The Transformative Potential of Large Language Models in Mining Electronic Health Records Data: Content Analysis

Background In this study, we evaluate the accuracy, efficiency, and cost-effectiveness of large language models in extracting and structuring information from free-text clinical reports, particularly in identifying and classifying patient comorbidities within oncology electronic health records. We specifically compare the performance of gpt-3.5-turbo-1106 and gpt-4-1106-preview models against that of specialized human evaluators. Objective We specifically compare the performance of gpt-3.5-turbo-1106 and gpt-4-1106-preview models against that of specialized human evaluators. Methods We implemented a script using the OpenAI application programming interface to extract structured information in JavaScript object notation format from comorbidities reported in 250 personal history reports. These reports were manually reviewed in batches of 50 by 5 specialists in radiation oncology. We compared the results using metrics such as sensitivity, specificity, precision, accuracy, F-value, κ index, and the McNemar test, in addition to examining the common causes of errors in both humans and generative pretrained transformer (GPT) models. Results The GPT-3.5 model exhibited slightly lower performance compared to physicians across all metrics, though the differences were not statistically significant (McNemar test, P=.79). GPT-4 demonstrated clear superiority in several key metrics (McNemar test, P<.001). Notably, it achieved a sensitivity of 96.8%, compared to 88.2% for GPT-3.5 and 88.8% for physicians. However, physicians marginally outperformed GPT-4 in precision (97.7% vs 96.8%). GPT-4 showed greater consistency, replicating the exact same results in 76% of the reports across 10 repeated analyses, compared to 59% for GPT-3.5, indicating more stable and reliable performance. Physicians were more likely to miss explicit comorbidities, while the GPT models more frequently inferred nonexplicit comorbidities, sometimes correctly, though this also resulted in more false positives. Conclusions This study demonstrates that, with well-designed prompts, the large language models examined can match or even surpass medical specialists in extracting information from complex clinical reports. Their superior efficiency in time and costs, along with easy integration with databases, makes them a valuable tool for large-scale data mining and real-world evidence generation.