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feat: negative-set robustness — Phase 2 benchmark honesty - #7
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…ves, 53 tests Phase 2: Negative-set robustness — pipeline must enrich AMP-like sequences above negatives regardless of negative type, not just against easy all-repeat controls. - Add examples/negative/poly_cationic.csv: 5 poly-K/R sequences with high charge density but no hydrophobic face (a harder negative set than degenerate repeats) - Add examples/negative/poly_hydrophobic.csv: 5 poly-L/I/V sequences with high hydrophobic fraction but zero charge (another harder negative class) - Add examples/benchmark/robustness_positives.csv: 3 canonical AMP-like positives used across all robustness tests - Add test_negative_robustness.py: 16 tests verifying: - Poly-cationic sequences have correct physicochemical properties (high charge, zero hydro) - Poly-hydrophobic sequences have correct properties (high hydro, zero charge) - Safety scorer penalizes both classes (excess charge / excess hydrophobicity) - EF > 1.0 vs degenerate, poly-cationic, AND poly-hydrophobic negatives - recall@3 = 1.0 (all 3 positives in top-3) vs both hard negative sets - Mean positive ensemble score > mean negative ensemble across all negative types - Add recall_at_k, random_recall_at_k, enrichment_factor, benchmark_summary to evaluate.py - Fix ruff F401 unused imports in pipeline.py, test_cli.py, test_pipeline_filters.py - 53 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Superseded by PR #11 (feat/integrate-all-phases), which merges all Phase 2 + Phase 3 work into a single consolidation PR with 251 tests passing.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: Negative-set robustness from AGENTS.md:
A pipeline that only outperforms trivial negatives (all-A, all-G) cannot be trusted. This PR verifies the pipeline still enriches AMP-like sequences against harder, more realistic negative classes.
New negative datasets
poly_cationic.csvpoly_hydrophobic.csvThese represent one-dimensional negatives — sequences that have one AMP-like property but lack the balance that makes real AMPs work.
What the tests prove
Test plan
make test— 53 tests passruff check src tests— clean