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import logging
from typing import Optional, Tuple, Union
import torch
import torch.nn as nn
from torch.nn import BCEWithLogitsLoss, CrossEntropyLoss, MSELoss
from torch.nn.modules.utils import consume_prefix_in_state_dict_if_present
from transformers import BertPreTrainedModel
from transformers.modeling_outputs import SequenceClassifierOutput
from huggingface_hub import hf_hub_download
from safetensors.torch import load_file
from .bert_layers_mosa import BertModel
from .configuration_bert import BertConfig
logger = logging.getLogger(__name__)
class ClinicalMosaicForEmbeddingGeneration(BertPreTrainedModel):
config_class = BertConfig
def __init__(self, config, **kwargs):
"""
Initializes the BertEmbeddings class.
Args:
config (BertConfig): The configuration for the BERT model.
add_pooling_layer (bool, optional): Whether to add a pooling layer. Defaults to False.
"""
super().__init__(config)
self.config = config
self.bert = BertModel(config, add_pooling_layer=False)
# this resets the weights
self.post_init()
@classmethod
def from_pretrained(
cls, pretrained_checkpoint, state_dict=None, config=None, *inputs, **kwargs
):
"""Load from pre-trained."""
# this gets a fresh init model
model = cls(config, *inputs, **kwargs)
# Download the model file
archive_file = hf_hub_download(
repo_id=pretrained_checkpoint,
filename="model.safetensors",
)
# Load the state_dict
state_dict = load_file(archive_file)
# add missing bert prefix
state_dict = {f'bert.{key}': value for key, value in state_dict.items()}
missing_keys, unexpected_keys = model.load_state_dict(state_dict, strict=False)
if len(missing_keys) > 0:
logger.warning(
f"Found these missing keys in the checkpoint: {', '.join(missing_keys)}"
)
logger.warning(f"the number of which is equal to {len(missing_keys)}")
if len(unexpected_keys) > 0:
logger.warning(
f"Found these unexpected keys in the checkpoint: {', '.join(unexpected_keys)}",
)
logger.warning(f"the number of which is equal to {len(unexpected_keys)}")
return model
def forward(
self,
input_ids: Optional[torch.Tensor] = None,
attention_mask: Optional[torch.Tensor] = None,
token_type_ids: Optional[torch.Tensor] = None,
position_ids: Optional[torch.Tensor] = None,
subset_mask: Optional[torch.Tensor] = None,
output_all_encoded_layers: bool = True,
) -> torch.Tensor:
embedding_output = self.bert.embeddings(input_ids, token_type_ids, position_ids)
encoder_outputs_all = self.bert.encoder(
embedding_output,
attention_mask,
output_all_encoded_layers=output_all_encoded_layers,
subset_mask=subset_mask,
)
# batch_size, hidden_dim
return encoder_outputs_all
class ClinicalMosaicForSequenceClassification(BertPreTrainedModel):
"""Bert Model transformer with a sequence classification/regression head.
This head is just a linear layer on top of the pooled output.
"""
config_class = BertConfig
def __init__(self, config, **kwargs):
super().__init__(config)
self.num_labels = config.num_labels
self.config = config
self.bert = BertModel(config, add_pooling_layer=True)
classifier_dropout = (
config.classifier_dropout
if config.classifier_dropout is not None
else config.hidden_dropout_prob
)
self.dropout = nn.Dropout(classifier_dropout)
self.classifier = nn.Linear(config.hidden_size, config.num_labels)
# this resets the weights
self.post_init()
@classmethod
def from_pretrained(
cls, pretrained_checkpoint, state_dict=None, config=None, *inputs, **kwargs
):
"""Load from pre-trained."""
