# ------------------------------------------------------------------------------------------ # 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, CXRBertTokenizer 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