A new AI-assisted data standard accelerates interoperability in biomedical research.

Abstract

In this paper, we leveraged Large Language Models(LLMs) to accelerate data wrangling and automate labor-intensive aspects of data discovery and harmonization. This work promotes interoperability standards and enhances data discovery, facilitating AI-readiness in biomedical science with the generation of Common Data Elements (CDEs) as key to harmonizing multiple datasets. Thirty-one studies, various ontologies, and medical coding systems served as source material to create CDEs from which available metadata and context was sent as an API request to 4th-generation OpenAI GPT models to populate each metadata field. A human-in-the-loop (HITL) approach was used to assess quality and accuracy of the generated CDEs. To regulate CDE generation, we employed ElasticSearch and HITL to avoid duplicate CDEs and instead, added them as potential aliases for existing CDEs. The generated CDEs are foundational to assess the interoperability potential of datasets by determining how many data set column headers can be correctly mapped to CDEs as well as quantifying compliance with permissible values and data types. Subject matter experts reviewed generated CDEs and determined that 94.0% of generated metadata fields did not require manual revisions. Data tables from the Alzheimer's Disease Neuroimaging Initiative (ADNI) and the Global Parkinson's Genetic Program (GP2) were used as test cases for interoperability assessments. Column headers from all test cases were successfully mapped to generated CDEs at a rate of 32.4% via elastic search.The interoperability score, a metric for dataset compatibility to CDEs and other connected datasets, based on relevant criteria such as data field completeness and compliance with common harmonization standards averaged 53.8 out of 100 for test cases. With this project, we aim to automate the most tedious aspects of data harmonization, enhancing efficiency and scalability in biomedical research while decreasing activation energy for federated research.