# this gets a fresh init model
model = cls(config, *inputs, **kwargs)
# Download the model file
archive_file = hf_hub_download(
repo_id=pretrained_checkpoint,
filename="model.safetensors",
)
# Load the state_dict
state_dict = load_file(archive_file)
# add missing bert prefix
state_dict = {f'bert.{key}': value for key, value in state_dict.items()}
missing_keys, unexpected_keys = model.load_state_dict(state_dict, strict=False)
# Calculate classifier parameters
num_classifier_params = config.hidden_size * config.num_labels + config.num_labels
classifier_keys = {"classifier.weight", "classifier.bias", "bert.pooler.dense.weight", "bert.pooler.dense.bias"}
# Check if only the classification layer is missing
if set(missing_keys) == classifier_keys:
print(
f"Checkpoint does not contain the classification layer "
f"({config.hidden_size}x{config.num_labels} + {config.num_labels} = {num_classifier_params} params). "
"It will be randomly initialized."
)
elif len(missing_keys) > 0:
logger.warning(
f"Checkpoint is missing {len(missing_keys)} parameters, including possibly critical ones: "
f"{', '.join(missing_keys)}"
)
if len(unexpected_keys) > 0:
logger.warning(
f"Found these unexpected keys in the checkpoint: {', '.join(unexpected_keys)}",
)
logger.warning(f"the number of which is equal to {len(unexpected_keys)}")
return model
def forward(
self,
input_ids: Optional[torch.Tensor] = None,
attention_mask: Optional[torch.Tensor] = None,
token_type_ids: Optional[torch.Tensor] = None,
position_ids: Optional[torch.Tensor] = None,
head_mask: Optional[torch.Tensor] = None,
inputs_embeds: Optional[torch.Tensor] = None,
labels: Optional[torch.Tensor] = None,
output_attentions: Optional[bool] = None,
output_hidden_states: Optional[bool] = None,
return_dict: Optional[bool] = None,
) -> Union[Tuple[torch.Tensor], SequenceClassifierOutput]:
return_dict = (
return_dict if return_dict is not None else self.config.use_return_dict
)
outputs = self.bert(
input_ids,
attention_mask=attention_mask,
token_type_ids=token_type_ids,
position_ids=position_ids,
head_mask=head_mask,
inputs_embeds=inputs_embeds,
output_attentions=output_attentions,
output_hidden_states=output_hidden_states,
return_dict=return_dict,
)
pooled_output = outputs[1]
pooled_output = self.dropout(pooled_output)
logits = self.classifier(pooled_output)
loss = None
if labels is not None:
if self.config.problem_type is None:
if self.num_labels == 1:
self.config.problem_type = "regression"
elif self.num_labels > 1 and (
labels.dtype == torch.long or labels.dtype == torch.int
):
self.config.problem_type = "single_label_classification"
else:
self.config.problem_type = "multi_label_classification"
if self.config.problem_type == "regression":
loss_fct = MSELoss()
if self.num_labels == 1:
loss = loss_fct(logits.squeeze(), labels.squeeze())
else:
loss = loss_fct(logits, labels)
elif self.config.problem_type == "single_label_classification":
loss_fct = CrossEntropyLoss()
loss = loss_fct(logits.view(-1, self.num_labels), labels.view(-1))
elif self.config.problem_type == "multi_label_classification":
loss_fct = BCEWithLogitsLoss()
loss = loss_fct(logits, labels)
if not return_dict:
output = (logits,) + outputs[2:]
return ((loss,) + output) if loss is not None else output
return SequenceClassifierOutput(
loss=loss,
logits=logits,
hidden_states=None,
attentions=None,
)
class ClinicalMosaicForForMaskedLM(BertPreTrainedModel):
config_class = BertConfig
def __init__(self, config):
super().__init__(config)
if config.is_decoder:
warnings.warn(
'If you want to use `BertForMaskedLM` make sure `config.is_decoder=False` for '
'bi-directional self-attention.')
