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docs: overhaul EXPERT_REVIEW_PACK.md for 7-seed pilot panel - #88
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The previous version was outdated (pipeline v0.1.0, 5 seeds, stale phase3 candidates, old batch stats). Updated to reflect current state: - Pipeline version 0.5.x, AUROC 0.8420, 7 seed families - Current 20-candidate pilot panel table with novelty categories (16 NOVEL, 3 KNOWN_VARIANT, 1 CLOSE_RELATIVE from PR #86) - SEED-003 annotated as KNOWN_VARIANT (82% similar to RRWQWRMKKLG) - Gold-standard calibration section with Melittin safety blind spot - Per-family summary table with P(active), reviewer focus, serum notes - Updated reviewer questions targeting current 7-seed specific issues - Updated next steps: serum stability first, MRSA USA300, external predictor checklist requirement before synthesis - Updated pipeline limitations table with Melittin blind spot, serum model edge cases, Pro-rich stability caveat - Document cross-reference index to all companion docs Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Summary
Complete overhaul of
docs/EXPERT_REVIEW_PACK.md— the document an expert microbiologist reads before signing off on synthesis. The previous version was significantly outdated (pipeline v0.1.0, 5 seeds, stale phase3 batch stats, old candidate table).What changed
Metadata: Pipeline v0.5.x, AUROC 0.8420, 7 seed families (was 5), 20-candidate pilot panel (was 89-candidate phase3 pool)
Section 1 — Overview: Added 8-stage scoring table (vs 6-stage old); documents serum stability scorer, cross-term, Trp-weighted aromatic bonus, face segregation
Section 2 — Seeds + Reference Set: Updated to 7 seeds; added broad novelty check summary (16 NOVEL, 3 KNOWN_VARIANT, 1 CLOSE_RELATIVE)
Section 3 — Pilot Panel: Full 20-candidate table with broad novelty category column; replaces old top-20 table with stale Phase3 candidates
Section 4 — Gold-Standard Calibration: New section documenting Melittin safety blind spot; LL-37/Cecropin-A below-panel explanation
Section 5 — Per-Family Summary: New section with P(active) estimates, SEED-008 Trp disagreement note, SEED-009 media note for reviewer
Section 6 — Reviewer Questions: Updated to current 7-seed specifics; added MRSA, RPMI, serum stability sequencing, SEED-003 novelty question
Section 7 — Next Steps: Updated order: serum stability first, external predictor checklist before synthesis, novelty pre-registration, MRSA USA300 Priority 3
Section 8 — Limitations: Updated with Melittin blind spot, SEED-008/009 model edge cases, Pro-rich stability caveat, LL-37 length bias explanation
Section 9 — Cross-References: New index to all companion docs (ASSAY_PREREGISTRATION, WET_LAB_HANDOFF, NOVELTY_BROAD_CHECK, etc.)
Test plan
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