Medical Data Pecking: A Context-Aware Approach for Automated Quality Evaluation of Structured Medical Data

TL;DR

This paper introduces Medical Data Pecking, a novel context-aware method that uses large language models and software testing concepts to automatically evaluate and improve the quality of structured medical data in electronic health records.

Contribution

It presents a new approach combining software testing and medical knowledge, implemented in the MDPT tool, for systematic and automated EHR data quality assessment.

Findings

Successfully identified 20-43 data issues across datasets

Generated 55-73 tests per cohort for quality evaluation

Demonstrated the effectiveness of LLM-based test suites in medical data quality

Abstract

Background: The use of Electronic Health Records (EHRs) for epidemiological studies and artificial intelligence (AI) training is increasing rapidly. The reliability of the results depends on the accuracy and completeness of EHR data. However, EHR data often contain significant quality issues, including misrepresentations of subpopulations, biases, and systematic errors, as they are primarily collected for clinical and billing purposes. Existing quality assessment methods remain insufficient, lacking systematic procedures to assess data fitness for research. Methods: We present the Medical Data Pecking approach, which adapts unit testing and coverage concepts from software engineering to identify data quality concerns. We demonstrate our approach using the Medical Data Pecking Tool (MDPT), which consists of two main components: (1) an automated test generator that uses large language models and grounding techniques to create a test suite from data and study descriptions, and (2) a data testing framework that executes these tests, reporting potential errors and coverage. Results: We evaluated MDPT on three datasets: All of Us (AoU), MIMIC-III, and SyntheticMass, generating 55-73 tests per cohort across four conditions. These tests correctly identified 20-43 non-aligned or non-conforming data issues. We present a detailed analysis of the LLM-generated test suites in terms of reference grounding and value accuracy. Conclusion: Our approach incorporates external medical knowledge to enable context-sensitive data quality testing as part of the data analysis workflow to improve the validity of its outcomes. Our approach tackles these challenges from a quality assurance perspective, laying the foundation for further development such as additional data modalities and improved grounding methods.