arXiv:2602.19661cs.LG2026-02被引 1

用大模型将病历时间信息转化为文本,提升疾病分类准确率。

PaReGTA: An LLM-based EHR Data Encoding Approach to Capture Temporal Information

  • 将就诊记录转为带时间线索的文本模板,保留时间顺序信息。
  • 在3.9万例偏头痛患者上分类效果优于传统方法,且不依赖复杂训练。
  • 支持未来新模型升级,还能量化临床因素重要性,适合医疗研究者使用。

结构化电子健康记录(EHR)中的时间信息常因稀疏的独热编码或计数表示而丢失,而序列模型又存在计算成本高、需大量数据的问题。我们提出PaReGTA,一种基于大语言模型的编码框架:(i) 将纵向EHR事件转换为包含明确时间线索的就诊级文本模板;(ii) 通过轻量级对比微调预训练句向量模型,学习领域适配的就诊嵌入;(iii) 采用混合时间池化策略,聚合就诊嵌入生成固定维度的患者表征,兼顾近期与全局重要就诊。由于无需从头训练,仅依赖预训练大模型,该方法在数据有限的队列中仍表现良好。此外,该框架具有模型无关性,可受益于未来的专用句向量模型。为增强可解释性,引入PaReGTA-RSS(表示转移得分),通过移除特定临床因素后重新计算表示,并利用机器学习模型投影表示变化,量化临床因素的重要性。在来自‘全民研究计划’的39,088例偏头痛患者数据上,PaReGTA在偏头痛类型分类任务中优于稀疏基线,而深度序列模型在本队列中表现不稳定。

原文摘要 · Abstract (English)

Temporal information in structured electronic health records (EHRs) is often lost in sparse one-hot or count-based representations, while sequence models can be costly and data-hungry. We propose PaReGTA, an LLM-based encoding framework that (i) converts longitudinal EHR events into visit-level templated text with explicit temporal cues, (ii) learns domain-adapted visit embeddings via lightweight contrastive fine-tuning of a sentence-embedding model, and (iii) aggregates visit embeddings into a fixed-dimensional patient representation using hybrid temporal pooling that captures both recency and globally informative visits. Because PaReGTA does not require training from scratch but instead utilizes a pre-trained LLM, it can perform well even in data-limited cohorts. Furthermore, PaReGTA is model-agnostic and can benefit from future EHR-specialized sentence-embedding models. For interpretability, we introduce PaReGTA-RSS (Representation Shift Score), which quantifies clinically defined factor importance by recomputing representations after targeted factor removal and projecting representation shifts through a machine learning model. On 39,088 migraine patients from the All of Us Research Program, PaReGTA outperforms sparse baselines for migraine type classification while deep sequential models were unstable in our cohort.

医疗文本时间建模大模型应用可解释性

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