|
""" |
|
Geneformer precollator and pretrainer. |
|
|
|
Huggingface data collator and trainer modified to accommodate single-cell transcriptomics data. |
|
""" |
|
import collections |
|
import math |
|
import pickle |
|
import warnings |
|
from enum import Enum |
|
from typing import Dict, Iterator, List, Optional, Union |
|
|
|
import numpy as np |
|
import torch |
|
from datasets import Dataset |
|
from packaging import version |
|
from torch.utils.data.distributed import DistributedSampler |
|
from torch.utils.data.sampler import RandomSampler |
|
from transformers import ( |
|
BatchEncoding, |
|
DataCollatorForLanguageModeling, |
|
SpecialTokensMixin, |
|
Trainer, |
|
) |
|
from transformers.file_utils import is_datasets_available, is_sagemaker_dp_enabled |
|
from transformers.trainer_pt_utils import ( |
|
DistributedLengthGroupedSampler, |
|
DistributedSamplerWithLoop, |
|
LengthGroupedSampler, |
|
) |
|
from transformers.training_args import ParallelMode |
|
from transformers.utils import is_tf_available, is_torch_available, logging, to_py_obj |
|
from transformers.utils.generic import _is_tensorflow, _is_torch |
|
|
|
logger = logging.get_logger(__name__) |
|
EncodedInput = List[int] |
|
VERY_LARGE_INTEGER = int( |
|
1e30 |
|
) |
|
LARGE_INTEGER = int( |
|
1e20 |
|
) |
|
|
|
if is_sagemaker_dp_enabled(): |
|
import smdistributed.dataparallel.torch.distributed as dist |
|
else: |
|
import torch.distributed as dist |
|
|
|
_is_torch_generator_available = False |
|
if version.parse(torch.__version__) >= version.parse("1.6"): |
|
_is_torch_generator_available = True |
|
|
|
|
|
class ExplicitEnum(Enum): |
|
""" |
|
Enum with more explicit error message for missing values. |
|
""" |
|
|
|
@classmethod |
|
def _missing_(cls, value): |
|
raise ValueError( |
|
"%r is not a valid %s, please select one of %s" |
|
% (value, cls.__name__, str(list(cls._value2member_map_.keys()))) |
|
) |
|
|
|
|
|
class TruncationStrategy(ExplicitEnum): |
|
""" |
|
Possible values for the ``truncation`` argument in :meth:`PreTrainedTokenizerBase.__call__`. Useful for |
|
tab-completion in an IDE. |
|
""" |
|
|
|
ONLY_FIRST = "only_first" |
|
ONLY_SECOND = "only_second" |
|
LONGEST_FIRST = "longest_first" |
|
DO_NOT_TRUNCATE = "do_not_truncate" |
|
|
|
|
|
class PaddingStrategy(ExplicitEnum): |
|
""" |
|
Possible values for the ``padding`` argument in :meth:`PreTrainedTokenizerBase.__call__`. Useful for tab-completion |
|
in an IDE. |
|
""" |
|
|
|
LONGEST = "longest" |
|
MAX_LENGTH = "max_length" |
|
DO_NOT_PAD = "do_not_pad" |
|
|
|
|
|
class TensorType(ExplicitEnum): |
|
""" |
|
Possible values for the ``return_tensors`` argument in :meth:`PreTrainedTokenizerBase.__call__`. Useful for |
|
tab-completion in an IDE. |
|
""" |
|
|
|
PYTORCH = "pt" |
|
TENSORFLOW = "tf" |
|
NUMPY = "np" |
|
JAX = "jax" |
|
|
|
|
|
class GeneformerPreCollator(SpecialTokensMixin): |
|
def __init__(self, *args, **kwargs) -> None: |
|
super().__init__(mask_token="<mask>", pad_token="<pad>") |
|
|
|
self.token_dictionary = kwargs.get("token_dictionary") |
|
self.padding_side = "right" |
|
self.model_input_names = ["input_ids"] |
|
|
|
def convert_ids_to_tokens(self, value): |
|
return self.token_dictionary.get(value) |
|
|
|
def _get_padding_truncation_strategies( |
|
self, |
|
padding=False, |
|
truncation=False, |
|
max_length=None, |
|
pad_to_multiple_of=None, |
|
verbose=True, |
|
**kwargs, |
|
): |
|
""" |
