From c501951b0fc22504ce90f6e0d96c99fc0572add8 Mon Sep 17 00:00:00 2001 From: gbanyan Date: Wed, 11 Feb 2026 20:50:00 +0800 Subject: [PATCH] docs(04-02): complete QC and validation plan - 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 --- .planning/STATE.md | 26 ++-- .../04-scoring-integration/04-02-SUMMARY.md | 146 ++++++++++++++++++ 2 files changed, 161 insertions(+), 11 deletions(-) create mode 100644 .planning/phases/04-scoring-integration/04-02-SUMMARY.md diff --git a/.planning/STATE.md b/.planning/STATE.md index 0f3bc67..0f705e8 100644 --- a/.planning/STATE.md +++ b/.planning/STATE.md @@ -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 diff --git a/.planning/phases/04-scoring-integration/04-02-SUMMARY.md b/.planning/phases/04-scoring-integration/04-02-SUMMARY.md new file mode 100644 index 0000000..8a2ea77 --- /dev/null +++ b/.planning/phases/04-scoring-integration/04-02-SUMMARY.md @@ -0,0 +1,146 @@ +--- +phase: 04-scoring-integration +plan: 02 +subsystem: scoring +tags: [qc, validation, quality-control, outlier-detection, positive-controls, mad, percentile-rank] + +# Dependency graph +requires: + - phase: 04-scoring-integration + plan: 01 + provides: scored_genes table, known_genes compilation + - phase: 01-data-infrastructure + provides: PipelineStore, DuckDB persistence +provides: + - Quality control checks for missing data, distributions, outliers + - MAD-based robust outlier detection per evidence layer + - Positive control validation against known gene rankings + - PERCENT_RANK window function validation + - QC orchestrator with composite score statistics +affects: [04-03, candidate-ranking, filtering, quality-assessment] + +# Tech tracking +tech-stack: + added: + - scipy>=1.14 for MAD-based outlier detection + patterns: + - MAD-based robust outlier detection (>3 MAD threshold) + - PERCENT_RANK window function for percentile ranking + - Threshold-based classification (warn/error levels) + - Temporary table pattern for DuckDB joins + +key-files: + created: + - src/usher_pipeline/scoring/quality_control.py + - src/usher_pipeline/scoring/validation.py + modified: + - pyproject.toml + - src/usher_pipeline/scoring/__init__.py + +key-decisions: + - "scipy.stats.median_abs_deviation for MAD computation (robust to outliers)" + - "Missing data thresholds: 50% warn, 80% error" + - "Outlier threshold: >3 MAD from median per layer" + - "PERCENT_RANK computed across ALL genes before exclusion (validates scoring system)" + - "Top quartile validation: median percentile >= 0.75 for known genes" + - "Temporary table pattern for known gene join (avoids external temp files)" + +patterns-established: + - "QC orchestrator pattern: run_qc_checks combines all checks with pass/fail boolean" + - "Composite score percentiles (p10, p25, p50, p75, p90) for distribution analysis" + - "Human-readable validation reports with formatted tables" + - "NULL-aware statistics: only compute on non-NULL values per layer" + +# Metrics +duration: 2m 54s +completed: 2026-02-11 +--- + +# Phase 04 Plan 02: Quality Control and Positive Control Validation Summary + +**MAD-based outlier detection and PERCENT_RANK validation ensuring scoring system credibility before candidate ranking** + +## Performance + +- **Duration:** 2 minutes 54 seconds (174 seconds) +- **Started:** 2026-02-11T12:45:12Z +- **Completed:** 2026-02-11T12:48:06Z +- **Tasks:** 2 +- **Files modified:** 4 + +## Accomplishments +- Added scipy>=1.14 dependency for robust statistical methods +- Implemented compute_missing_data_rates() with warn (>50%) and error (>80%) thresholds +- Created compute_distribution_stats() detecting no variation (std < 0.01) and out-of-range values +- Built detect_outliers() using MAD-based detection (>3 MAD from median per layer) +- Developed run_qc_checks() orchestrator with composite score percentiles (p10-p90) +- Implemented validate_known_gene_ranking() using PERCENT_RANK window function +- Created generate_validation_report() with human-readable formatted output +- Exported run_qc_checks, validate_known_gene_ranking, generate_validation_report from scoring module + +## Task Commits + +Each task was committed atomically: + +1. **Task 1: Quality control checks for scoring results** - `ba2f97a` (feat) +2. **Task 2: Positive control validation against known gene rankings** - `70a5d6e` (feat) + +## Files Created/Modified +- `src/usher_pipeline/scoring/quality_control.py` - QC checks with MAD-based outlier detection +- `src/usher_pipeline/scoring/validation.py` - Known gene ranking validation with PERCENT_RANK +- `pyproject.toml` - Added scipy>=1.14 dependency +- `src/usher_pipeline/scoring/__init__.py` - Export QC and validation functions + +## Decisions Made + +1. **scipy for MAD computation:** Used scipy.stats.median_abs_deviation with scale="normal" for robust outlier detection. MAD is less sensitive to outliers than standard deviation, making it ideal for detecting anomalous genes in scored datasets. + +2. **Missing data threshold classification:** 50% missing = warning (may still be usable), 80% missing = error (too sparse to trust). This dual-threshold approach allows for graduated QC feedback. + +3. **Outlier threshold calibration:** >3 MAD from median flags outliers. This is a standard robust statistics threshold balancing sensitivity and specificity. Layers with MAD=0 (no variation) skip outlier detection. + +4. **PERCENT_RANK validation timing:** Validation computes percentile ranks BEFORE known gene exclusion to validate the scoring system itself (not post-filtering artifacts). Uses temporary table pattern for efficient DuckDB join. + +5. **Top quartile validation criterion:** Median percentile >= 0.75 ensures known cilia/Usher genes rank in top 25% of all genes. This threshold confirms scoring logic prioritizes cilia-relevant features. + +6. **Composite score percentiles:** Included p10, p25, p50, p75, p90 in run_qc_checks() for distribution analysis. These percentiles help identify skewness, outliers, and score concentration patterns. + +## Deviations from Plan + +None - plan executed exactly as written. + +## Issues Encountered + +None. Both verification tests passed on first attempt. + +## User Setup Required + +None - scipy installed automatically in virtual environment. + +## Next Phase Readiness + +Ready for Phase 04 Plan 03 (ranked candidate list generation and filtering): +- QC checks available via run_qc_checks() for post-scoring validation +- Positive control validation confirms scoring system works correctly +- Outlier detection identifies anomalous genes per layer +- Composite score percentiles provide distribution context for threshold selection + +No blockers. Next plan can implement: +- Known gene exclusion filtering +- Quality flag filtering (sufficient_evidence threshold) +- Composite score ranking +- Top-N candidate selection with provenance + +## Self-Check: PASSED + +All claimed files and commits verified: +- src/usher_pipeline/scoring/quality_control.py - FOUND +- src/usher_pipeline/scoring/validation.py - FOUND +- pyproject.toml - FOUND +- Commit ba2f97a (Task 1) - FOUND +- Commit 70a5d6e (Task 2) - FOUND + +--- +*Phase: 04-scoring-integration* +*Plan: 02* +*Completed: 2026-02-11*