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# ------------------------------------------------------------------------------------------
# Copyright (c) Microsoft Corporation. All rights reserved.
# Licensed under the MIT License (MIT). See LICENSE in the repo root for license information.
# ------------------------------------------------------------------------------------------
from typing import Any, Optional, Tuple, Union
import torch
import torch.nn.functional as F
from torch import nn
from torch import Tensor as T
from transformers import BertForMaskedLM
from transformers.modeling_outputs import ModelOutput
from .configuration_cxrbert import CXRBertConfig
BERTTupleOutput = Tuple[T, T, T, T, T]
class CXRBertOutput(ModelOutput):
last_hidden_state: torch.FloatTensor
prediction_logits: torch.FloatTensor
cls_projected_embedding: Optional[torch.FloatTensor] = None
hidden_states: Optional[Tuple[torch.FloatTensor]] = None
attentions: Optional[Tuple[torch.FloatTensor]] = None
class BertProjectionHead(nn.Module):
'''
Projection head to be used with BERT CLS token, it's similar to `BertPredictionHeadTransform` in HuggingFace library.
:param config: CXRBertConfig
:return: (batch_size, output_size)
'''
def __init__(self, config: CXRBertConfig) -> None:
super().__init__()
self.dense_to_hidden = nn.Linear(config.hidden_size, config.projection_size)
self.transform_act_fn = nn.functional.gelu
self.LayerNorm = nn.LayerNorm(config.projection_size, eps=1e-12)
self.dense_to_output = nn.Linear(config.projection_size, config.projection_size)
def forward(self, hidden_states: torch.Tensor) -> torch.Tensor:
hidden_states = self.dense_to_hidden(hidden_states)
hidden_states = self.transform_act_fn(hidden_states)
hidden_states = self.LayerNorm(hidden_states)
hidden_states = self.dense_to_output(hidden_states)
return hidden_states
class CXRBertModel(BertForMaskedLM):
"""
Implements the CXR-BERT model outlined in the manuscript:
Boecking et al. "Making the Most of Text Semantics to Improve Biomedical Vision-Language Processing", 2022
https://arxiv.org/abs/2204.09817
Extends the HuggingFace BertForMaskedLM model by adding a separate projection head. The projection "[CLS]" token is used to align
the latent vectors of image and text modalities.
"""
config_class = CXRBertConfig
def __init__(self, config: CXRBertConfig):
super().__init__(config)
self.cls_projection_head = BertProjectionHead(config)
self.init_weights()
def forward(
self,
input_ids: torch.Tensor,
attention_mask: torch.Tensor,
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,
output_attentions: Optional[bool] = None,
output_hidden_states: Optional[bool] = None,
output_cls_projected_embedding: Optional[bool] = None,
return_dict: Optional[bool] = None,
**kwargs: Any
) -> Union[BERTTupleOutput, CXRBertOutput]:
return_dict = return_dict if return_dict is not None else self.config.use_return_dict
bert_for_masked_lm_output = super().forward(input_ids=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=True,
return_dict=True)
last_hidden_state = bert_for_masked_lm_output.hidden_states[-1]
cls_projected_embedding = self.cls_projection_head(last_hidden_state[:, 0, :]) if output_cls_projected_embedding else None
if return_dict:
return CXRBertOutput(
last_hidden_state=last_hidden_state,
prediction_logits=bert_for_masked_lm_output.logits,
cls_projected_embedding=cls_projected_embedding,
hidden_states=bert_for_masked_lm_output.hidden_states if output_hidden_states else None,
attentions=bert_for_masked_lm_output.attentions,
)
else:
return (
last_hidden_state,
bert_for_masked_lm_output.logits,
cls_projected_embedding,
bert_for_masked_lm_output.hidden_states,
bert_for_masked_lm_output.attentions,)
def get_projected_text_embeddings(self, input_ids: torch.Tensor, attention_mask: torch.Tensor) -> torch.Tensor:
"""
Returns l2-normalised projected cls token embeddings for the given input token ids and attention mask.
The joint latent space is trained using a contrastive objective between image and text data modalities.
:param input_ids: (batch_size, sequence_length)
:param attention_mask: (batch_size, sequence_length)
:return: (batch_size, projection_size)
"""
outputs = self.forward(input_ids=input_ids, attention_mask=attention_mask,
output_cls_projected_embedding=True, return_dict=True)
assert isinstance(outputs, CXRBertOutput)
normalized_cls_embedding = F.normalize(outputs.cls_projected_embedding, dim=1)
return normalized_cls_embedding
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