def converted(self) -> Tokenizer:
from .models.roformer.tokenization_utils import JiebaPreTokenizer
vocab = self.original_tokenizer.vocab
tokenizer = Tokenizer(
WordPiece(vocab, unk_token=str(self.original_tokenizer.unk_token)))
strip_accents = False
do_lower_case = False
if hasattr(self.original_tokenizer, "basic_tokenizer"):
strip_accents = self.original_tokenizer.basic_tokenizer.strip_accents
do_lower_case = self.original_tokenizer.basic_tokenizer.do_lower_case
tokenizer.normalizer = normalizers.BertNormalizer(
clean_text=True,
handle_chinese_chars=False,
strip_accents=strip_accents,
lowercase=do_lower_case,
)
tokenizer.pre_tokenizer = pre_tokenizers.PreTokenizer.custom(
JiebaPreTokenizer(vocab))
cls = str(self.original_tokenizer.cls_token)
sep = str(self.original_tokenizer.sep_token)
cls_token_id = self.original_tokenizer.cls_token_id
sep_token_id = self.original_tokenizer.sep_token_id
tokenizer.post_processor = processors.TemplateProcessing(
single=f"{cls}:0 $A:0 {sep}:0",
pair=f"{cls}:0 $A:0 {sep}:0 $B:1 {sep}:1",
special_tokens=[
(cls, cls_token_id),
(sep, sep_token_id),
],
)
tokenizer.decoder = decoders.WordPiece(prefix="##")
return tokenizer
def converted(self) -> Tokenizer:
vocab = self.original_tokenizer.vocab
tokenizer = Tokenizer(
WordPiece(vocab, unk_token=str(self.original_tokenizer.unk_token)))
tokenize_chinese_chars = False
strip_accents = False
do_lower_case = False
if hasattr(self.original_tokenizer, "basic_tokenizer"):
tokenize_chinese_chars = self.original_tokenizer.basic_tokenizer.tokenize_chinese_chars
strip_accents = self.original_tokenizer.basic_tokenizer.strip_accents
do_lower_case = self.original_tokenizer.basic_tokenizer.do_lower_case
tokenizer.normalizer = normalizers.BertNormalizer(
clean_text=True,
handle_chinese_chars=tokenize_chinese_chars,
strip_accents=strip_accents,
lowercase=do_lower_case,
)
tokenizer.pre_tokenizer = pre_tokenizers.BertPreTokenizer()
cls = str(self.original_tokenizer.cls_token)
sep = str(self.original_tokenizer.sep_token)
cls_token_id = self.original_tokenizer.cls_token_id
sep_token_id = self.original_tokenizer.sep_token_id
tokenizer.post_processor = processors.TemplateProcessing(
single=
f"{cls}:2 $A:0 {sep}:0", # token_type_id is 2 for Funnel transformer
pair=f"{cls}:2 $A:0 {sep}:0 $B:1 {sep}:1",
special_tokens=[
(cls, cls_token_id),
(sep, sep_token_id),
],
)
tokenizer.decoder = decoders.WordPiece(prefix="##")
return tokenizer
def from_file(vocab: str, **kwargs):
vocab = WordPiece.read_file(vocab)
return BertWordPieceTokenizer(vocab, **kwargs)
def __init__(
self,
vocab: Optional[Union[str, Dict[str, int]]] = None,
unk_token: Union[str, AddedToken] = "[UNK]",
sep_token: Union[str, AddedToken] = "[SEP]",
cls_token: Union[str, AddedToken] = "[CLS]",
pad_token: Union[str, AddedToken] = "[PAD]",
mask_token: Union[str, AddedToken] = "[MASK]",
clean_text: bool = True,
handle_chinese_chars: bool = True,
strip_accents: Optional[bool] = None,
lowercase: bool = True,
wordpieces_prefix: str = "##",
):
if vocab is not None:
tokenizer = Tokenizer(WordPiece(vocab, unk_token=str(unk_token)))
else:
tokenizer = Tokenizer(WordPiece(unk_token=str(unk_token)))
# Let the tokenizer know about special tokens if they are part of the vocab
if tokenizer.token_to_id(str(unk_token)) is not None:
tokenizer.add_special_tokens([str(unk_token)])
if tokenizer.token_to_id(str(sep_token)) is not None:
tokenizer.add_special_tokens([str(sep_token)])
if tokenizer.token_to_id(str(cls_token)) is not None:
tokenizer.add_special_tokens([str(cls_token)])
if tokenizer.token_to_id(str(pad_token)) is not None:
