Automated Insomnia Phenotyping from Electronic Health Records: Leveraging Large Language Models to Decode Clinical Narratives
Lopez-Garcia, G.; Weissenbacher, D.; Stadler, M.; O'Connor, K.; Xu, D.; Gryboski, L.; Heavens, J.; Abu-el-Rub, N.; Mazzotti, D. R.; Chakravorty, S.; Gonzalez-Hernandez, G.
Show abstract
Insomnia is a highly prevalent but often underdiagnosed condition in clinical practice. Its inconsistent documentation in electronic health records (EHRs) limits population-level analyses and obstructs efforts to evaluate treatment patterns or outcomes. We present a novel, fully automated approach for phenotyping insomnia directly from unstructured clinical notes using generative large language models (LLMs). Leveraging prompt engineering with few-shot learning and chain-of-thought reasoning, we evaluated our system on two distinct corpora: inpatient clinical notes from MIMIC-III and outpatient primary care notes from the University of Kansas Health System (KUMC). Our models--Llama 70B and Llama 405B--achieved F1 scores of 93.0 on the MIMIC corpus and 85.7 on the KUMC corpus, substantially outperforming domain-adapted BERT-based classifiers. Ultimately, our framework offers a scalable and interpretable solution for clinical phenotyping of insomnia and can serve as a blueprint for similar efforts targeting other underdiagnosed or under-documented conditions in the EHR.
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