Electronic health records (EHR) offer unprecedented opportunities for in-depth clinical phenotyping and prediction of clinical outcomes. Combining multiple data sources is crucial to generate a complete picture of disease prevalence, incidence and trajectories. The standard approach to combining clinical data involves collating clinical terms across different terminology systems using curated maps, which are often inaccurate and/or incomplete. Here, we propose sEHR-CE, a novel framework based on transformers to enable integrated phenotyping and analyses of heterogeneous clinical datasets without relying on these mappings. We unify clinical terminologies using textual descriptors of concepts, and represent individuals' EHR as sections of text. We then fine-tune pre-trained language models to predict disease phenotypes more accurately than non-text and single terminology approaches. We validate our approach using primary and secondary care data from the UK Biobank, a large-scale research study. Finally, we illustrate in a type 2 diabetes use case how sEHR-CE identifies individuals without diagnosis that share clinical characteristics with patients.

本文提出了一种基于Transformers的新型框架sEHR-CE，可以在不需要映射的情况下，对异构临床数据集进行集成表型和分析。使用预训练的语言模型来预测疾病表型的准确性高于非文本和单个术语方法，并且用2型糖尿病为例说明如何识别没有诊断但具有与患者相似临床特征的个体。

sEHR-CE: 结构化电子病历语言建模，用于高效和可推广的患者队列扩展