|
Find the correct padding/truncation strategy with backward compatibility for old arguments (truncation_strategy |
|
and pad_to_max_length) and behaviors. |
|
""" |
|
old_truncation_strategy = kwargs.pop("truncation_strategy", "do_not_truncate") |
|
old_pad_to_max_length = kwargs.pop("pad_to_max_length", False) |
|
|
|
|
|
|
|
if max_length is not None and padding is False and truncation is False: |
|
if verbose: |
|
if not self.deprecation_warnings.get( |
|
"Truncation-not-explicitly-activated", False |
|
): |
|
logger.warning( |
|
"Truncation was not explicitly activated but `max_length` is provided a specific value, " |
|
"please use `truncation=True` to explicitly truncate examples to max length. " |
|
"Defaulting to 'longest_first' truncation strategy. " |
|
"If you encode pairs of sequences (GLUE-style) with the tokenizer you can select this strategy " |
|
"more precisely by providing a specific strategy to `truncation`." |
|
) |
|
self.deprecation_warnings["Truncation-not-explicitly-activated"] = True |
|
truncation = "longest_first" |
|
|
|
|
|
if padding is False and old_pad_to_max_length: |
|
if verbose: |
|
warnings.warn( |
|
"The `pad_to_max_length` argument is deprecated and will be removed in a future version, " |
|
"use `padding=True` or `padding='longest'` to pad to the longest sequence in the batch, or " |
|
"use `padding='max_length'` to pad to a max length. In this case, you can give a specific " |
|
"length with `max_length` (e.g. `max_length=45`) or leave max_length to None to pad to the " |
|
"maximal input size of the model (e.g. 512 for Bert).", |
|
FutureWarning, |
|
) |
|
if max_length is None: |
|
padding_strategy = PaddingStrategy.LONGEST |
|
else: |
|
padding_strategy = PaddingStrategy.MAX_LENGTH |
|
elif padding is not False: |
|
if padding is True: |
|
padding_strategy = ( |
|
PaddingStrategy.LONGEST |
|
) |
|
elif not isinstance(padding, PaddingStrategy): |
|
padding_strategy = PaddingStrategy(padding) |
|
elif isinstance(padding, PaddingStrategy): |
|
padding_strategy = padding |
|
else: |
|
padding_strategy = PaddingStrategy.DO_NOT_PAD |
|
|
|
|
|
if truncation is False and old_truncation_strategy != "do_not_truncate": |
|
if verbose: |
|
warnings.warn( |
|
"The `truncation_strategy` argument is deprecated and will be removed in a future version, " |
|
"use `truncation=True` to truncate examples to a max length. You can give a specific " |
|
"length with `max_length` (e.g. `max_length=45`) or leave max_length to None to truncate to the " |
|
"maximal input size of the model (e.g. 512 for Bert). " |
|
" If you have pairs of inputs, you can give a specific truncation strategy selected among " |
|
"`truncation='only_first'` (will only truncate the first sentence in the pairs) " |
|
"`truncation='only_second'` (will only truncate the second sentence in the pairs) " |
|
"or `truncation='longest_first'` (will iteratively remove tokens from the longest sentence in the pairs).", |
|
FutureWarning, |
|
) |
|
truncation_strategy = TruncationStrategy(old_truncation_strategy) |
|
elif truncation is not False: |
|
if truncation is True: |
|
truncation_strategy = ( |
|
TruncationStrategy.LONGEST_FIRST |
|
) |
|
elif not isinstance(truncation, TruncationStrategy): |
|
truncation_strategy = TruncationStrategy(truncation) |
|
elif isinstance(truncation, TruncationStrategy): |
|
truncation_strategy = truncation |
|
else: |
|