tokenizer.add_special_tokens([str(pad_token)])
if tokenizer.token_to_id(str(mask_token)) is not None:
tokenizer.add_special_tokens([str(mask_token)])
tokenizer.normalizer = BertNormalizer(
clean_text=clean_text,
handle_chinese_chars=handle_chinese_chars,
strip_accents=strip_accents,
lowercase=lowercase,
)
tokenizer.pre_tokenizer = BertPreTokenizer()
if vocab is not None:
sep_token_id = tokenizer.token_to_id(str(sep_token))
if sep_token_id is None:
raise TypeError("sep_token not found in the vocabulary")
cls_token_id = tokenizer.token_to_id(str(cls_token))
if cls_token_id is None:
raise TypeError("cls_token not found in the vocabulary")
tokenizer.post_processor = BertProcessing(
(str(sep_token), sep_token_id), (str(cls_token), cls_token_id))
tokenizer.decoder = decoders.WordPiece(prefix=wordpieces_prefix)
parameters = {
"model": "BertWordPiece",
"unk_token": unk_token,
"sep_token": sep_token,
"cls_token": cls_token,
"pad_token": pad_token,
"mask_token": mask_token,
"clean_text": clean_text,
"handle_chinese_chars": handle_chinese_chars,
"strip_accents": strip_accents,
"lowercase": lowercase,
"wordpieces_prefix": wordpieces_prefix,
}
super().__init__(tokenizer, parameters)
for line in tqdm(fin):
dp = json.loads(line.strip())
for d in enumerate(dp):
if "value" in d:
if "," in d["value"]:
print('Not cleaned up')
# Extract value/types from trees and store in comma separated raw file (all_raw.json)
with open("output/all_new_trees.json") as fin, open("output/all_raw.json",
"w") as fout:
for i, line in enumerate(tqdm(fin)):
dp = json.loads(line)
token_list = []
for d in dp:
if "value" in d:
token_list.append(d["value"])
elif "type" in d:
token_list.append(d["type"])
raw = ",".join(token_list)
print(json.dumps(raw), file=fout)
# Train tokenizer on raw file
tokenizer = Tokenizer(WordPiece(unk_token="[UNK]"))
tokenizer.pre_tokenizer = CharDelimiterSplit(delimiter=",")
trainer = WordPieceTrainer(special_tokens=["[UNK]", "[PAD]"])
tokenizer.train(["output/all_raw.json"], trainer)
tokenizer.save("output/tokenizer.json")
def __init__(
self,
vocab_file: Optional[str] = None,
add_special_tokens: bool = True,
unk_token: str = "[UNK]",
sep_token: str = "[SEP]",
cls_token: str = "[CLS]",
clean_text: bool = True,
handle_chinese_chars: bool = True,
strip_accents: bool = True,
lowercase: bool = True,
wordpieces_prefix: str = "##",
):
if vocab_file is not None:
tokenizer = Tokenizer(WordPiece.from_files(vocab_file, unk_token=unk_token))
else:
tokenizer = Tokenizer(WordPiece.empty())
# Let the tokenizer know about special tokens if they are part of the vocab
if tokenizer.token_to_id(unk_token) is not None:
tokenizer.add_special_tokens([unk_token])
if tokenizer.token_to_id(sep_token) is not None:
tokenizer.add_special_tokens([sep_token])
if tokenizer.token_to_id(cls_token) is not None:
tokenizer.add_special_tokens([cls_token])
tokenizer.normalizer = BertNormalizer(
clean_text=clean_text,
handle_chinese_chars=handle_chinese_chars,
strip_accents=strip_accents,
lowercase=lowercase,
)
tokenizer.pre_tokenizer = BertPreTokenizer()
if add_special_tokens and vocab_file is not None:
sep_token_id = tokenizer.token_to_id(sep_token)
if sep_token_id is None:
raise TypeError("sep_token not found in the vocabulary")
cls_token_id = tokenizer.token_to_id(cls_token)
if cls_token_id is None:
raise TypeError("cls_token not found in the vocabulary")
tokenizer.post_processor = BertProcessing(
(sep_token, sep_token_id), (cls_token, cls_token_id)
)
tokenizer.decoder = decoders.WordPiece(prefix=wordpieces_prefix)
