EAGLE-AI: A large language model workflow for automated extraction and scoring of literature evidence linking genes to autism spectrum disorder
Bibliographic record
Abstract
We previously developed the Evaluation of Autism Gene Link Evidence (EAGLE) curation framework and used it to characterise 219 autism-associated genes. However, this took years of human work. We present EAGLE-AI, an automated curation system incorporating large language models (LLMs). On screened paper sets, it achieves F1 91% and scoring error 17.2%, near human performance. EAGLE-AI performs worse on unscreened papers due to table parsing and context overload, which we address using if-else scoring and computer vision tools. Handling of supplementary materials remains an unsolved problem. Our findings demonstrate proof-of-concept for automating most of a clinical genomics curation process.
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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 | 0.010 | 0.022 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.002 |
| Bibliometrics | 0.009 | 0.004 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.004 | 0.002 |
| Open science | 0.002 | 0.003 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.018 | 0.012 |
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".