model_on_device if ( self.is_model_parallel or args.deepspeed or ((args.fp16_full_eval or args.bf16_full_eval) and not args.do_train) or (self.sharded_ddp in [ShardedDDPOption.ZERO_DP_2, ShardedDDPOption.ZERO_DP_3]) or (self.fsdp is not None) ): self.place_model_on_device = False default_collator = default_data_collator if tokenizer is None else DataCollatorWithPadding(tokenizer) self.data_collator = data_collator if data_collator is not None else default_collator self.train_dataset = train_dataset self.eval_dataset = eval_dataset self.tokenizer = tokenizer if self.place_model_on_device and not getattr(model, "is_loaded_in_8bit", False): self._move_model_to_device(model, args.device) # Force n_gpu to 1 to avoid DataParallel as MP will manage the GPUs if self.is_model_parallel: self.args._n_gpu = 1 # later use `self.model is self.model_wrapped` to check if it's wrapped or not self.model_wrapped = model self.model = model self.compute_metrics = compute_metrics self.preprocess_logits_for_metrics = preprocess_logits_for_metrics self.optimizer, self.lr_scheduler = optimizers if model_init is not None and (self.optimizer is not None or self.lr_scheduler is not None): raise RuntimeError( "Passing a `model_init` is incompatible with providing the `optimizers` argument. " "You should subclass `Trainer` and override the `create_optimizer_and_scheduler` method." ) if is_torch_tpu_available() and self.optimizer is not None: for param in self.model.parameters(): model_device = param.device break for param_group in self.optimizer.param_groups: if len(param_group["params"]) > 0: optimizer_device = param_group["params"][0].device break if model_device != optimizer_device: raise ValueError( "The model and the optimizer parameters are not on the same device, which probably means you" " created an optimizer around your model **before** putting on the device and passing it to the" " `Trainer`. Make sure the lines `import torch_xla.core.xla_model as xm` and" " `model.to(xm.xla_device())` is performed before the optimizer creation in your script." ) if ((self.sharded_ddp is not None) or args.deepspeed or (self.fsdp is not None)) and ( self.optimizer is not None or self.lr_scheduler is not None ): raise RuntimeError( "Passing `optimizers` is not allowed if Fairscale, Deepspeed or PyTorch FSDP is enabled." "You should subclass `Trainer` and override the `create_optimizer_and_scheduler` method." ) default_callbacks = DEFAULT_CALLBACKS + get_reporting_integration_callbacks(self.args.report_to) callbacks = default_callbacks if callbacks is None else default_callbacks + callbacks self.callback_handler = CallbackHandler( callbacks, self.model, self.tokenizer, self.optimizer, self.lr_scheduler ) self.add_callback(PrinterCallback if self.args.disable_tqdm else DEFAULT_PROGRESS_CALLBACK) # Will be set to True by `self._setup_loggers()` on first call to `self.log()`. self._loggers_initialized = False # Create clone of distant repo and output directory if needed if self.args.push_to_hub: self.init_git_repo(at_init=True) # In case of pull, we need to make sure every process has the latest. if is_torch_tpu_available(): xm.rendezvous("init git repo") elif args.local_rank != -1: dist.barrier() if self.args.should_save: os.makedirs(self.args.output_dir, exist_ok=True) if not callable(self.data_collator) and callable(getattr(self.data_collator, "collate_batch", None)): raise ValueError("The `data_collator` should be a simple callable (function, class with `__call__`).") if args.max_steps > 0: logger.info("max_steps is given, it will override any value given in num_train_epochs") if train_dataset is not None and not has_length(train_dataset) and args.max_steps <= 0: raise ValueError( "The train_dataset does not implement __len__, max_steps has to be specified. " "The number of steps needs to be known in advance for the learning rate scheduler." ) if ( train_dataset is not None and isinstance(train_dataset, torch.utils.data.IterableDataset) and args.group_by_length ): raise ValueError("the `--group_by_length` option is only available for `Dataset`, not `IterableDataset") self._signature_columns = None # Mixed precision setup self.use_apex = False self.use_cuda_amp = False self.use_cpu_amp = False # Mixed precision setup for SageMaker Model Parallel if is_sagemaker_mp_enabled(): # BF16 + model parallelism in SageMaker: currently not supported, raise an error if args.bf16: raise ValueError("SageMaker Model Parallelism does not support BF16 yet. Please use FP16 instead ") if IS_SAGEMAKER_MP_POST_1_10: # When there's mismatch between SMP config and trainer argument, use SMP config as truth if args.fp16 != smp.state.cfg.fp16: logger.warning( f"FP16 provided in SM_HP_MP_PARAMETERS is {smp.state.cfg.fp16}," f"but FP16 provided in trainer argument is {args.fp16}," f"setting to {smp.state.cfg.fp16}" ) args.fp16 = smp.state.cfg.fp16 else: # smp < 1.10 does not support fp16 in trainer. if hasattr(smp.state.cfg, "fp16"): logger.warning( f"FP16 provided in SM_HP_MP_PARAMETERS is {smp.state.cfg.fp16}, " "but SageMaker Model Parallelism < 1.10 does not support FP16 in trainer." ) if args.fp16 or args.bf16: if args.half_precision_backend == "auto": if args.device == torch.device("cpu"): if args.fp16: raise ValueError("Tried to use `fp16` but it is not supported on cpu") elif _is_native_cpu_amp_available: args.half_precision_backend = "cpu_amp" else: raise ValueError("Tried to use cpu amp but native cpu amp is not available") else: args.half_precision_backend = "cuda_amp" logger.info(f"Using {args.half_precision_backend} half precision backend") self.do_grad_scaling = False if (args.fp16 or args.bf16) and not (args.deepspeed or is_sagemaker_mp_enabled()): # deepspeed and SageMaker Model Parallel manage their own half precision if args.half_precision_backend == "cuda_amp": self.use_cuda_amp = True self.amp_dtype = torch.float16 if args.fp16 else torch.bfloat16 # bf16 does not need grad scaling self.do_grad_scaling = self.amp_dtype == torch.float16 if self.do_grad_scaling: if self.sharded_ddp is not None: self.scaler = ShardedGradScaler() elif self.fsdp is not None: from torch.distributed.fsdp.sharded_grad_scaler import ( ShardedGradScaler as FSDPShardedGradScaler, ) self.scaler = FSDPShardedGradScaler() elif is_torch_tpu_available(): from torch_xla.amp import GradScaler self.scaler = GradScaler() else: self.scaler = torch.cuda.amp.GradScaler() elif args.half_precision_backend == "cpu_amp": self.use_cpu_amp = True self.amp_dtype = torch.bfloat16 else: if not is_apex_available(): raise ImportError( "Using FP16 with APEX but APEX is not installed, please refer to" " https://www.github.com/nvidia/apex." ) self.use_apex = True # FP16 + model parallelism in SageMaker: gradient clipping does not work for now so we raise a helpful error. if ( is_sagemaker_mp_enabled() and self.use_cuda_amp and args.max_grad_norm is not None and args.max_grad_norm > 0 ): raise ValueError( "SageMaker Model Parallelism in mixed precision mode does not support gradient clipping yet. Pass " "along 'max_grad_norm': 0 in your hyperparameters." ) # Label smoothing if self.args.label_smoothing_factor != 0: self.label_smoother = LabelSmoother(epsilon=self.args.label_smoothing_factor) else: self.label_smoother = None self.state = TrainerState( is_local_process_zero=self.is_local_process_zero(), is_world_process_zero=self.is_world_process_zero(), ) self.control = TrainerControl() # Internal variable to count flos in each process, will be accumulated in `self.state.total_flos` then # returned to 0 every time flos need to be logged self.current_flos = 0 self.hp_search_backend = None self.use_tune_checkpoints = False default_label_names = find_labels(self.model.__class__) self.label_names = default_label_names if self.args.label_names is None else self.args.label_names self.can_return_loss = can_return_loss(self.model.__class__) self.control = self.callback_handler.on_init_end(self.args, self.state, self.control) # Internal variables to keep track of the original batch size self._train_batch_size = args.train_batch_size # very last self._memory_tracker.stop_and_update_metrics() # torch.compile if args.torch_compile and not is_torch_compile_available(): raise RuntimeError("Using torch.compile requires PyTorch 2.0 or higher.") def add_callback(self, callback): """ Add a callback to the current list of [`~transformer.TrainerCallback`]. Args: callback (`type` or [`~transformer.TrainerCallback`]): A [`~transformer.TrainerCallback`] class or an instance of a [`~transformer.TrainerCallback`]. In the first case, will instantiate a member of that class. """ self.callback_handler.add_callback(callback) def pop_callback(self, callback): """ Remove a callback from the current list of [`~transformer.TrainerCallback`] and returns it. If the callback is not found, returns `None` (and no error is raised). Args: callback (`type` or [`~transformer.TrainerCallback`]): A [`~transformer.TrainerCallback`] class or an instance of a [`~transformer.TrainerCallback`]. In the first case, will pop the first member of that class found in the list of callbacks. Returns: [`~transformer.TrainerCallback`]: The callback removed, if found. """ return self.callback_handler.pop_callback(callback) def remove_callback(self, callback): """ Remove a callback from the current list of [`~transformer.TrainerCallback`]. Args: callback (`type` or [`~transformer.TrainerCallback`]): A [`~transformer.TrainerCallback`] class or an instance of a [`~transformer.TrainerCallback`]. In the first case, will remove the first member of that class found in the list of callbacks. """ self.callback_handler.remove_callback(callback) def _move_model_to_device(self, model, device): model = model.to(device) # Moving a model to an XLA device disconnects the tied weights, so we have to retie them. if self.args.parallel_mode == ParallelMode.TPU and hasattr(model, "tie_weights"): model.tie_weights() def _set_signature_columns_if_needed(self): if self._signature_columns is None: # Inspect model forward signature to keep only the arguments it accepts. signature = inspect.signature(self.model.forward) self._signature_columns = list(signature.parameters.keys()) # Labels may be named label or label_ids, the default data collator handles that. self._signature_columns += list(set(["label", "label_ids"] + self.label_names)) def _remove_unused_columns(self, dataset: "datasets.Dataset", description: Optional[str] = None): if not self.args.remove_unused_columns: return dataset self._set_signature_columns_if_needed() signature_columns = self._signature_columns ignored_columns = list(set(dataset.column_names) - set(signature_columns)) if len(ignored_columns) > 0: dset_description = "" if description is None else f"in the {description} set" logger.info( f"The following columns {dset_description} don't have a corresponding argument in " f"`{self.model.__class__.__name__}.forward` and have been ignored: {', '.join(ignored_columns)}." f" If {', '.join(ignored_columns)} are not expected by `{self.model.__class__.__name__}.forward`, " " you can safely ignore this message." ) columns = [k for k in signature_columns if k in dataset.column_names] if version.parse(datasets.__version__) < version.parse("1.4.0"): dataset.set_format( type=dataset.format["type"], columns=columns, format_kwargs=dataset.format["format_kwargs"] ) return dataset else: return dataset.remove_columns(ignored_columns) def _get_collator_with_removed_columns( self, data_collator: Callable, description: Optional[str] = None ) -> Callable: """Wrap the data collator in a callable removing unused columns.""" if not self.args.remove_unused_columns: return data_collator self._set_signature_columns_if_needed() signature_columns = self._signature_columns remove_columns_collator = RemoveColumnsCollator( data_collator=data_collator, signature_columns=signature_columns, logger=logger, description=description, model_name=self.model.__class__.__name__, ) return remove_columns_collator def _get_train_sampler(self) -> Optional[torch.utils.data.Sampler]: if self.train_dataset is None or not has_length(self.train_dataset): return None generator = None if self.args.world_size <= 1: generator = torch.Generator() # for backwards compatibility, we generate a seed here (which is sampled from a generator seeded with # `args.seed`) if data_seed isn't provided. # Further on in this method, we default to `args.seed` instead. if self.args.data_seed is None: seed = int(torch.empty((), dtype=torch.int64).random_().item()) else: seed = self.args.data_seed generator.manual_seed(seed) seed = self.args.data_seed if self.args.data_seed is not None else self.args.seed # Build the sampler. if self.args.group_by_length: if is_datasets_available() and isinstance(self.train_dataset, datasets.Dataset): lengths = ( self.train_dataset[self.args.length_column_name] if self.args.length_column_name in self.train_dataset.column_names else None ) else: lengths = None model_input_name = self.tokenizer.model_input_names[0] if self.tokenizer is not None else None if self.args.world_size <= 1: return LengthGroupedSampler( self.args.train_batch_size * self.args.gradient_accumulation_steps, dataset=self.train_dataset, lengths=lengths, model_input_name=model_input_name, generator=generator, ) else: return DistributedLengthGroupedSampler( self.args.train_batch_size * self.args.gradient_accumulation_steps, dataset=self.train_dataset, num_replicas=self.args.world_size, rank=self.args.process_index, lengths=lengths, model_input_name=model_input_name, seed=seed, ) else: if self.args.world_size <= 1: return RandomSampler(self.train_dataset, generator=generator) elif ( self.args.parallel_mode in [ParallelMode.TPU, ParallelMode.SAGEMAKER_MODEL_PARALLEL] and not self.args.dataloader_drop_last ): # Use a loop for TPUs when drop_last is False to have all batches have the same size. return DistributedSamplerWithLoop( self.train_dataset, batch_size=self.args.per_device_train_batch_size, num_replicas=self.args.world_size, rank=self.args.process_index, seed=seed, ) else: return DistributedSampler( self.train_dataset, num_replicas=self.args.world_size, rank=self.args.process_index, seed=seed, ) def get_train_dataloader(self) -> DataLoader: """ Returns the training [`~torch.utils.data.DataLoader`]. Will use no sampler if `train_dataset` does not implement `__len__`, a random sampler (adapted to distributed training if necessary) otherwise. Subclass and override this method if you want to inject some custom behavior. """ if self.train_dataset is None: raise ValueError("Trainer: training requires a train_dataset.") train_dataset = self.train_dataset data_collator = self.data_collator if is_datasets_available() and isinstance(train_dataset, datasets.Dataset): train_dataset = self._remove_unused_columns(train_dataset, description="training") else: data_collator = self._get_collator_with_removed_columns(data_collator, description="training") if isinstance(train_dataset, torch.utils.data.IterableDataset): if self.args.world_size > 1: train_dataset = IterableDatasetShard( train_dataset, batch_size=self._train_batch_size, drop_last=self.args.dataloader_drop_last, num_processes=self.args.world_size, process_index=self.args.process_index, ) return DataLoader( train_dataset, batch_size=self._train_batch_size, collate_fn=data_collator, num_workers=self.args.dataloader_num_workers, pin_memory=self.args.dataloader_pin_memory, ) ### 吴超逸加 ### if self.args.data_sampler != None: #print(self.args.world_size,self.args.process_index,self.args.batch_size_2D,self.args.batch_size_3D) train_sampler = self.args.data_sampler( dataset=self.train_dataset, num_replicas=self.args.world_size, rank=self.args.process_index, batch_size_2D = self.args.batch_size_2D, batch_size_3D = self.args.batch_size_3D, ) return DataLoader( train_dataset, batch_sampler=train_sampler, collate_fn=data_collator, num_workers=self.args.dataloader_num_workers, pin_memory=self.args.dataloader_pin_memory, worker_init_fn=seed_worker, ) else: ### 吴超逸加 ### train_sampler = self._get_train_sampler() return DataLoader( train_dataset, batch_size=self._train_batch_size, sampler=train_sampler, collate_fn=data_collator, drop_last=self.args.dataloader_drop_last, num_workers=self.args.dataloader_num_workers, pin_memory=self.args.dataloader_pin_memory, worker_init_fn=seed_worker, ) def _get_eval_sampler(self, eval_dataset: Dataset) -> Optional[torch.utils.data.Sampler]: # Deprecated code if self.args.use_legacy_prediction_loop: if is_torch_tpu_available(): return SequentialDistributedSampler( eval_dataset, num_replicas=xm.xrt_world_size(), rank=xm.get_ordinal() ) elif is_sagemaker_mp_enabled(): return SequentialDistributedSampler( eval_dataset, num_replicas=smp.dp_size(), rank=smp.dp_rank(), batch_size=self.args.per_device_eval_batch_size, ) elif self.args.local_rank != -1: return SequentialDistributedSampler(eval_dataset) else: return SequentialSampler(eval_dataset) if self.args.world_size <= 1: return SequentialSampler(eval_dataset) else: return ShardSampler( eval_dataset, batch_size=self.args.per_device_eval_batch_size, num_processes=self.args.world_size, process_index=self.args.process_index, ) def get_eval_dataloader(self, eval_dataset: Optional[Dataset] = None) -> DataLoader: """ Returns the evaluation [`~torch.utils.data.DataLoader`]. Subclass and override this method if you want to inject some custom behavior. Args: eval_dataset (`torch.utils.data.Dataset`, *optional*): If provided, will override `self.eval_dataset`. If it is a [`~datasets.Dataset`], columns not accepted by the `model.forward()` method are automatically removed. It must implement `__len__`. """ if eval_dataset is None and self.eval_dataset is None: raise ValueError("Trainer: evaluation requires an eval_dataset.") eval_dataset = eval_dataset if eval_dataset is not None else self.eval_dataset data_collator = self.data_collator if is_datasets_available() and isinstance(eval_dataset, datasets.Dataset): eval_dataset = self._remove_unused_columns(eval_dataset, description="evaluation") else: data_collator = self._get_collator_with_removed_columns(data_collator, description="evaluation") if isinstance(eval_dataset, torch.utils.data.IterableDataset): if self.args.world_size > 1: eval_dataset = IterableDatasetShard( eval_dataset, batch_size=self.args.per_device_eval_batch_size, drop_last=self.args.dataloader_drop_last, num_processes=self.args.world_size, process_index=self.args.process_index, ) return DataLoader( eval_dataset, batch_size=self.args.eval_batch_size, collate_fn=data_collator, num_workers=self.args.dataloader_num_workers, pin_memory=self.args.dataloader_pin_memory, ) eval_sampler = self._get_eval_sampler(eval_dataset) return DataLoader( eval_dataset, sampler=eval_sampler, batch_size=self.args.eval_batch_size, collate_fn=data_collator, drop_last=self.args.dataloader_drop_last, num_workers=self.args.dataloader_num_workers, pin_memory=self.args.dataloader_pin_memory, ) def get_test_dataloader(self, test_dataset: Dataset) -> DataLoader: """ Returns the test [`~torch.utils.data.DataLoader`]. Subclass and override this method if you want to inject some custom behavior. Args: test_dataset (`torch.utils.data.Dataset`, *optional*): The test dataset to use. If it is a [`~datasets.Dataset`], columns not accepted by the `model.forward()` method are automatically removed. It must implement `__len__`. """ data_collator = self.data_collator if is_datasets_available() and isinstance(test_dataset, datasets.Dataset): test_dataset = self._remove_unused_columns(test_dataset, description="test") else: data_collator = self._get_collator_with_removed_columns(data_collator, description="test") if isinstance(test_dataset, torch.utils.data.IterableDataset): if self.args.world_size > 1: test_dataset = IterableDatasetShard( test_dataset, batch_size=self.args.eval_batch_size, drop_last=self.args.dataloader_drop_last, num_processes=self.args.world_size, process_index=self.args.process_index, ) return DataLoader( test_dataset, batch_size=self.args.eval_batch_size, collate_fn=data_collator, num_workers=self.args.dataloader_num_workers, pin_memory=self.args.dataloader_pin_memory, ) test_sampler = self._get_eval_sampler(test_dataset) # We use the same batch_size as for eval. return DataLoader( test_dataset, sampler=test_sampler, batch_size=self.args.eval_batch_size, collate_fn=data_collator, drop_last=self.args.dataloader_drop_last, num_workers=self.args.dataloader_num_workers, pin_memory=self.args.dataloader_pin_memory, ) def create_optimizer_and_scheduler(self, num_training_steps: int): """ Setup the optimizer and the learning rate scheduler. We provide a reasonable default that works well. If you want to use something else, you can pass a tuple in the Trainer's init through `optimizers`, or subclass and override this method (or `create_optimizer` and/or `create_scheduler`) in a subclass. """ self.create_optimizer() if IS_SAGEMAKER_MP_POST_1_10 and smp.state.cfg.fp16: # If smp >= 1.10 and fp16 is enabled, we unwrap the optimizer optimizer = self.optimizer.optimizer else: optimizer = self.optimizer self.create_scheduler(num_training_steps=num_training_steps, optimizer=optimizer) def create_optimizer(self): """ Setup the optimizer. We provide a reasonable default that works well. If you want to use something else, you can pass a tuple in the Trainer's init through `optimizers`, or subclass and override this method in a subclass. """ opt_model = self.model_wrapped if is_sagemaker_mp_enabled() else self.model if self.optimizer is None: decay_parameters = get_parameter_names(opt_model, ALL_LAYERNORM_LAYERS) decay_parameters = [name for name in decay_parameters if "bias" not in name] optimizer_grouped_parameters = [ { "params": [ p for n, p in opt_model.named_parameters() if (n in decay_parameters and p.requires_grad) ], "weight_decay": self.args.weight_decay, }, { "params": [ p for n, p in opt_model.named_parameters() if (n not in decay_parameters and p.requires_grad) ], "weight_decay": 0.0, }, ] optimizer_cls, optimizer_kwargs = Trainer.get_optimizer_cls_and_kwargs(self.args) if self.sharded_ddp == ShardedDDPOption.SIMPLE: self.optimizer = OSS( params=optimizer_grouped_parameters, optim=optimizer_cls, **optimizer_kwargs, ) else: self.optimizer = optimizer_cls(optimizer_grouped_parameters, **optimizer_kwargs) if optimizer_cls.