Utilizing Open-Source Large Language Models to Extract Genitourinary Symptoms from Clinical Notes
Yunbing Bai, Wanting Cui, Joseph Finkelstein · Studies in health technology and informatics · 2025
Accurately identifying patient signs and symptoms from clinical notes is essential for effective diagnosis, treatment planning, and medical research. In this study, we evaluated the performance of the Meta Llama model in extracting signs and symptoms related to the genitourinary system, along with their corresponding ICD-10 codes, from urological clinical notes in the MTSamples dataset. The dataset was manually annotated to compare the extraction results of large language models (LLMs) output. We utilized Llama 3.3-70B and performed prompt engineering. The findings suggest that the best performance was achieved when the prompt included a predefined list of definitions of corresponding ICD-10 codes and restricted the model from making assumptions. Under these conditions, Llama 3.3-70B achieved an average recall of 0.96, precision of 0.89, and F1-score of 0.92 for S&S extraction, as well as an average recall of 0.93, precision of 0.85, and F1-score of 0.89 for ICD-10 code generation.