Criteria2Query 3.0: Leveraging generative large language models for clinical trial eligibility query generation

Automated identification of eligible patients is a bottleneck of clinical research. We propose Criteria2Query (C2Q) 3.0, a system that leverages GPT-4 for the semi-automatic transformation of clinical trial eligibility criteria text into executable clinical database queries.

C2Q 3.0 integrated three GPT-4 prompts for concept extraction, SQL query generation, and reasoning. Each prompt was designed and evaluated separately. The concept extraction prompt was benchmarked against manual annotations from 20 clinical trials by two evaluators, who later also measured SQL generation accuracy and identified errors in GPT-generated SQL queries from 5 clinical trials. The reasoning prompt was assessed by three evaluators on four metrics: readability, correctness, coherence, and usefulness, using corrected SQL queries and an open-ended feedback questionnaire.

Out of 518 concepts from 20 clinical trials, GPT-4 achieved an F1-score of 0.891 in concept extraction. For SQL generation, 29 errors spanning seven categories were detected, with logic errors being the most common (n = 10; 34.48 %). Reasoning evaluations yielded a high coherence rating, with the mean score being 4.70 but relatively lower readability, with a mean of 3.95. Mean scores of correctness and usefulness were identified as 3.97 and 4.37, respectively.

GPT-4 significantly improves the accuracy of extracting clinical trial eligibility criteria concepts in C2Q 3.0. Continued research is warranted to ensure the reliability of large language models.