parameters = {
"model": "BertWordPiece",
"add_special_tokens": add_special_tokens,
"unk_token": unk_token,
"sep_token": sep_token,
"cls_token": cls_token,
"clean_text": clean_text,
"handle_chinese_chars": handle_chinese_chars,
"strip_accents": strip_accents,
"lowercase": lowercase,
"wordpieces_prefix": wordpieces_prefix,
}
super().__init__(tokenizer, parameters)
if args.type == "gpt2":
print("Running GPT-2 tokenizer")
tok_p = GPT2Tokenizer.from_pretrained("gpt2")
# Create a Tokenizer using BPE
tok_r = Tokenizer(BPE(args.vocab, args.merges))
# Use ByteLevel PreTokenizer
tok_r.pre_tokenizer = pre_tokenizers.ByteLevel(add_prefix_space=False)
# Use ByteLevel Decoder
tok_r.decoder = decoders.ByteLevel()
elif args.type == "bert":
print("Running Bert tokenizer")
tok_p = BertTokenizer.from_pretrained(args.vocab)
tok_r = Tokenizer(WordPiece(args.vocab, unk_token="[UNK]", max_input_chars_per_word=100))
tok_r.normalizer = BertNormalizer(
clean_text=True,
handle_chinese_chars=True,
strip_accents=True,
lowercase=True,
)
# tok_r.pre_tokenizer = pre_tokenizers.Whitespace()
tok_r.pre_tokenizer = pre_tokenizers.BertPreTokenizer()
tok_r.decoder = decoders.WordPiece()
tok_r.post_processor = BertProcessing(
("[SEP]", tok_r.token_to_id("[SEP]")),
("[CLS]", tok_r.token_to_id("[CLS]")),
)
else:
raise Exception(f"Unknown type {args.type}")
print("Running GPT-2 tokenizer")
tok_p = GPT2Tokenizer.from_pretrained('gpt2')
# Create a Tokenizer using BPE
tok_r = Tokenizer(BPE.from_files(args.vocab, args.merges))
# Use ByteLevel PreTokenizer
tok_r.pre_tokenizer = pre_tokenizers.ByteLevel(add_prefix_space=False)
# Use ByteLevel Decoder
tok_r.decoder = decoders.ByteLevel()
elif args.type == "bert":
print("Running Bert tokenizer")
tok_p = BertTokenizer.from_pretrained(args.vocab)
tok_r = Tokenizer(
WordPiece.from_files(args.vocab,
unk_token="[UNK]",
max_input_chars_per_word=100))
tok_r.normalizer = BertNormalizer(
clean_text=True,
handle_chinese_chars=True,
strip_accents=True,
lowercase=True,
)
# tok_r.pre_tokenizer = pre_tokenizers.Whitespace()
tok_r.pre_tokenizer = pre_tokenizers.BertPreTokenizer()
tok_r.decoder = decoders.WordPiece()
tok_r.post_processor = BertProcessing(
("[SEP]", tok_r.token_to_id("[SEP]")),
("[CLS]", tok_r.token_to_id("[CLS]")),
)
else:
def train_custom_tokenizer(dataset,
token_model,
tknzr_file,
vocab_size,
vocab=None,
pretrain_fast=False,
max_input_chars_per_word=None,
eos_token=None,
bos_token=None,
pad_token=None,
mask_token=None,
unk_token=None):
"""
Building a Tokenizer using HuggingFace library. The pipeline seems to be:
- Model : algorithm that tokenizes, it is a mandatory
component. There are only 4 models implemented
(BPE, Unigram, WordLevel, WordPiece)
- Normalizer : some preprocessing that could happen before, but
doesn't necessarily have to
- Pre-Tokenizer : splitting the input according to some rules
- Post-Processing : needing to add some tokens/input after (mostly seems
to be eos, bos tokens)
- Decoder : certain previous pipeline steps need to be reversed
for proper decoding
- Trainer : The corresponding training algorithm for the model
Note : Some pre-processing might need to happen beforehand in previous
functions (might be easier using pandas before)
Input
token_model (str) : algorithm to use for tokenization
dataset (class) : a python iterator that goes through the data
to be used for training
token_dir (str) : directory with tokenizers
vocab_size (int) : size of the vocabulary to use
tokenFilename (str) : filename of particular token we want to
train. Will overwrite previously save files.