truncation_strategy = TruncationStrategy.DO_NOT_TRUNCATE |
|
|
|
|
|
if max_length is None: |
|
if padding_strategy == PaddingStrategy.MAX_LENGTH: |
|
if self.model_max_length > LARGE_INTEGER: |
|
if verbose: |
|
if not self.deprecation_warnings.get( |
|
"Asking-to-pad-to-max_length", False |
|
): |
|
logger.warning( |
|
"Asking to pad to max_length but no maximum length is provided and the model has no predefined maximum length. " |
|
"Default to no padding." |
|
) |
|
self.deprecation_warnings["Asking-to-pad-to-max_length"] = True |
|
padding_strategy = PaddingStrategy.DO_NOT_PAD |
|
else: |
|
max_length = self.model_max_length |
|
|
|
if truncation_strategy != TruncationStrategy.DO_NOT_TRUNCATE: |
|
if self.model_max_length > LARGE_INTEGER: |
|
if verbose: |
|
if not self.deprecation_warnings.get( |
|
"Asking-to-truncate-to-max_length", False |
|
): |
|
logger.warning( |
|
"Asking to truncate to max_length but no maximum length is provided and the model has no predefined maximum length. " |
|
"Default to no truncation." |
|
) |
|
self.deprecation_warnings[ |
|
"Asking-to-truncate-to-max_length" |
|
] = True |
|
truncation_strategy = TruncationStrategy.DO_NOT_TRUNCATE |
|
else: |
|
max_length = self.model_max_length |
|
|
|
|
|
if padding_strategy != PaddingStrategy.DO_NOT_PAD and ( |
|
not self.pad_token or self.pad_token_id < 0 |
|
): |
|
raise ValueError( |
|
"Asking to pad but the tokenizer does not have a padding token. " |
|
"Please select a token to use as `pad_token` `(tokenizer.pad_token = tokenizer.eos_token e.g.)` " |
|
"or add a new pad token via `tokenizer.add_special_tokens({'pad_token': '[PAD]'})`." |
|
) |
|
|
|
|
|
if ( |
|
truncation_strategy != TruncationStrategy.DO_NOT_TRUNCATE |
|
and padding_strategy != PaddingStrategy.DO_NOT_PAD |
|
and pad_to_multiple_of is not None |
|
and max_length is not None |
|
and (max_length % pad_to_multiple_of != 0) |
|
): |
|
raise ValueError( |
|
f"Truncation and padding are both activated but " |
|
f"truncation length ({max_length}) is not a multiple of pad_to_multiple_of ({pad_to_multiple_of})." |
|
) |
|
|
|
return padding_strategy, truncation_strategy, max_length, kwargs |
|
|
|
def pad( |
|
self, |
|
encoded_inputs: Union[ |
|
BatchEncoding, |
|
List[BatchEncoding], |
|
Dict[str, EncodedInput], |
|
Dict[str, List[EncodedInput]], |
|
List[Dict[str, EncodedInput]], |
|
], |
|
padding: Union[bool, str, PaddingStrategy] = True, |
|
max_length: Optional[int] = None, |
|
pad_to_multiple_of: Optional[int] = None, |
|
return_attention_mask: Optional[bool] = True, |
|
return_tensors: Optional[Union[str, TensorType]] = None, |
|
verbose: bool = True, |
|
) -> BatchEncoding: |
|
""" |
|
Pad a single encoded input or a batch of encoded inputs up to predefined length or to the max sequence length |
|
in the batch. |
|
|
|
Padding side (left/right) padding token ids are defined at the tokenizer level (with ``self.padding_side``, |
|
``self.pad_token_id`` and ``self.pad_token_type_id``) |
|
|
|
.. note:: |
|
|
|
If the ``encoded_inputs`` passed are dictionary of numpy arrays, PyTorch tensors or TensorFlow tensors, the |
|
result will use the same type unless you provide a different tensor type with ``return_tensors``. In the |
|
case of PyTorch tensors, you will lose the specific device of your tensors however. |
|
|
|
Args: |
|
encoded_inputs (:class:`~transformers.BatchEncoding`, list of :class:`~transformers.BatchEncoding`, :obj:`Dict[str, List[int]]`, :obj:`Dict[str, List[List[int]]` or :obj:`List[Dict[str, List[int]]]`): |
