Enhancing biomarker based oncology trial matching using large language models

Clinical trials are an essential component of drug development for new cancer treatments, yet the information required to determine a patient's eligibility for enrollment is scattered in large amounts of unstructured text. Genomic biomarkers are especially important in precision medicine and targeted therapies, making them essential for matching patients to appropriate trials. Large language models (LLMs) offer a promising solution for extracting this information from clinical trial study descriptions (e.g., brief summary, eligibility criteria), aiding in identifying suitable patient matches in downstream applications. In this study, we explore various strategies for extracting genetic biomarkers from oncology trials. Therefore, our focus is on structuring unstructured clinical trial data, not processing individual patient records. Our results show that open-source language models, when applied out-of-the-box, effectively capture complex logical expressions and structure genomic biomarkers, outperforming closed-source models such as GPT-4. Furthermore, fine-tuning these open-source models with additional data significantly enhances their performance.