vocab (list of str) : models other than BPE can use non-mandatory
vocab as input
max_input_chars_per_word : used for WordPiece
Output
tokenizer : huggingFace Tokenizer object, our fully
trainer tokenizer
"""
special_token_lst = [
pad_token, bos_token, eos_token, mask_token, unk_token
]
# NFKC
normalizer_lst = []
pre_tokenizer_lst = [Whitespace, ByteLevel]
decoder_lst = []
bos_idx = special_token_lst.index(bos_token)
eos_idx = special_token_lst.index(eos_token)
if token_model == 'BPE':
model = BPE(unk_token=unk_token)
Trainer = BpeTrainer
elif token_model == 'Unigram':
model = Unigram(vocab=vocab)
Trainer = UnigramTrainer
elif token_model == 'WordLevel':
model = WordLevel(unk_token=unk_token, vocab=vocab)
Trainer = WordLevelTrainer
elif token_model == 'WordPiece':
model = WordPiece(unk_token=unk_token,
vocab=vocab,
max_input_chars_per_word=max_input_chars_per_word)
Trainer = WordPieceTrainer
else:
error_msg = f'Error: token_model ({token_model}) not an algorithm in%s' \
% VALID_TOKENIZATIONS
raise SystemExit(error_msg)
# instantiation
tokenizer = Tokenizer(model)
# Select a tokenization trainer
if vocab_size is None:
trainer = Trainer(show_progress=True, special_tokens=special_token_lst)
else:
trainer = Trainer(vocab_size=vocab_size,
show_progress=True,
special_tokens=special_token_lst)
# Set the normalizer
tokenizer.normalizer = normalizers.Sequence(
[fcn() for fcn in normalizer_lst])
# Set the pre-tokenizer
tokenizer.pre_tokenizer = pre_tokenizers.Sequence(
[fcn() for fcn in pre_tokenizer_lst])
# Set the post-processing
tokenizer.post_processor = processors.TemplateProcessing(
single=bos_token + " $A " + eos_token,
special_tokens=[(bos_token, bos_idx), (eos_token, eos_idx)],
# pair=bos_token+" $A "+eos_token" $B:1 "+eos_token+":1",
)
# Set the decoder
if ByteLevel in pre_tokenizer_lst:
tokenizer.decoder = decoders.ByteLevel()
if Metaspace in pre_tokenizer_lst:
tokenizer.decoder = decoders.Metaspace()
if token_model == 'WordPiece':
tokenizer.decoder = decoders.WordPiece()
# creating iterator
def batch_iterator():
for i in np.arange(0, len(dataset)):
yield dataset[i]
# train call
tokenizer.train_from_iterator(trainer=trainer,
iterator=batch_iterator(),
length=len(dataset))
if Path(tknzr_file).exists():
print(f"Warning : overwriting previously save tokenizer with\
same filename ( {tknzr_file} ).")
tokenizer.save(tknzr_file)
if pretrain_fast:
tokenizer = PreTrainedTokenizerFast(tokenizer_file=tknzr_file)
else:
tokenizer = PreTrainedTokenizer(tokenizer_file=tknzr_file)
tokenizer.pad_token = pad_token
tokenizer.mask_token = mask_token
return tokenizer
def test_instantiate(self, bert_files):
assert isinstance(WordPiece.empty(), Model)
assert isinstance(WordPiece.from_files(bert_files["vocab"]), Model)
def load_vocab(self, vocab, merges):
vocab, merges = tok_model.read_file(vocab, merges)
self.tokenizer.model = tok_model(vocab, merges)
def prepare_tokenizer(self):
tokenizer = Tokenizer(WordPiece(unk_token='[UNK]'))
tokenizer.pre_tokenizer = Whitespace()
tokenizer.normalizer = Sequence([Lowercase(), NFKC()])
return tokenizer
def preprocess_data(args):
label_counter = Counter([])
examples_per_file = Counter()
print("Reading all files for labels.")