|
Tokenized inputs. Can represent one input (:class:`~transformers.BatchEncoding` or :obj:`Dict[str, |
|
List[int]]`) or a batch of tokenized inputs (list of :class:`~transformers.BatchEncoding`, `Dict[str, |
|
List[List[int]]]` or `List[Dict[str, List[int]]]`) so you can use this method during preprocessing as |
|
well as in a PyTorch Dataloader collate function. |
|
|
|
Instead of :obj:`List[int]` you can have tensors (numpy arrays, PyTorch tensors or TensorFlow tensors), |
|
see the note above for the return type. |
|
padding (:obj:`bool`, :obj:`str` or :class:`~transformers.tokenization_utils_base.PaddingStrategy`, `optional`, defaults to :obj:`True`): |
|
Select a strategy to pad the returned sequences (according to the model's padding side and padding |
|
index) among: |
|
|
|
* :obj:`True` or :obj:`'longest'`: Pad to the longest sequence in the batch (or no padding if only a |
|
single sequence if provided). |
|
* :obj:`'max_length'`: Pad to a maximum length specified with the argument :obj:`max_length` or to the |
|
maximum acceptable input length for the model if that argument is not provided. |
|
* :obj:`False` or :obj:`'do_not_pad'` (default): No padding (i.e., can output a batch with sequences of |
|
different lengths). |
|
max_length (:obj:`int`, `optional`): |
|
Maximum length of the returned list and optionally padding length (see above). |
|
pad_to_multiple_of (:obj:`int`, `optional`): |
|
If set will pad the sequence to a multiple of the provided value. |
|
|
|
This is especially useful to enable the use of Tensor Cores on NVIDIA hardware with compute capability |
|
>= 7.5 (Volta). |
|
return_attention_mask (:obj:`bool`, `optional`): |
|
Whether to return the attention mask. If left to the default, will return the attention mask according |
|
to the specific tokenizer's default, defined by the :obj:`return_outputs` attribute. |
|
|
|
`What are attention masks? <../glossary.html#attention-mask>`__ |
|
return_tensors (:obj:`str` or :class:`~transformers.tokenization_utils_base.TensorType`, `optional`): |
|
If set, will return tensors instead of list of python integers. Acceptable values are: |
|
|
|
* :obj:`'tf'`: Return TensorFlow :obj:`tf.constant` objects. |
|
* :obj:`'pt'`: Return PyTorch :obj:`torch.Tensor` objects. |
|
* :obj:`'np'`: Return Numpy :obj:`np.ndarray` objects. |
|
verbose (:obj:`bool`, `optional`, defaults to :obj:`True`): |
|
Whether or not to print more information and warnings. |
|
""" |
|
|
|
|
|
if isinstance(encoded_inputs, (list, tuple)) and isinstance( |
|
encoded_inputs[0], (dict, BatchEncoding) |
|
): |
|
encoded_inputs = { |
|
key: [example[key] for example in encoded_inputs] |
|
for key in encoded_inputs[0].keys() |
|
} |
|
|
|
|
|
if self.model_input_names[0] not in encoded_inputs: |
|
raise ValueError( |
|
"You should supply an encoding or a list of encodings to this method" |
|
f"that includes {self.model_input_names[0]}, but you provided {list(encoded_inputs.keys())}" |
|
) |
|
|
|
required_input = encoded_inputs[self.model_input_names[0]] |
|
|
|
if not required_input: |
|
if return_attention_mask: |
|
encoded_inputs["attention_mask"] = [] |
|
return encoded_inputs |
|
|
|
|
|
|
|
|
|
|
|
first_element = required_input[0] |
|
if isinstance(first_element, (list, tuple)): |
|
|
|
index = 0 |
|
while len(required_input[index]) == 0: |
