Large Language Models for Accurate Medical Chart Abstraction: Enabling Scalable and Secure Artificial Intelligence Deployment in Stroke

Zhusi Zhong, Carl M. Porto, David Hong, Miranda Gonzales, Revyn Kim +11

Medical chart abstraction transforms unstructured clinical narratives into structured variables for research and quality monitoring. We evaluated a prompting-based large language model (LLM) framework for extracting eight clinical variables from 2,416 neurointerventional acute stroke intervention reports across three hospitals. Twenty-two instruction-tuned open-source LLMs were evaluated across architectures, model sizes, and biomedical adaptations using Quick Response and Chain-of-Thought (CoT) prompting. Non-expert staff annotations served as the cross-model reference standard. Evaluation was restricted to report-variable pairs with a valid LLaMA3.3-70B CoT prediction and a corresponding reference label. Performance measures included extraction accuracy, inference latency, and agreement with expert adjudication. Twenty discordant cases per variable underwent review by two senior physicians and four medical students. LLaMA3.3-70B achieved the highest overall accuracy (94.8%). CoT improved performance on inference-dependent variables such as site of occlusion, while Quick Response was optimal for directly stated procedural fields. Expert adjudication showed that AI predictions…