SYMBOL INDEX (144 symbols across 16 files)

FILE: clasp/clasp.py
  class CLASP (line 5) | class CLASP(nn.Module):
    method __init__ (line 6) | def __init__(
    method forward (line 17) | def forward(

FILE: clasp/positional.py
  function rotate_every_two (line 7) | def rotate_every_two(x):
  function apply_rotary_pos_emb (line 13) | def apply_rotary_pos_emb(q, k, sinu_pos):
  class SinuEmb (line 20) | class SinuEmb(nn.Module):
    method __init__ (line 21) | def __init__(self, dim, max_seq_len):
    method forward (line 29) | def forward(self, x):

FILE: clasp/reversible.py
  function route_args (line 8) | def route_args(router, args, depth):
  class Deterministic (line 20) | class Deterministic(nn.Module):
    method __init__ (line 21) | def __init__(self, net):
    method record_rng (line 29) | def record_rng(self, *args):
    method forward (line 35) | def forward(self, *args, record_rng = False, set_rng = False, **kwargs):
  class ReversibleBlock (line 54) | class ReversibleBlock(nn.Module):
    method __init__ (line 55) | def __init__(self, f, g):
    method forward (line 60) | def forward(self, x, f_args = {}, g_args = {}):
    method backward_pass (line 70) | def backward_pass(self, y, dy, f_args = {}, g_args = {}):
  class _ReversibleFunction (line 108) | class _ReversibleFunction(Function):
    method forward (line 110) | def forward(ctx, x, blocks, args):
    method backward (line 119) | def backward(ctx, dy):
  class SequentialSequence (line 126) | class SequentialSequence(nn.Module):
    method __init__ (line 127) | def __init__(self, layers, args_route = {}):
    method forward (line 133) | def forward(self, x, **kwargs):
  class ReversibleSequence (line 142) | class ReversibleSequence(nn.Module):
    method __init__ (line 143) | def __init__(self, blocks, args_route = {}):
    method forward (line 148) | def forward(self, x, **kwargs):

FILE: clasp/simple_tokenizer.py
  function default_bpe (line 14) | def default_bpe():
  function bytes_to_unicode (line 18) | def bytes_to_unicode():
  function get_pairs (line 30) | def get_pairs(word):
  function basic_clean (line 38) | def basic_clean(text):
  function whitespace_clean (line 43) | def whitespace_clean(text):
  class SimpleTokenizer (line 48) | class SimpleTokenizer(object):
    method __init__ (line 49) | def __init__(self, bpe_path = default_bpe()):
    method bpe (line 68) | def bpe(self, token):
    method encode (line 109) | def encode(self, text):
    method decode (line 117) | def decode(self, tokens, remove_start_end = True):
  function tokenize (line 127) | def tokenize(texts, context_length = 256, add_start = False, add_end = F...

FILE: clasp/transformer.py
  function exists (line 17) | def exists(val):
  function uniq (line 20) | def uniq(arr):
  function cast_tuple (line 23) | def cast_tuple(val, depth = 1):
  function default (line 28) | def default(val, d):
  function max_neg_value (line 33) | def max_neg_value(t):
  class Attention (line 38) | class Attention(nn.Module):
    method __init__ (line 39) | def __init__(self, dim, seq_len, heads = 8, dim_head = 64, dropout = 0.):
    method apply_rel_pos_emb (line 52) | def apply_rel_pos_emb(self, q, k, rel_pos_emb = None):
    method forward (line 61) | def forward(self, x, mask = None, rel_pos_emb = None):
  class SparseAttention (line 86) | class SparseAttention(Attention):
    method __init__ (line 87) | def __init__(
    method forward (line 111) | def forward(self, x, mask = None, rel_pos_emb = None):
  class LayerScale (line 138) | class LayerScale(nn.Module):
    method __init__ (line 139) | def __init__(self, dim, depth, fn):
    method forward (line 151) | def forward(self, x, **kwargs):
  class PreNorm (line 154) | class PreNorm(nn.Module):
    method __init__ (line 155) | def __init__(self, dim, fn):
    method forward (line 160) | def forward(self, x, **kwargs):
  class GEGLU (line 163) | class GEGLU(nn.Module):
    method forward (line 164) | def forward(self, x):
  class FeedForward (line 168) | class FeedForward(nn.Module):
    method __init__ (line 169) | def __init__(self, dim, dropout = 0., mult = 4.):
    method forward (line 178) | def forward(self, x):
  class Transformer (line 181) | class Transformer(nn.Module):
    method __init__ (line 182) | def __init__(
    method forward (line 241) | def forward(self, x, mask = None):

