SYMBOL INDEX (138 symbols across 25 files)

FILE: blue/bert/create_cdr_bert.py
  function _find_toks (line 8) | def _find_toks(sentences, start, end):
  function convert (line 20) | def convert(src, dest, entity_type, validate_mentions=None):
  class Commend (line 52) | class Commend:
    method chemical (line 53) | def chemical(self, input, output):
    method disease (line 56) | def disease(self, input, output):

FILE: blue/bert/create_chemprot_bert.py
  function find_entities (line 13) | def find_entities(sentence, entities, entity_type):
  function find_relations (line 23) | def find_relations(relations, chem, prot):
  function replace_text (line 33) | def replace_text(text, offset, ann1, ann2):
  function print_rel_debug (line 64) | def print_rel_debug(sentences, entities, id1, id2):
  function merge_sentences (line 84) | def merge_sentences(sentences):
  function convert (line 101) | def convert(abstract_file, entities_file, relation_file, output):
  function create_chemprot_bert (line 168) | def create_chemprot_bert(data_dir, output_dir):

FILE: blue/bert/create_clefe_bert.py
  function pattern_repl (line 14) | def pattern_repl(matchobj, prefix):
  function _find_toks (line 22) | def _find_toks(sentences, start, end):
  function read_text (line 34) | def read_text(pathname):
  function map_anns (line 48) | def map_anns(sentences, ann_file):
  function convert (line 71) | def convert(text_dir, ann_dir, dest, validate_mentions=None):
  function convert_train_gs_to_text (line 93) | def convert_train_gs_to_text(src_dir, dest_dir):
  function split_development (line 132) | def split_development(data_path, devel_docids_pathname):
  function create_clefe_bert (line 149) | def create_clefe_bert(gold_directory, output_directory):

FILE: blue/bert/create_ddi_bert.py
  function get_ann (line 11) | def get_ann(arg, obj):
  function replace_text (line 18) | def replace_text(text, offset, ann1, ann2):
  function create_ddi_bert (line 44) | def create_ddi_bert(gold_directory, output):

FILE: blue/bert/create_i2b2_bert.py
  function read_text (line 19) | def read_text(pathname):
  function _get_ann_offset (line 50) | def _get_ann_offset(sentences, match_obj: Match,
  function read_annotations (line 72) | def read_annotations(pathname, sentences):
  function _find_anns (line 97) | def _find_anns(anns, start, end):
  function read_relations (line 104) | def read_relations(pathname, sentences, cons):
  function find_relations (line 129) | def find_relations(relations, ann1, ann2):
  function convert (line 140) | def convert(top_dir, dest):
  function split_doc (line 180) | def split_doc(train1, train2, dev_docids, dest_dir):
  function create_i2b2_bert (line 200) | def create_i2b2_bert(gold_directory, output_directory):

FILE: blue/bert/create_mednli_bert.py
  function convert (line 11) | def convert(src, dest):
  function create_mednli (line 21) | def create_mednli(input_dir, output_dir):

FILE: blue/eval_hoc.py
  function get_p_r_f_arrary (line 13) | def get_p_r_f_arrary(test_predict_label, test_true_label):
  function eval_hoc (line 58) | def eval_hoc(true_file, pred_file):

FILE: blue/eval_mednli.py
  function eval_mednli (line 9) | def eval_mednli(gold_file, pred_file):

FILE: blue/eval_ner.py
  function has_strict (line 9) | def has_strict(target: Annotation, lst: List[Annotation]):
  function eval_cdr (line 16) | def eval_cdr(gold_file, pred_file):

FILE: blue/eval_rel.py
  function _read_relations (line 12) | def _read_relations(pathname):
  function eval_chemprot (line 23) | def eval_chemprot(gold_file, pred_file):

FILE: blue/eval_sts.py
  function eval_sts (line 5) | def eval_sts(true_file, pred_file):