|
index += 1 |
|
if index < len(required_input): |
|
first_element = required_input[index][0] |
|
|
|
if not isinstance(first_element, (int, list, tuple)): |
|
if is_tf_available() and _is_tensorflow(first_element): |
|
return_tensors = "tf" if return_tensors is None else return_tensors |
|
elif is_torch_available() and _is_torch(first_element): |
|
return_tensors = "pt" if return_tensors is None else return_tensors |
|
elif isinstance(first_element, np.ndarray): |
|
return_tensors = "np" if return_tensors is None else return_tensors |
|
else: |
|
raise ValueError( |
|
f"type of {first_element} unknown: {type(first_element)}. " |
|
f"Should be one of a python, numpy, pytorch or tensorflow object." |
|
) |
|
|
|
for key, value in encoded_inputs.items(): |
|
encoded_inputs[key] = to_py_obj(value) |
|
|
|
|
|
padding_strategy, _, max_length, _ = self._get_padding_truncation_strategies( |
|
padding=padding, max_length=max_length, verbose=verbose |
|
) |
|
|
|
required_input = encoded_inputs[self.model_input_names[0]] |
|
if required_input and not isinstance(required_input[0], (list, tuple)): |
|
encoded_inputs = self._pad( |
|
encoded_inputs, |
|
max_length=max_length, |
|
padding_strategy=padding_strategy, |
|
pad_to_multiple_of=pad_to_multiple_of, |
|
return_attention_mask=return_attention_mask, |
|
) |
|
return BatchEncoding(encoded_inputs, tensor_type=return_tensors) |
|
|
|
batch_size = len(required_input) |
|
assert all( |
|
len(v) == batch_size for v in encoded_inputs.values() |
|
), "Some items in the output dictionary have a different batch size than others." |
|
|
|
if padding_strategy == PaddingStrategy.LONGEST: |
|
max_length = max(len(inputs) for inputs in required_input) |
|
padding_strategy = PaddingStrategy.MAX_LENGTH |
|
|
|
batch_outputs = {} |
|
for i in range(batch_size): |
|
inputs = dict((k, v[i]) for k, v in encoded_inputs.items()) |
|
outputs = self._pad( |
|
inputs, |
|
max_length=max_length, |
|
padding_strategy=padding_strategy, |
|
pad_to_multiple_of=pad_to_multiple_of, |
|
return_attention_mask=return_attention_mask, |
|
) |
|
|
|
for key, value in outputs.items(): |
|
if key not in batch_outputs: |
|
batch_outputs[key] = [] |
|
batch_outputs[key].append(value) |
|
|
|
return BatchEncoding(batch_outputs, tensor_type=return_tensors) |
|
|
|
def _pad( |
|
self, |
|
encoded_inputs: Union[Dict[str, EncodedInput], BatchEncoding], |
|
max_length: Optional[int] = None, |
|
padding_strategy: PaddingStrategy = PaddingStrategy.DO_NOT_PAD, |
|
pad_to_multiple_of: Optional[int] = None, |
|
return_attention_mask: Optional[bool] = None, |
|
) -> dict: |
|
""" |
|
Pad encoded inputs (on left/right and up to predefined length or max length in the batch) |
|
|
|
Args: |
|
encoded_inputs: Dictionary of tokenized inputs (`List[int]`) or batch of tokenized inputs (`List[List[int]]`). |
|
max_length: maximum length of the returned list and optionally padding length (see below). |
|
Will truncate by taking into account the special tokens. |
|
padding_strategy: PaddingStrategy to use for padding. |
|
|
|
- PaddingStrategy.LONGEST Pad to the longest sequence in the batch |
|
- PaddingStrategy.MAX_LENGTH: Pad to the max length (default) |
|
- PaddingStrategy.DO_NOT_PAD: Do not pad |
|
The tokenizer padding sides are defined in self.padding_side: |
|
|
|
- 'left': pads on the left of the sequences |
|
- 'right': pads on the right of the sequences |
|
