Add PubTator3 annotation, train/eval pipeline, and MLflow tracking - #1
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ghofrangaddeh50-web wants to merge 4 commits into
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Add PubTator3 annotation, train/eval pipeline, and MLflow tracking#1ghofrangaddeh50-web wants to merge 4 commits into
ghofrangaddeh50-web wants to merge 4 commits into
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ghofrangaddeh50-web
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Jun 2, 2026
ghofrangaddeh50-web
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- annotation_client: PubTator3 collector with BERN2 fallback, normalized to the existing BERN2 output shape so downstream NER preprocessing is unchanged
- trainer: stratified train/val/test split, StratifiedKFold CV, held-out evaluation (accuracy/precision/recall/f1/roc_auc), MLflow tracking + artifacts
- plain-Python entrypoints (train.py, demo_predict.py) so training/prediction run on native Windows where Metaflow cannot; Metaflow flows kept as thin wrappers over the same core logic
- requirements.txt, .gitignore, configs, and README workflow docs
- annotation_client: PubTator3 collector with BERN2 fallback, normalized to the existing BERN2 output shape so downstream NER preprocessing is unchanged - trainer: stratified train/val/test split, StratifiedKFold CV, held-out evaluation (accuracy/precision/recall/f1/roc_auc), MLflow tracking + artifacts - plain-Python entrypoints (train.py, demo_predict.py) so training/prediction run on native Windows where Metaflow cannot; Metaflow flows kept as thin wrappers over the same core logic - requirements.txt, .gitignore, configs, and README workflow docs Co-Authored-By: Claude <noreply@anthropic.com>
Add tests/ covering 7 failure scenarios (PubTator3 down, partial coverage, both down, fallback disabled, HTTP 429, log assertions, and a live integration test), plus conftest and shared fixtures. Add pytest.ini, requirements-dev.txt, a no-fallback config, and French docs explaining and exercising the fallback. Ignore test artifacts. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Keep the fallback explanation and testing guides local-only; they are not part of the shared codebase. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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