# models/text_encoder.py """ 文本编码器模块:使用PubMedBERT对药物治疗文本进行编码 """ import torch import torch.nn as nn from transformers import AutoTokenizer, AutoModel class DrugTextEncoder(nn.Module): """ 使用PubMedBERT编码药物治疗文本 支持冻结/微调模式 """ def __init__( self, model_name: str = "microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext", freeze: bool = False, output_dim: int = 768, max_length: int = 512, use_pooler_output: bool = True, ): super().__init__() self.max_length = max_length self.use_pooler_output = use_pooler_output # 加载预训练的tokenizer和模型 self.tokenizer = AutoTokenizer.from_pretrained(model_name) self.bert = AutoModel.from_pretrained(model_name) # 是否冻结BERT参数 if freeze: for param in self.bert.parameters(): param.requires_grad = False # 投影层(可选,如果需要改变输出维度) self.projection = None if output_dim != 768: self.projection = nn.Linear(768, output_dim) self.output_dim = output_dim def forward(self, texts): """ Args: texts: List[str] or str, 药物治疗的JSON字符串 Returns: embeddings: [B, output_dim] """ # 如果是单个字符串,转为列表 if isinstance(texts, str): texts = [texts] # Tokenization encoded = self.tokenizer( texts, padding=True, truncation=True, max_length=self.max_length, return_tensors='pt' ) # 移到正确的设备 device = next(self.bert.parameters()).device encoded = {k: v.to(device) for k, v in encoded.items()} # BERT编码 outputs = self.bert(**encoded) # 旧版 checkpoint 更可能依赖 BERT pooler_output,而不是直接取 CLS hidden state if self.use_pooler_output and getattr(outputs, "pooler_output", None) is not None: cls_embeddings = outputs.pooler_output else: cls_embeddings = outputs.last_hidden_state[:, 0, :] # [B, 768] # 可选的投影 if self.projection is not None: cls_embeddings = self.projection(cls_embeddings) return cls_embeddings def unfreeze(self): """解冻BERT参数,用于微调""" for param in self.bert.parameters(): param.requires_grad = True def freeze(self): """冻结BERT参数""" for param in self.bert.parameters(): param.requires_grad = False # 测试代码 if __name__ == "__main__": encoder = DrugTextEncoder(freeze=True) # 模拟输入 sample_text = '{"pre":{"tp":"T1","therapies":[{"type":"chemotherapy","agents":[{"name":"Temozolomide","dose":"75mg/m2"}]}]}}' embedding = encoder([sample_text, sample_text]) print(f"Output shape: {embedding.shape}") # [2, 768]