pad_to_multiple_of: (optional) Integer if set will pad the sequence to a multiple of the provided value. |
|
This is especially useful to enable the use of Tensor Core on NVIDIA hardware with compute capability |
|
>= 7.5 (Volta). |
|
return_attention_mask: (optional) Set to False to avoid returning attention mask (default: set to model specifics) |
|
""" |
|
|
|
if return_attention_mask is None: |
|
return_attention_mask = "attention_mask" in self.model_input_names |
|
|
|
required_input = encoded_inputs[self.model_input_names[0]] |
|
|
|
if padding_strategy == PaddingStrategy.LONGEST: |
|
max_length = len(required_input) |
|
|
|
if ( |
|
max_length is not None |
|
and pad_to_multiple_of is not None |
|
and (max_length % pad_to_multiple_of != 0) |
|
): |
|
max_length = ((max_length // pad_to_multiple_of) + 1) * pad_to_multiple_of |
|
|
|
needs_to_be_padded = ( |
|
padding_strategy != PaddingStrategy.DO_NOT_PAD |
|
and len(required_input) != max_length |
|
) |
|
|
|
if needs_to_be_padded: |
|
difference = max_length - len(required_input) |
|
if self.padding_side == "right": |
|
if return_attention_mask: |
|
encoded_inputs["attention_mask"] = [1] * len(required_input) + [ |
|
0 |
|
] * difference |
|
if "token_type_ids" in encoded_inputs: |
|
encoded_inputs["token_type_ids"] = ( |
|
encoded_inputs["token_type_ids"] |
|
+ [self.pad_token_type_id] * difference |
|
) |
|
if "special_tokens_mask" in encoded_inputs: |
|
encoded_inputs["special_tokens_mask"] = ( |
|
encoded_inputs["special_tokens_mask"] + [1] * difference |
|
) |
|
encoded_inputs[self.model_input_names[0]] = ( |
|
required_input + [self.pad_token_id] * difference |
|
) |
|
elif self.padding_side == "left": |
|
if return_attention_mask: |
|
encoded_inputs["attention_mask"] = [0] * difference + [1] * len( |
|
required_input |
|
) |
|
if "token_type_ids" in encoded_inputs: |
|
encoded_inputs["token_type_ids"] = [ |
|
self.pad_token_type_id |
|
] * difference + encoded_inputs["token_type_ids"] |
|
if "special_tokens_mask" in encoded_inputs: |
|
encoded_inputs["special_tokens_mask"] = [ |
|
1 |
|
] * difference + encoded_inputs["special_tokens_mask"] |
|
encoded_inputs[self.model_input_names[0]] = [ |
|
self.pad_token_id |
|
] * difference + required_input |
|
else: |
|
raise ValueError("Invalid padding strategy:" + str(self.padding_side)) |
|
elif return_attention_mask and "attention_mask" not in encoded_inputs: |
|
encoded_inputs["attention_mask"] = [1] * len(required_input) |
|
|
|
return encoded_inputs |
|
|
|
def get_special_tokens_mask( |
|
self, |
|
token_ids_0: List[int], |
|
token_ids_1: Optional[List[int]] = None, |
|
already_has_special_tokens: bool = False, |
|
) -> List[int]: |
|
""" |
|
Retrieves sequence ids from a token list that has no special tokens added. This method is called when adding |
|
special tokens using the tokenizer ``prepare_for_model`` or ``encode_plus`` methods. |
|
Args: |
|
token_ids_0 (:obj:`List[int]`): |
|
List of ids of the first sequence. |
|
token_ids_1 (:obj:`List[int]`, `optional`): |
|
List of ids of the second sequence. |
|
already_has_special_tokens (:obj:`bool`, `optional`, defaults to :obj:`False`): |
|
Whether or not the token list is already formatted with special tokens for the model. |
|
Returns: |
|
A list of integers in the range [0, 1]: 1 for a special token, 0 for a sequence token. |
|
""" |
|
assert already_has_special_tokens and token_ids_1 is None, ( |
|
