Labcoat biomedical ml hygiene
Skill qchiujunhao/labcoat/skills/labcoat-biomedical-ml-hygiene
Biomedical ML hygiene for leakage, patient-level splits, subject/sample identifiers, site/batch leakage, label leakage, calibration, external validation, and preprocessing fit-before-split risks. Use when building or reviewing ML code for biomedical data.From its SKILL.md
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SKILL.md
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Biomedical ML Hygiene
Prevent optimistic biomedical ML results.
Decision Ladder
- Identify prediction unit: patient, subject, sample, slide, cell, visit, site, or batch.
- Split by independent unit before preprocessing fit.
- Use group-aware cross-validation when repeated samples exist.
- Check label leakage, site/batch proxies, and duplicate-derived features.
- Require calibration and external validation language for deployment claims.
Allowed
- Flag leakage risks and suggest group-aware splitting.
- Ask for cohort structure and prediction unit.
- Use minimal tests that fail when patient IDs cross splits.
Disallowed
- Do not report clinical performance as validated without external evidence.
- Do not fit scalers/normalizers on the full dataset before splitting.
- Do not ignore patient/site/batch grouping.
Output
Use:
- Prediction unit:
- Leakage risks:
- Split strategy:
- Validation limits:
Read references/leakage-patterns.md for patterns.
What ships with it: 1 file
358 B alongside SKILL.md
references/
- leakage-patterns.md358 B