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feat: 10-seed mechanism matrix, 5 external predictors, Wave 2 plan, negative result protocol - #60
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…egative result protocol 10-seed mechanism matrix (DISCOVERY_PREDICTION.md): - Table updated from 8 seeds to all 10 (SEED-009 Bac2A + SEED-010 KR-12) - Added mechanism class column: 7 distinct mechanisms documented - sel_proxy and cytotox_risk computed from pipeline for new seeds - Summary: first pipeline with complete mechanistic diversity statement External predictor checklist (reports/external_predict.py): - Added AntiCP 2.0 (Raghava lab, SVM for cytotoxicity-tested AMPs) - Added Macrel (command-line Random Forest trained on DRAMP v2; reports AMP probability + hemolytic probability independently) - Agreement threshold updated: ≥3/5 tools (was ≥2/3) - Table updated to include all 5 predictor columns - Added Macrel hemolytic probability flag guidance Wave 2 active-learning plan (docs/WAVE2_PLAN.md): - Pre-specifies strategy for each outcome: Scenario A (0 hits), B (active-but-toxic), C (confirmed hit with TI ≥ 10) - Includes D-amino acid variant plan, MDR strain panel, mechanism confirmation assays, and per-scenario budget estimates - Learning loop table: 5 calibration signals to extract from Wave 1 Negative result protocol (docs/WET_LAB_HANDOFF.md): - Full negative result reporting section with schema field mapping - Diagnostic checklist for inactive candidates (aggregation, synthesis failure, seed-family failure, scoring model error) - Archive path: outputs/negative_results/<id>_<date>_negative.json
- WAVE2_PLAN: replace ATCC 19606 (susceptible reference) with ATCC BAA-1710 (clinical MDR A. baumannii ESKAPE panel representative) [HIGH] - WAVE2_PLAN: correct ATCC BAA-2146 label from 'ESBL' to 'NDM-1 carbapenemase-producing; carbapenem-resistant' [MEDIUM] - WET_LAB_HANDOFF: change JSON negative result example result_value from null to 128.0 (highest concentration tested); add clarifying note [MEDIUM] - external_predict: clarify AntiCP 2.0 predicts anticancer peptides (ACPs) not AMPs directly; update positive_label and note to prevent misclassification [LOW]
4 tasks done
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Summary
Four improvements that complete the pre-wet-lab documentation and reduce post-assay ambiguity:
1. 10-seed mechanism diversity table
2. 5 external predictors (was 3)
3. Wave 2 active-learning plan (
docs/WAVE2_PLAN.md)4. Negative result reporting protocol
schemas/lab_result.schema.jsonexplicitlyTest plan
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