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v0.5.58 — Simulation Cheap-Baseline Benchmark (Loop 36) - #152

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loop36-simulation-baselines
Jul 6, 2026
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Per-signal comparison: does each simulation output beat its cheapest meaningful heuristic baseline?

Primary: scripts/benchmark_simulation_baselines.py — compares 4 simulation signals vs cheap baselines on the within-AMP hemolysis task. make bench-simulation-baselines.

Honest finding: 0/4 signals beat their cheapest baseline.

  • bacterial_binding (0.4876) vs mean_eisenberg (0.5469): delta=-0.0593
  • selectivity_ratio (0.3615) vs selectivity_proxy (0.3905): delta=-0.0290
  • helix_weight (0.6458) vs helix_propensity (0.6489): delta=-0.0031
  • non_helical (0.4124) vs proline_fraction (0.4929): delta=-0.0805

Consequence: All simulation modules remain permanently experimental. Weighted mode stays blocked. Future work needs fundamentally richer modeling, not 1D propensities.

Tests: 13 tests covering baselines, AUROC, all-blocked verdict, CLI output.

Doc updates: 50_LOOP_PLAN (Loop 36 complete), ROADMAP (v0.5.58), METRICS_CURRENT (v0.5.58, 1953 tests), BENCHMARKING (22 targets match Makefile).

1953 tests passing (pre-push full suite).

Per-signal comparison: does each simulation output beat its cheapest
meaningful heuristic baseline on the within-AMP hemolysis task?

Changes:
- scripts/benchmark_simulation_baselines.py -- compares 4 simulation
  signals against their cheapest heuristic baselines.
- Makefile -- added bench-simulation-baselines target.
- tests/test_benchmark_simulation_baselines.py -- 13 tests.
- docs/50_LOOP_PLAN.md -- Loop 36 complete, next Loop 38.
- docs/ROADMAP.md -- v0.5.58 entry.
- docs/METRICS_CURRENT.md -- Pipeline v0.5.58, 1953 tests.
- docs/BENCHMARKING.md -- Added bench-simulation-baselines.

Honest finding: 0/4 simulation signals beat their cheapest baseline.
All modules remain permanently experimental. Weighted mode blocked.
@cschanhniem
cschanhniem merged commit 0adceb8 into main Jul 6, 2026
@cschanhniem
cschanhniem deleted the loop36-simulation-baselines branch July 6, 2026 08:08
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