FILE: blue/ext/data_structure.py
  class Span (line 5) | class Span:
    method __init__ (line 6) | def __init__(self, start: int, end: int, text: str):
    method __str__ (line 11) | def __str__(self):
    method __repr__ (line 14) | def __repr__(self):
  class Annotation (line 18) | class Annotation:
    method __init__ (line 19) | def __init__(self, id: str, docid: str, spans: List[Span], type: str):
    method __str__ (line 25) | def __str__(self):
    method __repr__ (line 28) | def __repr__(self):
    method strict_equal (line 31) | def strict_equal(self, another: 'Annotation') -> bool:
    method relaxed_equal (line 43) | def relaxed_equal(self, another: 'Annotation') -> bool:
    method to_obj (line 53) | def to_obj(self) -> Dict:
    method from_obj (line 62) | def from_obj(obj: Any) -> "Annotation":
  function read_annotations (line 68) | def read_annotations(pathname)->List[Annotation]:

FILE: blue/ext/pmetrics.py
  class Report (line 38) | class Report(object):
    method __init__ (line 39) | def __init__(self):
    method sensitivity (line 47) | def sensitivity(self, targetclass):
    method specificity (line 50) | def specificity(self, targetclass):
    method precision (line 53) | def precision(self, targetclass):
    method recall (line 56) | def recall(self, targetclass):
    method f1 (line 59) | def f1(self, targetclass):
    method sub_report (line 62) | def sub_report(self, targetclasses, *_, **kwargs) -> 'Report':
  function divide (line 115) | def divide(x, y):
  function tpr (line 119) | def tpr(tp, tn, fp, fn):
  function tnr (line 124) | def tnr(tp, tn, fp, fn):
  function tp_tn_fp_fn (line 129) | def tp_tn_fp_fn(confusion_matrix):
  function ppv (line 137) | def ppv(tp, tn, fp, fn):
  function npv (line 142) | def npv(tp, tn, fp, fn):
  function fpr (line 147) | def fpr(tp, tn, fp, fn):
  function fnr (line 152) | def fnr(tp, tn, fp, fn):
  function fdr (line 157) | def fdr(tp, tn, fp, fn):
  function accuracy (line 162) | def accuracy(tp, tn, fp, fn):
  function f1 (line 167) | def f1(precision, recall):
  function cohen_kappa (line 171) | def cohen_kappa(confusion, weights=None):
  function micro (line 194) | def micro(tp, tn, fp, fn):
  function overall_acc (line 208) | def overall_acc(tp, tn, fp, fn):
  function weighted_acc (line 213) | def weighted_acc(tp, tn, fp, fn):
  function micro_weighted (line 220) | def micro_weighted(tp, tn, fp, fn):
  function confusion_matrix_report (line 237) | def confusion_matrix_report(confusion_matrix, *_, **kwargs) -> 'Report':
  function auc (line 291) | def auc(y_true, y_score, y_column: int = 1):
  function multi_class_auc (line 304) | def multi_class_auc(y_true, y_score):
  function classification_report (line 326) | def classification_report(y_true, y_pred, *_, **kwargs) -> 'Report':
  function precision_recall_fscore_multilabel (line 343) | def precision_recall_fscore_multilabel(y_true, y_pred, *_, **kwargs):
  function test_cm1 (line 371) | def test_cm1():
  function test_cm2 (line 380) | def test_cm2():
  function test_kappa (line 406) | def test_kappa():
  function test_precision_recall_fscore_multilabel (line 417) | def test_precision_recall_fscore_multilabel():

FILE: blue/ext/preprocessing.py
  function split_punct (line 10) | def split_punct(text, start):
  function tokenize_text (line 15) | def tokenize_text(text, id):
  function print_ner_debug (line 36) | def print_ner_debug(sentences, start, end):
  function write_bert_ner_file (line 58) | def write_bert_ner_file(dest, total_sentences):

FILE: blue/ext/pstring.py
  function printable (line 206) | def printable(s: str, greeklish=False, verbose=False, replacement=' ') -...

