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v0.5.55 — Within-AMP Simulation Ablation (Loop 34) - #149
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Extended the simulation ablation benchmark to test modules on their designed task: within-AMP hemolysis detection. Changes: - scripts/benchmark_simulation_ablation.py -- Extended with --mode within-amp flag. Tests 45 hemolytic vs 125 selective AMPs. - Makefile -- Added bench-simulation-ablation-within-amp target. - docs/50_LOOP_PLAN.md -- Loop 34 complete (re-interpreted). - docs/ROADMAP.md -- v0.5.55 entry. - docs/METRICS_CURRENT.md -- Pipeline v0.5.55, 1928 tests. Honest finding: simulation modules do NOT improve over existing rich_selectivity (0.7453) for hemolysis detection. Best simulation score: helix_weight AUROC 0.6458 (hemolytic AMPs are more helical). 1928 tests passing.
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Extended simulation ablation benchmark with within-AMP hemolysis detection mode.
Primary:
scripts/benchmark_simulation_ablation.py --mode within-amp— tests MembraneProxy + StructureProxy on 45 hemolytic vs 125 selective AMPs from existing hemolysis_reference.csv.Honest finding:
helix_weightAUROC 0.6458 (hemolytic AMPs are more helical)rich_selectivityremains the best detector at 0.7453Tests: 23 tests (6 new for within-AMP mode).
Doc updates: 50_LOOP_PLAN (Loop 34 complete, re-interpreted), ROADMAP, METRICS_CURRENT v0.5.55, BENCHMARKING (21 targets matching Makefile).
1928 tests passing (pre-push full suite).