Reliable Curation of EHR Dataset via Large Language Models under Environmental Constraints

TL;DR

This paper presents CELEC, an LLM-based framework that enables secure, accurate, and efficient natural language querying of EHR databases, facilitating biomedical research without compromising patient privacy.

Contribution

Introduces CELEC, a novel LLM-powered system that translates natural language to SQL for EHR data extraction, ensuring privacy and high accuracy with a robust prompting strategy.

Findings

CELEC achieves accuracy comparable to existing systems.

CELEC maintains strict privacy by only accessing metadata.

Ablation studies highlight the importance of few-shot demonstrations.

Abstract

Electronic health records (EHRs) are central to modern healthcare delivery and research; yet, many researchers lack the database expertise necessary to write complex SQL queries or generate effective visualizations, limiting efficient data use and scientific discovery. To address this barrier, we introduce CELEC, a large language model (LLM)-powered framework for automated EHR data extraction and analytics. CELEC translates natural language queries into SQL using a prompting strategy that integrates schema information, few-shot demonstrations, and chain-of-thought reasoning, which together improve accuracy and robustness. CELEC also adheres to strict privacy protocols: the LLM accesses only database metadata (e.g., table and column names), while all query execution occurs securely within the institutional environment, ensuring that no patient-level data is ever transmitted to or shared with the LLM. On a subset of the EHRSQL benchmark, CELEC achieves execution accuracy comparable to prior systems while maintaining low latency, cost efficiency, and strict privacy by exposing only database metadata to the LLM. Ablation studies confirm that each component of the SQL generation pipeline, particularly the few-shot demonstrations, plays a critical role in performance. By lowering technical barriers and enabling medical researchers to query EHR databases directly, CELEC streamlines research workflows and accelerates biomedical discovery.