__name__ == "Adam8bit": import bitsandbytes manager = bitsandbytes.optim.GlobalOptimManager.get_instance() skipped = 0 for module in opt_model.modules(): if isinstance(module, nn.Embedding): skipped += sum({p.data_ptr(): p.numel() for p in module.parameters()}.values()) print(f"skipped {module}: {skipped/2**20}M params") manager.register_module_override(module, "weight", {"optim_bits": 32}) logger.debug(f"bitsandbytes: will optimize {module} in fp32") print(f"skipped: {skipped/2**20}M params") if is_sagemaker_mp_enabled(): self.optimizer = smp.DistributedOptimizer(self.optimizer) return self.optimizer @staticmethod def get_optimizer_cls_and_kwargs(args: TrainingArguments) -> Tuple[Any, Any]: """ Returns the optimizer class and optimizer parameters based on the training arguments. Args: args (`transformers.training_args.TrainingArguments`): The training arguments for the training session. """ # parse args.optim_args optim_args = {} if args.optim_args: for mapping in args.optim_args.replace(" ", "").split(","): key, value = mapping.split("=") optim_args[key] = value optimizer_kwargs = {"lr": args.learning_rate} adam_kwargs = { "betas": (args.adam_beta1, args.adam_beta2), "eps": args.adam_epsilon, } if args.optim == OptimizerNames.ADAFACTOR: optimizer_cls = Adafactor optimizer_kwargs.update({"scale_parameter": False, "relative_step": False}) elif args.optim == OptimizerNames.ADAMW_HF: from .optimization import AdamW optimizer_cls = AdamW optimizer_kwargs.update(adam_kwargs) elif args.optim in [OptimizerNames.ADAMW_TORCH, OptimizerNames.ADAMW_TORCH_FUSED]: from torch.optim import AdamW optimizer_cls = AdamW optimizer_kwargs.update(adam_kwargs) if args.optim == OptimizerNames.ADAMW_TORCH_FUSED: optimizer_kwargs.update({"fused": True}) elif args.optim == OptimizerNames.ADAMW_TORCH_XLA: try: from torch_xla.amp.syncfree import AdamW optimizer_cls = AdamW optimizer_kwargs.update(adam_kwargs) except ImportError: raise ValueError("Trainer failed to import syncfree AdamW from torch_xla.") elif args.optim == OptimizerNames.ADAMW_APEX_FUSED: try: from apex.optimizers import FusedAdam optimizer_cls = FusedAdam optimizer_kwargs.update(adam_kwargs) except ImportError: raise ValueError("Trainer tried to instantiate apex FusedAdam but apex is not installed!") elif args.optim == OptimizerNames.ADAMW_BNB: try: from bitsandbytes.optim import Adam8bit optimizer_cls = Adam8bit optimizer_kwargs.update(adam_kwargs) except ImportError: raise ValueError("Trainer tried to instantiate bnb Adam8bit but bnb is not installed!") elif args.optim == OptimizerNames.ADAMW_ANYPRECISION: try: from torchdistx.optimizers import AnyPrecisionAdamW optimizer_cls = AnyPrecisionAdamW optimizer_kwargs.update(adam_kwargs) # TODO Change dtypes back to M=FP32, Var = BF16, Kahan = False once they can be cast together in torchdistx. optimizer_kwargs.update( { "use_kahan_summation": strtobool(optim_args.get("use_kahan_summation", "False")), "momentum_dtype": getattr(torch, optim_args.get("momentum_dtype", "float32")), "variance_dtype": getattr(torch, optim_args.get("variance_dtype", "float32")), "compensation_buffer_dtype": getattr( torch, optim_args.get("compensation_buffer_dtype", "bfloat16") ), } ) except ImportError: raise ValueError("Please install https://github.com/pytorch/torchdistx") elif args.optim == OptimizerNames.SGD: optimizer_cls = torch.optim.SGD elif args.optim == OptimizerNames.ADAGRAD: optimizer_cls = torch.optim.Adagrad else: raise ValueError(f"Trainer cannot instantiate unsupported optimizer: {args.optim}") return optimizer_cls, optimizer_kwargs def create_scheduler(self, num_training_steps: int, optimizer: torch.optim.Optimizer = None): """ Setup the scheduler. The optimizer of the trainer must have been set up either before this method is called or passed as an argument. Args: num_training_steps (int): The number of training steps to do. """ if self.lr_scheduler is None: self.lr_scheduler = get_scheduler( self.args.lr_scheduler_type, optimizer=self.optimizer if optimizer is None else optimizer, num_warmup_steps=self.args.get_warmup_steps(num_training_steps), num_training_steps=num_training_steps, ) return self.lr_scheduler def num_examples(self, dataloader: DataLoader) -> int: """ Helper to get number of samples in a [`~torch.utils.data.DataLoader`] by accessing its dataset. When dataloader.dataset does not exist or has no length, estimates as best it can """ try: dataset = dataloader.dataset # Special case for IterableDatasetShard, we need to dig deeper if isinstance(dataset, IterableDatasetShard): return len(dataloader.dataset.dataset) return len(dataloader.dataset) except (NameError, AttributeError, TypeError): # no dataset or length, estimate by length of dataloader return len(dataloader) * self.args.per_device_train_batch_size def _hp_search_setup(self, trial: Union["optuna.Trial", Dict[str, Any]]): """HP search setup code""" self._trial = trial if self.hp_search_backend is None or trial is None: return if self.hp_search_backend == HPSearchBackend.OPTUNA: params = self.hp_space(trial) elif self.hp_search_backend == HPSearchBackend.RAY: params = trial params.pop("wandb", None) elif self.hp_search_backend == HPSearchBackend.SIGOPT: params = {k: int(v) if isinstance(v, str) else v for k, v in trial.assignments.items()} elif self.hp_search_backend == HPSearchBackend.WANDB: params = trial for key, value in params.items(): if not hasattr(self.args, key): logger.warning( f"Trying to set {key} in the hyperparameter search but there is no corresponding field in" " `TrainingArguments`." ) continue old_attr = getattr(self.args, key, None) # Casting value to the proper type if old_attr is not None: value = type(old_attr)(value) setattr(self.args, key, value) if self.hp_search_backend == HPSearchBackend.OPTUNA: logger.info(f"Trial: {trial.params}") if self.hp_search_backend == HPSearchBackend.SIGOPT: logger.info(f"SigOpt Assignments: {trial.assignments}") if self.hp_search_backend == HPSearchBackend.WANDB: logger.info(f"W&B Sweep parameters: {trial}") if self.args.deepspeed: # Rebuild the deepspeed config to reflect the updated training parameters from transformers.deepspeed import HfTrainerDeepSpeedConfig self.args.hf_deepspeed_config = HfTrainerDeepSpeedConfig(self.args.deepspeed) self.args.hf_deepspeed_config.trainer_config_process(self.args) def _report_to_hp_search(self, trial: Union["optuna.Trial", Dict[str, Any]], step: int, metrics: Dict[str, float]): if self.hp_search_backend is None or trial is None: return self.objective = self.compute_objective(metrics.copy()) if self.hp_search_backend == HPSearchBackend.OPTUNA: import optuna trial.report(self.objective, step) if trial.should_prune(): self.callback_handler.on_train_end(self.args, self.state, self.control) raise optuna.TrialPruned() elif self.hp_search_backend == HPSearchBackend.RAY: from ray import tune if self.control.should_save: self._tune_save_checkpoint() tune.report(objective=self.objective, **metrics) def _tune_save_checkpoint(self): from ray import tune if not self.use_tune_checkpoints: return with tune.checkpoint_dir(step=self.state.global_step) as checkpoint_dir: output_dir = os.path.join(checkpoint_dir, f"{PREFIX_CHECKPOINT_DIR}-{self.state.global_step}") self.save_model(output_dir, _internal_call=True) if self.args.should_save: self.state.save_to_json(os.path.join(output_dir, TRAINER_STATE_NAME)) torch.save(self.optimizer.state_dict(), os.path.join(output_dir, OPTIMIZER_NAME)) torch.save(self.lr_scheduler.state_dict(), os.path.join(output_dir, SCHEDULER_NAME)) def call_model_init(self, trial=None): model_init_argcount = number_of_arguments(self.model_init) if model_init_argcount == 0: model = self.model_init() elif model_init_argcount == 1: model = self.model_init(trial) else: raise RuntimeError("model_init should have 0 or 1 argument.") if model is None: raise RuntimeError("model_init should not return None.") return model def torch_jit_model_eval(self, model, dataloader, training=False): if not training: if dataloader is None: logger.warning("failed to use PyTorch jit mode due to current dataloader is none.") return model example_batch = next(iter(dataloader)) example_batch = self._prepare_inputs(example_batch) try: jit_model = model.eval() with ContextManagers([self.autocast_smart_context_manager(cache_enabled=False), torch.no_grad()]): if version.parse(version.parse(torch.__version__).base_version) >= version.parse("1.14.0"): if isinstance(example_batch, dict): jit_model = torch.jit.trace(jit_model, example_kwarg_inputs=example_batch, strict=False) else: jit_model = torch.jit.trace( jit_model, example_kwarg_inputs={key: example_batch[key] for key in example_batch}, strict=False, ) else: jit_inputs = [] for key in example_batch: example_tensor = torch.ones_like(example_batch[key]) jit_inputs.append(example_tensor) jit_inputs = tuple(jit_inputs) jit_model = torch.jit.trace(jit_model, jit_inputs, strict=False) jit_model = torch.jit.freeze(jit_model) with torch.no_grad(): jit_model(**example_batch) jit_model(**example_batch) model = jit_model self.use_cpu_amp = False self.use_cuda_amp = False except (RuntimeError, TypeError, ValueError, NameError, IndexError) as e: logger.warning(f"failed to use PyTorch jit mode due to: {e}.") return model def ipex_optimize_model(self, model, training=False, dtype=torch.float32): if not is_ipex_available(): raise ImportError( "Using IPEX but IPEX is not installed or IPEX's version does not match current PyTorch, please refer" " to https://github.com/intel/intel-extension-for-pytorch." ) import intel_extension_for_pytorch as ipex if not training: model.eval() dtype = torch.bfloat16 if not self.is_in_train and self.args.bf16_full_eval else dtype # conv_bn_folding is disabled as it fails in symbolic tracing, resulting in ipex warnings model = ipex.optimize(model, dtype=dtype, level="O1", conv_bn_folding=False, inplace=not self.is_in_train) else: if not model.training: model.train() model, self.optimizer = ipex.optimize( model, dtype=dtype, optimizer=self.optimizer, inplace=True, level="O1" ) return model def _wrap_model(self, model, training=True, dataloader=None): if self.args.use_ipex: dtype = torch.bfloat16 if self.use_cpu_amp else torch.float32 model = self.ipex_optimize_model(model, training, dtype=dtype) if is_sagemaker_mp_enabled(): # Wrapping the base model twice in a DistributedModel will raise an error. if isinstance(self.model_wrapped, smp.model.DistributedModel): return self.model_wrapped return smp.DistributedModel(model, backward_passes_per_step=self.args.gradient_accumulation_steps) # already initialized its own DDP and AMP if self.deepspeed: return self.deepspeed # train/eval could be run multiple-times - if already wrapped, don't re-wrap it again if unwrap_model(model) is not model: return model # Mixed precision training with apex (torch < 1.6) if self.use_apex and training: model, self.optimizer = amp.initialize(model, self.optimizer, opt_level=self.args.fp16_opt_level) # Multi-gpu training (should be after apex fp16 initialization) / 8bit models does not support DDP if self.args.n_gpu > 1 and not getattr(model, "is_loaded_in_8bit", False): model = nn.DataParallel(model) if self.args.jit_mode_eval: start_time = time.time() model = self.torch_jit_model_eval(model, dataloader, training) self.jit_compilation_time = round(time.time() - start_time, 4) # Note: in torch.distributed mode, there's no point in wrapping the model # inside a DistributedDataParallel as we'll be under `no_grad` anyways. if not training: return model # Distributed training (should be after apex fp16 initialization) if self.sharded_ddp is not None: # Sharded DDP! if self.sharded_ddp == ShardedDDPOption.SIMPLE: model = ShardedDDP(model, self.optimizer) else: mixed_precision = self.args.fp16 or self.args.bf16 cpu_offload = ShardedDDPOption.OFFLOAD in self.args.sharded_ddp zero_3 = self.sharded_ddp == ShardedDDPOption.ZERO_DP_3 # XXX: Breaking the self.model convention but I see no way around it for now. if ShardedDDPOption.AUTO_WRAP in self.args.sharded_ddp: model = auto_wrap(model) self.model = model = FullyShardedDDP( model, mixed_precision=mixed_precision, reshard_after_forward=zero_3, cpu_offload=cpu_offload, ).to(self.args.device) # Distributed training using PyTorch FSDP elif self.fsdp is not None: if not self.args.fsdp_config["xla"]: # PyTorch FSDP! from torch.distributed.fsdp.fully_sharded_data_parallel import CPUOffload, MixedPrecision from torch.distributed.fsdp.fully_sharded_data_parallel import FullyShardedDataParallel as FSDP from torch.distributed.fsdp.wrap import size_based_auto_wrap_policy, transformer_auto_wrap_policy if FSDPOption.OFFLOAD in self.args.fsdp: cpu_offload = CPUOffload(offload_params=True) else: cpu_offload = CPUOffload(offload_params=False) auto_wrap_policy = None if FSDPOption.AUTO_WRAP in self.args.fsdp: if self.args.fsdp_config["fsdp_min_num_params"] > 0: auto_wrap_policy = functools.partial( size_based_auto_wrap_policy, min_num_params=self.args.fsdp_config["fsdp_min_num_params"] ) elif self.args.fsdp_config.get("fsdp_transformer_layer_cls_to_wrap", None) is not None: transformer_cls_to_wrap = set() for layer_class in self.args.fsdp_config["fsdp_transformer_layer_cls_to_wrap"]: transformer_cls = get_module_class_from_name(model, layer_class) if transformer_cls is None: raise Exception("Could not find the transformer layer class to wrap in the model.") else: transformer_cls_to_wrap.add(transformer_cls) auto_wrap_policy = functools.partial( transformer_auto_wrap_policy, # Transformer layer class to wrap transformer_layer_cls=transformer_cls_to_wrap, ) mixed_precision_policy = None dtype = None if self.args.fp16: dtype = torch.float16 elif self.args.bf16: dtype = torch.bfloat16 if dtype is not None: mixed_precision_policy = MixedPrecision(param_dtype=dtype, reduce_dtype=dtype, buffer_dtype=dtype) if type(model) != FSDP: # XXX: Breaking the self.model convention but I see no way around it for now. signature = inspect.signature(FSDP.__init__).parameters.keys() kwargs = {} for arg in ["limit_all_gathers", "forward_prefetch", "backward_prefetch"]: if arg in signature: kwargs[arg] = getattr(self, arg) self.model = model = FSDP( model, sharding_strategy=self.fsdp, cpu_offload=cpu_offload, auto_wrap_policy=auto_wrap_policy, mixed_precision=mixed_precision_policy, device_id=self.args.device, **kwargs, ) else: try: from torch_xla.distributed.fsdp import XlaFullyShardedDataParallel as FSDP from torch_xla.distributed.fsdp import checkpoint_module from torch_xla.distributed.fsdp.wrap import ( size_based_auto_wrap_policy, transformer_auto_wrap_policy, ) except ImportError: raise ImportError("Missing XLA FSDP related module; please make sure to use torch-xla >= 2.0.") auto_wrap_policy = None auto_wrapper_callable = None if self.args.fsdp_config["fsdp_min_num_params"] > 0: auto_wrap_policy = functools.partial( size_based_auto_wrap_policy, min_num_params=self.args.fsdp_config["fsdp_min_num_params"] ) elif self.args.fsdp_config.get("fsdp_transformer_layer_cls_to_wrap", None) is not None: transformer_cls_to_wrap = set() for layer_class in self.args.fsdp_config["fsdp_transformer_layer_cls_to_wrap"]: transformer_cls = get_module_class_from_name(model, layer_class) if transformer_cls is None: raise Exception("Could not find the transformer layer class to wrap in the model.") else: transformer_cls_to_wrap.add(transformer_cls) auto_wrap_policy = functools.partial( transformer_auto_wrap_policy, # Transformer layer class to wrap transformer_layer_cls=transformer_cls_to_wrap, ) fsdp_kwargs = self.args.xla_fsdp_config if self.args.fsdp_config["xla_fsdp_grad_ckpt"]: # Apply gradient checkpointing to auto-wrapped sub-modules if specified def auto_wrapper_callable(m, *args, **kwargs): return FSDP(checkpoint_module(m), *args, **kwargs) # Wrap the base model with an outer FSDP wrapper self.model = model = FSDP( model, auto_wrap_policy=auto_wrap_policy, auto_wrapper_callable=auto_wrapper_callable, **fsdp_kwargs, ) # Patch `xm.optimizer_step` should not reduce gradients in this case, # as FSDP does not need gradient reduction over sharded parameters. def patched_optimizer_step(optimizer, barrier=False, optimizer_args={}): loss = optimizer.step(**optimizer_args) if barrier: xm.mark_step() return loss xm.optimizer_step = patched_optimizer_step elif is_sagemaker_dp_enabled(): model = nn.parallel.DistributedDataParallel( model, device_ids=[int(os.getenv("SMDATAPARALLEL_LOCAL_RANK"))] ) elif self.args.local_rank != -1: kwargs = {} if self.args.ddp_find_unused_parameters is not None: kwargs["find_unused_parameters"] = self.args.ddp_find_unused_parameters elif isinstance(model, PreTrainedModel): # find_unused_parameters breaks checkpointing as per # https://github.com/huggingface/transformers/pull/4659#issuecomment-643356021 kwargs["find_unused_parameters"] = not model.is_gradient_checkpointing else: kwargs["find_unused_parameters"] = True if self.args.ddp_bucket_cap_mb is not None: kwargs["bucket_cap_mb"] = self.args.ddp_bucket_cap_mb if is_torch_neuroncore_available(): return model model = nn.parallel.DistributedDataParallel( model, device_ids=[self.args.local_rank] if self.args._n_gpu != 0 else None, output_device=self.args.local_rank if self.args._n_gpu != 0 else None, **kwargs, ) # torch.compile() needs to be called after wrapping the model with FSDP or DDP # to ensure that it accounts for the graph breaks required by those wrappers if self.args.torch_compile: model = torch.compile(model, backend=self.args.torch_compile_backend, mode=self.args.torch_compile_mode) return model def train( self, resume_from_checkpoint: Optional[Union[str, bool]] = None, trial: Union["optuna.Trial", Dict[str, Any]] = None, ignore_keys_for_eval: Optional[List[str]] = None, **kwargs, ): """ Main training entry point. Args: resume_from_checkpoint (`str` or `bool`, *optional*): If a `str`, local path to a saved checkpoint as saved by a previous instance of [`Trainer`]. If a `bool` and equals `True`, load the last checkpoint in *args.output_dir* as saved by a previous instance of [`Trainer`]. If present, training will resume from the model/optimizer/scheduler states loaded here. trial (`optuna.Trial` or `Dict[str, Any]`, *optional*): The trial run or the hyperparameter dictionary for hyperparameter search. ignore_keys_for_eval (`List[str]`, *optional*) A list of keys in the output of your model (if it is a dictionary) that should be ignored when gathering predictions for evaluation during the training. kwargs: Additional keyword arguments used to hide deprecated arguments """ if resume_from_checkpoint is False: resume_from_checkpoint = None # memory metrics - must set up as early as possible self._memory_tracker.start() args = self.args self.is_in_train = True # do_train is not a reliable argument, as it might not be set and .train() still called, so # the following is a workaround: if (args.fp16_full_eval or args.bf16_full_eval) and not args.do_train: self._move_model_to_device(self.model, args.device) if "model_path" in kwargs: resume_from_checkpoint = kwargs.pop("model_path") warnings.warn( "`model_path` is deprecated and will be removed in a future version. Use `resume_from_checkpoint` " "instead.", FutureWarning, ) if len(kwargs) > 0: raise TypeError(f"train() received got unexpected keyword arguments: {', '.join(list(kwargs.keys()))}.") # This might change the seed so needs to run first. self._hp_search_setup(trial) self._train_batch_size = self.args.train_batch_size # Model re-init model_reloaded = False if self.model_init is not None: # Seed must be set before instantiating the model when using model_init. enable_full_determinism(self.args.seed) if self.args.full_determinism else set_seed(self.args.seed) self.model = self.call_model_init(trial) model_reloaded = True # Reinitializes optimizer and scheduler self.optimizer, self.lr_scheduler = None, None # Load potential model checkpoint if isinstance(resume_from_checkpoint, bool) and resume_from_checkpoint: resume_from_checkpoint = get_last_checkpoint(args.output_dir) if resume_from_checkpoint is None: raise ValueError(f"No valid checkpoint found in output directory ({args.output_dir})") if resume_from_checkpoint is not None and not is_sagemaker_mp_enabled() and args.deepspeed is None: self._load_from_checkpoint(resume_from_checkpoint) # If model was re-initialized, put it on the right device and update self.model_wrapped if model_reloaded: if self.place_model_on_device: self._move_model_to_device(self.model, args.device) self.model_wrapped = self.model inner_training_loop = find_executable_batch_size( self._inner_training_loop, self._train_batch_size, args.auto_find_batch_size ) return inner_training_loop( args=args, resume_from_checkpoint=resume_from_checkpoint, trial=trial, ignore_keys_for_eval=ignore_keys_for_eval, ) def _inner_training_loop( self, batch_size=None, args=None, resume_from_checkpoint=None, trial=None, ignore_keys_for_eval=None ): self._train_batch_size = batch_size # Data loader and number of training steps train_dataloader = self.get_train_dataloader() # Setting up training control variables: # number of training epochs: num_train_epochs # number of training steps per epoch: num_update_steps_per_epoch # total number of training steps to