v0.5.31 — Order-dependent features benchmark (Loop 13)

[cschanhniem]

Class

Benchmark honesty / scientific credibility (Priority 1)

Why it matters

The pipeline's strict triage AUROC (0.572) showed it's predominantly composition-based. We didn't know WHICH features depend on sequence order, or whether order-dependent features could improve discrimination. This benchmark answers both questions.

Key findings

1. dipeptide_order_score is the feat: enforce config filters, add run manifest, bench leakage CLI, 37 tests #1 order-dependent feature (AUROC 0.7861 on AMP-vs-scrambled), beating hydrophobic moment (0.7483)
2. Only 7/31 features survive scrambling — all are amphipathicity/helix-wheel properties + new dipeptide score
3. All composition features are EXACTLY position-independent (AUROC = 0.5000, identical means)
4. Some features are anti-order-dependent (aggregation 0.4325, hydrophilic face mean h 0.3506 — scrambling creates patterns not found in native AMPs)

Changes

• src/openamp_foundry/features/dipeptide.py — new module: dipeptide frequencies + order score with pre-computed log-odds reference
• src/openamp_foundry/features/dipeptide_log_odds.json — 400-entry reference for AMP-vs-scrambled discrimination
• src/openamp_foundry/features/physchem.py — dipeptide_order_score added to compute_features() (31st scalar feature)
• src/openamp_foundry/features/__init__.py — exports for new module
• scripts/benchmark_order_dependent.py — analyzes which features survive scrambling
• Makefile — make bench-order-dependent target
• .github/workflows/ci.yml — informational CI step
• docs/50_LOOP_PLAN.md — Loop 13 ✅
• docs/METRICS_CURRENT.md — Order-Dependent Features Benchmark section
• docs/ROADMAP.md — v0.5.31 entry

Verification

• ✅ 1723 tests pass
• ✅ Lint clean on all new/modified files
• ✅ dipeptide_order_score accessible via openamp_foundry.features API

Risk / uncertainty

• The log-odds reference is pre-computed from the 500-AMP benchmark; it will need periodic recalibration as the AMP corpus grows
• Not yet integrated into the ensemble scoring — integration requires re-baselining the benchmark gate
• Some signal may come from position-specific residue patterns (e.g., N-terminal K) rather than true dipeptide preferences

Next loop

Loop 14 — Cross-dataset generalization (train on APD6, test on DRAMP or vice versa)