for input_file in args.input_files:
with xopen(input_file, "rt") as f:
for example, labels in input_readers[args.task](f):
examples_per_file[input_file] += 1
label_counter.update(labels)
if args.top_n_labels > 0:
mlb_full = MultiLabelBinarizer(sparse_output=True)
mlb_full = mlb_full.fit(label_counter.keys())
label_counter = dict(label_counter.most_common(args.top_n_labels))
mlb = MultiLabelBinarizer(sparse_output=True)
# Passing a list in a list because that's what the function wants.
if args.labels_in:
labels = json.load(open(args.labels_in))
mlb = mlb.fit([labels])
else:
mlb = mlb.fit([[pair for pair in label_counter]])
# Save list of partial -> full mapping if doing top N labels.
if args.top_n_labels > 0:
label_mapping = np.where(np.in1d(mlb_full.classes_,
mlb.classes_))[0].tolist()
with xopen(args.label_mapping, "wt") as f:
f.write(json.dumps(label_mapping))
# Also save the full labels.
with xopen(args.full_labels, "wt") as f:
f.write(json.dumps(list(mlb_full.classes_)))
# Save list of labels.
with xopen(args.labels_out, "wt") as f:
f.write(json.dumps(list(mlb.classes_)))
# Set parallel tokenization thread count.
os.environ["RAYON_NUM_THREADS"] = str(args.processes)
from tokenizers import Tokenizer, decoders, trainers
from tokenizers.models import WordPiece
from tokenizers.normalizers import BertNormalizer
from tokenizers.pre_tokenizers import BertPreTokenizer
from tokenizers.processors import BertProcessing
if args.task == 'cafa':
# Define our custom tokenizer.
# It is exactly the same as the default BERT tokenizer, except for max_input_chars_per_word
# being 20000 instead of 100. This tokenizer is very slow on the long protein sequences.
tokenizer = WordPiece.from_files(args.vocab,
unk_token="[UNK]",
max_input_chars_per_word=20000)
tokenizer = Tokenizer(tokenizer)
tokenizer.add_special_tokens(["[UNK]", "[SEP]", "[CLS]"])
tokenizer.normalizer = BertNormalizer(lowercase=args.do_lower_case)
tokenizer.pre_tokenizer = BertPreTokenizer()
tokenizer.post_processor = BertProcessing(
("[SEP]", tokenizer.token_to_id("[SEP]")),
("[CLS]", tokenizer.token_to_id("[CLS]")))
tokenizer.decoder = decoders.WordPiece(prefix='##')
else:
tokenizer = BertWordPieceTokenizer(args.vocab,
lowercase=args.do_lower_case)
tokenizer.enable_padding(max_length=args.seq_len)
tokenizer.enable_truncation(max_length=args.seq_len)
for input_file in args.input_files:
with xopen(input_file, 'rt') as in_f:
file_name = generate_out_filename(input_file, args)
with xopen(file_name, "wt") as out_f:
print("Processing to: ", file_name)
# Write the shape as the first row, useful for the finetuning.
if args.labels_in:
n_labels = len(json.load(open(args.labels_in)))
else:
n_labels = len(label_counter)
out_f.write(
json.dumps((examples_per_file[input_file], n_labels)) +
'\n')
batch_size = min(examples_per_file[input_file],
args.processes * 100)
example_batch = []
labels_batch = []
doc_idx_batch = []
with ParallelGenerator(input_readers[args.task](in_f),
max_lookahead=batch_size) as g:
START_POS = int(args.window_start) / 100
for doc_idx, (example, labels) in enumerate(g):
#example = ' '.join(example.split(' ')[-510:])
example_batch.append(example)
labels_batch.append(labels)
doc_idx_batch.append(doc_idx)
if len(example_batch) == batch_size:
example_batch = tokenizer.encode_batch(
example_batch)
labels_batch = mlb.transform(labels_batch)
for example, labels, doc_idx in zip(
example_batch, labels_batch,
doc_idx_batch):
