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feat: Phase W W1 novelty challenge harness schema (NCH-) - #1003

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cschanhniem merged 1 commit into
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feat/w1-novelty-challenge-harness
Jul 10, 2026
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cschanhniem merged 1 commit into
mainfrom
feat/w1-novelty-challenge-harness

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Summary

  • Adds NCH- (novelty challenge harness) schema: batch-level gate documenting what fraction of top candidates have ≥80% sequence identity to known AMPs in a reference database
  • Verdict auto-computed: novel_batch (≤20% near-neighbors), mixed_novelty (20-60%), near_neighbor_dominated (≥60%), challenge_not_run (empty input)
  • 6 reference databases (APD3, DRAMP, DBAASP, CAMP, LAMP, custom); configurable identity threshold
  • NCHCandidateResult helper stores per-candidate identity and near-neighbor flag
  • Blocks "novel family" batch-level overclaims without machine-verifiable evidence
  • Adds Phase W definition (W1-W5) to NEXT_100_PR_MAP: batch-level benchmark hardness phase
  • dry_lab_only=True enforced; empty limitations rejected; 63 tests

Test plan

  • python3 -m pytest tests/evidence/test_novelty_challenge_harness.py -- 63 passed
  • Regression BASELINE=9830, tolerance=491; 63 new tests within tolerance

…el novelty gate blocking novel_batch claim when near-neighbor fraction exceeds 20%; VALID_NCH_VERDICTS (4), VALID_REFERENCE_DATABASES (6), identity threshold 0.80, NCHCandidateResult helper; 63 tests; adds Phase W to NEXT_100_PR_MAP
@cschanhniem
cschanhniem merged commit ce48497 into main Jul 10, 2026
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