Text2Cohort: Democratizing the NCI Imaging Data Commons with Natural Language Cohort Discovery
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The Imaging Data Commons (IDC) is a cloud-based database that provides researchers with open access to cancer imaging data, with the goal of facilitating collaboration in medical imaging research. However, querying the IDC database for cohort discovery and access to imaging data has a significant learning curve for researchers due to its complex nature. We developed Text2Cohort, a large language model (LLM) based toolkit to facilitate user-friendly and intuitive natural language cohort discovery in the IDC. Text2Cohorts translates user input into IDC database queries using prompt engineering and autocorrection and returns the query's response to the user. Autocorrection resolves errors in queries by passing the errors back to the model for interpretation and correction. We evaluate Text2Cohort on 50 natural language user inputs ranging from information extraction to cohort discovery. The resulting queries and outputs were verified by two computer scientists to measure Text2Cohort's accuracy and F1 score. Text2Cohort successfully generated queries and their responses with an 88 it failed to generate queries for 6/50 (12 semantic errors. Our results indicate that Text2Cohort succeeded at generating queries with correct responses, but occasionally failed due to a lack of understanding of the data schema. Despite these shortcomings, Text2Cohort demonstrates the utility of LLMs to enable researchers to discover and curate cohorts using data hosted on IDC with high levels of accuracy using natural language in a more intuitive and user-friendly way.
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