Integrating large language models with human expertise for disease detection in electronic health records
Bibliographic record
Abstract
OBJECTIVE: Electronic health records (EHR) are widely available to complement administrative data-based disease surveillance and healthcare performance evaluation. Defining conditions from EHR is labour-intensive and requires extensive manual labelling of disease outcomes. This study developed an efficient strategy based on advanced large language models to identify multiple conditions from EHR clinical notes. METHODS: We linked a cardiac registry cohort in 2015 with an EHR system in Alberta, Canada. We developed a pipeline that leveraged a generative large language model (LLM) to analyze, understand, and interpret EHR notes by prompts based on specific diagnosis, treatment management, and clinical guidelines. The pipeline was applied to detect acute myocardial infarction (AMI), diabetes, and hypertension. The performance was compared against clinician-validated diagnoses as the reference standard and widely adopted International Classification of Diseases (ICD) codes-based methods. RESULTS: The study cohort accounted for 3088 patients and 551,095 clinical notes. The prevalence was 55.4 %, 27.7 %, 65.9 % and for AMI, diabetes, and hypertension, respectively. The performance of the LLM-based pipeline for detecting conditions varied: AMI had 88 % sensitivity, 63 % specificity, and 77 % positive predictive value (PPV); diabetes had 91 % sensitivity, 86 % specificity, and 71 % PPV; and hypertension had 94 % sensitivity, 32 % specificity, and 72 % PPV. Compared with ICD codes, the LLM-based method demonstrated improved sensitivity and negative predictive value across all conditions. The monthly percentage trends from the detected cases by LLM and reference standard showed consistent patterns. CONCLUSION: The proposed LLM-based pipeline demonstrated reasonable accuracy and high efficiency in disease detection for multiple conditions. Human expert knowledge can be integrated into the pipeline to guide EHR note analysis without manually curated labels. The method could enable comprehensive real-time disease surveillance using EHRs.
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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 | 0.008 | 0.029 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.003 |
| Bibliometrics | 0.002 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.002 | 0.003 |
| Open science | 0.002 | 0.003 |
| Research integrity | 0.001 | 0.003 |
| Insufficient payload (model declined to judge) | 0.002 | 0.002 |
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".