# Convert sparse arrays to python lists for json dumping.
# print(labels);input()
labels = labels.nonzero()[1].tolist()
"""try:
[][0]
print("DOC_LEN:",len(example.overflowing)+1)
mid = len(example.overflowing)//2
out_f.write(json.dumps( [example.overflowing[mid].ids, labels, len(example.overflowing)+1] ) + '\n')
except IndexError:
out_f.write(json.dumps( [example.ids, labels, len(example.overflowing)+1] ) + '\n')"""
if args.all_blocks or args.n_blocks > 0:
blocks = [example.ids] + [
blk.ids for blk in example.overflowing
]
#print("BLOCKS:%d,TOKENS:%d" % (len(list(blocks)), sum([len(list(tokens)) for tokens in blocks])))
for b, block in enumerate(blocks, 2):
if b > args.n_blocks and args.n_blocks > 0:
break
out_f.write(
json.dumps(
[block, labels, doc_idx]) +
'\n')
else:
window = get_window(example, START_POS)
assert len(window) == 512
assert all(
[type(y) is int for y in window])
out_f.write(
json.dumps([window, labels]) + '\n')
example_batch = []
labels_batch = []
# Write out whatever is left in the last smaller batch.
example_batch = tokenizer.encode_batch(example_batch)
labels_batch = mlb.transform(labels_batch)
for example, labels, doc_idx in zip(
example_batch, labels_batch, doc_idx_batch):
# Convert sparse arrays to python lists for json dumping.
# print(labels);input()
labels = labels.nonzero()[1].tolist()
"""try:
[][0]
print("DOC_LEN:",len(example.overflowing)+1)
mid = len(example.overflowing)//2
out_f.write(json.dumps( [example.overflowing[mid].ids, labels, len(example.overflowing)+1] ) + '\n')
except IndexError:
out_f.write(json.dumps( [example.ids, labels, len(example.overflowing)+1] ) + '\n')"""
if args.all_blocks or args.n_blocks > 0:
blocks = [example.ids] + [
blk.ids for blk in example.overflowing
]
#print("BLOCKS:%d,TOKENS:%d" % (len(list(blocks)), sum([len(list(tokens)) for tokens in blocks])))
for b, block in enumerate(blocks, 2):
if b > args.n_blocks and args.n_blocks > 0:
break
out_f.write(
json.dumps([block, labels, doc_idx]) +
'\n')
else:
out_f.write(
json.dumps(
[get_window(example, START_POS), labels]) +
'\n')
from tokenizers import Tokenizer
from tokenizers.models import WordPiece
from tokenizers.trainers import WordPieceTrainer
from tokenizers.pre_tokenizers import Whitespace
from tokenizers.normalizers import Sequence, NFD, Lowercase, Strip
def train(dataset_path,
output_dir='data/tokenizer/',
vocab_size=30_000,
min_frequency=3):
trainer = WordPieceTrainer(vocab_size=vocab_size,
min_frequency=min_frequency,
special_tokens=['[UNK]', '[CLS]', '[SEP]', '[PAD]', '[MASK]'])
tokenizer = Tokenizer(WordPiece())
tokenizer.pre_tokenizer = Whitespace()
tokenizer.normalizer = Sequence([NFD(), Lowercase(), Strip()])
files = [dataset_path]
tokenizer.train(trainer, files)
files = tokenizer.model.save(output_dir)
tokenizer.model = WordPiece.from_file(*files, unk_token='[UNK]')
tokenizer.save(f'{output_dir}tokenizer.json')
if __name__ == '__main__':
fire.Fire(train)
def preprocess_data(args):
label_counter = Counter([])
examples_per_file = Counter()
print("Reading all files for labels.")
