Large Language Model Applications for Health Information Extraction in Oncology: Scoping Review
Bibliographic record
Abstract
Background: Natural language processing systems for data extraction from unstructured clinical text require expert-driven input for labeled annotations and model training. The natural language processing competency of large language models (LLM) can enable automated data extraction of important patient characteristics from electronic health records, which is useful for accelerating cancer clinical research and informing oncology care. Objective: This scoping review aims to map the current landscape, including definitions, frameworks, and future directions of LLMs applied to data extraction from clinical text in oncology. Methods: We queried Ovid MEDLINE for primary, peer-reviewed research studies published since 2000 on June 2, 2024, using oncology- and LLM-related keywords. This scoping review included studies that evaluated the performance of an LLM applied to data extraction from clinical text in oncology contexts. Study attributes and main outcomes were extracted to outline key trends of research in LLM-based data extraction. Results: The literature search yielded 24 studies for inclusion. The majority of studies assessed original and fine-tuned variants of the BERT LLM (n=18, 75%) followed by the Chat-GPT conversational LLM (n=6, 25%). LLMs for data extraction were commonly applied in pan-cancer clinical settings (n=11, 46%), followed by breast (n=4, 17%), and lung (n=4, 17%) cancer contexts, and were evaluated using multi-institution datasets (n=18, 75%). Comparing the studies published in 2022-2024 versus 2019-2021, both the total number of studies (18 vs 6) and the proportion of studies using prompt engineering increased (5/18, 28% vs 0/6, 0%), while the proportion using fine-tuning decreased (8/18, 44.4% vs 6/6, 100%). Advantages of LLMs included positive data extraction performance and reduced manual workload. Conclusions: LLMs applied to data extraction in oncology can serve as useful automated tools to reduce the administrative burden of reviewing patient health records and increase time for patient-facing care. Recent advances in prompt-engineering and fine-tuning methods, and multimodal data extraction present promising directions for future research. Further studies are needed to evaluate the performance of LLM-enabled data extraction in clinical domains beyond the training dataset and to assess the scope and integration of LLMs into real-world clinical environments.
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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 | 0.040 | 0.205 |
| Meta-epidemiology (narrow) | 0.002 | 0.002 |
| Meta-epidemiology (broad) | 0.005 | 0.010 |
| Bibliometrics | 0.023 | 0.022 |
| Science and technology studies | 0.001 | 0.002 |
| Scholarly communication | 0.005 | 0.007 |
| Open science | 0.004 | 0.004 |
| Research integrity | 0.003 | 0.003 |
| Insufficient payload (model declined to judge) | 0.007 | 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".