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docs(04-02): complete QC and validation plan

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- Add SUMMARY for quality control and positive control validation
- Update STATE.md: Plan 2 of 3 in Phase 04 complete
- Progress: 70% (14/20 plans complete)
- Decisions: scipy MAD outlier detection, PERCENT_RANK validation
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gbanyan
2026-02-11 20:50:00 +08:00
parent 70a5d6eff8
commit c501951b0f
2 changed files with 161 additions and 11 deletions
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.planning/STATE.md
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@@ -10,18 +10,18 @@ See: .planning/PROJECT.md (updated 2026-02-11)
## Current Position
Phase: 4 of 6 (Scoring and Integration)
Plan: 1 of 3 in current phase (in progress)
Status: Plan 04-01 complete — known gene compilation and weighted scoring integration
Last activity: 2026-02-11 — Completed 04-01-PLAN.md
Plan: 2 of 3 in current phase (in progress)
Status: Plan 04-02 complete — quality control and positive control validation
Last activity: 2026-02-11 — Completed 04-02-PLAN.md
Progress: [██████░░░░] 65.0% (13/20 plans complete across all phases)
Progress: [███████░░░] 70.0% (14/20 plans complete across all phases)
## Performance Metrics
**Velocity:**
- Total plans completed: 13
- Average duration: 5.5 min
- Total execution time: 1.2 hours
- Total plans completed: 14
- Average duration: 5.4 min
- Total execution time: 1.3 hours
**By Phase:**
@@ -30,17 +30,17 @@ Progress: [██████░░░░] 65.0% (13/20 plans complete across al
| 01 - Data Infrastructure | 4/4 | 14 min | 3.5 min/plan |
| 02 - Prototype Evidence Layer | 2/2 | 8 min | 4.0 min/plan |
| 03 - Core Evidence Layers | 6/6 | 52 min | 8.7 min/plan |
| 04 - Scoring Integration | 1/3 | 4 min | 4.0 min/plan |
| 04 - Scoring Integration | 2/3 | 7 min | 3.5 min/plan |
**Recent Plan Details:**
| Plan | Duration | Tasks | Files |
|------|----------|-------|-------|
| Phase 03 P02 | 12 min | 2 tasks | 9 files |
| Phase 03 P03 | 11 min | 2 tasks | 7 files |
| Phase 03 P04 | 8 min | 2 tasks | 8 files |
| Phase 03 P05 | 10 min | 2 tasks | 8 files |
| Phase 03 P06 | 13 min | 2 tasks | 10 files |
| Phase 04 P01 | 4 min | 2 tasks | 4 files |
| Phase 04 P02 | 3 min | 2 tasks | 4 files |
## Accumulated Context
@@ -103,6 +103,10 @@ Recent decisions affecting current work:
- [04-01]: Quality flags based on evidence_count (>=4 sufficient, >=2 moderate, >=1 sparse, 0 no_evidence)
- [04-01]: Per-layer contribution tracking (score * weight) for explainability
- [04-01]: ScoringWeights validation enforcing sum = 1.0 ± 1e-6 tolerance
- [04-02]: scipy MAD-based outlier detection (>3 MAD threshold) for robust anomaly detection
- [04-02]: Missing data thresholds: 50% warn, 80% error for graduated QC feedback
- [04-02]: PERCENT_RANK validation computed before known gene exclusion (validates scoring system)
- [04-02]: Top quartile validation criterion (median percentile >= 0.75 for known genes)
### Pending Todos
@@ -115,5 +119,5 @@ None yet.
## Session Continuity
Last session: 2026-02-11 - Plan execution
Stopped at: Completed 04-01-PLAN.md (Known gene compilation and weighted scoring)
Resume file: .planning/phases/04-scoring-integration/04-01-SUMMARY.md
Stopped at: Completed 04-02-PLAN.md (Quality control and positive control validation)
Resume file: .planning/phases/04-scoring-integration/04-02-SUMMARY.md