from typing import List, Optional, Tuple, Union import torch import torch.nn as nn from torch.nn import BCEWithLogitsLoss, CrossEntropyLoss, MSELoss from transformers.models.bert.modeling_bert import BertModel as TransformersBertModel from transformers.models.bert.modeling_bert import BertForMaskedLM as TransformersBertForMaskedLM from transformers.models.bert.modeling_bert import BertPreTrainedModel from transformers.modeling_outputs import SequenceClassifierOutput class BertModel(TransformersBertModel): def __init__(self, config): super().__init__(config) class BertForMaskedLM(TransformersBertForMaskedLM): def __init__(self, config): super().__init__(config) class DNABertForSequenceClassification(BertPreTrainedModel): def __init__(self, config): super().__init__(config) self.num_labels = config.num_labels self.config = config self.bert = BertModel(config) 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) # Initialize weights and apply final processing self.post_init() 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]: r""" labels (`torch.LongTensor` of shape `(batch_size,)`, *optional*): Labels for computing the sequence classification/regression loss. Indices should be in `[0, ..., config.num_labels - 1]`. If `config.num_labels == 1` a regression loss is computed (Mean-Square loss), If `config.num_labels > 1` a classification loss is computed (Cross-Entropy). """ return_dict = return_dict if return_dict is not None else self.config.use_return_dict # get the size of input_ids batch_size, seq_len = input_ids.shape if seq_len > 512: assert seq_len % 512 == 0, "seq_len should be a multiple of 512" # split the input_ids into multiple chunks input_ids = input_ids.view(-1, 512) attention_mask = attention_mask.view(-1, 512) if attention_mask is not None else None token_type_ids = token_type_ids.view(-1, 512) if token_type_ids is not None else None position_ids = None 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] if seq_len > 512: # reshape the pooled_output pooled_output = pooled_output.view(batch_size, -1, pooled_output.shape[-1]) # take the mean of the pooled_output pooled_output = torch.mean(pooled_output, dim=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=outputs.hidden_states, attentions=outputs.attentions, )