execute: max_steps total_train_batch_size = args.train_batch_size * args.gradient_accumulation_steps * args.world_size len_dataloader = None if has_length(train_dataloader): len_dataloader = len(train_dataloader) num_update_steps_per_epoch = len_dataloader // args.gradient_accumulation_steps num_update_steps_per_epoch = max(num_update_steps_per_epoch, 1) num_examples = self.num_examples(train_dataloader) if args.max_steps > 0: max_steps = args.max_steps num_train_epochs = args.max_steps // num_update_steps_per_epoch + int( args.max_steps % num_update_steps_per_epoch > 0 ) # May be slightly incorrect if the last batch in the training dataloader has a smaller size but it's # the best we can do. num_train_samples = args.max_steps * total_train_batch_size else: max_steps = math.ceil(args.num_train_epochs * num_update_steps_per_epoch) num_train_epochs = math.ceil(args.num_train_epochs) num_train_samples = self.num_examples(train_dataloader) * args.num_train_epochs elif args.max_steps > 0: # Rely on max_steps when dataloader does not have a working size max_steps = args.max_steps # Setting a very large number of epochs so we go as many times as necessary over the iterator. num_train_epochs = sys.maxsize num_update_steps_per_epoch = max_steps num_examples = total_train_batch_size * args.max_steps num_train_samples = args.max_steps * total_train_batch_size else: raise ValueError( "args.max_steps must be set to a positive value if dataloader does not have a length, was" f" {args.max_steps}" ) if DebugOption.UNDERFLOW_OVERFLOW in self.args.debug: if self.args.n_gpu > 1: # nn.DataParallel(model) replicates the model, creating new variables and module # references registered here no longer work on other gpus, breaking the module raise ValueError( "Currently --debug underflow_overflow is not supported under DP. Please use DDP" " (torch.distributed.launch)." ) else: debug_overflow = DebugUnderflowOverflow(self.model) # noqa delay_optimizer_creation = ( self.sharded_ddp is not None and self.sharded_ddp != ShardedDDPOption.SIMPLE or is_sagemaker_mp_enabled() or self.fsdp is not None ) if args.deepspeed: deepspeed_engine, optimizer, lr_scheduler = deepspeed_init( self, num_training_steps=max_steps, resume_from_checkpoint=resume_from_checkpoint ) self.model = deepspeed_engine.module self.model_wrapped = deepspeed_engine self.deepspeed = deepspeed_engine self.optimizer = optimizer self.lr_scheduler = lr_scheduler elif not delay_optimizer_creation: self.create_optimizer_and_scheduler(num_training_steps=max_steps) self.state = TrainerState() self.state.is_hyper_param_search = trial is not None # Activate gradient checkpointing if needed if args.gradient_checkpointing: self.model.gradient_checkpointing_enable() model = self._wrap_model(self.model_wrapped) if is_sagemaker_mp_enabled() and resume_from_checkpoint is not None: self._load_from_checkpoint(resume_from_checkpoint, model) # for the rest of this function `model` is the outside model, whether it was wrapped or not if model is not self.model: self.model_wrapped = model if delay_optimizer_creation: self.create_optimizer_and_scheduler(num_training_steps=max_steps) # Check if saved optimizer or scheduler states exist self._load_optimizer_and_scheduler(resume_from_checkpoint) # important: at this point: # self.model is the Transformers Model # self.model_wrapped is DDP(Transformers Model), Deepspeed(Transformers Model), etc. # Train! logger.info("***** Running training *****") logger.info(f" Num examples = {num_examples:,}") logger.info(f" Num Epochs = {num_train_epochs:,}") logger.info(f" Instantaneous batch size per device = {args.per_device_train_batch_size:,}") logger.info(f" Total train batch size (w. parallel, distributed & accumulation) = {total_train_batch_size:,}") logger.info(f" Gradient Accumulation steps = {args.gradient_accumulation_steps}") logger.info(f" Total optimization steps = {max_steps:,}") logger.info(f" Number of trainable parameters = {get_model_param_count(model, trainable_only=True):,}") self.state.epoch = 0 start_time = time.time() epochs_trained = 0 steps_trained_in_current_epoch = 0 steps_trained_progress_bar = None # Check if continuing training from a checkpoint if resume_from_checkpoint is not None and os.path.isfile( os.path.join(resume_from_checkpoint, TRAINER_STATE_NAME) ): self.state = TrainerState.load_from_json(os.path.join(resume_from_checkpoint, TRAINER_STATE_NAME)) epochs_trained = self.state.global_step // num_update_steps_per_epoch if not args.ignore_data_skip: steps_trained_in_current_epoch = self.state.global_step % (num_update_steps_per_epoch) steps_trained_in_current_epoch *= args.gradient_accumulation_steps else: steps_trained_in_current_epoch = 0 logger.info(" Continuing training from checkpoint, will skip to saved global_step") logger.info(f" Continuing training from epoch {epochs_trained}") logger.info(f" Continuing training from global step {self.state.global_step}") if not args.ignore_data_skip: if skip_first_batches is None: logger.info( f" Will skip the first {epochs_trained} epochs then the first" f" {steps_trained_in_current_epoch} batches in the first epoch. If this takes a lot of time," " you can install the latest version of Accelerate with `pip install -U accelerate`.You can" " also add the `--ignore_data_skip` flag to your launch command, but you will resume the" " training on data already seen by your model." ) else: logger.info( f" Will skip the first {epochs_trained} epochs then the first" f" {steps_trained_in_current_epoch} batches in the first epoch." ) if self.is_local_process_zero() and not args.disable_tqdm and skip_first_batches is None: steps_trained_progress_bar = tqdm(total=steps_trained_in_current_epoch) steps_trained_progress_bar.set_description("Skipping the first batches") # Update the references self.callback_handler.model = self.model self.callback_handler.optimizer = self.optimizer self.callback_handler.lr_scheduler = self.lr_scheduler self.callback_handler.train_dataloader = train_dataloader if self.hp_name is not None and self._trial is not None: # use self._trial because the SigOpt/Optuna hpo only call `_hp_search_setup(trial)` instead of passing trial # parameter to Train when using DDP. self.state.trial_name = self.hp_name(self._trial) if trial is not None: assignments = trial.assignments if self.hp_search_backend == HPSearchBackend.SIGOPT else trial self.state.trial_params = hp_params(assignments) else: self.state.trial_params = None # This should be the same if the state has been saved but in case the training arguments changed, it's safer # to set this after the load. self.state.max_steps = max_steps self.state.num_train_epochs = num_train_epochs self.state.is_local_process_zero = self.is_local_process_zero() self.state.is_world_process_zero = self.is_world_process_zero() # tr_loss is a tensor to avoid synchronization of TPUs through .item() tr_loss = torch.tensor(0.0).to(args.device) # _total_loss_scalar is updated everytime .item() has to be called on tr_loss and stores the sum of all losses self._total_loss_scalar = 0.0 self._globalstep_last_logged = self.state.global_step model.zero_grad() self.control = self.callback_handler.on_train_begin(args, self.state, self.control) # Skip the first epochs_trained epochs to get the random state of the dataloader at the right point. if not args.ignore_data_skip: for epoch in range(epochs_trained): is_random_sampler = hasattr(train_dataloader, "sampler") and isinstance( train_dataloader.sampler, RandomSampler ) if is_torch_less_than_1_11 or not is_random_sampler: # We just need to begin an iteration to create the randomization of the sampler. # That was before PyTorch 1.11 however... for _ in train_dataloader: break else: # Otherwise we need to call the whooooole sampler cause there is some random operation added # AT THE VERY END! _ = list(train_dataloader.sampler) total_batched_samples = 0 for epoch in range(epochs_trained, num_train_epochs): ### 吴超逸加 ### if isinstance(train_dataloader, DataLoader) and (isinstance(train_dataloader.sampler, DistributedSampler) or self.args.data_sampler != None): train_dataloader.sampler.set_epoch(epoch) elif hasattr(train_dataloader, "dataset") and (isinstance(train_dataloader.sampler, DistributedSampler) or self.args.data_sampler != None): train_dataloader.dataset.set_epoch(epoch) if is_torch_tpu_available(): parallel_loader = pl.ParallelLoader(train_dataloader, [args.device]).per_device_loader(args.device) epoch_iterator = parallel_loader else: epoch_iterator = train_dataloader # Reset the past mems state at the beginning of each epoch if necessary. if args.past_index >= 0: self._past = None steps_in_epoch = ( len(epoch_iterator) if len_dataloader is not None else args.max_steps * args.gradient_accumulation_steps ) self.control = self.callback_handler.on_epoch_begin(args, self.state, self.control) if epoch == epochs_trained and resume_from_checkpoint is not None and steps_trained_in_current_epoch == 0: self._load_rng_state(resume_from_checkpoint) rng_to_sync = False steps_skipped = 0 if skip_first_batches is not None and steps_trained_in_current_epoch > 0: epoch_iterator = skip_first_batches(epoch_iterator, steps_trained_in_current_epoch) steps_skipped = steps_trained_in_current_epoch steps_trained_in_current_epoch = 0 rng_to_sync = True step = -1 for step, inputs in enumerate(epoch_iterator): total_batched_samples += 1 if rng_to_sync: self._load_rng_state(resume_from_checkpoint) rng_to_sync = False # Skip past any already trained steps if resuming training if steps_trained_in_current_epoch > 0: steps_trained_in_current_epoch -= 1 if steps_trained_progress_bar is not None: steps_trained_progress_bar.update(1) if steps_trained_in_current_epoch == 0: self._load_rng_state(resume_from_checkpoint) continue elif steps_trained_progress_bar is not None: steps_trained_progress_bar.close() steps_trained_progress_bar = None if step % args.gradient_accumulation_steps == 0: self.control = self.callback_handler.on_step_begin(args, self.state, self.control) if ( (total_batched_samples % args.gradient_accumulation_steps != 0) and args.local_rank != -1 and args._no_sync_in_gradient_accumulation ): # Avoid unnecessary DDP synchronization since there will be no backward pass on this example. with model.no_sync(): tr_loss_step = self.training_step(model, inputs) else: tr_loss_step = self.training_step(model, inputs) if ( args.logging_nan_inf_filter and not is_torch_tpu_available() and (torch.isnan(tr_loss_step) or torch.isinf(tr_loss_step)) ): # if loss is nan or inf simply add the average of previous logged losses tr_loss += tr_loss / (1 + self.state.global_step - self._globalstep_last_logged) else: tr_loss += tr_loss_step self.current_flos += float(self.floating_point_ops(inputs)) # Optimizer step for deepspeed must be called on every step regardless of the value of gradient_accumulation_steps if self.deepspeed: self.deepspeed.step() if total_batched_samples % args.gradient_accumulation_steps == 0 or ( # last step in epoch but step is always smaller than gradient_accumulation_steps steps_in_epoch <= args.gradient_accumulation_steps and (step + 1) == steps_in_epoch ): # Gradient clipping if args.max_grad_norm is not None and args.max_grad_norm > 0 and not self.deepspeed: # deepspeed does its own clipping if self.do_grad_scaling: # Reduce gradients first for XLA if is_torch_tpu_available(): gradients = xm._fetch_gradients(self.optimizer) xm.all_reduce("sum", gradients, scale=1.0 / xm.xrt_world_size()) # AMP: gradients need unscaling self.scaler.unscale_(self.optimizer) if is_sagemaker_mp_enabled() and args.fp16: self.optimizer.clip_master_grads(args.max_grad_norm) elif hasattr(self.optimizer, "clip_grad_norm"): # Some optimizers (like the sharded optimizer) have a specific way to do gradient clipping self.optimizer.clip_grad_norm(args.max_grad_norm) elif hasattr(model, "clip_grad_norm_"): # Some models (like FullyShardedDDP) have a specific way to do gradient clipping model.clip_grad_norm_(args.max_grad_norm) else: # Revert to normal clipping otherwise, handling Apex or full precision nn.utils.clip_grad_norm_( amp.master_params(self.optimizer) if self.use_apex else model.parameters(), args.max_grad_norm, ) # Optimizer step optimizer_was_run = True if self.deepspeed: pass # called outside the loop elif is_torch_tpu_available(): if self.do_grad_scaling: self.scaler.step(self.optimizer) self.scaler.update() else: xm.optimizer_step(self.optimizer) elif self.do_grad_scaling: scale_before = self.scaler.get_scale() self.scaler.step(self.optimizer) self.scaler.update() scale_after = self.scaler.get_scale() optimizer_was_run = scale_before <= scale_after else: self.optimizer.step() if optimizer_was_run and not self.deepspeed: self.lr_scheduler.step() model.zero_grad() self.state.global_step += 1 self.state.epoch = epoch + (step + 1 + steps_skipped) / steps_in_epoch self.control = self.callback_handler.on_step_end(args, self.state, self.control) self._maybe_log_save_evaluate(tr_loss, model, trial, epoch, ignore_keys_for_eval) else: self.control = self.callback_handler.on_substep_end(args, self.state, self.control) if self.control.should_epoch_stop or self.control.should_training_stop: break if step < 0: logger.warning( "There seems to be not a single sample in your epoch_iterator, stopping training at step" f" {self.state.global_step}! This is expected if you're using an IterableDataset and set" f" num_steps ({max_steps}) higher than the number of available samples." ) self.control.should_training_stop = True self.control = self.callback_handler.on_epoch_end(args, self.state, self.control) self._maybe_log_save_evaluate(tr_loss, model, trial, epoch, ignore_keys_for_eval) if DebugOption.TPU_METRICS_DEBUG in self.args.debug: if is_torch_tpu_available(): # tpu-comment: Logging debug metrics for PyTorch/XLA (compile, execute times, ops, etc.) xm.master_print(met.metrics_report()) else: logger.warning( "You enabled PyTorch/XLA debug metrics but you don't have a TPU " "configured. Check your training configuration if this is unexpected." ) if self.control.should_training_stop: break if args.past_index and hasattr(self, "_past"): # Clean the state at the end of training delattr(self, "_past") logger.info("\n\nTraining completed. Do not forget to share your model on huggingface.co/models =)\n\n") if args.load_best_model_at_end and self.state.best_model_checkpoint is not None: # Wait for everyone to get here so we are sur the model has been saved by process 0. if is_torch_tpu_available(): xm.rendezvous("load_best_model_at_end") elif args.local_rank != -1: dist.barrier() elif is_sagemaker_mp_enabled(): smp.barrier() self._load_best_model() # add remaining tr_loss self._total_loss_scalar += tr_loss.item() train_loss = self._total_loss_scalar / self.state.global_step metrics = speed_metrics("train", start_time, num_samples=num_train_samples, num_steps=self.state.max_steps) self.store_flos() metrics["total_flos"] = self.state.total_flos metrics["train_loss"] = train_loss self.is_in_train = False self._memory_tracker.stop_and_update_metrics(metrics) self.log(metrics) run_dir = self._get_output_dir(trial) checkpoints_sorted = self._sorted_checkpoints(use_mtime=False, output_dir=run_dir) # Delete the last checkpoint when save_total_limit=1 if it's different from the best checkpoint and process allowed to save. if self.args.should_save and self.state.best_model_checkpoint is not None and self.args.save_total_limit == 1: for checkpoint in checkpoints_sorted: if checkpoint != self.state.best_model_checkpoint: logger.info(f"Deleting older checkpoint [{checkpoint}] due to args.save_total_limit") shutil.rmtree(checkpoint) self.control = self.callback_handler.on_train_end(args, self.state, self.control) return TrainOutput(self.state.global_step, train_loss, metrics) def _get_output_dir(self, trial): if self.hp_search_backend is not None and trial is not None: if self.hp_search_backend == HPSearchBackend.OPTUNA: run_id = trial.number elif self.hp_search_backend == HPSearchBackend.RAY: from ray import tune run_id = tune.get_trial_id() elif self.hp_search_backend == HPSearchBackend.SIGOPT: run_id = trial.id elif self.hp_search_backend == HPSearchBackend.WANDB: import wandb run_id = wandb.run.id run_name = self.hp_name(trial) if self.hp_name is not None else f"run-{run_id}" run_dir = os.path.join(self.args.output_dir, run_name) else: run_dir = self.args.output_dir return run_dir def _load_from_checkpoint(self, resume_from_checkpoint, model=None): if model is None: model = self.model config_file = os.path.join(resume_from_checkpoint, CONFIG_NAME) weights_file = os.path.join(resume_from_checkpoint, WEIGHTS_NAME) weights_index_file = os.path.join(resume_from_checkpoint, WEIGHTS_INDEX_NAME) safe_weights_file = os.path.join(resume_from_checkpoint, SAFE_WEIGHTS_NAME) safe_weights_index_file = os.path.join(resume_from_checkpoint, SAFE_WEIGHTS_INDEX_NAME) if not any( [os.path.isfile(f) for f in [weights_file, safe_weights_file, weights_index_file, safe_weights_index_file]] ): raise ValueError(f"Can't find a valid checkpoint at {resume_from_checkpoint}") logger.info(f"Loading model from {resume_from_checkpoint}.") if os.path.isfile(config_file): config = PretrainedConfig.from_json_file(config_file) checkpoint_version = config.transformers_version if checkpoint_version is not None and checkpoint_version != __version__: logger.warning( f"You are resuming training from a checkpoint trained with {checkpoint_version} of " f"Transformers but your current version is {__version__}. This is not recommended and could " "yield to errors or unwanted behaviors." ) if os.path.isfile(weights_file) or os.path.isfile(safe_weights_file): # If the model is on the GPU, it still works! if is_sagemaker_mp_enabled(): if os.path.isfile(os.path.join(resume_from_checkpoint, "user_content.pt")): # If the 'user_content.pt' file exists, load with the new smp api. # Checkpoint must have been saved with the new smp api. smp.resume_from_checkpoint( path=resume_from_checkpoint, tag=WEIGHTS_NAME, partial=False, load_optimizer=False ) else: # If the 'user_content.pt' file does NOT exist, load with the old smp api. # Checkpoint must have been saved with the old smp api. if hasattr(self.args, "fp16") and self.args.fp16 is True: logger.warning( "Enabling FP16 and loading from smp < 1.10 checkpoint together is not suppported." ) state_dict = torch.load(weights_file, map_location="cpu") # Required for smp to not auto-translate state_dict from hf to smp (is already smp). state_dict["_smp_is_partial"] = False load_result = model.load_state_dict(state_dict, strict=True) # release memory del state_dict else: # We load the model state dict on the CPU to avoid an OOM error. if self.args.save_safetensors and os.path.isfile(safe_weights_file): state_dict = safetensors.torch.load_file(safe_weights_file, device="cpu") else: state_dict = torch.load(weights_file, map_location="cpu") # workaround for FSDP bug https://github.com/pytorch/pytorch/issues/82963 # which takes *args instead of **kwargs load_result = model.load_state_dict(state_dict, False) # release memory del state_dict self._issue_warnings_after_load(load_result) else: # We load the sharded checkpoint load_result = load_sharded_checkpoint( model, resume_from_checkpoint, strict=is_sagemaker_mp_enabled(), prefer_safe=self.args.save_safetensors ) if not is_sagemaker_mp_enabled(): self._issue_warnings_after_load(load_result) def _load_best_model(self): logger.info(f"Loading best model from {self.state.best_model_checkpoint} (score: {self.state.best_metric}).") best_model_path = os.path.join(self.state.best_model_checkpoint, WEIGHTS_NAME) best_safe_model_path = os.path.join(self.state.best_model_checkpoint, SAFE_WEIGHTS_NAME) model = self.model_wrapped if is_sagemaker_mp_enabled() else self.model if os.path.exists(best_model_path) or os.path.exists(best_safe_model_path): if self.deepspeed: if self.model_wrapped is not None: # this removes the pre-hooks from the previous engine self.model_wrapped.destroy() self.model_wrapped = None # temp hack until Deepspeed fixes the problem with resume from an existing engine that did some stepping deepspeed_engine, optimizer, lr_scheduler = deepspeed_init( self, num_training_steps=self.args.max_steps, resume_from_checkpoint=self.state.best_model_checkpoint, ) self.model = deepspeed_engine.module self.model_wrapped = deepspeed_engine self.deepspeed = deepspeed_engine self.optimizer = optimizer self.lr_scheduler = lr_scheduler else: if is_sagemaker_mp_enabled(): if os.path.isfile(os.path.join(self.state.best_model_checkpoint, "user_content.pt")): # If the 'user_content.pt' file exists, load with the new smp api. # Checkpoint must have been saved with the new smp api. smp.resume_from_checkpoint( path=self.state.best_model_checkpoint, tag=WEIGHTS_NAME, partial=False, load_optimizer=False, ) else: # If the 'user_content.pt' file does NOT exist, load with the old smp api. # Checkpoint must have been saved with the old smp api. if self.args.save_safetensors and os.path.isfile(best_safe_model_path): state_dict = safetensors.torch.load_file(best_safe_model_path, device="cpu") else: state_dict = torch.load(best_model_path, map_location="cpu") state_dict["_smp_is_partial"] = False load_result = model.load_state_dict(state_dict, strict=True) else: # We load the model state dict on the CPU to avoid an OOM error. if self.args.save_safetensors and os.path.isfile(best_safe_model_path): state_dict = safetensors.torch.load_file(best_safe_model_path, device="cpu") else: state_dict = torch.load(best_model_path, map_location="cpu") # If the model is on the GPU, it still works! # workaround for FSDP bug https://github.com/pytorch/pytorch/issues/82963 # which takes *args instead of **kwargs load_result = model.load_state_dict(state_dict, False) if