FILE: blue/ext/pubtator.py
  class Pubtator (line 9) | class Pubtator:
    method __init__ (line 11) | def __init__(self, pmid: str=None, title: str=None, abstract: str=None):
    method __str__ (line 18) | def __str__(self):
    method __iter__ (line 28) | def __iter__(self):
    method text (line 36) | def text(self):
  class PubtatorAnn (line 46) | class PubtatorAnn:
    method __init__ (line 47) | def __init__(self, pmid, start, end, text, type, id):
    method __str__ (line 56) | def __str__(self):
    method __iter__ (line 59) | def __iter__(self):
  class PubtatorRel (line 68) | class PubtatorRel:
    method __init__ (line 69) | def __init__(self, pmid, type, id1, id2):
    method __str__ (line 76) | def __str__(self):
    method __iter__ (line 79) | def __iter__(self):
  function loads (line 90) | def loads(s: str) -> List[Pubtator]:
  function load (line 100) | def load(fp) -> List[Pubtator]:
  function __iterparse (line 113) | def __iterparse(line_iterator):

FILE: blue/gs/create_cdr_test_gs.py
  function create_test_gs (line 9) | def create_test_gs(input, output, type):

FILE: blue/gs/create_chemprot_test_gs.py
  function _read_entities (line 9) | def _read_entities(pathname):
  function _read_relations (line 18) | def _read_relations(pathname):
  function create_test_gs (line 29) | def create_test_gs(entities, relations, output):

FILE: blue/gs/create_clefe_test_gs.py
  function pattern_repl (line 14) | def pattern_repl(matchobj, prefix):
  function _proprocess_text (line 22) | def _proprocess_text(text):
  function create_test_gs (line 31) | def create_test_gs(reports_dir, anns_dir, output):

FILE: blue/gs/create_ddi_test_gs.py
  function create_test_gs (line 10) | def create_test_gs(input_dir, output):

FILE: blue/gs/create_hoc.py
  function split_doc (line 8) | def split_doc(docid_file, data_dir, dest):
  function create_hoc (line 27) | def create_hoc(hoc_dir):

FILE: blue/gs/create_i2b2_test_gs.py
  function read_text (line 19) | def read_text(pathname):
  function _get_ann_offset (line 50) | def _get_ann_offset(sentences, match_obj: Match,
  function read_annotations (line 73) | def read_annotations(pathname, sentences):
  function _find_anns (line 98) | def _find_anns(anns, start, end):
  function read_relations (line 105) | def read_relations(pathname, sentences, cons):
  function find_relations (line 130) | def find_relations(relations, ann1, ann2):
  function create_test_gs (line 141) | def create_test_gs(input_dir, output_dir):

FILE: blue/gs/create_mednli_test_gs.py
  function create_mednli_test_gs (line 10) | def create_mednli_test_gs(input, output):

FILE: blue_plus/dataset.py
  class BaseDataset (line 4) | class BaseDataset(object):
    method __init__ (line 7) | def __init__(self, config_file):
    method full_name (line 18) | def full_name(self):
    method download (line 22) | def download(self, download_dir='blue_plus_data', override=False):
    method evaluate (line 39) | def evaluate(self, test_file, prediction_file, output_file):

FILE: blue_plus/example_dataset/biosses_dataset.py
  class BIOSSES_Dataset (line 15) | class BIOSSES_Dataset(BaseDataset):
    method download (line 16) | def download(self, download_dir='blue_plus_data', override=False):
    method evaluate (line 27) | def evaluate(self, test_file, prediction_file, results_file):
    method evaluate_bert (line 38) | def evaluate_bert(self, test_file, prediction_file, results_file):
    method prepare_bert_format (line 41) | def prepare_bert_format(self, input_file, output_file):
  function main (line 48) | def main():