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v0.5.29 — Expanded 500-AMP benchmark (Loop 11) - #139
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- Curated 500 public-domain AMPs + 500 length-matched decoys (n=1000) from UniProt-reviewed (CC BY 4.0) and APD6 natural sources - Pipeline AUROC 0.7792 (CI₉₅: 0.7505–0.8065) — signal generalizes - Cluster-aware CI: 0.746–0.8102 (width 0.064, ~2.3× tighter) - Representative AUROC 0.778 ≈ full AUROC 0.7792 (less redundancy) - Makefile targets: bench-500, bench-cluster-split-500 - CI gate: expanded benchmark AUROC > 0.70 enforced - Docs: METRICS_CURRENT.md, ROADMAP.md, 50_LOOP_PLAN.md updated - Curation script: scripts/curate_500_amp_benchmark.py (reproducible)
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Class
Benchmark honesty / scientific credibility (Priority 1)
Why it matters
The previous benchmark (95 AMPs + 96 decoys, n=191) gave a CI width of ±0.07. The expanded set (500 + 500, n=1000) gives ~2.3× tighter CIs and tests the pipeline against more diverse AMP classes. The old benchmark's representative AUROC (0.7607) was notably below full AUROC (0.7832), suggesting near-duplicate inflation. The expanded set's representative AUROC (0.778) nearly equals full AUROC (0.7792).
Changes
bench-500,bench-cluster-split-500targetsResults
Verification
Next loop
Loop 12 — Time-split benchmark