for input_file in args.input_files:
with xopen(input_file, "rt") as f:
for example, labels in input_readers[args.task](f):
examples_per_file[input_file] += 1
label_counter.update(labels)
if args.top_n_labels > 0:
mlb_full = MultiLabelBinarizer(sparse_output=True)
mlb_full = mlb_full.fit(label_counter.keys())
label_counter = dict(label_counter.most_common(args.top_n_labels))
mlb = MultiLabelBinarizer(sparse_output=True)
# Passing a list in a list because that's what the function wants.
mlb = mlb.fit([[pair for pair in label_counter]])
# Save list of partial -> full mapping if doing top N labels.
if args.top_n_labels > 0:
label_mapping = np.where(np.in1d(mlb_full.classes_,
mlb.classes_))[0].tolist()
with xopen(args.label_mapping, "wt") as f:
f.write(json.dumps(label_mapping))
# Also save the full labels.
with xopen(args.full_labels, "wt") as f:
f.write(json.dumps(list(mlb_full.classes_)))
# Save list of labels.
with xopen(args.labels_out, "wt") as f:
f.write(json.dumps(list(mlb.classes_)))
# Set parallel tokenization thread count.
os.environ["RAYON_NUM_THREADS"] = str(args.processes)
from tokenizers import Tokenizer, decoders, trainers
from tokenizers.models import WordPiece
from tokenizers.normalizers import BertNormalizer
from tokenizers.pre_tokenizers import BertPreTokenizer
from tokenizers.processors import BertProcessing
if args.task == 'cafa':
# Define our custom tokenizer.
# It is exactly the same as the default BERT tokenizer, except for max_input_chars_per_word
# being 20000 instead of 100. This tokenizer is very slow on the long protein sequences.
tokenizer = WordPiece.from_files(args.vocab,
unk_token="[UNK]",
max_input_chars_per_word=20000)
tokenizer = Tokenizer(tokenizer)
tokenizer.add_special_tokens(["[UNK]", "[SEP]", "[CLS]"])
tokenizer.normalizer = BertNormalizer(lowercase=args.do_lower_case)
tokenizer.pre_tokenizer = BertPreTokenizer()
tokenizer.post_processor = BertProcessing(
("[SEP]", tokenizer.token_to_id("[SEP]")),
("[CLS]", tokenizer.token_to_id("[CLS]")))
tokenizer.decoder = decoders.WordPiece(prefix='##')
else:
tokenizer = BertWordPieceTokenizer(args.vocab,
lowercase=args.do_lower_case)
tokenizer.enable_padding(max_length=args.seq_len)
tokenizer.enable_truncation(max_length=args.seq_len)
for input_file in args.input_files:
with xopen(input_file, 'rt') as in_f:
file_name = generate_out_filename(input_file, args)
with xopen(file_name, "wt") as out_f:
print("Processing to: ", file_name)
# Write the shape as the first row, useful for the finetuning.
out_f.write(
json.dumps((examples_per_file[input_file],
len(label_counter))) + '\n')
batch_size = min(examples_per_file[input_file],
args.processes * 100)
example_batch = []
labels_batch = []
with ParallelGenerator(input_readers[args.task](in_f),
max_lookahead=batch_size) as g:
for example, labels in g:
example_batch.append(example)
labels_batch.append(labels)
if len(example_batch) == batch_size:
example_batch = tokenizer.encode_batch(
example_batch)
labels_batch = mlb.transform(labels_batch)
for example, labels in zip(example_batch,
labels_batch):
# Convert sparse arrays to python lists for json dumping.
# print(labels);input()
labels = labels.nonzero()[1].tolist()
out_f.write(
json.dumps([example.ids, labels]) + '\n')
example_batch = []
labels_batch = []
# Write out whatever is left in the last smaller batch.
example_batch = tokenizer.encode_batch(example_batch)
labels_batch = mlb.transform(labels_batch)
for example, labels in zip(example_batch, labels_batch):
