usher-exploring/.planning/phases/04-scoring-integration/04-01-SUMMARY.md

phase, plan, subsystem, tags, requires, provides, affects, tech-stack, key-files, key-decisions, patterns-established, duration, completed

phase	plan	subsystem	tags	requires	provides	affects	tech-stack	key-files	key-decisions	patterns-established	duration	completed
04-scoring-integration	01	scoring	scoring known-genes weighted-average duckdb polars multi-evidence	phase provides 01-data-infrastructure PipelineStore, DuckDB persistence, gene_universe table phase provides 02-prototype-evidence-layer gnomad_constraint table with loeuf_normalized phase provides 03-core-evidence-layers tissue_expression, annotation_completeness, subcellular_localization, animal_model_phenotypes, literature_evidence tables	Known cilia/Usher gene set compilation (OMIM + SYSCILIA SCGS v2) ScoringWeights validation enforcing sum constraint Multi-evidence weighted scoring with NULL-preserving weighted average join_evidence_layers() - LEFT JOIN all 6 evidence tables compute_composite_scores() - weighted_sum / available_weight pattern persist_scored_genes() - DuckDB persistence with quality flags	04-02 04-03 ranking filtering validation	added patterns NULL-preserving weighted average (weighted_sum / available_weight) Evidence quality flags (sufficient/moderate/sparse/no_evidence) Per-layer contribution tracking for explainability Known gene compilation from multiple sources	created modified src/usher_pipeline/scoring/__init__.py src/usher_pipeline/scoring/known_genes.py src/usher_pipeline/scoring/integration.py src/usher_pipeline/config/schema.py	OMIM Usher genes: 10 genes as disease positive controls SYSCILIA SCGS v2 core: ~28 genes as ciliary positive controls (subset of 686 full list) Known genes preserve multi-source provenance (duplicate gene_symbols with different sources) ScoringWeights validation: sum must equal 1.0 ± 1e-6 tolerance NULL-preserving weighted average: available_weight = sum of weights for non-NULL layers only Quality flags based on evidence_count: >=4 sufficient, >=2 moderate, >=1 sparse, 0 no_evidence Per-layer contributions computed as score * weight (NULL if score is NULL) for explainability	NULL-preserving scoring pattern: COALESCE for weighted_sum, but available_weight excludes NULL layers LEFT JOIN all evidence tables to gene_universe preserving all genes Quality flag classification based on evidence layer count Contribution tracking for transparency (each layer's impact on composite score)	4min	2026-02-11

Phase 04 Plan 01: Known Gene Compilation and Multi-Evidence Scoring Summary

NULL-preserving weighted scoring engine joining 6 evidence layers with configurable weights, plus OMIM/SYSCILIA known gene compilation for validation

Performance

• Duration: 4 minutes (228 seconds)
• Started: 2026-02-11T12:38:05Z
• Completed: 2026-02-11T12:42:13Z
• Tasks: 2
• Files modified: 4

Accomplishments

• Compiled 38 known cilia/Usher genes from OMIM (10 genes) and SYSCILIA SCGS v2 core (28 genes)
• Implemented ScoringWeights.validate_sum() enforcing weight sum constraint (1.0 ± 1e-6)
• Created join_evidence_layers() LEFT JOINing all 6 evidence tables preserving NULLs
• Built compute_composite_scores() with NULL-preserving weighted average (weighted_sum / available_weight)
• Added quality flag classification (sufficient/moderate/sparse/no_evidence) based on evidence count
• Included per-layer contribution columns for explainability

Task Commits

Each task was committed atomically:

1. Task 1: Known gene compilation and ScoringWeights validation - 0cd2f7c (feat)
2. Task 2: Multi-evidence weighted scoring integration - f441e8c (feat)

Files Created/Modified

• src/usher_pipeline/scoring/__init__.py - Scoring module exports
• src/usher_pipeline/scoring/known_genes.py - OMIM_USHER_GENES (10), SYSCILIA_SCGS_V2_CORE (28), compile_known_genes()
• src/usher_pipeline/scoring/integration.py - join_evidence_layers(), compute_composite_scores(), persist_scored_genes()
• src/usher_pipeline/config/schema.py - Added ScoringWeights.validate_sum() method

Decisions Made

1. Known gene curation: Limited SYSCILIA SCGS v2 to ~28 core genes (subset of 686 full list) for initial positive control validation. Future enhancement can add fetch_scgs_v2() to download complete list from publication supplementary data.

2. Multi-source provenance: compile_known_genes() does NOT de-duplicate gene_symbols across sources. A gene appearing in both OMIM and SYSCILIA will have two rows (one per source). This preserves provenance for validation and analysis.

3. NULL-preserving weighted average: Implemented weighted_sum / available_weight pattern where available_weight = sum of weights for non-NULL layers only. Genes with 0 evidence layers receive NULL composite_score (not 0), preserving semantic distinction between "no evidence" and "weak evidence".

4. Quality flags: Classification based on evidence_count thresholds (>=4 sufficient, >=2 moderate, >=1 sparse, 0 no_evidence) to guide downstream filtering and prioritization.

5. Explainability: Per-layer contribution columns (score * weight) enable tracing which evidence layers drove a gene's composite score. Critical for manual review and trust.

Deviations from Plan

None - plan executed exactly as written.

Issues Encountered

None. Both verification tests passed on first attempt.

User Setup Required

None - no external service configuration required.

Next Phase Readiness

Ready for Phase 04 Plan 02 (ranked candidate list generation):

• Known gene set compiled and ready for exclusion filtering
• Composite scoring engine functional with NULL preservation
• Quality flags available for filtering
• Per-layer contributions available for ranking criteria

No blockers. Next plan can implement:

• Exclusion of known genes
• Ranking by composite score
• Quality flag filtering
• Top-N candidate selection

Self-Check: PASSED

All claimed files and commits verified:

• src/usher_pipeline/scoring/init.py - FOUND
• src/usher_pipeline/scoring/known_genes.py - FOUND
• src/usher_pipeline/scoring/integration.py - FOUND
• Commit 0cd2f7c (Task 1) - FOUND
• Commit f441e8c (Task 2) - FOUND

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Phase: 04-scoring-integration Plan: 01 Completed: 2026-02-11