not is_sagemaker_mp_enabled(): self._issue_warnings_after_load(load_result) elif os.path.exists(os.path.join(self.state.best_model_checkpoint, WEIGHTS_INDEX_NAME)): load_result = load_sharded_checkpoint( model, self.state.best_model_checkpoint, strict=is_sagemaker_mp_enabled() ) if not is_sagemaker_mp_enabled(): self._issue_warnings_after_load(load_result) else: logger.warning( f"Could not locate the best model at {best_model_path}, if you are running a distributed training " "on multiple nodes, you should activate `--save_on_each_node`." ) def _issue_warnings_after_load(self, load_result): if len(load_result.missing_keys) != 0: if self.model._keys_to_ignore_on_save is not None and set(load_result.missing_keys) == set( self.model._keys_to_ignore_on_save ): self.model.tie_weights() else: logger.warning(f"There were missing keys in the checkpoint model loaded: {load_result.missing_keys}.") if len(load_result.unexpected_keys) != 0: logger.warning( f"There were unexpected keys in the checkpoint model loaded: {load_result.unexpected_keys}." ) def _maybe_log_save_evaluate(self, tr_loss, model, trial, epoch, ignore_keys_for_eval): if self.control.should_log: if is_torch_tpu_available(): xm.mark_step() logs: Dict[str, float] = {} # all_gather + mean() to get average loss over all processes tr_loss_scalar = self._nested_gather(tr_loss).mean().item() # reset tr_loss to zero tr_loss -= tr_loss logs["loss"] = round(tr_loss_scalar / (self.state.global_step - self._globalstep_last_logged), 4) logs["learning_rate"] = self._get_learning_rate() self._total_loss_scalar += tr_loss_scalar self._globalstep_last_logged = self.state.global_step self.store_flos() self.log(logs) metrics = None if self.control.should_evaluate: if isinstance(self.eval_dataset, dict): metrics = {} for eval_dataset_name, eval_dataset in self.eval_dataset.items(): dataset_metrics = self.evaluate( eval_dataset=eval_dataset, ignore_keys=ignore_keys_for_eval, metric_key_prefix=f"eval_{eval_dataset_name}", ) metrics.update(dataset_metrics) else: metrics = self.evaluate(ignore_keys=ignore_keys_for_eval) self._report_to_hp_search(trial, self.state.global_step, metrics) if self.control.should_save: self._save_checkpoint(model, trial, metrics=metrics) self.control = self.callback_handler.on_save(self.args, self.state, self.control) def _load_rng_state(self, checkpoint): # Load RNG states from `checkpoint` if checkpoint is None: return if self.args.world_size > 1: process_index = self.args.process_index rng_file = os.path.join(checkpoint, f"rng_state_{process_index}.pth") if not os.path.isfile(rng_file): logger.info( f"Didn't find an RNG file for process {process_index}, if you are resuming a training that " "wasn't launched in a distributed fashion, reproducibility is not guaranteed." ) return else: rng_file = os.path.join(checkpoint, "rng_state.pth") if not os.path.isfile(rng_file): logger.info( "Didn't find an RNG file, if you are resuming a training that was launched in a distributed " "fashion, reproducibility is not guaranteed." ) return checkpoint_rng_state = torch.load(rng_file) random.setstate(checkpoint_rng_state["python"]) np.random.set_state(checkpoint_rng_state["numpy"]) torch.random.set_rng_state(checkpoint_rng_state["cpu"]) if torch.cuda.is_available(): if self.args.local_rank != -1: torch.cuda.random.set_rng_state(checkpoint_rng_state["cuda"]) else: try: torch.cuda.random.set_rng_state_all(checkpoint_rng_state["cuda"]) except Exception as e: logger.info( f"Didn't manage to set back the RNG states of the GPU because of the following error:\n {e}" "\nThis won't yield the same results as if the training had not been interrupted." ) if is_torch_tpu_available(): xm.set_rng_state(checkpoint_rng_state["xla"]) def _save_checkpoint(self, model, trial, metrics=None): # In all cases, including ddp/dp/deepspeed, self.model is always a reference to the model we # want to save except FullyShardedDDP. # assert unwrap_model(model) is self.model, "internal model should be a reference to self.model" # Save model checkpoint checkpoint_folder = f"{PREFIX_CHECKPOINT_DIR}-{self.state.global_step}" if self.hp_search_backend is None and trial is None: self.store_flos() run_dir = self._get_output_dir(trial=trial) output_dir = os.path.join(run_dir, checkpoint_folder) self.save_model(output_dir, _internal_call=True) if self.deepspeed: # under zero3 model file itself doesn't get saved since it's bogus! Unless deepspeed # config `stage3_gather_16bit_weights_on_model_save` is True self.deepspeed.save_checkpoint(output_dir) # Save optimizer and scheduler if self.sharded_ddp == ShardedDDPOption.SIMPLE: self.optimizer.consolidate_state_dict() if is_torch_tpu_available(): xm.rendezvous("saving_optimizer_states") xm.save(self.optimizer.state_dict(), os.path.join(output_dir, OPTIMIZER_NAME)) with warnings.catch_warnings(record=True) as caught_warnings: xm.save(self.lr_scheduler.state_dict(), os.path.join(output_dir, SCHEDULER_NAME)) reissue_pt_warnings(caught_warnings) elif is_sagemaker_mp_enabled(): opt_state_dict = self.optimizer.local_state_dict(gather_if_shard=False) smp.barrier() if smp.rdp_rank() == 0 or smp.state.cfg.shard_optimizer_state: smp.save( opt_state_dict, os.path.join(output_dir, OPTIMIZER_NAME), partial=True, v3=smp.state.cfg.shard_optimizer_state, ) if self.args.should_save: with warnings.catch_warnings(record=True) as caught_warnings: torch.save(self.lr_scheduler.state_dict(), os.path.join(output_dir, SCHEDULER_NAME)) reissue_pt_warnings(caught_warnings) if self.do_grad_scaling: torch.save(self.scaler.state_dict(), os.path.join(output_dir, SCALER_NAME)) elif self.args.should_save and not self.deepspeed: # deepspeed.save_checkpoint above saves model/optim/sched torch.save(self.optimizer.state_dict(), os.path.join(output_dir, OPTIMIZER_NAME)) with warnings.catch_warnings(record=True) as caught_warnings: torch.save(self.lr_scheduler.state_dict(), os.path.join(output_dir, SCHEDULER_NAME)) reissue_pt_warnings(caught_warnings) if self.do_grad_scaling: torch.save(self.scaler.state_dict(), os.path.join(output_dir, SCALER_NAME)) # Determine the new best metric / best model checkpoint if metrics is not None and self.args.metric_for_best_model is not None: metric_to_check = self.args.metric_for_best_model if not metric_to_check.startswith("eval_"): metric_to_check = f"eval_{metric_to_check}" metric_value = metrics[metric_to_check] operator = np.greater if self.args.greater_is_better else np.less if ( self.state.best_metric is None or self.state.best_model_checkpoint is None or operator(metric_value, self.state.best_metric) ): self.state.best_metric = metric_value self.state.best_model_checkpoint = output_dir # Save the Trainer state if self.args.should_save: self.state.save_to_json(os.path.join(output_dir, TRAINER_STATE_NAME)) # Save RNG state in non-distributed training rng_states = { "python": random.getstate(), "numpy": np.random.get_state(), "cpu": torch.random.get_rng_state(), } if torch.cuda.is_available(): if self.args.local_rank == -1: # In non distributed, we save the global CUDA RNG state (will take care of DataParallel) rng_states["cuda"] = torch.cuda.random.get_rng_state_all() else: rng_states["cuda"] = torch.cuda.random.get_rng_state() if is_torch_tpu_available(): rng_states["xla"] = xm.get_rng_state() # A process can arrive here before the process 0 has a chance to save the model, in which case output_dir may # not yet exist. os.makedirs(output_dir, exist_ok=True) if self.args.world_size <= 1: torch.save(rng_states, os.path.join(output_dir, "rng_state.pth")) else: torch.save(rng_states, os.path.join(output_dir, f"rng_state_{self.args.process_index}.pth")) if self.args.push_to_hub: self._push_from_checkpoint(output_dir) # Maybe delete some older checkpoints. if self.args.should_save: self._rotate_checkpoints(use_mtime=True, output_dir=run_dir) def _load_optimizer_and_scheduler(self, checkpoint): """If optimizer and scheduler states exist, load them.""" if checkpoint is None: return if self.deepspeed: # deepspeed loads optimizer/lr_scheduler together with the model in deepspeed_init return checkpoint_file_exists = ( glob.glob(os.path.join(checkpoint, OPTIMIZER_NAME) + "_*") if is_sagemaker_mp_enabled() else os.path.isfile(os.path.join(checkpoint, OPTIMIZER_NAME)) ) if checkpoint_file_exists and os.path.isfile(os.path.join(checkpoint, SCHEDULER_NAME)): # Load in optimizer and scheduler states if is_torch_tpu_available(): # On TPU we have to take some extra precautions to properly load the states on the right device. optimizer_state = torch.load(os.path.join(checkpoint, OPTIMIZER_NAME), map_location="cpu") with warnings.catch_warnings(record=True) as caught_warnings: lr_scheduler_state = torch.load(os.path.join(checkpoint, SCHEDULER_NAME), map_location="cpu") reissue_pt_warnings(caught_warnings) xm.send_cpu_data_to_device(optimizer_state, self.args.device) xm.send_cpu_data_to_device(lr_scheduler_state, self.args.device) self.optimizer.load_state_dict(optimizer_state) self.lr_scheduler.load_state_dict(lr_scheduler_state) else: if is_sagemaker_mp_enabled(): if os.path.isfile(os.path.join(checkpoint, "user_content.pt")): # Optimizer checkpoint was saved with smp >= 1.10 def opt_load_hook(mod, opt): opt.load_state_dict(smp.load(os.path.join(checkpoint, OPTIMIZER_NAME), partial=True)) else: # Optimizer checkpoint was saved with smp < 1.10 def opt_load_hook(mod, opt): if IS_SAGEMAKER_MP_POST_1_10: opt.load_state_dict( smp.load(os.path.join(checkpoint, OPTIMIZER_NAME), partial=True, back_compat=True) ) else: opt.load_state_dict(smp.load(os.path.join(checkpoint, OPTIMIZER_NAME), partial=True)) self.model_wrapped.register_post_step_hook(opt_load_hook) else: # We use the CPU when training on one GPU to avoid OOM for GPU RAM when training big models. # In distributed training however, we load directly on each GPU and risk the GPU OOM as it's more # likely to get OOM on CPU (since we load num_gpu times the optimizer state map_location = self.args.device if self.args.world_size > 1 else "cpu" self.optimizer.load_state_dict( torch.load(os.path.join(checkpoint, OPTIMIZER_NAME), map_location=map_location) ) with warnings.catch_warnings(record=True) as caught_warnings: self.lr_scheduler.load_state_dict(torch.load(os.path.join(checkpoint, SCHEDULER_NAME))) reissue_pt_warnings(caught_warnings) if self.do_grad_scaling and os.path.isfile(os.path.join(checkpoint, SCALER_NAME)): self.scaler.load_state_dict(torch.load(os.path.join(checkpoint, SCALER_NAME))) def hyperparameter_search( self, hp_space: Optional[Callable[["optuna.Trial"], Dict[str, float]]] = None, compute_objective: Optional[Callable[[Dict[str, float]], float]] = None, n_trials: int = 20, direction: str = "minimize", backend: Optional[Union["str", HPSearchBackend]] = None, hp_name: Optional[Callable[["optuna.Trial"], str]] = None, **kwargs, ) -> BestRun: """ Launch an hyperparameter search using `optuna` or `Ray Tune` or `SigOpt`. The optimized quantity is determined by `compute_objective`, which defaults to a function returning the evaluation loss when no metric is provided, the sum of all metrics otherwise. To use this method, you need to have provided a `model_init` when initializing your [`Trainer`]: we need to reinitialize the model at each new run. This is incompatible with the `optimizers` argument, so you need to subclass [`Trainer`] and override the method [`~Trainer.create_optimizer_and_scheduler`] for custom optimizer/scheduler. Args: hp_space (`Callable[["optuna.Trial"], Dict[str, float]]`, *optional*): A function that defines the hyperparameter search space. Will default to [`~trainer_utils.default_hp_space_optuna`] or [`~trainer_utils.default_hp_space_ray`] or [`~trainer_utils.default_hp_space_sigopt`] depending on your backend. compute_objective (`Callable[[Dict[str, float]], float]`, *optional*): A function computing the objective to minimize or maximize from the metrics returned by the `evaluate` method. Will default to [`~trainer_utils.default_compute_objective`]. n_trials (`int`, *optional*, defaults to 100): The number of trial runs to test. direction (`str`, *optional*, defaults to `"minimize"`): Whether to optimize greater or lower objects. Can be `"minimize"` or `"maximize"`, you should pick `"minimize"` when optimizing the validation loss, `"maximize"` when optimizing one or several metrics. backend (`str` or [`~training_utils.HPSearchBackend`], *optional*): The backend to use for hyperparameter search. Will default to optuna or Ray Tune or SigOpt, depending on which one is installed. If all are installed, will default to optuna. hp_name (`Callable[["optuna.Trial"], str]]`, *optional*): A function that defines the trial/run name. Will default to None. kwargs (`Dict[str, Any]`, *optional*): Additional keyword arguments passed along to `optuna.create_study` or `ray.tune.run`. For more information see: - the documentation of [optuna.create_study](https://optuna.readthedocs.io/en/stable/reference/generated/optuna.study.create_study.html) - the documentation of [tune.run](https://docs.ray.io/en/latest/tune/api_docs/execution.html#tune-run) - the documentation of [sigopt](https://app.sigopt.com/docs/endpoints/experiments/create) Returns: [`trainer_utils.BestRun`]: All the information about the best run. Experiment summary can be found in `run_summary` attribute for Ray backend. """ if backend is None: backend = default_hp_search_backend() if backend is None: raise RuntimeError( "At least one of optuna or ray should be installed. " "To install optuna run `pip install optuna`. " "To install ray run `pip install ray[tune]`. " "To install sigopt run `pip install sigopt`." ) backend = HPSearchBackend(backend) if backend == HPSearchBackend.OPTUNA and not is_optuna_available(): raise RuntimeError("You picked the optuna backend, but it is not installed. Use `pip install optuna`.") if backend == HPSearchBackend.RAY and not is_ray_tune_available(): raise RuntimeError( "You picked the Ray Tune backend, but it is not installed. Use `pip install 'ray[tune]'`." ) if backend == HPSearchBackend.SIGOPT and not is_sigopt_available(): raise RuntimeError("You picked the sigopt backend, but it is not installed. Use `pip install sigopt`.") if backend == HPSearchBackend.WANDB and not is_wandb_available(): raise RuntimeError("You picked the wandb backend, but it is not installed. Use `pip install wandb`.") self.hp_search_backend = backend if self.model_init is None: raise RuntimeError( "To use hyperparameter search, you need to pass your model through a model_init function." ) self.hp_space = default_hp_space[backend] if hp_space is None else hp_space self.hp_name = hp_name self.compute_objective = default_compute_objective if compute_objective is None else compute_objective backend_dict = { HPSearchBackend.OPTUNA: run_hp_search_optuna, HPSearchBackend.RAY: run_hp_search_ray, HPSearchBackend.SIGOPT: run_hp_search_sigopt, HPSearchBackend.WANDB: run_hp_search_wandb, } best_run = backend_dict[backend](self, n_trials, direction, **kwargs) self.hp_search_backend = None return best_run def log(self, logs: Dict[str, float]) -> None: """ Log `logs` on the various objects watching training. Subclass and override this method to inject custom behavior. Args: logs (`Dict[str, float]`): The values to log. """ if self.state.epoch is not None: logs["epoch"] = round(self.state.epoch, 2) output = {**logs, **{"step": self.state.global_step}} self.state.log_history.append(output) self.control = self.callback_handler.on_log(self.args, self.state, self.control, logs) def _prepare_input(self, data: Union[torch.Tensor, Any]) -> Union[torch.Tensor, Any]: """ Prepares one `data` before feeding it to the model, be it a tensor or a nested list/dictionary of tensors. """ if isinstance(data, Mapping): return type(data)({k: self._prepare_input(v) for k, v in data.items()}) elif isinstance(data, (tuple, list)): return type(data)(self._prepare_input(v) for v in data) elif isinstance(data, torch.Tensor): kwargs = {"device": self.args.device} if self.deepspeed and (torch.is_floating_point(data) or torch.is_complex(data)): # NLP models inputs are int/uint and those get adjusted to the right dtype of the # embedding. Other models such as wav2vec2's inputs are already float and thus # may need special handling to match the dtypes of the model kwargs.update({"dtype": self.args.hf_deepspeed_config.dtype()}) return data.to(**kwargs) return data def _prepare_inputs(self, inputs: Dict[str, Union[torch.Tensor, Any]]) -> Dict[str, Union[torch.Tensor, Any]]: """ Prepare `inputs` before feeding them to the model, converting them to tensors if they are not already and handling potential state. """ inputs = self._prepare_input(inputs) if len(inputs) == 0: raise ValueError( "The batch received was empty, your model won't be able to train on it. Double-check that your " f"training dataset contains keys expected by the model: {','.join(self._signature_columns)}." ) if self.args.past_index >= 0 and self._past is not None: inputs["mems"] = self._past return inputs def compute_loss_context_manager(self): """ A helper wrapper to group together context managers. """ return self.autocast_smart_context_manager() def autocast_smart_context_manager(self, cache_enabled: Optional[bool] = True): """ A helper wrapper that creates an appropriate context manager for `autocast` while feeding it the desired arguments, depending on the situation. """ if self.use_cuda_amp or self.use_cpu_amp: if is_torch_greater_or_equal_than_1_10: ctx_manager = ( torch.cpu.amp.autocast(cache_enabled=cache_enabled, dtype=self.amp_dtype) if self.use_cpu_amp else torch.cuda.amp.autocast(cache_enabled=cache_enabled, dtype=self.amp_dtype) ) else: ctx_manager = torch.cuda.amp.autocast() else: ctx_manager = contextlib.nullcontext() if sys.version_info >= (3, 7) else contextlib.suppress() return ctx_manager def training_step(self, model: nn.Module, inputs: Dict[str, Union[torch.Tensor, Any]]) -> torch.Tensor: """ Perform a training step on a batch of inputs. Subclass and override to inject custom behavior. Args: model (`nn.Module`): The model to train. inputs (`Dict[str, Union[torch.Tensor, Any]]`): The inputs and targets of the model. The dictionary will be unpacked before being fed to the model. Most models expect the targets under the argument `labels`. Check your model's documentation for all accepted arguments. Return: `torch.Tensor`: The tensor with training loss on this batch. """ model.train() inputs = self._prepare_inputs(inputs) if is_sagemaker_mp_enabled(): loss_mb = smp_forward_backward(model, inputs, self.args.gradient_accumulation_steps) return loss_mb.reduce_mean().detach().to(self.args.device) with self.compute_loss_context_manager(): loss = self.compute_loss(model, inputs) if self.args.n_gpu > 1: loss = loss.mean() # mean() to average on multi-gpu parallel training if self.args.gradient_accumulation_steps > 1 and not self.deepspeed: # deepspeed handles loss scaling by gradient_accumulation_steps in its `backward` loss = loss / self.args.gradient_accumulation_steps if self.do_grad_scaling: self.scaler.scale(loss).backward() elif self.use_apex: with amp.scale_loss(loss, self.optimizer) as scaled_loss: scaled_loss.backward() elif self.deepspeed: # loss gets scaled under gradient_accumulation_steps in deepspeed loss = self.deepspeed.backward(loss) else: loss.backward() return loss.detach() def compute_loss(self, model, inputs, return_outputs=False): """ How the loss is computed by Trainer. By default, all models return the loss in the first element. Subclass and override for custom behavior. """ if self.label_smoother is not None and "labels" in inputs: labels = inputs.pop("labels") else: labels = None outputs = model(**inputs) # Save past state if it exists # TODO: this needs to be fixed and made cleaner later. if self.args.past_index >= 0: self._past = outputs[self.args.past_index] if labels is not None: if unwrap_model(model)._get_name() in MODEL_FOR_CAUSAL_LM_MAPPING_NAMES.values(): loss = self.label_smoother(outputs, labels, shift_labels=True) else: loss = self.label_smoother(outputs, labels) else: if isinstance(outputs, dict) and "loss" not in outputs: raise ValueError( "The model did not return a loss from the inputs, only the following keys: " f"{','.join(outputs.keys())}. For reference, the inputs it received are {','.join(inputs.keys())}." ) # We don't use .loss here since the model may return tuples instead of ModelOutput. loss = outputs["loss"] if isinstance(outputs, dict) else outputs[0] return (loss, outputs) if return_outputs else loss def is_local_process_zero(self) -> bool: """ Whether or not this process is the local (e.g., on one machine if training in a distributed fashion on several machines) main process. """ return self.args.local_process_index == 0 def is_world_process_zero(self) -> bool: """ Whether or not this process is the global main process (when training in a distributed fashion on several machines, this is only going to be `True` for one process). """ # Special case for SageMaker ModelParallel since there process_index is dp_process_index, not the global # process index. if is_sagemaker_mp_enabled(): return smp.rank() == 0 else: return self.args.process_index == 0 def save_model(self, output_dir: Optional[str] = None, _internal_call: bool = False): """ Will save the model, so you can reload it using `from_pretrained()`. Will only save from the main process. """ if output_dir is None: output_dir = self.args.output_dir if is_torch_tpu_available(): self._save_tpu(output_dir) elif is_sagemaker_mp_enabled(): # Calling the state_dict needs to be done on the wrapped model and on all processes. os.makedirs(output_dir, exist_ok=True) state_dict = self.model_wrapped.state_dict() if self.args.should_save: self._save(output_dir, state_dict=state_dict) if