# Convert sparse arrays to python lists for json dumping.
# print(labels);input()
labels = labels.nonzero()[1].tolist()
out_f.write(json.dumps([example.ids, labels]) + '\n')
def test_instantiation_from_tokenizers(self):
bert_tokenizer = Tokenizer(WordPiece(unk_token="[UNK]"))
PreTrainedTokenizerFast(tokenizer_object=bert_tokenizer)
def test_instantiate(self, bert_files):
assert isinstance(WordPiece(), Model)
assert isinstance(WordPiece(), WordPiece)
assert isinstance(WordPiece(bert_files["vocab"]), Model)
def test_instantiation_from_tokenizers_json_file(self):
bert_tokenizer = Tokenizer(WordPiece(unk_token="[UNK]"))
with tempfile.TemporaryDirectory() as tmpdirname:
bert_tokenizer.save(os.path.join(tmpdirname, "tokenizer.json"))
PreTrainedTokenizerFast(
tokenizer_file=os.path.join(tmpdirname, "tokenizer.json"))
def __init__(self, **kwargs):
super().__init__(**kwargs)
self.tokenizer = _get_module_or_attr("tokenizers",
"Tokenizer")(WordPiece())
self.trainer = WordPieceTrainer
def __init__(self,
vocab_file: Optional[str] = None,
unk_token: Union[str, AddedToken] = "<unk>",
sep_token: Union[str, AddedToken] = "</s>",
cls_token: Union[str, AddedToken] = "<s>",
nl_token: Union[str, AddedToken] = "<nl>",
pad_token: Union[str, AddedToken] = "<pad>",
mask_token: Union[str, AddedToken] = "<mask>",
clean_text: bool = True,
handle_chinese_chars: bool = True,
separate_numbers: bool = True,
strip_accents: bool = True,
lowercase: bool = True,
wordpieces_prefix: str = "##",
special_chars: str = SPECIAL_CHARS,
zh_norm: bool = True,
handle_simpl: bool = True,
do_postprocess: bool = False):
if vocab_file is not None:
tokenizer = Tokenizer(
WordPiece(vocab_file, unk_token=str(unk_token)))
else:
tokenizer = Tokenizer(WordPiece())
# Let the tokenizer know about special tokens if they are part of the vocab
if tokenizer.token_to_id(str(unk_token)) is not None:
tokenizer.add_special_tokens([str(unk_token)])
if tokenizer.token_to_id(str(sep_token)) is not None:
tokenizer.add_special_tokens([str(sep_token)])
if tokenizer.token_to_id(str(cls_token)) is not None:
tokenizer.add_special_tokens([str(cls_token)])
if tokenizer.token_to_id(str(pad_token)) is not None:
tokenizer.add_special_tokens([str(pad_token)])
if tokenizer.token_to_id(str(nl_token)) is not None:
tokenizer.add_special_tokens([str(nl_token)])
if tokenizer.token_to_id(str(mask_token)) is not None:
tokenizer.add_special_tokens([str(mask_token)])
if tokenizer.token_to_id(str(mask_token)) is not None:
tokenizer.add_special_tokens([str(mask_token)])
tokenizer.normalizer = Sequence([
NFKC(),
BertNormalizer(clean_text=clean_text,
handle_chinese_chars=handle_chinese_chars,
separate_numbers=separate_numbers,
strip_accents=strip_accents,
lowercase=lowercase,
special_chars=special_chars,
zh_norm=zh_norm,
handle_simpl=handle_simpl)
])
tokenizer.pre_tokenizer = BertPreTokenizer()
if vocab_file is not None and do_postprocess:
sep_token_id = tokenizer.token_to_id(str(sep_token))
if sep_token_id is None:
raise TypeError("sep_token not found in the vocabulary")
cls_token_id = tokenizer.token_to_id(str(cls_token))
if cls_token_id is None:
raise TypeError("cls_token not found in the vocabulary")
tokenizer.post_processor = BertProcessing(
(str(sep_token), sep_token_id), (str(cls_token), cls_token_id))
tokenizer.decoder = decoders.WordPiece(prefix=wordpieces_prefix)
parameters = {
"model": "BertWordPiece",
"unk_token": unk_token,
"sep_token": sep_token,
"cls_token": cls_token,
"nl_token": nl_token,
"pad_token": pad_token,
"mask_token": mask_token,
"clean_text": clean_text,
"handle_chinese_chars": handle_chinese_chars,
"separate_numbers": separate_numbers,
"strip_accents": strip_accents,
"lowercase": lowercase,
"special_chars": special_chars,
"zh_norm": zh_norm,
"handle_simpl": handle_simpl,
"wordpieces_prefix": wordpieces_prefix,
}
super().__init__(tokenizer, parameters)
