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feat: novelty pressure tests — Phase 2 benchmark honesty - #8
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Phase 2: Novelty pressure — top candidates must not be mere copies of known AMP motifs. - Add examples/benchmark/novelty_pressure_pool.csv: 11 sequences including 3 near-dups of known references (NOV-DUP-*), 3 genuinely novel AMP-like sequences (NOV-NEW-*), and 5 non-AMP negatives (NOV-NEG-*) - Add test_novelty_pressure.py: 13 tests verifying: - Exact reference copies receive novelty = 0.0 - 1-substitution near-dups receive novelty < 0.20 (below min_novelty threshold) - Genuinely novel sequences receive novelty >= 0.20 - Novelty decreases monotonically with increasing reference similarity - nearest_reference field is populated for near-duplicate candidates - Pipeline min_novelty filter excludes near-dups from selection - Exact reference copies never appear in selected batch - Novel AMP-like candidates preferentially selected over near-dups - Near-dups do not dominate the top-5 ranked (novelty weighting has effect) - Add recall_at_k, random_recall_at_k, enrichment_factor, benchmark_summary to evaluate.py - Fix ruff F401 unused imports across 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Superseded by PR #11 (feat/integrate-all-phases), which merges all Phase 2 + Phase 3 work into a single consolidation PR with 251 tests passing.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: Novelty pressure from AGENTS.md:
This PR verifies that the pipeline actively penalizes near-duplicate copies of known AMPs and selects genuinely novel sequences instead.
Test dataset:
examples/benchmark/novelty_pressure_pool.csvWhat the tests prove
nearest_referencepopulated for near-dupsTest plan
make test— 50 tests passruff check src tests— clean