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feat: serum stability in pipeline scores and pilot panel priority - #32
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- pipeline.py: compute serum_stability_score(features) for every candidate and store it under scores["serum_stability"] in the JSONL output - pilot.py: update _pilot_priority() to include 0.05 × serum_stability as a light tiebreaker (max +0.05 gain, does not override ensemble) - pilot_panel.py: add serum_stability column to CSV output and markdown table; update priority-formula comment to reflect the new term - tests: update correct_columns assertion for new CSV field; add test for higher_stability_higher_priority; fix missing-disagreement default test for updated formula Regenerated outputs show SEED-004 variants (stability 0.85+) now rank slightly higher than equally-scored SEED-003 variants (stability 0.27), correctly de-emphasising the most protease-sensitive family. 858 tests passing
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Jun 28, 2026
…ity assessment (#33) - Add 29 well-characterized AMP sequences from published literature to the curated reference set, spanning LL-37 fragments (KR-12, FK-13, FK-16), cathelicidins (BMAP-27, BMAP-28, mCRAMP), proline-rich (apidaecin, oncocin, pyrrhocoricin), marine (pleurocidin, clavanin A), and engineered (WLBU2, BP100, omiganan) families — total 44 → 72 unique sequences - Remove duplicate REF-GIG-001 (identical to REF-MAG-001) - Add tests/test_reference_set.py: 14 tests guarding structure, uniqueness, canonical amino acids, family coverage (≥20 families, ≥70 sequences) - Update docs/DISCOVERY_PREDICTION.md: mark PRs #31–#32 completed, revise serum stability probability 10–20% → 25–40% based on updated pilot panel composition, revise combined "breaking news" probability 5–12% → 10–25% with root cause analysis of remaining gap
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Summary
serum_stability_score(features)is now computed for every candidate and stored underscores["serum_stability"]in the JSONL output alongside activity, safety, synthesis, and novelty._pilot_priority()now adds0.05 × serum_stabilityas a light tiebreaker. Max gain = +0.05 (does not override ensemble score ordering). Candidates with fewer interior protease sites rank slightly higher when ensemble scores are close.serum_stabilitycolumn. Priority formula comment updated.Impact
Before: SEED-003 variants (stability 0.27) and equally-scored SEED-004 variants (stability 0.85) sorted identically.
After: SEED-004 (more serum-stable, fewer K/R sites) correctly ranks above equally-scored SEED-003 candidates within the same seed slot.
Test plan
correct_columnstest updated for new CSV fieldhigher_stability_higher_prioritytest addedmissing_disagreement_defaults_to_0_5test updated for new formula🤖 Generated with Claude Code