FILE: clasp/utils.py
  function basic_sampler (line 11) | def basic_sampler(seq, sample_len):
  function basic_rand_sampler (line 23) | def basic_rand_sampler(seq, sample_len):
  function basic_aa_tokenizer (line 40) | def basic_aa_tokenizer(seq, context_length, return_mask=True):
  class CLASPDataset (line 56) | class CLASPDataset(Dataset):
    method __init__ (line 61) | def __init__(self, path, text_sampler, bioseq_sampler, text_tok, biose...
    method __len__ (line 79) | def __len__(self):
    method __getitem__ (line 82) | def __getitem__(self, idx):
  class RankSplitDataset (line 99) | class RankSplitDataset(Dataset):
    method __init__ (line 100) | def __init__(self, file_path, offset_dict, rank, world_size, logger=No...
    method __len__ (line 131) | def __len__(self):
    method __getitem__ (line 134) | def __getitem__(self, idx):
  class CLASPRankSplitDataset (line 138) | class CLASPRankSplitDataset(RankSplitDataset):
    method __init__ (line 144) | def __init__(self, file_path, offset_dict, rank, world_size, logger,
    method __getitem__ (line 154) | def __getitem__(self, idx):

FILE: preproc/create_offset_dict.py
  function get_args (line 7) | def get_args():
  function main (line 20) | def main():

FILE: preproc/preprocess_data.py
  function get_csv (line 68) | def get_csv(path, fields):

FILE: preproc/preprocess_data_reduced.py
  function get_csv (line 69) | def get_csv(path, fields):

FILE: train/example_inference_multigpu.py
  function get_args (line 34) | def get_args():
  function setup (line 100) | def setup(rank, world_size):
  function cleanup (line 107) | def cleanup():
  function run (line 111) | def run(func, world_size):
  function trainer (line 118) | def trainer(rank, world_size):

FILE: train/inference_multigpu_ecpred_test.py
  function get_args (line 35) | def get_args():
  function set_requires_grad (line 105) | def set_requires_grad(model, option=False):
  class ECPredEnzymePredDataset (line 110) | class ECPredEnzymePredDataset(Dataset):
    method __init__ (line 111) | def __init__(self, path, bioseq_sampler, bioseq_tok):
    method __len__ (line 121) | def __len__(self):
    method __getitem__ (line 124) | def __getitem__(self, idx):
  function setup (line 135) | def setup(rank, world_size):
  function cleanup (line 142) | def cleanup():
  function run (line 146) | def run(func, world_size):
  function inferer (line 153) | def inferer(rank, world_size):

FILE: train/inference_multigpu_loss_test.py
  function get_args (line 35) | def get_args():
  function set_requires_grad (line 101) | def set_requires_grad(model, option=False):
  function setup (line 106) | def setup(rank, world_size):
  function cleanup (line 113) | def cleanup():
  function run (line 117) | def run(func, world_size):
  function inferer (line 124) | def inferer(rank, world_size):

FILE: train/inference_multigpu_simple_query_test.py
  function get_args (line 36) | def get_args():
  function set_requires_grad (line 102) | def set_requires_grad(model, option=False):
  function setup (line 107) | def setup(rank, world_size):
  function cleanup (line 114) | def cleanup():
  function run (line 118) | def run(func, world_size):
  function inferer (line 125) | def inferer(rank, world_size):

FILE: train/train.py
  function get_args (line 30) | def get_args():
  function create_logger (line 96) | def create_logger(path_log, file_name):
  function setup (line 117) | def setup(rank, world_size):
  function cleanup (line 124) | def cleanup():
  class AverageMeter (line 128) | class AverageMeter(object):
    method __init__ (line 130) | def __init__(self):
    method reset (line 133) | def reset(self):
    method update (line 139) | def update(self, val, n=1):
  function reduce_tensor (line 147) | def reduce_tensor(tensor, n):
  function train_ddp (line 160) | def train_ddp(args, model, optimizer, dl_train, epochs, logger=None, wri...
  function run (line 266) | def run(func, world_size):
  function trainer (line 273) | def trainer(rank, world_size):

FILE: train/train_multigpusim.py
  function get_args (line 32) | def get_args():
  function create_logger (line 106) | def create_logger(path_log, file_name):
  function setup (line 127) | def setup(rank, world_size):
  function cleanup (line 133) | def cleanup():
  class AverageMeter (line 137) | class AverageMeter(object):
    method __init__ (line 139) | def __init__(self):
    method reset (line 142) | def reset(self):
    method update (line 148) | def update(self, val, n=1):
  function reduce_tensor (line 156) | def reduce_tensor(tensor, n):
  function train_ddp (line 163) | def train_ddp(args, model, optimizer, dl_train, dl_valid_id, dl_valid_oo...
  function run (line 365) | def run(func, world_size):
  function trainer (line 372) | def trainer(rank, world_size):

FILE: train/train_multigpusim_wandb.py
  function get_args (line 34) | def get_args():
  function create_logger (line 108) | def create_logger(path_log, file_name):
  function setup (line 129) | def setup(rank, world_size):
  function cleanup (line 135) | def cleanup():
  class AverageMeter (line 139) | class AverageMeter(object):
    method __init__ (line 141) | def __init__(self):
    method reset (line 144) | def reset(self):
    method update (line 150) | def update(self, val, n=1):
  function reduce_tensor (line 158) | def reduce_tensor(tensor, n):
  function train_ddp (line 165) | def train_ddp(args, model, optimizer, dl_train, dl_valid_id, dl_valid_oo...
  function run (line 382) | def run(func, world_size):
  function trainer (line 389) | def trainer(rank, world_size):