Customizing Open Source LLMs for Quantitative Medication Attribute Extraction across Heterogeneous EHR Systems

TL;DR

This paper presents a framework that customizes open source large language models to extract standardized medication attributes from heterogeneous EHR data, enabling consistent analysis of opioid use disorder treatments across multiple clinics.

Contribution

The study introduces a practical pipeline that adapts open source LLMs for extracting MOUD prescription data from diverse EHR systems, improving coverage and accuracy while supporting privacy-preserving deployment.

Findings

Qwen2.5-32B achieves 93.4% coverage and 93.0% accuracy

MedGemma-27B achieves 93.1% coverage and 92.2% accuracy

Error analysis led to targeted fixes for missing data and unit misinterpretations.

Abstract

Harmonizing medication data across Electronic Health Record (EHR) systems is a persistent barrier to monitoring medications for opioid use disorder (MOUD). In heterogeneous EHR systems, key prescription attributes are scattered across differently formatted fields and freetext notes. We present a practical framework that customizes open source large language models (LLMs), including Llama, Qwen, Gemma, and MedGemma, to extract a unified set of MOUD prescription attributes (prescription date, drug name, duration, total quantity, daily quantity, and refills) from heterogeneous, site specific data and compute a standardized metric of medication coverage, \emph{MOUD days}, per patient. Our pipeline processes records directly in a fixed JSON schema, followed by lightweight normalization and cross-field consistency checks. We evaluate the system on prescription level EHR data from five clinics in a national OUD study (25{,}605 records from 1{,}257 patients), using a previously annotated benchmark of 10{,}369 records (776 patients) as the ground truth. Performance is reported as coverage (share of records with a valid, matchable output) and record-level exact-match accuracy. Larger models perform best overall: Qwen2.5-32B achieves \textbf{93.4\%} coverage with \textbf{93.0\%} exact-match accuracy across clinics, and MedGemma-27B attains \textbf{93.1\%}/\textbf{92.2\%}. A brief error review highlights three common issues and fixes: imputing missing dosage fields using within-drug norms, handling monthly/weekly injectables (e.g., Vivitrol) by setting duration from the documented schedule, and adding unit checks to prevent mass units (e.g., ``250 g'') from being misread as daily counts. By removing brittle, site-specific ETL and supporting local, privacy-preserving deployment, this approach enables consistent cross-site analyses of MOUD exposure, adherence, and retention in real-world settings.