用统一模型同时预测疾病和生成病历,提升医疗数据利用效率。
Generative Foundation Model for Structured and Unstructured Electronic Health Records
- 用CNN-Transformer融合时间序列与文本,跨模态注意力实现多源数据理解。
- 在MIMIC-IV上预测心衰的准确率达0.923,生成病历质量优于现有方法。
- 适合临床决策支持、电子病历自动生成,可扩展至更多医疗数据类型。
电子健康记录(EHR)包含结构化数据(如人口统计、生命体征、检验结果、编码)与非结构化临床笔记等多模态信息。当前主流方法将数值型数据简单转为文本,易丢失时序与量化细节。本文提出生成式深度患者模型(GDP),采用CNN-Transformer编码器原生处理结构化时间序列,并通过交叉注意力融合非结构化文本,接入LLaMA解码器。训练分两阶段:1)生成预训练,学习从患者时间线生成临床叙述,同时进行掩码特征预测(MFP)和下一步预测(NTP)以捕捉时序动态;2)多任务微调,用于心衰、2型糖尿病、30天再入院等临床预测。在MIMIC-IV数据集上,心衰预测AUROC为0.923,2型糖尿病为0.817,30天再入院为0.627。叙事生成方面,ROUGE-L达0.135,BERTScore-F1为0.545。盲测中,GDP-Instruct在忠实性、流畅性和临床实用性上得分最高,表明可减轻医院文书负担而不牺牲准确性。结果证明,单一多模态基础模型可兼具临床预测与高质量病历生成能力,其灵活架构还可拓展至其他模态。
原文摘要 · Abstract (English)
Electronic health records (EHRs) are rich clinical data sources but complex repositories of patient data, spanning structured elements (demographics, vitals, lab results, codes), unstructured clinical notes and other modalities of data. Harnessing this heterogeneity is critical for improving patient outcomes. Recent advances in large language models (LLMs) have enabled foundation models that can learn from multiple data modalities and support clinical tasks. However, most current approaches simply serialize numeric EHR data into text, which risks losing temporal and quantitative detail. We introduce Generative Deep Patient (GDP), a multimodal foundation model that natively encodes structured EHR time-series via a CNN-Transformer encoder and fuses it with unstructured EHRs through cross-modal attention into a LLaMA-based decoder. GDP is trained in two stages: (1) generative pretraining, where it learns to produce clinical narratives from raw patient timelines while also performing masked feature prediction (MFP) and next time-step prediction (NTP) to capture temporal dynamics; and (2) multi-task fine-tuning for clinically meaningful predictions (e.g., heart failure, type 2 diabetes, 30-day readmission). In clinical prediction, GDP demonstrated superior performance on MIMIC-IV: heart failure AUROC = 0.923, type 2 diabetes AUROC = 0.817, and 30-day readmission AUROC = 0.627. For narrative generation, GDP achieved ROUGE-L = 0.135 and BERTScore-F1 = 0.545. In a blinded human evaluation, GDP-Instruct scored highest on faithfulness, fluency, and overall clinical utility, suggesting reduced hospital documentation workload without sacrificing accuracy. Our results demonstrate that a single multimodal foundation model can both predict clinically actionable events and generate high-quality clinical narratives. Furthermore, GDP's flexible architecture can be extended to additional modalities.
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