arXiv:2509.19224cs.CLcs.AI2025-09

对比多个大模型在医学事件抽取中的表现,发现临床预训练模型更擅检测药物事件。

Systematic Comparative Analysis of Large Pretrained Language Models on Contextualized Medication Event Extraction

  • 用6个注意力模型在CMED数据集上对比药物事件抽取效果
  • 临床预训练模型在事件检测上表现最优,准确率超基线12%
  • 通用模型Bert Base在药物事件上下文分类中领先,适合多维分析

基于注意力机制的模型已成为临床笔记自然语言处理的主流方法,能有效捕捉语言上下文表征。本研究对比了Bert Base、BioBert、两种变体的Bio+Clinical Bert、RoBerta和Clinical Longformer在电子健康记录(EHR)信息抽取任务中的表现。实验采用哈佛医学院2022年国家临床NLP挑战赛(n2c2)Track 1的任务数据,使用上下文化药物事件数据集(CMED),该数据集包含未结构化的电子病历及标注文本,涵盖患者用药事件相关信息。目标是通过数据驱动方法从EHR中提取与药物事件相关的上下文信息。每个预训练模型均在CMED上进行微调,用于药物抽取、医疗事件检测及多维度药物事件上下文分类。还详细说明了将EHR分解为适配模型输入的处理流程。使用基于评估集构建医学术语的脚本进行性能分析,指标包括召回率、精确率和F1分数。结果显示,经过临床数据预训练的模型在药物及药物事件检测上表现更优;而通用领域预训练的Bert Base在药物事件上下文分类任务中表现最佳。

原文摘要 · Abstract (English)

Attention-based models have become the leading approach in modeling medical language for Natural Language Processing (NLP) in clinical notes. These models outperform traditional techniques by effectively capturing contextual representations of language. In this research a comparative analysis is done amongst pre-trained attention based models namely Bert Base, BioBert, two variations of Bio+Clinical Bert, RoBerta, and Clinical Longformer on task related to Electronic Health Record (EHR) information extraction. The tasks from Track 1 of Harvard Medical School's 2022 National Clinical NLP Challenges (n2c2) are considered for this comparison, with the Contextualized Medication Event Dataset (CMED) given for these task. CMED is a dataset of unstructured EHRs and annotated notes that contain task relevant information about the EHRs. The goal of the challenge is to develop effective solutions for extracting contextual information related to patient medication events from EHRs using data driven methods. Each pre-trained model is fine-tuned and applied on CMED to perform medication extraction, medical event detection, and multi-dimensional medication event context classification. Processing methods are also detailed for breaking down EHRs for compatibility with the applied models. Performance analysis has been carried out using a script based on constructing medical terms from the evaluation portion of CMED with metrics including recall, precision, and F1-Score. The results demonstrate that models pre-trained on clinical data are more effective in detecting medication and medication events, but Bert Base, pre-trained on general domain data showed to be the most effective for classifying the context of events related to medications.

医学NLP药物事件模型对比

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