SciDEX — Task: [Agora] Add gene-expression context to 20 hypothes

967 active hypotheses lack substantive gene_expression_context, limiting biological interpretability. ## Acceptance criteria - 20 hypotheses gain gene_expression_context grounded in cited datasets, papers, or KG annotations - Context distinguishes cell type, brain region, disease stage, or uncertainty where available - Remaining hypotheses missing expression context is <= 947 ## Approach 1. Select hypotheses with target_gene values and high debate/market relevance. 2. Use existing SciDEX papers/KG links and public expression evidence where available. 3. Persist concise expression context and verify hypothesis pages render. Generated by the quest-engine low-queue cycle after live DB gap verification. Re-check for duplicate recent work before editing, and document any stronger framing you find.

Last Error

cli-get-next: phantom running task — linked run 9fcb190f-a9b already terminal (abandoned); requeued immediately

Spec File

Goal

Populate data_support_score for active hypotheses so quality gates can distinguish computationally grounded hypotheses from literature-only or speculative claims. Scores should reflect actual linked analyses, datasets, KG edges, citations, or an explicit lack of supporting data.

Acceptance Criteria

☐ The selected active hypotheses have data_support_score values between 0 and 1

☐ Each score has a concise rationale from linked data, citations, KG edges, or caveats

☐ No support is fabricated where the evidence is absent

☐ The before/after missing-score count is recorded

Approach

Query active hypotheses where data_support_score IS NULL, ordered by impact, market, or composite score.

Inspect linked analyses, papers, datasets, KG edges, and existing evidence fields.

Assign calibrated scores and rationale using existing database write patterns.

Verify score ranges and count reduction.

Dependencies

quest-engine-ci - Generates this task when queue depth is low and data-support gaps exist.

Dependents

Hypothesis ranking, quality gates, and Exchange allocation depend on data-support scores.

Work Log

2026-04-21 21:55 PT — Slot 76 (MiniMax)

Started: Task spec + AGENTS.md read
Approach: Calibrated scoring from 5 dimensions:

- KG edge count (0-0.3): strong grounding gets 0.3, none gets 0
- Evidence citations (0-0.4): count + quality (high/medium/year ≥ 2020)
- Debate count (0-0.15): more scrutiny = higher score
- Analysis linkage (0-0.1): formal derivation from debate
- Artifact links (0-0.05): notebooks/datasets = computational grounding

Output: scripts/score_data_support.py — reusable, well-documented
Results:

- Before: 203 promoted/debated missing, 747 total missing
- 20 hypotheses scored: range 0.600–0.950
- After: 183 promoted/debated missing, 727 total missing
- All 20 scores verified in [0, 1] range

Scores: h-var-95b0f9a6bc (0.950, MAPT), h-var-261452bfb4 (0.950, ACSL4), h-var-22c38d11cd (0.950, ACSL4), h-var-ce41f0efd7 (0.950, TREM2), h-var-97b18b880d (0.950, ALOX15), h-0e675a41 (0.950, HDAC3), h-42f50a4a (0.950, APOE), h-var-f96e38ec20 (0.950, ACSL4), h-11795af0 (0.900, APOE), h-856feb98 (0.900, BDNF), h-var-9e8fc8fd3d (0.900, PVALB), h-d0a564e8 (0.900, APOE), h-807d7a82 (0.900, AQP4), h-48858e2a (0.900, TREM2), h-43f72e21 (0.900, PRKAA1), h-3f02f222 (0.900, BCL2L1), h-var-e4cae9d286 (0.850, LPCAT3), h-var-c56b26facf (0.850, LPCAT3), h-9e9fee95 (0.700, HCRTR1/HCRTR2), hyp-SDA-2026-04-12-20260411-082446-2c1c9e2d-2 (0.600, CHRNA7/BACE1 — no KG edges)
Committed: scripts/score_data_support.py [task:f7f4133c-4b99-48ef-888b-fa1b08387a24]
Result: Done — 20 hypotheses scored with validated evidence-based rationales

2026-04-26 19:40 UTC — Slot 42 (Claude Sonnet 4.6) [task:4a7ec4f5-b5f5-443c-89db-1a22b67165e9]

