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docs(04-01): complete known gene compilation and weighted scoring plan

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- Known genes: 38 (10 OMIM Usher + 28 SYSCILIA SCGS v2 core)
- ScoringWeights.validate_sum() enforcing weight sum = 1.0
- NULL-preserving weighted average (weighted_sum / available_weight)
- Quality flags based on evidence_count thresholds
- Per-layer contributions for explainability
- 2 tasks, 4 files, 4 min duration
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gbanyan
2026-02-11 20:44:09 +08:00
parent f441e8c1ad
commit 71c4e8f736
2 changed files with 166 additions and 11 deletions
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.planning/STATE.md
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@@ -5,23 +5,23 @@
See: .planning/PROJECT.md (updated 2026-02-11)
**Core value:** Produce a high-confidence, multi-evidence-backed ranked list of under-studied cilia/Usher candidate genes that is fully traceable — every gene's inclusion is explainable by specific evidence, and every gap is documented.
**Current focus:** Phase 3 complete — ready for Phase 4
**Current focus:** Phase 4 in progress — Scoring and Integration
## Current Position
Phase: 3 of 6 (Core Evidence Layers)
Plan: 6 of 6 in current phase (phase complete)
Status: Phase 3 complete — verified (6/6 success criteria, 20/20 requirements)
Last activity: 2026-02-11 — Phase 3 verified and complete
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
Progress: [██████░░░░] 60.0% (12/20 plans complete across all phases)
Progress: [██████░░░░] 65.0% (13/20 plans complete across all phases)
## Performance Metrics
**Velocity:**
- Total plans completed: 12
- Average duration: 5.6 min
- Total execution time: 1.1 hours
- Total plans completed: 13
- Average duration: 5.5 min
- Total execution time: 1.2 hours
**By Phase:**
@@ -30,11 +30,17 @@ Progress: [██████░░░░] 60.0% (12/20 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 |
**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 |
## Accumulated Context
@@ -92,6 +98,11 @@ Recent decisions affecting current work:
- [03-06]: Quality-weighted scoring uses log2 normalization to mitigate well-studied gene bias (prevents TP53-like dominance)
- [03-06]: Context weights cilia/sensory=2.0, cytoskeleton/polarity=1.0 for primary target prioritization
- [03-06]: Rate limiting via decorator pattern (3 req/sec default, 10 req/sec with NCBI API key)
- [04-01]: OMIM Usher genes (10) and SYSCILIA SCGS v2 core (28) as known gene positive controls
- [04-01]: NULL-preserving weighted average: weighted_sum / available_weight (only non-NULL layers contribute)
- [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
### Pending Todos
@@ -104,5 +115,5 @@ None yet.
## Session Continuity
Last session: 2026-02-11 - Plan execution
Stopped at: Completed 03-06-PLAN.md (Literature Evidence layer) - Phase 3 complete
Resume file: .planning/phases/03-core-evidence-layers/03-06-SUMMARY.md
Stopped at: Completed 04-01-PLAN.md (Known gene compilation and weighted scoring)
Resume file: .planning/phases/04-scoring-integration/04-01-SUMMARY.md