IS_SAGEMAKER_MP_POST_1_10: # 'user_content.pt' indicates model state_dict saved with smp >= 1.10 Path(os.path.join(output_dir, "user_content.pt")).touch() elif ( ShardedDDPOption.ZERO_DP_2 in self.args.sharded_ddp or ShardedDDPOption.ZERO_DP_3 in self.args.sharded_ddp or self.fsdp is not None ): state_dict = self.model.state_dict() if self.args.should_save: self._save(output_dir, state_dict=state_dict) elif self.deepspeed: # this takes care of everything as long as we aren't under zero3 if self.args.should_save: self._save(output_dir) if is_deepspeed_zero3_enabled(): # It's too complicated to try to override different places where the weights dump gets # saved, so since under zero3 the file is bogus, simply delete it. The user should # either user deepspeed checkpoint to resume or to recover full weights use # zero_to_fp32.py stored in the checkpoint. if self.args.should_save: file = os.path.join(output_dir, WEIGHTS_NAME) if os.path.isfile(file): # logger.info(f"deepspeed zero3: removing {file}, see zero_to_fp32.py to recover weights") os.remove(file) # now save the real model if stage3_gather_16bit_weights_on_model_save=True # if false it will not be saved. # This must be called on all ranks if not self.deepspeed.save_16bit_model(output_dir, WEIGHTS_NAME): logger.warning( "deepspeed.save_16bit_model didn't save the model, since" " stage3_gather_16bit_weights_on_model_save=false. Saving the full checkpoint instead, use" " zero_to_fp32.py to recover weights" ) self.deepspeed.save_checkpoint(output_dir) elif self.args.should_save: self._save(output_dir) # Push to the Hub when `save_model` is called by the user. if self.args.push_to_hub and not _internal_call: self.push_to_hub(commit_message="Model save") def _save_tpu(self, output_dir: Optional[str] = None): output_dir = output_dir if output_dir is not None else self.args.output_dir logger.info(f"Saving model checkpoint to {output_dir}") if xm.is_master_ordinal(): os.makedirs(output_dir, exist_ok=True) torch.save(self.args, os.path.join(output_dir, TRAINING_ARGS_NAME)) # Save a trained model and configuration using `save_pretrained()`. # They can then be reloaded using `from_pretrained()` xm.rendezvous("saving_checkpoint") if not isinstance(self.model, PreTrainedModel): if isinstance(unwrap_model(self.model), PreTrainedModel): unwrap_model(self.model).save_pretrained( output_dir, is_main_process=self.args.should_save, state_dict=self.model.state_dict(), save_function=xm.save, ) else: logger.info("Trainer.model is not a `PreTrainedModel`, only saving its state dict.") state_dict = self.model.state_dict() xm.save(state_dict, os.path.join(output_dir, WEIGHTS_NAME)) else: self.model.save_pretrained(output_dir, is_main_process=self.args.should_save, save_function=xm.save) if self.tokenizer is not None and self.args.should_save: self.tokenizer.save_pretrained(output_dir) def _save(self, output_dir: Optional[str] = None, state_dict=None): # If we are executing this function, we are the process zero, so we don't check for that. output_dir = output_dir if output_dir is not None else self.args.output_dir os.makedirs(output_dir, exist_ok=True) logger.info(f"Saving model checkpoint to {output_dir}") # Save a trained model and configuration using `save_pretrained()`. # They can then be reloaded using `from_pretrained()` if not isinstance(self.model, PreTrainedModel): if state_dict is None: state_dict = self.model.state_dict() if isinstance(unwrap_model(self.model), PreTrainedModel): unwrap_model(self.model).save_pretrained( output_dir, state_dict=state_dict, safe_serialization=self.args.save_safetensors ) else: logger.info("Trainer.model is not a `PreTrainedModel`, only saving its state dict.") if self.args.save_safetensors: safetensors.torch.save_file(state_dict, os.path.join(output_dir, SAFE_WEIGHTS_NAME)) else: torch.save(state_dict, os.path.join(output_dir, WEIGHTS_NAME)) else: self.model.save_pretrained( output_dir, state_dict=state_dict, safe_serialization=self.args.save_safetensors ) if self.tokenizer is not None: self.tokenizer.save_pretrained(output_dir) # Good practice: save your training arguments together with the trained model torch.save(self.args, os.path.join(output_dir, TRAINING_ARGS_NAME)) def store_flos(self): # Storing the number of floating-point operations that went into the model if self.args.local_rank != -1: self.state.total_flos += ( distributed_broadcast_scalars([self.current_flos], device=self.args.device).sum().item() ) self.current_flos = 0 else: self.state.total_flos += self.current_flos self.current_flos = 0 def _sorted_checkpoints( self, output_dir=None, checkpoint_prefix=PREFIX_CHECKPOINT_DIR, use_mtime=False ) -> List[str]: ordering_and_checkpoint_path = [] glob_checkpoints = [str(x) for x in Path(output_dir).glob(f"{checkpoint_prefix}-*") if os.path.isdir(x)] for path in glob_checkpoints: if use_mtime: ordering_and_checkpoint_path.append((os.path.getmtime(path), path)) else: regex_match = re.match(f".*{checkpoint_prefix}-([0-9]+)", path) if regex_match is not None and regex_match.groups() is not None: ordering_and_checkpoint_path.append((int(regex_match.groups()[0]), path)) checkpoints_sorted = sorted(ordering_and_checkpoint_path) checkpoints_sorted = [checkpoint[1] for checkpoint in checkpoints_sorted] # Make sure we don't delete the best model. if self.state.best_model_checkpoint is not None: best_model_index = checkpoints_sorted.index(str(Path(self.state.best_model_checkpoint))) for i in range(best_model_index, len(checkpoints_sorted) - 2): checkpoints_sorted[i], checkpoints_sorted[i + 1] = checkpoints_sorted[i + 1], checkpoints_sorted[i] return checkpoints_sorted def _rotate_checkpoints(self, use_mtime=False, output_dir=None) -> None: if self.args.save_total_limit is None or self.args.save_total_limit <= 0: return # Check if we should delete older checkpoint(s) checkpoints_sorted = self._sorted_checkpoints(use_mtime=use_mtime, output_dir=output_dir) if len(checkpoints_sorted) <= self.args.save_total_limit: return # If save_total_limit=1 with load_best_model_at_end=True, we could end up deleting the last checkpoint, which # we don't do to allow resuming. save_total_limit = self.args.save_total_limit if ( self.state.best_model_checkpoint is not None and self.args.save_total_limit == 1 and checkpoints_sorted[-1] != self.state.best_model_checkpoint ): save_total_limit = 2 number_of_checkpoints_to_delete = max(0, len(checkpoints_sorted) - save_total_limit) checkpoints_to_be_deleted = checkpoints_sorted[:number_of_checkpoints_to_delete] for checkpoint in checkpoints_to_be_deleted: logger.info(f"Deleting older checkpoint [{checkpoint}] due to args.save_total_limit") shutil.rmtree(checkpoint, ignore_errors=True) def evaluate( self, eval_dataset: Optional[Dataset] = None, ignore_keys: Optional[List[str]] = None, metric_key_prefix: str = "eval", ) -> Dict[str, float]: """ Run evaluation and returns metrics. The calling script will be responsible for providing a method to compute metrics, as they are task-dependent (pass it to the init `compute_metrics` argument). You can also subclass and override this method to inject custom behavior. Args: eval_dataset (`Dataset`, *optional*): Pass a dataset if you wish to override `self.eval_dataset`. If it is a [`~datasets.Dataset`], columns not accepted by the `model.forward()` method are automatically removed. It must implement the `__len__` method. ignore_keys (`List[str]`, *optional*): A list of keys in the output of your model (if it is a dictionary) that should be ignored when gathering predictions. metric_key_prefix (`str`, *optional*, defaults to `"eval"`): An optional prefix to be used as the metrics key prefix. For example the metrics "bleu" will be named "eval_bleu" if the prefix is "eval" (default) Returns: A dictionary containing the evaluation loss and the potential metrics computed from the predictions. The dictionary also contains the epoch number which comes from the training state. """ # memory metrics - must set up as early as possible self._memory_tracker.start() eval_dataloader = self.get_eval_dataloader(eval_dataset) start_time = time.time() eval_loop = self.prediction_loop if self.args.use_legacy_prediction_loop else self.evaluation_loop output = eval_loop( eval_dataloader, description="Evaluation", # No point gathering the predictions if there are no metrics, otherwise we defer to # self.args.prediction_loss_only prediction_loss_only=True if self.compute_metrics is None else None, ignore_keys=ignore_keys, metric_key_prefix=metric_key_prefix, ) total_batch_size = self.args.eval_batch_size * self.args.world_size if f"{metric_key_prefix}_jit_compilation_time" in output.metrics: start_time += output.metrics[f"{metric_key_prefix}_jit_compilation_time"] output.metrics.update( speed_metrics( metric_key_prefix, start_time, num_samples=output.num_samples, num_steps=math.ceil(output.num_samples / total_batch_size), ) ) self.log(output.metrics) if DebugOption.TPU_METRICS_DEBUG in self.args.debug: # tpu-comment: Logging debug metrics for PyTorch/XLA (compile, execute times, ops, etc.) xm.master_print(met.metrics_report()) self.control = self.callback_handler.on_evaluate(self.args, self.state, self.control, output.metrics) self._memory_tracker.stop_and_update_metrics(output.metrics) return output.metrics def predict( self, test_dataset: Dataset, ignore_keys: Optional[List[str]] = None, metric_key_prefix: str = "test" ) -> PredictionOutput: """ Run prediction and returns predictions and potential metrics. Depending on the dataset and your use case, your test dataset may contain labels. In that case, this method will also return metrics, like in `evaluate()`. Args: test_dataset (`Dataset`): Dataset to run the predictions on. If it is an `datasets.Dataset`, columns not accepted by the `model.forward()` method are automatically removed. Has to implement the method `__len__` ignore_keys (`List[str]`, *optional*): A list of keys in the output of your model (if it is a dictionary) that should be ignored when gathering predictions. metric_key_prefix (`str`, *optional*, defaults to `"test"`): An optional prefix to be used as the metrics key prefix. For example the metrics "bleu" will be named "test_bleu" if the prefix is "test" (default) If your predictions or labels have different sequence length (for instance because you're doing dynamic padding in a token classification task) the predictions will be padded (on the right) to allow for concatenation into one array. The padding index is -100. Returns: *NamedTuple* A namedtuple with the following keys: - predictions (`np.ndarray`): The predictions on `test_dataset`. - label_ids (`np.ndarray`, *optional*): The labels (if the dataset contained some). - metrics (`Dict[str, float]`, *optional*): The potential dictionary of metrics (if the dataset contained labels). """ # memory metrics - must set up as early as possible self._memory_tracker.start() test_dataloader = self.get_test_dataloader(test_dataset) start_time = time.time() eval_loop = self.prediction_loop if self.args.use_legacy_prediction_loop else self.evaluation_loop output = eval_loop( test_dataloader, description="Prediction", ignore_keys=ignore_keys, metric_key_prefix=metric_key_prefix ) total_batch_size = self.args.eval_batch_size * self.args.world_size if f"{metric_key_prefix}_jit_compilation_time" in output.metrics: start_time += output.metrics[f"{metric_key_prefix}_jit_compilation_time"] output.metrics.update( speed_metrics( metric_key_prefix, start_time, num_samples=output.num_samples, num_steps=math.ceil(output.num_samples / total_batch_size), ) ) self.control = self.callback_handler.on_predict(self.args, self.state, self.control, output.metrics) self._memory_tracker.stop_and_update_metrics(output.metrics) return PredictionOutput(predictions=output.predictions, label_ids=output.label_ids, metrics=output.metrics) def evaluation_loop( self, dataloader: DataLoader, description: str, prediction_loss_only: Optional[bool] = None, ignore_keys: Optional[List[str]] = None, metric_key_prefix: str = "eval", ) -> EvalLoopOutput: """ Prediction/evaluation loop, shared by `Trainer.evaluate()` and `Trainer.predict()`. Works both with or without labels. """ args = self.args prediction_loss_only = prediction_loss_only if prediction_loss_only is not None else args.prediction_loss_only # if eval is called w/o train init deepspeed here if args.deepspeed and not self.deepspeed: # XXX: eval doesn't have `resume_from_checkpoint` arg but we should be able to do eval # from the checkpoint eventually deepspeed_engine, _, _ = deepspeed_init( self, num_training_steps=0, resume_from_checkpoint=None, inference=True ) self.model = deepspeed_engine.module self.model_wrapped = deepspeed_engine self.deepspeed = deepspeed_engine model = self._wrap_model(self.model, training=False, dataloader=dataloader) # if full fp16 or bf16 eval is wanted and this ``evaluation`` or ``predict`` isn't called # while ``train`` is running, cast it to the right dtype first and then put on device if not self.is_in_train: if args.fp16_full_eval: model = model.to(dtype=torch.float16, device=args.device) elif args.bf16_full_eval: model = model.to(dtype=torch.bfloat16, device=args.device) batch_size = self.args.eval_batch_size logger.info(f"***** Running {description} *****") if has_length(dataloader): logger.info(f" Num examples = {self.num_examples(dataloader)}") else: logger.info(" Num examples: Unknown") logger.info(f" Batch size = {batch_size}") model.eval() self.callback_handler.eval_dataloader = dataloader # Do this before wrapping. eval_dataset = getattr(dataloader, "dataset", None) if is_torch_tpu_available(): dataloader = pl.ParallelLoader(dataloader, [args.device]).per_device_loader(args.device) if args.past_index >= 0: self._past = None # Initialize containers # losses/preds/labels on GPU/TPU (accumulated for eval_accumulation_steps) losses_host = None preds_host = None labels_host = None inputs_host = None # losses/preds/labels on CPU (final containers) all_losses = None all_preds = None all_labels = None all_inputs = None # Will be useful when we have an iterable dataset so don't know its length. observed_num_examples = 0 # Main evaluation loop for step, inputs in enumerate(dataloader): # Update the observed num examples observed_batch_size = find_batch_size(inputs) if observed_batch_size is not None: observed_num_examples += observed_batch_size # For batch samplers, batch_size is not known by the dataloader in advance. if batch_size is None: batch_size = observed_batch_size # Prediction step loss, logits, labels = self.prediction_step(model, inputs, prediction_loss_only, ignore_keys=ignore_keys) inputs_decode = self._prepare_input(inputs["input_ids"]) if args.include_inputs_for_metrics else None if is_torch_tpu_available(): xm.mark_step() # Update containers on host if loss is not None: losses = self._nested_gather(loss.repeat(batch_size)) losses_host = losses if losses_host is None else torch.cat((losses_host, losses), dim=0) if labels is not None: labels = self._pad_across_processes(labels) labels = self._nested_gather(labels) labels_host = labels if labels_host is None else nested_concat(labels_host, labels, padding_index=-100) if inputs_decode is not None: inputs_decode = self._pad_across_processes(inputs_decode) inputs_decode = self._nested_gather(inputs_decode) inputs_host = ( inputs_decode if inputs_host is None else nested_concat(inputs_host, inputs_decode, padding_index=-100) ) if logits is not None: logits = self._pad_across_processes(logits) logits = self._nested_gather(logits) if self.preprocess_logits_for_metrics is not None: logits = self.preprocess_logits_for_metrics(logits, labels) preds_host = logits if preds_host is None else nested_concat(preds_host, logits, padding_index=-100) self.control = self.callback_handler.on_prediction_step(args, self.state, self.control) # Gather all tensors and put them back on the CPU if we have done enough accumulation steps. if args.eval_accumulation_steps is not None and (step + 1) % args.eval_accumulation_steps == 0: if losses_host is not None: losses = nested_numpify(losses_host) all_losses = losses if all_losses is None else np.concatenate((all_losses, losses), axis=0) if preds_host is not None: logits = nested_numpify(preds_host) all_preds = logits if all_preds is None else nested_concat(all_preds, logits, padding_index=-100) if inputs_host is not None: inputs_decode = nested_numpify(inputs_host) all_inputs = ( inputs_decode if all_inputs is None else nested_concat(all_inputs, inputs_decode, padding_index=-100) ) if labels_host is not None: labels = nested_numpify(labels_host) all_labels = ( labels if all_labels is None else nested_concat(all_labels, labels, padding_index=-100) ) # Set back to None to begin a new accumulation losses_host, preds_host, inputs_host, labels_host = None, None, None, None if args.past_index and hasattr(self, "_past"): # Clean the state at the end of the evaluation loop delattr(self, "_past") # Gather all remaining tensors and put them back on the CPU if losses_host is not None: losses = nested_numpify(losses_host) all_losses = losses if all_losses is None else np.concatenate((all_losses, losses), axis=0) if preds_host is not None: logits = nested_numpify(preds_host) all_preds = logits if all_preds is None else nested_concat(all_preds, logits, padding_index=-100) if inputs_host is not None: inputs_decode = nested_numpify(inputs_host) all_inputs = ( inputs_decode if all_inputs is None else nested_concat(all_inputs, inputs_decode, padding_index=-100) ) if labels_host is not None: labels = nested_numpify(labels_host) all_labels = labels if all_labels is None else nested_concat(all_labels, labels, padding_index=-100) # Number of samples if has_length(eval_dataset): num_samples = len(eval_dataset) # The instance check is weird and does not actually check for the type, but whether the dataset has the right # methods. Therefore we need to make sure it also has the attribute. elif isinstance(eval_dataset, IterableDatasetShard) and getattr(eval_dataset, "num_examples", 0) > 0: num_samples = eval_dataset.num_examples else: if has_length(dataloader): num_samples = self.num_examples(dataloader) else: # both len(dataloader.dataset) and len(dataloader) fail num_samples = observed_num_examples if num_samples == 0 and observed_num_examples > 0: num_samples = observed_num_examples # Number of losses has been rounded to a multiple of batch_size and in a distributed training, the number of # samplers has been rounded to a multiple of batch_size, so we truncate. if all_losses is not None: all_losses = all_losses[:num_samples] if all_preds is not None: all_preds = nested_truncate(all_preds, num_samples) if all_labels is not None: all_labels = nested_truncate(all_labels, num_samples) if all_inputs is not None: all_inputs = nested_truncate(all_inputs, num_samples) # Metrics! if self.compute_metrics is not None and all_preds is not None and all_labels is not None: if args.include_inputs_for_metrics: metrics = self.compute_metrics( EvalPrediction(predictions=all_preds, label_ids=all_labels, inputs=all_inputs) ) else: metrics = self.compute_metrics(EvalPrediction(predictions=all_preds, label_ids=all_labels)) else: metrics = {} # To be JSON-serializable, we need to remove numpy types or zero-d tensors metrics = denumpify_detensorize(metrics) if all_losses is not None: metrics[f"{metric_key_prefix}_loss"] = all_losses.mean().item() if hasattr(self, "jit_compilation_time"): metrics[f"{metric_key_prefix}_jit_compilation_time"] = self.jit_compilation_time # Prefix all keys with metric_key_prefix + '_' for key in list(metrics.keys()): if not key.startswith(f"{metric_key_prefix}_"): metrics[f"{metric_key_prefix}_{key}"] = metrics.pop(key) return EvalLoopOutput(predictions=all_preds, label_ids=all_labels, metrics=metrics, num_samples=num_samples) def _nested_gather(self, tensors, name=None): """ Gather value of `tensors` (tensor or list/tuple of nested tensors) and convert them to numpy before concatenating them to `gathered` """ if tensors is None: return if is_torch_tpu_available(): if name is None: name = "nested_gather" tensors = nested_xla_mesh_reduce(tensors, name) elif is_sagemaker_mp_enabled(): tensors = smp_gather(tensors) elif self.args.local_rank != -1: tensors = distributed_concat(tensors) return tensors # Copied from Accelerate. def _pad_across_processes(self, tensor, pad_index=-100): """ Recursively pad the tensors in a nested list/tuple/dictionary of tensors from all devices to the same size so they can safely be gathered. """ if isinstance(tensor, (list, tuple)): return type(tensor)(self._pad_across_processes(t, pad_index=pad_index) for t in tensor) elif isinstance(tensor, dict): return type(tensor)({k: self._pad_across_processes(v, pad_index=pad_index) for k, v in tensor.items()}) elif not isinstance(tensor, torch.Tensor): raise TypeError( f"Can't pad the values of type {type(tensor)}, only of nested list/tuple/dicts of tensors." ) if len(tensor.shape) < 2: return tensor # Gather all sizes size = torch.tensor(tensor.shape, device=tensor.device)[None] sizes = self._nested_gather(size).cpu() max_size = max(s[1] for s in sizes) # When extracting XLA graphs for compilation, max_size is 0, # so use inequality to avoid errors. if tensor.shape[1] >= max_size: return tensor # Then pad to the maximum size old_size = tensor.shape new_size = list(old_size) new_size[1] = max_size new_tensor = tensor.new_zeros(tuple(new_size)) + pad_index new_tensor[:, : old_size[1]] = tensor return new_tensor def prediction_step( self, model: nn.Module, inputs: Dict[str, Union[torch.Tensor, Any]], prediction_loss_only: bool, ignore_keys: Optional[List[str]] = None, ) -> Tuple[Optional[torch.Tensor], Optional[torch.Tensor], Optional[torch.Tensor]]: """ Perform an evaluation step on `model` using `inputs`. Subclass and override to inject custom behavior. Args: model (`nn.Module`): The model to evaluate. inputs (`Dict[str, Union[torch.Tensor, Any]]`): The inputs and targets of the model. The dictionary will be unpacked before being fed to the model. Most models expect the targets under the argument `labels`. Check your model's documentation for all accepted arguments. prediction_loss_only (`bool`): Whether or not to return the loss only. ignore_keys (`List[str]`, *optional*): A list of keys in the output of your model (if it is a dictionary) that should be ignored when gathering predictions. Return: Tuple[Optional[torch.Tensor], Optional[torch.Tensor], Optional[torch.Tensor]]: A tuple with the loss, logits and labels (each being optional). """ has_labels = False if len(self.label_names) == 0 else all(inputs.get(k) is not None for k in self.label_names) # For CLIP-like models capable of returning loss values. # If `return_loss` is not specified or being `None` in `inputs`, we check if the default value of `return_loss` # is `True` in `model.forward`. return_loss = inputs.get("return_loss", None) if return_loss is None: return_loss = self.can_return_loss loss_without_labels = True if len(self.label_names) == 0 and return_loss else False inputs = self._prepare_inputs(inputs) if ignore_keys is None: if hasattr(self.model, "config"): ignore_keys = getattr(self.model.config, "keys_to_ignore_at_inference", []) else: ignore_keys = [] # labels may be popped when computing the loss (label smoothing for instance) so we grab them first. if has_labels or loss_without_labels: labels = nested_detach(tuple(inputs.get(name) for name in self.label_names)) if len(labels) == 1: labels = labels[0] else: labels = None with torch.no_grad(): if is_sagemaker_mp_enabled(): raw_outputs = smp_forward_only(model, inputs) if has_labels or loss_without_labels: if isinstance(raw_outputs, dict): loss_mb = raw_outputs["loss"] logits_mb = tuple(v for k, v in raw_outputs.items() if k not in ignore_keys + ["loss"]) else: loss_mb = raw_outputs[0] logits_mb = raw_outputs[1:] loss = loss_mb.reduce_mean().detach().cpu() logits = smp_nested_concat(logits_mb) else: loss = None if isinstance(raw_outputs, dict): logits_mb = tuple(v for k, v in raw_outputs.items() if k not in ignore_keys) else: logits_mb = raw_outputs logits = smp_nested_concat(logits_mb) else: if has_labels or loss_without_labels: with self.compute_loss_context_manager(): loss, outputs = self.compute_loss(model, inputs, return_outputs=True) loss = loss.mean().detach() if isinstance(outputs, dict): logits = tuple(v for k, v in outputs.items() if k not in ignore_keys + ["loss"]) else: logits = outputs[1:] else: loss = None with self.compute_loss_context_manager(): outputs = model(**inputs) if isinstance(outputs, dict): logits = tuple(v for k, v in outputs.items() if k not in ignore_keys) else: logits = outputs # TODO: this needs to be fixed and made cleaner later. if self.args.past_index >= 0: self._past = outputs[self.args.past_index - 1] if prediction_loss_only: return (loss, None, None) logits = nested_detach(logits) if len(logits) == 1: logits = logits[0] return (loss, logits, labels) def floating_point_ops(self, inputs: Dict[str, Union[torch.Tensor, Any]]): """ For models that inherit from [`PreTrainedModel`], uses that method to compute the number of floating point operations for every backward + forward pass. If using another model, either implement such a method in the model or subclass and override this method. Args: inputs (`Dict[str, Union[torch.Tensor, Any]]`): The inputs and targets of the model. Returns: `int`: The number of floating-point operations. """ if hasattr(self.model, "floating_point_ops"): return self.model.floating_point_ops(inputs) else: return 0 def init_git_repo(self, at_init: bool = False): """ Initializes a git repo in `self.args.hub_model_id`. Args: at_init (`bool`, *optional*, defaults to `False`): Whether this function is called before any training or not. If `self.args.overwrite_output_dir` is `True` and `at_init` is `True`, the path to the repo (which is `self.args.output_dir`) might be wiped out. """ if not self.is_world_process_zero(): return if self.args.hub_model_id is None: repo_name = Path(self.args.output_dir).absolute().name else: repo_name = self.args.hub_model_id if "/" not in repo_name: repo_name = get_full_repo_name(repo_name, token=self.args.hub_token) # Make sure the repo exists. create_repo(repo_name, token=self.args.hub_token, private=self.args.hub_private_repo, exist_ok=True) try: self.repo = Repository(self.args.output_dir, clone_from=repo_name, token=self.args.hub_token) except EnvironmentError: if self.args.overwrite_output_dir and at_init: # Try again after wiping output_dir shutil.rmtree(self.args.output_dir) self.repo = Repository(self.args.output_dir, clone_from=repo_name, token=self.args.hub_token) else: raise self.repo.git_pull() # By default, ignore the checkpoint folders if ( not os.path.exists(os.path.join(self.args.output_dir, ".gitignore")) and self.args.hub_strategy != HubStrategy.ALL_CHECKPOINTS ): with open(os.path.join(self.args.output_dir, ".gitignore"), "w", encoding="utf-8") as writer: writer.writelines(["checkpoint-*/"]) # Add "*.sagemaker" to .gitignore if using SageMaker if os.environ.get("SM_TRAINING_ENV"): self._add_sm_patterns_to_gitignore() self.push_in_progress = None def create_model_card( self, language: Optional[str] = None, license: Optional[str] = None, tags: Union[str, List[str], None] = None, model_name: Optional[str] = None, finetuned_from: Optional[str] = None, tasks: Union[str, List[str], None] = None, dataset_tags: Union[str, List[str], None] = None, dataset: Union[str, List[str], None] = None, dataset_args: Union[str, List[str], None] = None, ): """ Creates a draft of a model card using the information available to the `Trainer`. Args: language (`str`, *optional*): The language of the model (if applicable) license (`str`, *optional*): The license of the model. Will default to the license of the pretrained model used, if the original model given to the `Trainer` comes from a repo on the Hub. tags (`str` or `List[str]`, *optional*): Some tags to be included in the metadata of the model card. model_name (`str`, *optional*): The name of the model. finetuned_from (`str`, *optional*): The name of the model used to fine-tune this one (if applicable). Will default to the name of the repo of the original model given to the `Trainer` (if it comes from the Hub). tasks (`str` or `List[str]`, *optional*): One or several task identifiers, to be included in the metadata of the model card. dataset_tags (`str` or `List[str]`, *optional*): One or several dataset tags, to be included in the metadata of the model card. dataset (`str` or `List[str]`, *optional*): One or several dataset identifiers, to be included in the metadata of the model card. dataset_args (`str` or `List[str]`, *optional*): One or several dataset arguments, to be included in the metadata of the model card. """ if not self.is_world_process_zero(): return training_summary = TrainingSummary.from_trainer( self, language=language, license=license, tags=tags, model_name=model_name, finetuned_from=finetuned_from, tasks=tasks, dataset_tags=dataset_tags, dataset=dataset, dataset_args=dataset_args, ) model_card = training_summary.to_model_card() with open(os.path.join(self.args.output_dir, "README.md"), "w") as f: f.write(model_card) def _push_from_checkpoint(self, checkpoint_folder): # Only push from one node. if not self.is_world_process_zero() or self.args.hub_strategy == HubStrategy.END: return # If we haven't finished the last push, we don't do this one. if self.push_in_progress is not None and not self.push_in_progress.is_done: return output_dir = self.args.output_dir # To avoid a new synchronization of all model weights, we just copy the file from the checkpoint folder modeling_files = [CONFIG_NAME, WEIGHTS_NAME, SAFE_WEIGHTS_NAME] for modeling_file in modeling_files: if os.path.isfile(os.path.join(checkpoint_folder, modeling_file)): shutil.copy(os.path.join(checkpoint_folder, modeling_file), os.path.join(output_dir, modeling_file)) # Saving the tokenizer is fast and we don't know how many files it may have spawned, so we resave it to be sure. if self.tokenizer is not None: self.tokenizer.save_pretrained(output_dir) # Same for the training arguments torch.save(self.args, os.path.join(output_dir, TRAINING_ARGS_NAME)) try: if self.args.hub_strategy == HubStrategy.CHECKPOINT: # Temporarily move the checkpoint just saved for the push tmp_checkpoint = os.path.join(output_dir, "last-checkpoint") # We have to remove the "last-checkpoint" dir if it exists, otherwise the checkpoint is moved as a # subfolder. if os.path.isdir(tmp_checkpoint): shutil.rmtree(tmp_checkpoint) shutil.move(checkpoint_folder, tmp_checkpoint) if self.args.save_strategy == IntervalStrategy.STEPS: commit_message = f"Training in progress, step {self.state.global_step}" else: commit_message = f"Training in progress, epoch {int(self.state.epoch)}" _, self.push_in_progress = self.repo.push_to_hub( commit_message=commit_message, blocking=False, auto_lfs_prune=True ) finally: if self.args.hub_strategy == HubStrategy.CHECKPOINT: # Move back the checkpoint to its place shutil.move(tmp_checkpoint, checkpoint_folder) def push_to_hub(self, commit_message: Optional[str] = "End of training", blocking: bool = True, **kwargs) -> str: """ Upload *self.model* and *self.tokenizer* to the 🤗 model hub on the repo *self.args.hub_model_id*. Parameters: commit_message (`str`, *optional*, defaults to `"End of training"`): Message to commit while pushing. blocking (`bool`, *optional*, defaults to `True`): Whether the function should return only when the `git push` has finished. kwargs: Additional keyword arguments passed along to [`~Trainer.create_model_card`]. Returns: The url of the commit of your model in the given repository if `blocking=False`, a tuple with the url of the commit and an object to track the progress of the commit if `blocking=True` """ # If a user calls manually `push_to_hub` with `self.args.push_to_hub = False`, we try to create the repo but # it might fail. if not hasattr(self, "repo"): self.init_git_repo() model_name = kwargs.pop("model_name", None) if model_name is None and self.args.should_save: if self.args.hub_model_id is None: model_name = Path(self.args.output_dir).name else: model_name = self.args.hub_model_id.split("/")[-1] # Needs to be executed on all processes for TPU training, but will only save on the processed determined by # self.args.should_save. self.save_model(_internal_call=True) # Only push from one node. if not self.is_world_process_zero(): return # Cancel any async push in progress if blocking=True. The commits will all be pushed together. if blocking and self.push_in_progress is not None and not self.push_in_progress.is_done: self.push_in_progress._process.kill() self.push_in_progress = None git_head_commit_url = self.repo.push_to_hub( commit_message=commit_message, blocking=blocking, auto_lfs_prune=True ) # push separately the model card to be independant from the rest of the model if self.args.should_save: self.create_model_card(model_name=model_name, **kwargs) try: self.repo.push_to_hub( commit_message="update model card README.md", blocking=blocking, auto_lfs_prune=True ) except EnvironmentError as exc: logger.error(f"Error pushing update to the model card. Please read logs and retry.\n${exc}") return git_head_commit_url # # Deprecated code # def prediction_loop( self, dataloader: DataLoader, description: str, prediction_loss_only: Optional[bool] = None, ignore_keys: Optional[List[str]] = None, metric_key_prefix: str = "eval", ) -> EvalLoopOutput: """ Prediction/evaluation loop, shared by `Trainer.evaluate()` and `Trainer.predict()`. Works both with or without labels. """ args = self.args if not has_length(dataloader): raise ValueError("dataloader must implement a working __len__") prediction_loss_only = prediction_loss_only if prediction_loss_only is not None else args.prediction_loss_only # if eval is called w/o train init deepspeed here if args.deepspeed and not self.deepspeed: # XXX: eval doesn't have `resume_from_checkpoint` arg but we should be able to do eval # from the checkpoint eventually deepspeed_engine, _, _ = deepspeed_init(self, num_training_steps=0, resume_from_checkpoint=None) self.model = deepspeed_engine.module self.model_wrapped = deepspeed_engine self.deepspeed = deepspeed_engine # XXX: we don't need optim/sched for inference, but this needs to be sorted out, since # for example the Z3-optimizer is a must for zero3 to work even for inference - what we # don't need is the deepspeed basic optimizer which is self.optimizer.optimizer deepspeed_engine.optimizer.optimizer = None deepspeed_engine.lr_scheduler = None model = self._wrap_model(self.model, training=False, dataloader=dataloader) # if full fp16 or bf16 eval is wanted and this ``evaluation`` or ``predict`` isn't called # while ``train`` is running, cast it to the right dtype first and then put on device if not self.is_in_train: if args.fp16_full_eval: model = model.to(dtype=torch.float16, device=args.device) elif args.bf16_full_eval: model = model.to(dtype=torch.bfloat16, device=args.device) batch_size = dataloader.batch_size num_examples = self.num_examples(dataloader) logger.info(f"***** Running {description} *****") logger.info(f" Num examples = {num_examples}") logger.info(f" Batch size = {batch_size}") losses_host: torch.Tensor = None preds_host: Union[torch.Tensor, List[torch.Tensor]] = None labels_host: Union[torch.Tensor, List[torch.Tensor]] = None inputs_host: Union[torch.Tensor, List[torch.Tensor]] = None world_size = max(1, args.world_size) eval_losses_gatherer = DistributedTensorGatherer(world_size, num_examples, make_multiple_of=batch_size) if not prediction_loss_only: # The actual number of eval_sample can be greater than num_examples in distributed settings (when we pass # a batch size to the sampler) make_multiple_of = None if hasattr(dataloader, "sampler") and isinstance(dataloader.sampler, SequentialDistributedSampler): make_multiple_of = dataloader.sampler.batch_size preds_gatherer = DistributedTensorGatherer(world_size, num_examples, make_multiple_of=make_multiple_of) labels_gatherer = DistributedTensorGatherer(world_size, num_examples, make_multiple_of=make_multiple_of) inputs_gatherer = DistributedTensorGatherer(world_size, num_examples, make_multiple_of=make_multiple_of) model.eval() if is_torch_tpu_available(): dataloader = pl.ParallelLoader(dataloader, [args.device]).per_device_loader(args.device) if args.past_index >= 0: self._past = None self.callback_handler.eval_dataloader = dataloader for step, inputs in enumerate(dataloader): loss, logits, labels = self.prediction_step(model, inputs, prediction_loss_only, ignore_keys=ignore_keys) inputs_decode = self._prepare_input(inputs["input_ids"]) if args.include_inputs_for_metrics else None if loss is not None: losses = loss.repeat(batch_size) losses_host = losses if losses_host is None else torch.cat((losses_host, losses), dim=0) if logits is not None: preds_host = logits if preds_host is None else nested_concat(preds_host, logits, padding_index=-100) if labels is not None: labels_host = labels if labels_host is None else nested_concat(labels_host, labels, padding_index=-100) if inputs_decode is not None: inputs_host = ( inputs_decode if inputs_host is None else nested_concat(inputs_host, inputs_decode, padding_index=-100) ) self.control = self.callback_handler.on_prediction_step(args, self.state, self.control) # Gather all tensors and put them back on the CPU if we have done enough accumulation steps. if args.eval_accumulation_steps is not None and (step + 1) % args.eval_accumulation_steps == 0: eval_losses_gatherer.add_arrays(self._gather_and_numpify(losses_host, "eval_losses")) if not prediction_loss_only: preds_gatherer.add_arrays(self._gather_and_numpify(preds_host, "eval_preds")) labels_gatherer.add_arrays(self._gather_and_numpify(labels_host, "eval_label_ids")) inputs_gatherer.add_arrays(self._gather_and_numpify(inputs_host, "eval_inputs_ids")) # Set back to None to begin a new accumulation losses_host, preds_host, labels_host, inputs_host = None, None, None, None if args.past_index and hasattr(self, "_past"): # Clean the state at the end of the evaluation loop delattr(self, "_past") # Gather all remaining tensors and put them back on the CPU eval_losses_gatherer.add_arrays(self._gather_and_numpify(losses_host, "eval_losses")) if not prediction_loss_only: preds_gatherer.add_arrays(self._gather_and_numpify(preds_host, "eval_preds")) labels_gatherer.add_arrays(self._gather_and_numpify(labels_host, "eval_label_ids")) inputs_gatherer.add_arrays(self._gather_and_numpify(inputs_host, "eval_inputs_ids")) eval_loss = eval_losses_gatherer.finalize() preds = preds_gatherer.finalize() if not prediction_loss_only else None label_ids = labels_gatherer.finalize() if not prediction_loss_only else None inputs_ids = inputs_gatherer.finalize() if not prediction_loss_only else None if self.compute_metrics is not None and preds is not None and label_ids is not None: if args.include_inputs_for_metrics: metrics = self.compute_metrics( EvalPrediction(predictions=preds, label_ids=label_ids, inputs=inputs_ids) ) else: metrics = self.compute_metrics(EvalPrediction(predictions=preds, label_ids=label_ids)) else: metrics = {} # To be JSON-serializable, we need to remove numpy types or zero-d tensors metrics = denumpify_detensorize(metrics) if eval_loss is not None: metrics[f"{metric_key_prefix}_loss"] = eval_loss.mean().item() # Prefix all keys with metric_key_prefix + '_' for key in list(metrics.keys()): if not key.startswith(f"{metric_key_prefix}_"): metrics[f"{metric_key_prefix}_{key}"] = metrics.pop(key) return EvalLoopOutput(predictions=preds, label_ids=label_ids, metrics=metrics, num_samples=num_examples) def _gather_and_numpify(self, tensors, name): """ Gather value of `tensors` (tensor or list/tuple of nested tensors) and convert them to numpy before concatenating them to `gathered` """ if tensors is None: return if is_torch_tpu_available(): tensors = nested_xla_mesh_reduce(tensors, name) elif is_sagemaker_mp_enabled(): tensors = smp_gather(tensors) elif self.args.local_rank != -1: tensors = distributed_concat(tensors) return nested_numpify(tensors) def _add_sm_patterns_to_gitignore(self) -> None: """Add SageMaker Checkpointing patterns to .gitignore file.""" # Make sure we only do this on the main process if not self.is_world_process_zero(): return patterns = ["*.sagemaker-uploading", "*.sagemaker-uploaded"] # Get current .gitignore content if os.path.exists(os.path.join(self.repo.local_dir, ".gitignore")): with open(os.path.join(self.repo.local_dir, ".gitignore"), "r") as f: current_content = f.read() else: current_content = "" # Add the patterns to .gitignore content = current_content for pattern in patterns: if pattern not in content: if content.endswith("\n"): content += pattern else: content += f"\n{pattern}" # Write the .gitignore file if it has changed if content != current_content: with open(os.path.join(self.repo.local_dir, ".gitignore"), "w") as f: logger.debug(f"Writing .gitignore file. Content: {content}") f.write(content) self.repo.git_add(".gitignore") # avoid race condition with git status time.sleep(0.5) if not self.repo.is_repo_clean(): self.repo.git_commit("Add *.sagemaker patterns to .gitignore.") self.repo.git_push() ================================================ FILE: src/datasampler.py ================================================ import torch.distributed as dist import math from torch.utils.data.sampler import Sampler from torch.utils.data.sampler import Sampler from torch.utils.data import DataLoader, DistributedSampler import random import torch from Dataset.multi_dataset import multi_dataset def make_batch(index_list, batch_size, drop_last): if drop_last: batches = [] whole_batch_num = len(index_list)//batch_size for _ in range(whole_batch_num): batches.append(index_list[batch_size*_:(batch_size*(_+1))]) else: batches = [] whole_batch_num = math.ceil(len(index_list)/batch_size) for _ in range(whole_batch_num): batches.append(index_list[batch_size*_:(batch_size*(_+1))]) return batches def batch_generation(dataset,batch_size_2D, batch_size_3D,drop_last=False,shuffle = True, seed = 0): len_2D = len(dataset.data_whole_2D) len_3D = len(dataset.data_whole_3D) index_2D = list(range(len_2D)) index_3D = list(range(len_2D,(len_2D+len_3D))) assert len(index_2D) + len(index_3D) == len(dataset.data_whole) if shuffle: # deterministically shuffle based on epoch and seed g = torch.Generator() g.manual_seed(seed) random.shuffle(index_2D) random.shuffle(index_3D) batch_2D = make_batch(index_2D, batch_size_2D, drop_last) batch_3D = make_batch(index_3D, batch_size_3D, drop_last) batch_chunk = batch_2D + batch_3D return batch_chunk class My_DistributedBatchSampler(Sampler): """ Iterable wrapper that distributes data across multiple workers. Args: iterable (iterable) num_replicas (int, optional): Number of processes participating in distributed training. rank (int, optional): Rank of the current process within ``num_replicas``. Example: >>> list(DistributedSampler(range(10), num_replicas=2, rank=0)) [0, 2, 4, 6, 8] >>> list(DistributedSampler(range(10), num_replicas=2, rank=1)) [1, 3, 5, 7, 9] """ def __init__(self, dataset, num_replicas=None, rank=None, batch_size_2D = 4, batch_size_3D = 1, drop_last = False, shuffle = True, seed: int = 0): self.num_replicas = num_replicas self.rank = rank self.drop_last = drop_last self.shuffle = shuffle self.dataset = dataset self.batch_size_2D = batch_size_2D self.batch_size_3D = batch_size_3D