"You cannot use ``already_has_special_tokens=False`` with this tokenizer. " |
|
"Please use a slow (full python) tokenizer to activate this argument." |
|
"Or set `return_special_tokens_mask=True` when calling the encoding method " |
|
"to get the special tokens mask in any tokenizer. " |
|
) |
|
|
|
all_special_ids = self.all_special_ids |
|
|
|
special_tokens_mask = [ |
|
1 if token in all_special_ids else 0 for token in token_ids_0 |
|
] |
|
|
|
return special_tokens_mask |
|
|
|
def convert_tokens_to_ids( |
|
self, tokens: Union[str, List[str]] |
|
) -> Union[int, List[int]]: |
|
""" |
|
Converts a token string (or a sequence of tokens) in a single integer id (or a sequence of ids), using the |
|
vocabulary. |
|
Args: |
|
tokens (:obj:`str` or :obj:`List[str]`): One or several token(s) to convert to token id(s). |
|
Returns: |
|
:obj:`int` or :obj:`List[int]`: The token id or list of token ids. |
|
""" |
|
if tokens is None: |
|
return None |
|
|
|
if isinstance(tokens, str): |
|
return self._convert_token_to_id_with_added_voc(tokens) |
|
|
|
ids = [] |
|
for token in tokens: |
|
ids.append(self._convert_token_to_id_with_added_voc(token)) |
|
return ids |
|
|
|
def _convert_token_to_id_with_added_voc(self, token): |
|
if token is None: |
|
return None |
|
|
|
return self.token_dictionary.get(token) |
|
|
|
def __len__(self): |
|
return len(self.token_dictionary) |
|
|
|
|
|
class GeneformerPretrainer(Trainer): |
|
def __init__(self, *args, **kwargs): |
|
data_collator = kwargs.get("data_collator", None) |
|
token_dictionary = kwargs.pop("token_dictionary") |
|
mlm = kwargs.pop("mlm", True) |
|
mlm_probability = kwargs.pop("mlm_probability", 0.15) |
|
|
|
if data_collator is None: |
|
precollator = GeneformerPreCollator(token_dictionary=token_dictionary) |
|
|
|
|
|
data_collator = DataCollatorForLanguageModeling( |
|
tokenizer=precollator, mlm=mlm, mlm_probability=mlm_probability |
|
) |
|
kwargs["data_collator"] = data_collator |
|
|
|
|
|
|
|
example_lengths_file = kwargs.pop("example_lengths_file") |
|
if example_lengths_file: |
|
with open(example_lengths_file, "rb") as f: |
|
self.example_lengths = pickle.load(f) |
|
else: |
|
raise Exception( |
|
"example_lengths_file is required; e.g. https://huggingface.co/datasets/ctheodoris/Genecorpus-30M/tree/main/genecorpus_30M_2048_sorted_lengths.pkl" |
|
) |
|
super().__init__(*args, **kwargs) |
|
|
|
|
|
def _get_train_sampler(self) -> Optional[torch.utils.data.sampler.Sampler]: |
|
if not isinstance(self.train_dataset, collections.abc.Sized): |
|
return None |
|
|
|
generator = None |
|
if self.args.world_size <= 1 and _is_torch_generator_available: |
|
generator = torch.Generator() |
|
generator.manual_seed( |
|
int(torch.empty((), dtype=torch.int64).random_().item()) |
|
) |
|
|
|
|
|
if self.args.group_by_length: |
|
if is_datasets_available() and isinstance(self.train_dataset, Dataset): |
|
lengths = self.example_lengths |
|
else: |
|
lengths = None |
|
model_input_name = ( |
|
self.tokenizer.model_input_names[0] |
|
if self.tokenizer is not None |
|
else None |
|
) |
|
return LengthGroupedSampler( |
|
dataset=self.train_dataset, |
|
batch_size=self.args.train_batch_size, |
|
lengths=lengths, |
|
model_input_name=model_input_name, |
|
generator=generator, |
|
) |
|
|
|
else: |
|
if _is_torch_generator_available: |
|
return RandomSampler(self.train_dataset, generator=generator) |
|
return RandomSampler(self.train_dataset) |
|
|