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arXiv · 2510.03844

On Using Large Language Models to Enhance Clinically-Driven Missing Data Recovery Algorithms in Electronic Health Records

Sarah C. Lotspeich·Abbey Collins·Brian J. Wells·Ashish K. Khanna·Joseph Rigdon·Lucy D'Agostino McGowan
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Abstract

Objective: Electronic health records (EHR) data are prone to missingness and errors. Previously, we devised an "enriched" chart review protocol where a "roadmap" of auxiliary diagnoses (anchors) was used to recover missing values in EHR data (e.g., a diagnosis of impaired glycemic control might imply that a missing hemoglobin A1c value would be considered unhealthy). Still, chart reviews are expensive and time-intensive, which limits the number of patients whose data can be reviewed. Now, we investigate the accuracy and scalability of a roadmap-driven algorithm, based on ICD-10 codes (International Classification of Diseases, 10th revision), to mimic expert chart reviews and recover missing values. Materials and Methods: In addition to the clinicians' original roadmap from our previous work, we consider new versions that were iteratively refined using large language models (LLM) in conjunction with clinical expertise to expand the list of auxiliary diagnoses. Using chart reviews for 100 patients from the EHR at an extensive learning health system, we examine algorithm performance with different roadmaps. Using the larger study of $1000$ patients, we applied the final algorithm, which used a roadmap with clinician-approved additions from the LLM. Results: The algorithm recovered as much, if not more, missing data as the expert chart reviewers, depending on the roadmap. Discussion: Clinically-driven algorithms (enhanced by LLM) can recover missing EHR data with similar accuracy to chart reviews and can feasibly be applied to large samples. Extending them to monitor other dimensions of data quality (e.g., plausability) is a promising future direction.

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Sarah C. Lotspeich, Abbey Collins, Brian J. Wells, Ashish K. Khanna, Joseph Rigdon, Lucy D'Agostino McGowan. 2025-10-04. On Using Large Language Models to Enhance Clinically-Driven Missing Data Recovery Algorithms in Electronic Health Records. https://doi.org/10.1093/jamiaopen%2Fooag080

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