Started: AGENTS.md read, DB connection established via scidex.core.database.get_db()
Before: 1008 hypotheses missing data_support_score (all statuses: proposed 722, archived 134, debated 97, promoted 41, active 9, open 5)
Approach: Same 5-dimension rubric. Fixed bug in score_hypothesis() where string items in evidence_for (PMID strings or claim text) caused AttributeError on .get(). Now handles mixed lists safely.
Processed: All 1008 hypotheses in 11 batches of 100, ordered by composite_score DESC.
After: 0 hypotheses missing data_support_score (1402 total; all have valid 0–1 scores)
Score distribution: 0.0–0.1: 128, 0.1–0.5: 174, 0.5–0.6: 582 (bulk with citations+debates), 0.6–0.9: 306, 0.9–1.0: 212
Script fix: Updated scripts/score_data_support.py to handle string items in evidence_for, fall back to citations_count column, and accept batch_size as CLI arg
Result: Done — all 1008 hypotheses now scored; DB updated directly

2026-04-26 12:30 PT — Slot 73 (MiniMax)

Started: AGENTS.md read, DB connection established via scidex.core.database.get_db()
Approach: Same 5-dimension calibrated scoring (KG edges 0-0.3, citations 0-0.4, debates 0-0.15, analysis linkage 0-0.1, artifacts 0-0.05). Rebased against latest main (ea2945ab9) before running.
Results:

- Before: 1294 hypotheses missing data_support_score
- 20 hypotheses scored: range 0.600–0.950
- After: 1274 missing (reduction of 20)
- Score distribution: low=16, mid=29, good=73, high=10 (of 128 total scored)
- All scores verified in [0, 1] range

20 scored hypotheses: h-var-70a95f9d57 (0.850, LPCAT3), hyp-SDA-2026-04-12-20260411-082446-2c1c9e2d-3 (0.600, CHRNA7/CHRM1), h-44195347 (0.900, APOE), h-b7898b79 (0.900, CLOCK), h-a20e0cbb (0.900, APOE), h-1a34778f (0.700, CGAS/STING1/DNASE2), h-fd1562a3 (0.900, COX4I1), h-d2722680 (0.900, TET2), h-seaad-v4-5a7a4079 (0.950, SIRT3), h-c8ccbee8 (0.900, AQP4), h-bb518928 (0.700, PLA2G6/PLA2G4A), h-7957bb2a (0.900, GPX4/SLC7A11), h-ec731b7a (0.900, G3BP1), h-84808267 (0.700, TFR1/LRP1/CAV1/ABCB1), h-a1b56d74 (0.900, HK2), h-98b431ba (0.900, TFAM), h-8fe389e8 (0.950, HDAC), h-99b4e2d2 (0.900, APOE), h-5706bbd7 (0.900, BMAL1), h-8d270062 (0.900, CACNA1G)
Verification:

- All 20 scores between 0 and 1
- Missing count reduced from 1294 to 1274 (-20)
- Prior scored hypotheses (h-var-95b0f9a6bc, h-0e675a41, etc.) retained their scores

Result: Done — 20 more hypotheses scored; no commit needed (DB-only change)

2026-04-26 23:33 UTC — Slot 52 (Codex) [task:0f26ef01-1934-4bce-b280-aa954e4a884a]

Started: AGENTS.md and shared Orchestra instructions read; staleness review found prior commit 5344be64d scored the then-missing NULL cohort, but the live DB still had 76 hypotheses with data_support_score IS NULL OR data_support_score = 0 (60 null, 16 zero).
Approach: Added scripts/score_missing_data_support_rubric.py, a reproducible one-shot scorer for the task's 4-point rubric. Because the current hypotheses schema does not have literal evidence_strength, data_source, or notes columns, mapped them to current fields: evidence count from evidence_for, strength from evidence_quality_score/evidence_validation_score, source from origin_type/analysis_id/source_collider_session_id, and reasoning from confidence_rationale/evidence_validation_details/score_breakdown/substantive description.
Results:

- Before: 76 hypotheses with data_support_score IS NULL OR data_support_score = 0
- Updated: 76 hypotheses scored by the rubric; scores ranged 0.50-1.00
- Rationale: populated confidence_rationale for 60 rows that lacked one; preserved existing rationale for 16 rows
- After: 0 hypotheses with data_support_score IS NULL OR data_support_score = 0

Verification:

- python3 scripts/score_missing_data_support_rubric.py --commit
- Independent DB check: total hypotheses 1489; null-or-zero data support 0; invalid range rows 0

Result: Done — current missing/zero data-support cohort scored with explicit rubric rationale where absent

Payload JSON

{
  "requirements": {
    "analysis": 7,
    "reasoning": 6
  }
}

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