self.seed = seed self.epoch = 0 if num_replicas is None or rank is None: # pragma: no cover if not torch.distributed.is_initialized(): raise RuntimeError('Requires `torch.distributed` to be initialized.') self.num_replicas = ( torch.distributed.get_world_size() if num_replicas is None else num_replicas) self.rank = torch.distributed.get_rank() if rank is None else rank indices = batch_generation(self.dataset,self.batch_size_2D,self.batch_size_3D,self.drop_last,self.shuffle) if self.rank >= self.num_replicas: raise IndexError('`rank` must be smaller than the `num_replicas`.') if self.drop_last and len(indices) % self.num_replicas != 0: # type: ignore[arg-type] # Split to nearest available length that is evenly divisible. # This is to ensure each rank receives the same amount of data when # using this Sampler. self.num_samples = math.ceil( (len(indices) - self.num_replicas) / self.num_replicas # type: ignore[arg-type] ) else: self.num_samples = math.ceil(len(indices) / self.num_replicas) # type: ignore[arg-type] self.total_size = self.num_samples * self.num_replicas def __iter__(self): indices = batch_generation(self.dataset,self.batch_size_2D,self.batch_size_3D,self.drop_last,self.shuffle,self.seed + self.epoch) # print(indices) if self.shuffle: # deterministically shuffle based on epoch and seed g = torch.Generator() g.manual_seed(self.seed + self.epoch) random.shuffle(indices) if not self.drop_last: # add extra samples to make it evenly divisible padding_size = self.total_size - len(indices) if padding_size <= len(indices): indices += indices[:padding_size] else: indices += (indices * math.ceil(padding_size / len(indices)))[:padding_size] else: # remove tail of data to make it evenly divisible. indices = indices[:self.total_size] assert len(indices) == self.total_size # subsample indices = indices[self.rank:self.total_size:self.num_replicas] assert len(indices) == self.num_samples return iter(indices) def __len__(self): return self.num_samples def set_epoch(self, epoch: int) -> None: r""" Set the epoch for this sampler. When :attr:`shuffle=True`, this ensures all replicas use a different random ordering for each epoch. Otherwise, the next iteration of this sampler will yield the same ordering. Args: epoch (int): Epoch number. """ self.epoch = epoch # print(My_DistributedBatchSampler) # Train_dataset = multi_dataset(text_tokenizer = '/mnt/petrelfs/share_data/zhangxiaoman/CODE/RadFM/src/Language_models/tokenizer') # DDP_sample_0 = list(My_DistributedBatchSampler(dataset= Train_dataset , num_replicas = 32, rank = 0,)) # DDP_sample_1 = list(My_DistributedBatchSampler(dataset= Train_dataset , num_replicas = 32, rank = 1,)) # for ii in DDP_sample_0: # print(ii) # for ii in DDP_sample_1: # print(ii) ================================================ FILE: src/output_csv_example/caption_example.csv ================================================ Question,Ground Truth,Pred,belong_to ['Could you provide an impression for this chest scan?'],['Impression: No acute cardiopulmonary process.'],['Impression: No pneumothorax.'],['chestxray_caption_dataset'] "[""I'm requesting a caption consists of findings and impression to clarify this X-ray image.""]",['Findings: Left PICC tip is seen terminating in the region of the distal left brachiocephalic vein. Tracheostomy tube is in unchanged standard position. The heart is moderately enlarged. Marked calcification of the aortic knob is again present. Mild pulmonary vascular congestion is similar. Bibasilar streaky airspace opacities are minimally improved. Previously noted left pleural effusion appears to have resolved. No pneumothorax is identified. Percutaneous gastrostomy tube is seen in the left upper quadrant. Impression: 1. Left PICC tip appears to terminate in the distal left brachiocephalic vein. 2. Mild pulmonary vascular congestion. 3. Interval improvement in aeration of the lung bases with residual streaky opacity likely reflective of atelectasis. Interval resolution of the left pleural effusion.'],['Findings: There is a moderate-sized left pleural effusion. Blunting of the right costophrenic angle may be secondary to a small pleural effusion. There is associated atelectasis at the left lung base. No pneumothorax is identified. Heart size is likely top normal. Impression: Moderate-sized left and possible small right pleural effusions.'],['chestxray_caption_dataset'] ['Please write a radiology report consists of findings that explains this X-ray image.'],['Findings: Single AP portable view of the chest. No prior. The lungs are clear of large confluent consolidation. Cardiac silhouette enlarged but could be accentuated by positioning and relatively low inspiratory effort. Calcifications noted at the aortic arch. Degenerative changes noted at the glenohumeral joints bilaterally. Osseous and soft tissue structures otherwise unremarkable. '],['Findings: The heart is mildly enlarged. The mediastinal and hilar contours appear unchanged. There is perihilar fullness and a central widespread diffuse abnormality with indistinct vascularity suggesting mild to moderate pulmonary congestion. There is no definite pleural effusion or pneumothorax. '],['chestxray_caption_dataset'] ['Please caption consists of findings this medical image'],"['Findings: A hazy opacity is present in the right lung which may represent aspiration, pleural effusion or hemorrhage. Retrocardiac opacity at the left base is unchanged. Moderate cardiomegaly is stable. Slight prominence of the pulmonary vasculature with cephalization and enlarged pulmonary arteries are consistent with mild pulmonary edema. Tracheostomy tube is in place. There are no displaced rib fractures. ']",['Findings: The endotracheal tube terminates 3.5 cm above the carina. A left IJ central venous catheter terminates at the upper SVC. External pacer wires are demonstrated. Large bilateral pleural effusions and mild central vascular congestion and edema are otherwise unchanged. There is no pneumothorax. '],['chestxray_caption_dataset'] ['Please write an impression for this X-ray scan.'],"['Impression: Mild residual retrocardiac opacification remains, pneumonia vs. atelectasis.']",['Impression: 1. Mild pulmonary edema. 2. Low lung volumes.'],['chestxray_caption_dataset'] ['Could you describe what this chest X-ray image shows in a caption consists of findings and impression?'],"['Findings: Single AP portable chest radiograph is obtained. Tracheostomy tube is present. There is no pneumothorax or pleural effusion. There is a hazy veil-like opacity in the right upper lung zone which may be consolidation, atelectasis or artifact. Heart size appears enlarged; however, this may be technical due to AP view. Bony structures are intact. Impression: Limited study with hazy opacity in the right upper and mid lungs which may be infectious in etiology, atelectasis or artifact.']","['Findings: The endotracheal tube terminates 3.5 cm above the carina. A left IJ central venous catheter terminates at the mid SVC. There is no pneumothorax. There is increased left basilar retrocardiac opacification, likely representing atelectasis. Impression: 1. Moderate left pleural effusion, increased since the prior study. 2. Increased left basilar retrocardiac atelectasis.']",['chestxray_caption_dataset'] ['Could you provide a caption consists of findings and impression for this X-ray image?'],['Findings: The lungs are clear bilaterally with no areas of focal consolidation. There is no pleural effusion or pneumothorax. Patient is status post CABG. Cardiomegaly is stable. Mediastinal silhouette is within normal limits. Impression: No evidence of pneumonia. Stable cardiomegaly.'],['Findings: The lungs are clear. The cardiomediastinal silhouette is within normal limits. No acute osseous abnormalities. Impression: No acute cardiopulmonary process.'],['chestxray_caption_dataset'] ['Can you offer a descriptive radiology report consists of findings for this chest X-ray scan?'],"['Findings: The lungs are well expanded and clear. The cardiomediastinal silhouette, hilar contours, and pleural surfaces are normal. No pleural effusion or pneumothorax is present. Sternal wires are intact. ']",['Findings: The lungs are clear without focal consolidation. No pleural effusion or pneumothorax is seen. The cardiac and mediastinal silhouettes are stable. '],['chestxray_caption_dataset'] ['Please given an impression this chest X-ray image'],['Impression: No acute cardiopulmonary process.'],['Impression: No acute cardiopulmonary process.'],['chestxray_caption_dataset'] ['Please given an impression this chest image'],"['Impression: No acute cardiopulmonary process. No significant interval change. Additionally, several pulmonary nodules measuring up to 3 mm are not not well appreciated on the current study-CT is more sensitive.']",['Impression: No acute cardiopulmonary process.'],['chestxray_caption_dataset'] ['Please given an impression this X-ray image'],['Impression: Bilateral lower lobe bronchiectasis with improved right lower medial lung peribronchial consolidation.'],['Impression: No acute cardiopulmonary process.'],['chestxray_caption_dataset'] ['Please write a radiology report consists of findings that explains this X-ray image.'],['Findings: Portable AP chest radiograph demonstrates a stable right pneumothorax. There are several radiodense lesions along the left hemithorax that may represent skin folds. There is no definite left pneumothorax. There is opacification of the left thorax consistent with a moderate left pleural effusion. There is also new engorgement of the pulmonary vasculature in the left lung. There is slight shift of the mediastinum to the right. Bilateral pigtail drains are noted at the costophrenic angles. The heart size is within normal limits. '],['Findings: The lungs are clear. There is no pneumothorax. The heart and mediastinum are within normal limits. Regional bones and soft tissues are unremarkable. '],['chestxray_caption_dataset'] ['Please caption this chest X-ray scan with findings and impression'],"['Findings: Following pigtail catheter placement in the right lower chest, moderate right pleural effusion has near completely resolved. Moderate-to-large left pleural effusion associated with left lower lung atelectasis and mediastinal shift to the right side is unchanged. There is no pneumothorax. Obscured left mediastinal and the heart borders by pleural effusion limited assessment of the cardiomediastinal silhouette. Impression: Folowing right pigtail catheter placement, moderate right pleural effusion has near completely resolved, whereas large left pleural effusion associated with passive collapse of adjacent lung and mediastinal shift to the right side is persisting. No pneumothorax.']",['Findings: There is a moderate left pleural effusion with adjacent compressive collapse. The right lung is clear. Cardiomediastinal and hilar contours are normal. No pneumothorax. Impression: Moderate left pleural effusion with adjacent compressive collapse.'],['chestxray_caption_dataset'] ['Please given an impression this X-ray image'],['Impression: 1. New mild-to-moderate left pneumothorax with mild rightward shift of the mediastinum. 2. Stable right pneumothorax. 3. Moderate left pleural effusion.'],['Impression: No acute cardiopulmonary process.'],['chestxray_caption_dataset'] ['Can you offer a descriptive caption consists of findings for this medical image?'],"['Findings: AP upright and lateral chest radiographs were obtained. Known interstitial lung disease contributes to a bilateral perihilar interstitial abnormality. In addition to the chronic findings there is bilateral ground-glass opacity and interstitial thickening, predominantly radiating from the hila. Cardiomegaly remains moderate. Aortic arch calcifications are unchanged. A right-sided PICC line terminates in the low SVC. A left chest Port-A-Cath terminates in the right atrium. Vertebroplasty changes are stable. ']","['Findings: Lung volumes are low. There is no focal consolidation, pleural effusion or pneumothorax. The aorta is tortuous. There is a hiatal hernia. Clips are present in the right upper quadrant. ']",['chestxray_caption_dataset'] ['A radiology report consists of findings and impression is needed to explain this chest X-ray scan.'],"['Findings: New left-sided Port-A-Cath is seen entering the left subclavian and terminating within the right atrium and can be withdrawn 3 cm and still remains within the low SVC. There is stable mild-to-moderate pulmonary edema and stable small bilateral pleural effusions. Again seen are low lung volumes. Heart is stably enlarged. There is no pneumothorax. . Impression: Left-sided Port-A-Cath placement, terminates within the right atrium. Can be withdrawn 3 cm and still remain within the low SVC.']",['Findings: The lungs are clear. There is no pneumothorax. The heart and mediastinum are within normal limits. Regional bones and soft tissues are unremarkable. Impression: Clear lungs with no evidence of pneumonia.'],['chestxray_caption_dataset'] ['Can you offer an impression for this chest scan?'],"['Impression: Mild pulmonary edema superimposed on known lung fibrosis. Severe chronic cardiomegaly and pulmonary hypertension. No displaced rib fracture. Multiple vertebroplasties, similar to prior.']",['Impression: No acute cardiopulmonary process.'],['chestxray_caption_dataset'] ['Please write an impression for this chest scan.'],['Impression: No acute intrathoracic process.'],['Impression: No acute cardiopulmonary process.'],['chestxray_caption_dataset'] ['A radiology report consists of findings and impression is needed to explain this medical scan.'],"['Findings: Lung volumes are low. Elevation of the right hemidiaphragm appears similar. Cardiomegaly is again noted. Minimal linear left basilar opacity appears similar and likely represents atelectasis. Of note, evaluation is slightly limited in the absence of lateral view. No pleural effusion or pneumothorax is seen on this single view. No focal consolidation is seen on this single view. Aortic calcifications are again noted. Radiopaque material in the left abdomen may represent previously ingested oral contrast. Impression: Stable frontal chest radiograph. Limited evaluation in the setting of single frontal view; lateral view would be helpful for more thorough evaluation.']",['Findings: The cardiomediastinal and hilar contours are within normal limits. Increased opacity at the right lung base could reflect atelectasis in the setting of low lung volumes. Aspiration however cannot be excluded. There is no definite pleural effusion or pneumothorax. Impression: Increased opacity at the right lung base could reflect atelectasis in the setting of low lung volumes. Aspiration however cannot be excluded.'],['chestxray_caption_dataset'] ['Could you provide an impression for this chest scan?'],['Impression: No acute cardiopulmonary process.'],['Impression: No acute cardiopulmonary process.'],['chestxray_caption_dataset'] "[""I'm requesting a radiology report consists of findings and impression to clarify this X-ray image.""]",['Findings: The nasogastric tube is in adequate position and there is a resolution of the gastric distention. There is still mild bibasilar atelectasis. There are no pneumothorax no pleural effusion. The cardiac and mediastinal contour are unchanged. Impression: The nasogastric tube is in adequate position and there is resolution of the gastric distention.'],['Findings: There is a moderate right pleural effusion with adjacent atelectasis. There is also a small left pleural effusion. There is mild interstitial edema. The cardiac silhouette is mildly enlarged. The aorta is calcified and tortuous. No pneumothorax is seen. Impression: Moderate right and small left pleural effusions with mild interstitial edema.'],['chestxray_caption_dataset'] ['Could you provide an impression for this X-ray scan?'],['Impression: Mild acute congestive heart failure.'],['Impression: 1. Mild pulmonary edema. 2. Moderate cardiomegaly.'],['chestxray_caption_dataset'] ['Could you provide a radiology report consists of findings for this X-ray scan?'],"['Findings: A left pectoral dual-lead pacer with trans-subclavian lead extending to the right atrium and right ventricle is in unchanged position. There is no pneumothorax or pleural effusion. Hyperexpansion suggests underlying chronic obstructive pulmonary disease. New from prior study, there are multifocal lower and middle lobe parenchymal opacities. Given the provided history and the apparent lack of infectious symptoms, these could represent amiodarone toxicity. The hilar and cardiomediastinal contours are unchanged. There is no pulmonary vascular congestion or pulmonary edema to suggest congestive failure. ']",['Findings: The lungs are well expanded and clear. The hila and pulmonary vasculature are normal. No pleural abnormalities or pneumothorax. The cardiomediastinal silhouette is normal. No fractures. '],['chestxray_caption_dataset'] ['Please write a caption consists of findings that explains this medical image.'],"['Findings: The lungs are clear of consolidation, effusion, or pneumothorax. Left chest wall dual lead pacing device is again seen. Moderate cardiomegaly is again noted. Upper thoracic dextroscoliosis is seen. No acute fracture identified based on this nondedicated exam. Surgical clips seen in the upper abdomen. ']",['Findings: The lungs are hyperinflated. There is no focal consolidation or pneumothorax. Blunting of the left costophrenic sulcus may be due to a small pleural effusion. Scarring in the right mid lung is again seen. '],['chestxray_caption_dataset'] ['A caption consists of findings and impression is needed to explain this chest X-ray scan.'],"[""Findings: Single portable view of the chest. Low lung volumes are again noted. Chronic changes compatible with patients pulmonary fibrosis are noted. More severely affected areas seen at the bases, left greater than right. Cardiomediastinal silhouette is stable. No acute osseous abnormalities identified. Impression: Findings again compatible with patient's known pulmonary fibrosis without definite superimposed acute process, noting that subtle change would be difficult to detect based on a portable film.""]","['Findings: There is a moderate-sized right pleural effusion. There is mild interstitial edema. Lung volumes are low, exaggerating heart and mediastinal contours; there is likely underlying mild cardiomegaly. The aorta is tortuous. Increased density at the right lung base likely represents atelectasis, but infection cannot be excluded. Impression: Moderate-sized right pleural effusion and mild interstitial edema. Increased density at the right lung base, likely atelectasis, but consolidation cannot be excluded. Follow-up imaging after treatment is recommended.']",['chestxray_caption_dataset'] ['Could you provide an impression for this chest scan?'],"['Impression: Right lower lobe pneumonia, which has not cleared, and small right pleural effusion.']",['Impression: Mild pulmonary edema.'],['chestxray_caption_dataset'] ['Please write a caption consists of findings that explains this chest X-ray scan.'],"['Findings: The patient is status post left upper lobectomy, with expected persistent left lung volume loss and shift of mediastinal structures. The cardiac, mediastinal, and hilar contours are unchanged, allowing for differences in technique and rotation of the patient. Biapical scarring is again seen. There is no pneumothorax or new consolidation. ']","['Findings: The lungs are clear without focal consolidation, effusion, or edema. Cardiomediastinal silhouette is within normal limits. Small hiatal hernia is noted. ']",['chestxray_caption_dataset'] ['Could you provide an impression for this chest X-ray image?'],['Impression: Cardiomegaly and venous congestion.'],['Impression: No acute cardiopulmonary process.'],['chestxray_caption_dataset'] "[""I'm requesting a radiology report consists of findings and impression to clarify this X-ray image.""]","[""Findings: AP single view of the chest has been obtained with patient in sitting semi-upright position. Again noted is status post sternotomy and significant enlargement of the cardiac silhouette. Previously described permanent pacer in left axillary position with two intracavitary electrodes in unchanged location. Unchanged position of left internal jugular approach central venous line terminating in upper portion of SVC. No pneumothorax has developed. Diffuse haze over both lung bases as before obliterating the diaphragmatic contours and indicative of bilateral pleural effusions partially layering posteriorly. The pulmonary venous congestive pattern persists. An intra-aortic balloon pump device is seen to terminate in the descending thoracic aorta about 3 cm below the level of the lower thoracic arch contour. This is unchanged. Impression: No significant interval changes during the last 24 hours interval. The described changes with postoperative status, CHF, pleural effusion and intra-aortic balloon pump device in place is of course compatible with the patient's hypoxia.""]",['Findings: The right IJ central venous catheter terminates in the mid SVC. Bibasilar subsegmental atelectasis with low lung volumes are present. There is stable elevation of the right hemidiaphragm. Impression: Right IJ terminating in the mid SVC. Bibasilar subsegmental atelectasis with low lung volumes.'],['chestxray_caption_dataset'] ['Could you provide a caption consists of findings and impression for this chest X-ray scan?'],"['Findings: The heart size is normal. Lung volumes are low. Biapical fibrotic changes with traction bronchiectasis is re- demonstrated. Minimal blunting of the left costophrenic angle suggests a trace left pleural effusion. Streaky bibasilar airspace opacities likely reflect atelectasis. No pneumothorax is identified. Known fracture of the left 11th rib is not clearly delineated on this exam. Clips are seen projecting over the left upper quadrant. No new fractures are seen. There is crowding of the bronchovascular structures but no overt pulmonary edema is demonstrated. Impression: Chronic fibrotic changes within both lung apices. Low lung volumes with probable bibasilar atelectasis, though infection or aspiration cannot be excluded. Small left pleural effusion. Known left 11th rib fracture is not clearly seen on the current exam.']",['Findings: The lungs are clear. The cardiomediastinal silhouette is within normal limits. No acute osseous abnormalities. Impression: No acute cardiopulmonary process.'],['chestxray_caption_dataset'] ['Can you offer a descriptive caption consists of findings and impression for this X-ray image?'],"['Findings: Endotracheal tube tip terminates approximately 3.8 cm from the carina. An orogastric tube tip is noted within the distal stomach. Lung volumes are low. Heart size is normal. Mediastinal contours are unremarkable. Crowding of the bronchovascular structures is noted, and mild pulmonary vascular congestion is likely present. Additionally, more focal somewhat linear opacities within both upper lobes appear to be associated with fibrotic changes. No pleural effusion or pneumothorax is identified, although the right costophrenic angle is excluded from the field of view. Diffuse gaseous distention of the bowel loops are noted within the upper abdomen. No acute osseous abnormality seen. Surgical anchors are noted projecting over the right shoulder. Impression: 1. Standard positions of the endotracheal and orogastric tubes. 