用预训练模型零样本预测患者未来医疗事件,省去繁琐调优。
Zero-shot Medical Event Prediction Using a Generative Pre-trained Transformer on Electronic Health Records
- 将医疗事件预测转为生成任务,仅靠预训练知识推断下一步
- 平均顶1精度0.614,召回率0.524,对12类疾病表现优异
- 无需标注数据,适合快速部署于多种临床预测场景
电子健康记录(EHR)中的纵向数据以编码概念序列形式记录个体临床史,涵盖诊断、操作、用药和检验等。生成式预训练变换器(GPT)可利用此类数据预测未来事件。尽管微调能提升特定任务性能,但面对众多临床预测任务时成本过高。相比之下,预训练基础模型可在零样本设定下使用,提供一种替代方案。本研究首次系统分析基于GPT的基础模型在EHR中实现零样本预测的可行性,提出一种新流程,将医疗概念预测建模为生成任务。与需大量标注数据的监督方法不同,该方法仅依赖预训练知识即可预测下一个医疗事件。我们在多个时间范围和临床类别上评估模型性能,证明其可捕捉潜在时间依赖性与复杂患者轨迹而无需任务监督。模型在预测下一个医疗概念时,平均顶1精度达0.614,召回率为0.524。针对12种主要诊断,模型展现出高真阳性率且误报率低。结果表明,基础型EHR-GPT模型能有效捕捉多样表型,实现稳健的零样本临床结局预测,增强预测模型的通用性并降低任务特异性训练需求,推动临床场景下的可扩展应用。
原文摘要 · Abstract (English)
Longitudinal data in electronic health records (EHRs) represent an individual`s clinical history through a sequence of codified concepts, including diagnoses, procedures, medications, and laboratory tests. Generative pre-trained transformers (GPT) can leverage this data to predict future events. While fine-tuning of these models can enhance task-specific performance, it becomes costly when applied to many clinical prediction tasks. In contrast, a pretrained foundation model can be used in zero-shot forecasting setting, offering a scalable alternative to fine-tuning separate models for each outcome. This study presents the first comprehensive analysis of zero-shot forecasting with GPT-based foundational models in EHRs, introducing a novel pipeline that formulates medical concept prediction as a generative modeling task. Unlike supervised approaches requiring extensive labeled data, our method enables the model to forecast a next medical event purely from a pretraining knowledge. We evaluate performance across multiple time horizons and clinical categories, demonstrating model`s ability to capture latent temporal dependencies and complex patient trajectories without task supervision. Model performance for predicting the next medical concept was evaluated using precision and recall metrics, achieving an average top1 precision of 0.614 and recall of 0.524. For 12 major diagnostic conditions, the model demonstrated strong zero-shot performance, achieving high true positive rates while maintaining low false positives. We demonstrate the power of a foundational EHR GPT model in capturing diverse phenotypes and enabling robust, zero-shot forecasting of clinical outcomes. This capability enhances the versatility of predictive healthcare models and reduces the need for task-specific training, enabling more scalable applications in clinical settings.
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