The Transformative Potential of Large Language Models in Mining Electronic Health Records Data: Content Analysis
Bibliographic record
Abstract
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.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.011 | 0.046 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.002 |
| Bibliometrics | 0.004 | 0.002 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.002 | 0.003 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 0.001 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".