self.bert = BertModel(config, add_pooling_layer=False)
self.cls = BertOnlyMLMHead(config,
self.bert.embeddings.word_embeddings.weight)
# Initialize weights and apply final processing
self.post_init()
def get_output_embeddings(self):
return self.cls.predictions.decoder
def set_output_embeddings(self, new_embeddings):
self.cls.predictions.decoder = new_embeddings
def forward(
self,
input_ids: Optional[torch.Tensor] = None,
attention_mask: Optional[torch.Tensor] = None,
token_type_ids: Optional[torch.Tensor] = None,
position_ids: Optional[torch.Tensor] = None,
head_mask: Optional[torch.Tensor] = None,
inputs_embeds: Optional[torch.Tensor] = None,
encoder_hidden_states: Optional[torch.Tensor] = None,
encoder_attention_mask: Optional[torch.Tensor] = None,
labels: Optional[torch.Tensor] = None,
output_attentions: Optional[bool] = None,
output_hidden_states: Optional[bool] = None,
return_dict: Optional[bool] = None,
) -> Union[Tuple[torch.Tensor], MaskedLMOutput]:
# labels should be a `torch.LongTensor` of shape
# `(batch_size, sequence_length)`. These are used for computing the
# masked language modeling loss.
#
# Indices should be in `[-100, 0, ..., config.vocab_size]` (see
# `input_ids` docstring) Tokens with indices set to `-100` are ignored
# (masked), the loss is only computed for the tokens with labels in `[0,
# ..., config.vocab_size]`
#
# Prediction scores are only computed for masked tokens and the (bs,
# seqlen) dimensions are flattened
if (input_ids is not None) == (inputs_embeds is not None):
raise ValueError('Must specify either input_ids or input_embeds!')
if labels is None:
masked_tokens_mask = None
else:
masked_tokens_mask = labels > 0
return_dict = return_dict if return_dict is not None else self.config.use_return_dict
outputs = self.bert(
input_ids,
attention_mask=attention_mask,
token_type_ids=token_type_ids,
position_ids=position_ids,
head_mask=head_mask,
inputs_embeds=inputs_embeds,
encoder_hidden_states=encoder_hidden_states,
encoder_attention_mask=encoder_attention_mask,
output_attentions=output_attentions,
output_hidden_states=output_hidden_states,
return_dict=return_dict,
masked_tokens_mask=masked_tokens_mask,
)
sequence_output = outputs[0]
prediction_scores = self.cls(sequence_output)
loss = None
if labels is not None:
# Compute loss
loss_fct = nn.CrossEntropyLoss()
masked_token_idx = torch.nonzero(labels.flatten() > 0,
as_tuple=False).flatten()
loss = loss_fct(prediction_scores,
labels.flatten()[masked_token_idx])
assert input_ids is not None, 'Coding error; please open an issue'
batch, seqlen = input_ids.shape[:2]
prediction_scores = rearrange(index_put_first_axis(
prediction_scores, masked_token_idx, batch * seqlen),
'(b s) d -> b s d',
b=batch)
if not return_dict:
output = (prediction_scores,) + outputs[2:]
return ((loss,) + output) if loss is not None else output
return MaskedLMOutput(
loss=loss,
logits=prediction_scores,
hidden_states=outputs[0],
attentions=None,
)
def prepare_inputs_for_generation(self, input_ids: torch.Tensor,
attention_mask: torch.Tensor,
**model_kwargs):
input_shape = input_ids.shape
effective_batch_size = input_shape[0]
# add a dummy token
if self.config.pad_token_id is None:
raise ValueError('The PAD token should be defined for generation')
attention_mask = torch.cat([
attention_mask,
attention_mask.new_zeros((attention_mask.shape[0], 1))
],
dim=-1)
dummy_token = torch.full((effective_batch_size, 1),
self.config.pad_token_id,
dtype=torch.long,
device=input_ids.device)
input_ids = torch.cat([input_ids, dummy_token], dim=1)
return {'input_ids': input_ids, 'attention_mask': attention_mask} |