arXiv:2509.04485cs.CLcs.AI2025-09

用临床表型增强的Transformer模型,从电子病历预测心血管风险。

ASCENDgpt: A Phenotype-Aware Transformer Model for Cardiovascular Risk Prediction from Electronic Health Records

  • 将4.7万条诊断码映射为176个表型词元,大幅压缩词汇量。
  • 在5种心血管结局上平均C指数达0.816,最高达0.842。
  • 兼顾可解释性与效率,适合临床风险评估场景。

我们提出ASCENDgpt,一种基于Transformer的模型,用于从纵向电子健康记录(EHRs)中预测心血管风险。该方法引入新型表型感知分词方案,将47,155条原始ICD代码映射为176个具有临床意义的表型词元,在保留语义信息的前提下实现了99.6%的诊断码整合率,总词表规模降至10,442,较直接使用原始ICD代码减少77.9%。我们在19,402名独立个体的序列上预训练ASCENDgpt,采用掩码语言建模目标,随后微调用于五类心血管结局的时间-事件预测:心肌梗死(MI)、卒中、主要不良心血管事件(MACE)、心血管死亡及全因死亡。在预留测试集上,模型平均C指数达0.816,各项表现优异(MI: 0.792,卒中: 0.824,MACE: 0.800,心血管死亡: 0.842,全因死亡: 0.824)。表型基础方法支持临床可解释性预测并保持计算高效。本研究证明了领域特定分词与预训练对EHR风险预测的有效性。

原文摘要 · Abstract (English)

We present ASCENDgpt, a transformer-based model specifically designed for cardiovascular risk prediction from longitudinal electronic health records (EHRs). Our approach introduces a novel phenotype-aware tokenization scheme that maps 47,155 raw ICD codes to 176 clinically meaningful phenotype tokens, achieving 99.6\% consolidation of diagnosis codes while preserving semantic information. This phenotype mapping contributes to a total vocabulary of 10,442 tokens - a 77.9\% reduction when compared with using raw ICD codes directly. We pretrain ASCENDgpt on sequences derived from 19402 unique individuals using a masked language modeling objective, then fine-tune for time-to-event prediction of five cardiovascular outcomes: myocardial infarction (MI), stroke, major adverse cardiovascular events (MACE), cardiovascular death, and all-cause mortality. Our model achieves excellent discrimination on the held-out test set with an average C-index of 0.816, demonstrating strong performance across all outcomes (MI: 0.792, stroke: 0.824, MACE: 0.800, cardiovascular death: 0.842, all-cause mortality: 0.824). The phenotype-based approach enables clinically interpretable predictions while maintaining computational efficiency. Our work demonstrates the effectiveness of domain-specific tokenization and pretraining for EHR-based risk prediction tasks.

心血管风险电子病历Transformer表型建模

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