2. Focal, somewhat linear opacities within both upper lobes which may be due to a chronic interstitial process. Correlation with prior imaging is recommended. Aspiration or infection, however, cannot be completely excluded. 3. Mild pulmonary vascular congestion in the setting of low lung volumes.']",['Findings: The lungs are clear. The cardiomediastinal silhouette is within normal limits. No acute osseous abnormalities. Impression: No acute cardiopulmonary process.'],['chestxray_caption_dataset'] "[""I'm requesting a radiology report consists of findings and impression to clarify this medical scan.""]",['Findings: PA and lateral views of the chest. Bilateral upper lobe scarring is seen with superior retraction of the hila. The lung volumes are relatively low. There is no evidence of superimposed acute process. Cardiomediastinal silhouette is stable. Surgical clips in the upper abdomen again noted. Osseous structures are essentially unremarkable noting probable right glenoid orthopedic hardware. Impression: Bilateral upper lobe scarring unchanged without evidence of superimposed acute process.'],['Findings: The lungs are clear without focal consolidation. No pleural effusion or pneumothorax is seen. The cardiac and mediastinal silhouettes are unremarkable. Impression: No acute cardiopulmonary process.'],['chestxray_caption_dataset'] ['Could you provide an impression for this chest X-ray image?'],['Impression: 1. Increase in moderate left loculated pleural effusion. 2. Worsening of left lung pneumonia.'],['Impression: 1. No evidence of pneumonia. 2. Mild pulmonary edema.'],['chestxray_caption_dataset'] "[""I'm requesting a caption consists of findings and impression to clarify this X-ray image.""]",['Findings: PA and lateral views of the chest were provided. Effusion is seen. No pneumothorax. No signs of pulmonary edema. The heart appears stable in size. The mediastinal contour is unchanged. Bony structures are intact. Anchors are partially imaged at the right glenoid. Impression: Resolving b/l upper lobe pneumonia.'],['Findings: The lungs are clear without focal consolidation. No pleural effusion or pneumothorax is seen. The cardiac and mediastinal silhouettes are unremarkable. Impression: No acute cardiopulmonary process.'],['chestxray_caption_dataset'] ['Can you offer a descriptive caption consists of findings for this chest X-ray image?'],"['Findings: The cardiac, mediastinal, and hilar contours appear unchanged. Multifocal opacities which persist in the upper lungs with volume loss suggest chronic scarring without definite superimposed disease. Blunting of the left posterior costophrenic sulcus is unchanged, suggesting either trace pleural effusion or pleural thickening. Bony structures are unremarkable. ']",['Findings: The lungs are clear without focal consolidation. No pleural effusion or pneumothorax is seen. The cardiac and mediastinal silhouettes are unremarkable. '],['chestxray_caption_dataset'] ['Can you offer an impression for this medical scan?'],['Impression: New right upper lobe consolidation worrisome for infection on background chronic scarring.'],['Impression: No acute cardiopulmonary process.'],['chestxray_caption_dataset'] ['Could you describe what this chest X-ray image shows in a radiology report consists of findings?'],"['Findings: Lung volumes are reduced. The left internal jugular central venous catheter has been removed. The heart size is borderline enlarged, but accentuated due to low inspiratory lung volumes. There is crowding of the bronchovascular structures with probable mild pulmonary vascular congestion. Worsening consolidative opacity in the right upper lung field as well as focal opacities within the left upper and bilateral lower lung fields are concerning for multifocal pneumonia. No pleural effusion or pneumothorax is seen. No acute osseous abnormalities visualized. Clips are demonstrated within the left upper quadrant of the abdomen. ']",['Findings: There is a large left pleural effusion. The right lung is clear. The cardiomediastinal silhouette is obscured. No pneumothorax is identified. Atherosclerotic calcifications of the aortic arch are noted. '],['chestxray_caption_dataset'] ['Please write a radiology report consists of findings and impression that explains this X-ray image.'],['Findings: Single frontal radiograph of the chest was performed and reveals no acute cardiopulmonary process. The cardiomediastinal and pleural structures are unremarkable. There is scarring in the upper lungs with superior traction of the hila. There is no pleural effusion or pneumothorax. Heart size is normal. Impression: No acute cardiopulmonary process.'],['Findings: The lungs are clear. The cardiomediastinal silhouette is within normal limits. No acute osseous abnormalities. Impression: No acute cardiopulmonary process.'],['chestxray_caption_dataset'] ['A caption consists of findings and impression is needed to explain this X-ray image.'],['Findings: The heart size is within normal limits. Mediastinal and hilar contours are normal. The previously described resolving right upper lobe pneumonia has improved. There is increasing density over most of the left lung with a small left-sided pleural effusion. There is no pneumothorax. Anchors are present within the right glenoid. Impression: Improving right upper lobe pneumonia and increasing left lung opacity concerning for worsening or new pneumonia.'],['Findings: The lungs are clear. The cardiomediastinal silhouette is within normal limits. No acute osseous abnormalities. Impression: No acute cardiopulmonary process.'],['chestxray_caption_dataset'] ['Can you offer an impression for this medical scan?'],['Impression: No evidence of pneumothorax.'],['Impression: No acute cardiopulmonary process.'],['chestxray_caption_dataset'] ['Could you provide an impression for this chest scan?'],"['Impression: Increased opacity projecting over the right hemi thorax likely due to increased right pleural effusion with overlying atelectasis, underlying infectious process not excluded.']",['Impression: 1. Mild pulmonary edema. 2. Moderate cardiomegaly. 3. No evidence of pneumonia.'],['chestxray_caption_dataset'] ['A caption consists of findings and impression is needed to explain this X-ray image.'],['Findings: Cardiomediastinal contours are unchanged. The lungs are hyperinflated. There is no pneumothorax. Loculated right pleural effusion has increased. Small left effusion is stable. There are no evident thickening lung abnormality. Degenerative changes in the thoracic spine are again noted Impression: Increase in size in loculated right pleural effusion'],"['Findings: There is a small right pleural effusion with overlying atelectasis. Right base opacity may be due to combination of pleural effusion and atelectasis, but consolidation due to pneumonia is not excluded. No pneumothorax is seen. The cardiac silhouette is enlarged. Mediastinal contours are stable. The aorta is calcified. No pulmonary edema is seen. Impression: Small right pleural effusion with overlying atelectasis. Right base opacity may be due to combination of pleural effusion and atelectasis but additional consolidation not excluded. Cardiomegaly. No pulmonary edema.']",['chestxray_caption_dataset'] ['Please write an impression for this chest X-ray image.'],['Impression: Diffusely increased opacity throughout the right lung is related to a chronic loculated right effusion and multifocal opacities worrisome for pneumonia.'],['Impression: No acute cardiopulmonary process.'],['chestxray_caption_dataset'] "[""I'm requesting a caption consists of findings to clarify this medical scan.""]","['Findings: There is a persistence of a moderate layering pulmonary effusion on the right. There are no new focal opacities concerning for pneumonia. There is no pneumothorax. The cardiomediastinal and hilar contours are stable, with mild cardiomegaly. Pulmonary vascularity is not increased. ']","['Findings: There is a small right pleural effusion with overlying atelectasis. Right base opacity may be due to combination of pleural effusion and atelectasis, but consolidation due to pneumonia is not excluded. No pneumothorax is seen. The cardiac silhouette is enlarged. Mediastinal contours are stable. The aorta is calcified. No pulmonary edema is seen. ']",['chestxray_caption_dataset'] ================================================ FILE: src/test.py ================================================ # Import necessary libraries for data processing, modeling, and utilities import tqdm.auto as tqdm import torch.nn.functional as F from typing import Optional, Dict, Sequence from typing import List, Optional, Tuple, Union import transformers from My_Trainer.trainer import Trainer from dataclasses import dataclass, field from Dataset.multi_dataset_test import multi_dataset from Model.RadFM.multimodality_model import MultiLLaMAForCausalLM from datasampler import My_DistributedBatchSampler import torch from torch.utils.data import DataLoader import csv import random import numpy as np def setup_seed(seed): """ Set random seeds for reproducibility across different libraries Args: seed: Integer seed value to use """ torch.manual_seed(seed) torch.cuda.manual_seed_all(seed) np.random.seed(seed) random.seed(seed) torch.backends.cudnn.deterministic = True # Set seed for reproducibility setup_seed(20) @dataclass class ModelArguments: """ Arguments related to model paths and configuration """ lang_encoder_path: Optional[str] = field(default="/home/cs/leijiayu/wuchaoyi/book_pretrain/Results/Book_mix_2048_13B_full/checkpoint-45800") tokenizer_path: str = field(default='/home/cs/leijiayu/wuchaoyi/Finetune_LLAMA/LLAMA_Model/tokenizer', metadata={"help": "Path to the tokenizer data."}) #vision_encoder_path: str = field(default='/home/cs/leijiayu/wuchaoyi/multi_modal/src/PMC-CLIP/checkpoint.pt', metadata={"help": "Path to the vision_encoder."}) @dataclass class DataArguments: """ Arguments related to dataset configuration and testing modes """ Mode: Optional[str] = field(default="Train") test_split: Optional[str] = field(default="open") @dataclass class TrainingArguments(transformers.TrainingArguments): """ Custom training arguments extending HuggingFace's TrainingArguments with additional parameters for multimodal training """ remove_unused_columns: bool = field(default = False) batch_size_2D: int = field(default = 4) # Batch size for 2D data batch_size_3D: int = field(default = 1) # Batch size for 3D data output_dir: Optional[str] = field(default="/home/cs/leijiayu/wuchaoyi/multi_modal/src/Results/BLIP_overfit/") cache_dir: Optional[str] = field(default=None) optim: str = field(default="adamw_torch") @dataclass class DataCollator(object): """ Data collator for preparing batches of multimodal inputs for the model """ def __call__(self, instances: Sequence[Dict]) -> Dict[str, torch.Tensor]: # Extract different components from the input instances vision_xs, lang_xs, attention_masks, labels = tuple( [instance[key] for instance in instances] for key in ('vision_x','lang_x', 'attention_mask', 'labels') ) # Stack language tensors along batch dimension lang_xs = torch.cat([_.unsqueeze(0) for _ in lang_xs], dim=0) attention_masks = torch.cat([_.unsqueeze(0) for _ in attention_masks], dim=0) labels = torch.cat([_.unsqueeze(0) for _ in labels], dim=0) # Set target dimensions for resizing vision inputs target_H = 512 target_W = 512 target_D = 4 MAX_D = 0 # Reduce resolution for single samples to save memory if len(vision_xs) == 1: target_H = 256 target_W = 256 # Define possible depth values for 3D data D_list = list(range(4,65,4)) # Adjust depth values for large inputs if len(vision_xs) == 1: if vision_xs[0].shape[0] > 6: D_list = list(range(4,33,4)) # Find maximum depth in current batch for ii in vision_xs: try: D = ii.shape[-1] if D > MAX_D: MAX_D = D except: continue # Select closest target depth from available options for temp_D in D_list: if abs(temp_D - MAX_D) < abs(target_D - MAX_D): target_D = temp_D # Resize all vision inputs to target dimensions vision_xs = [torch.nn.functional.interpolate(s, size=(target_H, target_W, target_D)) for s in vision_xs] # Pad sequence for variable-length vision inputs vision_xs = torch.nn.utils.rnn.pad_sequence( vision_xs, batch_first=True, padding_value=0 ) print(vision_xs.shape) # Return collated batch return dict( lang_x=lang_xs, vision_x=vision_xs, attention_mask=attention_masks, labels=labels, ) def main(): """ Main function to set up and run the inference process """ # Parse command-line arguments parser = transformers.HfArgumentParser((ModelArguments, DataArguments, TrainingArguments)) model_args, data_args, training_args = parser.parse_args_into_dataclasses() # Set custom data sampler training_args.data_sampler = My_DistributedBatchSampler print("Setup Data") # Initialize test dataset with specified split Test_dataset = multi_dataset(text_tokenizer=model_args.tokenizer_path, test_split=data_args.test_split) # Configure DataLoader for test dataset Test_dataloader = DataLoader( Test_dataset, batch_size=1, num_workers=1, pin_memory=True, sampler=None, shuffle=True, collate_fn=None, drop_last=False, ) print("Setup Model") # Initialize the multimodal model model = MultiLLaMAForCausalLM( lang_model_path=model_args.lang_encoder_path, ) # Load pre-trained model checkpoint ckpt = torch.load('/gpfs/home/cs/leijiayu/wuchaoyi/wangyingjie/src/Results/backup/checkpoint-17600/pytorch_model.bin', map_location='cpu') # ckpt.pop('embedding_layer.figure_token_weight') model.load_state_dict(ckpt, strict=False) model = model.to('cuda') model.eval() # Set model to evaluation mode # Create output CSV file for results with open('output_whole_2_epoch' + data_args.test_split + '.csv', mode='w') as outfile: writer = csv.writer(outfile) writer.writerow(["Question", "Ground Truth", "Pred", 'belong_to']) cc = 0 # Process each sample in the test dataset for sample in tqdm.tqdm(Test_dataloader): question = sample["question"] belong_to = sample['belong_to'] # img_pp = sample['img_path'] # Tokenize the question text lang_x = Test_dataset.text_tokenizer( question, max_length=2048, truncation=True, return_tensors="pt" )['input_ids'].to('cuda') # Get vision input vision_x = sample["vision_x"].to('cuda') answer = sample['answer'] try: # Generate text based on text and vision inputs generation = model.generate(lang_x, vision_x) generated_texts = Test_dataset.text_tokenizer.batch_decode(generation, skip_special_tokens=True) # Write results to CSV writer.writerow([question, answer, generated_texts, belong_to]) cc = cc + 1 # if cc >= 10000: # break except: continue if __name__ == "__main__": main() ================================================ FILE: src/train.py ================================================ # Import necessary libraries import tqdm.auto as tqdm import torch.nn.functional as F from typing import Optional, Dict, Sequence from typing import List, Optional, Tuple, Union import transformers from My_Trainer.trainer import Trainer from dataclasses import dataclass, field from Dataset.multi_dataset import multi_dataset from Model.RadFM.multimodality_model import MultiLLaMAForCausalLM from datasampler import My_DistributedBatchSampler from datasets import load_metric from Dataset.multi_dataset_test_for_close import multi_dataset_close import numpy as np import torch def compute_metrics(eval_preds): """ Compute evaluation metrics from prediction outputs. Returns the mean accuracy across all predictions. Args: eval_preds: Prediction outputs from the model Returns: Dictionary containing accuracy metric """ # metric = load_metric("glue", "mrpc") ACCs = eval_preds.predictions # print(ACCs) return {"accuracy": np.mean(ACCs, axis=-1)} @dataclass class ModelArguments: """ Arguments pertaining to which model/config/tokenizer we are going to fine-tune. """ lang_encoder_path: Optional[str] = field(default="/home/cs/leijiayu/wuchaoyi/book_pretrain/Results/Book_mix_2048_13B_full/checkpoint-45800") tokenizer_path: str = field(default='/home/cs/leijiayu/wuchaoyi/Finetune_LLAMA/LLAMA_Model/tokenizer', metadata={"help": "Path to the tokenizer data."}) @dataclass class DataArguments: """ Arguments pertaining to data processing mode. """ Mode: Optional[str] = field(default="Train") @dataclass class TrainingArguments(transformers.TrainingArguments): """ Custom training arguments extending the HuggingFace TrainingArguments class. Includes additional parameters specific to this multimodal training setup. """ remove_unused_columns: bool = field(default=False) batch_size_2D: int = field(default=4) # Batch size for 2D data batch_size_3D: int = field(default=1) # Batch size for 3D data output_dir: Optional[str] = field(default="/home/cs/leijiayu/wuchaoyi/multi_modal/src/Results/BLIP_overfit/") cache_dir: Optional[str] = field(default=None) optim: str = field(default="adamw_torch") @dataclass class DataCollator(object): """ Data collator that handles batching of multimodal inputs. Processes vision and language inputs, handles padding, and resizes vision inputs. """ def __call__(self, instances: Sequence[Dict]) -> Dict[str, torch.Tensor]: # Extract different data components from instances vision_xs, lang_xs, attention_masks, labels, loss_reweight, key_words_query = tuple( [instance[key] for instance in instances] for key in ('vision_x', 'lang_x', 'attention_mask', 'labels', 'loss_reweight', 'key_words_query') ) # Stack language tensors along batch dimension lang_xs = torch.cat([_.unsqueeze(0) for _ in lang_xs], dim=0) attention_masks = torch.cat([_.unsqueeze(0) for _ in attention_masks], dim=0) labels = torch.cat([_.unsqueeze(0) for _ in labels], dim=0) loss_reweight = torch.cat([_.unsqueeze(0) for _ in loss_reweight], dim=0) # Set target dimensions for vision input resizing target_H = 512 target_W = 512 target_D = 4 MAX_D = 0 # Define possible depth values for 3D data D_list = list(range(4, 65, 4)) # Adjust depth range for larger inputs if len(vision_xs) == 1: if vision_xs[0].shape[0] > 6: D_list = list(range(4, 33, 4)) # Find maximum depth in current batch for ii in vision_xs: try: D = ii.shape[-1] if D > MAX_D: MAX_D = D except: continue # Select closest target depth from available options for temp_D in D_list: if abs(temp_D - MAX_D) < abs(target_D - MAX_D): target_D = temp_D # Reduce image dimensions for larger depth inputs with small batch size if len(vision_xs) == 1 and target_D > 4: target_H = 256 target_W = 256 # Resize all vision inputs to target dimensions vision_xs = [torch.nn.functional.interpolate(s, size=(target_H, target_W, target_D)) for s in vision_xs] # Pad sequence for variable-length vision inputs vision_xs = torch.nn.utils.rnn.pad_sequence( vision_xs, batch_first=True, padding_value=0 ) print(vision_xs.shape, vision_xs.dtype) # Return collated batch return dict( lang_x=lang_xs, vision_x=vision_xs, attention_mask=attention_masks, labels=labels, loss_reweight=loss_reweight, key_words_query=key_words_query ) def main(): """ Main function to set up and run the training process. Parses arguments, initializes datasets, model, and trainer. """ # Parse command-line arguments parser = transformers.HfArgumentParser((ModelArguments, DataArguments, TrainingArguments)) model_args, data_args, training_args = parser.parse_args_into_dataclasses() # Set custom data sampler training_args.data_sampler = My_DistributedBatchSampler print("Setup Data") # Initialize training and evaluation datasets Train_dataset = multi_dataset(text_tokenizer=model_args.tokenizer_path) Eval_dataset = multi_dataset_close(text_tokenizer=model_args.tokenizer_path) print("Setup Model") # Initialize the multimodal model model = MultiLLaMAForCausalLM( lang_model_path=model_args.lang_encoder_path, ) # Setup trainer with model, datasets, and configurations trainer = Trainer( model=model, train_dataset=Train_dataset, eval_dataset=Eval_dataset, args=training_args, data_collator=DataCollator(), compute_metrics=compute_metrics ) # Start training trainer.train() # Save training state trainer.save_state() if __name__ == "__main__": main()