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Article

Bridging clinical narratives and structured phenotypes with large language models and sentence transformers.

Journal of genetics and genomics = Yi chuan xue bao - 1 Jul 2026

Cai Jihao, Li Guozhuang, Yang Yongxin, Xu Kexin, Zhao Sen, Hospedales Timothy, Zhao Lina, Yang Jianle, Wu Zhihong, Zhang Terry Jianguo, Chen Zefu, Wu Nan

Abstract excerpt

Structured phenotypes are important for Mendelian disorder diagnosis, gene-phenotype association studies, and standardized phenotypic data sharing. Although electronic health records (EHRs) contain abundant phenotypic information, much of it is unstructured. Early automated phenotyping methods are rule-based, limiting their ability to capture semantic variability and contextual information. Recent deep learning...

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PMID: 41698530
DOI: 10.1016/j.jgg.2026.02.009

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