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feat: toxicity penalty tests — Phase 2 benchmark honesty - #10
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Phase 2: Toxicity penalty — predicted hemolytic/toxic candidates are down-ranked. - Add test_toxicity_penalty.py: 13 tests covering the full toxicity penalty mechanism: Safety scorer penalty signals: - Hydrophobic fraction > 0.65 → hemolysis proxy penalty - Charge density > 0.55 → toxicity proxy penalty - Length > 35 aa → stability and synthesis penalty - Cysteine fraction > 0.25 → disulfide complexity penalty - Longest repeat run ≥ 6 → degenerate composition penalty Tests verify: - Extreme hydrophobicity reduces safety score (<0.6) - Extreme charge density reduces safety score (<0.6) - High cysteine fraction reduces safety (<0.9) - Very long sequences penalized - Long repeat runs penalized - All balanced AMP candidates score higher safety than poly-hydrophobic sequences - All balanced AMP candidates score higher safety than poly-cationic sequences - Monotonic safety reduction with increasing excess hydrophobicity - Double penalty (charge + repeat run) on poly-K - Mean AMP ensemble > mean high-risk ensemble in full pipeline - All AMPs outrank all high-risk candidates - Toxicity penalty propagates correctly through pipeline safety field - High-risk candidates excluded with strict max_safety_risk filter - Fix ruff F401 unused imports (pipeline.py, test_cli.py, test_pipeline_filters.py) - 50 tests passing, ruff clean
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Superseded by PR #11 (feat/integrate-all-phases), which merges all Phase 2 + Phase 3 work into a single consolidation PR with 251 tests passing. |
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Summary
Implements Phase 2: Toxicity penalty from AGENTS.md:
Safety scorer penalty signals tested
(hydro - 0.65) × 1.8(charge - 0.55) × 1.2+0.25+0.20+0.15These are computational proxies only. No biological safety claim is made.
What the tests prove
safetyfield in pipeline outputTest plan
make test— 50 tests passruff check src tests— clean