Reverso

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Author	SHA1	Message	Date
Junior B.	fd4591949c	Week 3: CMap connectivity scoring engine + ranked candidates Implement the matching engine (PLAN §6 Week 3): - src/scoring.py: weighted-KS/GSEA enrichment, weighted connectivity score (WTCS, Lamb 2006 / Subramanian 2017), signed NCS normalization, rank_drugs, and a sickle-pathway mechanistic prior - tests/test_scoring.py: real reference tests for the scorer (perfect reversal<null<mimic, same-sign->0, absent-gene invariance) + prior - week3_scoring.py: score 300 drugs -> ranked_candidates_v1.csv with a raw ranking and a secondary mechanistic-prior-weighted ranking Preliminary (formal recovery test is Week 4): hydroxyurea raw rank 40/300 (top 13%, just misses pre-registered top-10%), blended rank 7; L-glutamine WTCS=0 (ambiguous). Notably anti-inflammatory SCD drugs cluster in the raw top tier — the engine reverses the inflammation axis, not the erythroid axis, traceable to the 12% landmark-overlap caveat. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-06-23 22:34:56 +02:00
Junior B.	b731478f5d	Scaffold Reverso MVP pipeline structure Set up the project skeleton per PLAN.md §4: - src/ package: identifiers, disease, drugs, scoring, provenance with pydantic schemas and confidence-tier logic (working); data-pull/compute functions stubbed per their build week - 5 starter notebooks (01-05) with PLAN-referenced steps - tests/test_scoring.py: tier-assignment tests pass; scoring reference test xfail until Week 3 - docs/: recovery_test_report, data_sources, known_limitations skeletons - pyproject.toml (requires-python >=3.11,<3.14), .gitignore, README - data/ tree preserved via .gitkeep; raw/processed/results gitignored Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-06-23 20:20:09 +02:00

Author

SHA1

Message

Date

Junior B.

fd4591949c

Week 3: CMap connectivity scoring engine + ranked candidates

Implement the matching engine (PLAN §6 Week 3):
- src/scoring.py: weighted-KS/GSEA enrichment, weighted connectivity
  score (WTCS, Lamb 2006 / Subramanian 2017), signed NCS normalization,
  rank_drugs, and a sickle-pathway mechanistic prior
- tests/test_scoring.py: real reference tests for the scorer (perfect
  reversal<null<mimic, same-sign->0, absent-gene invariance) + prior
- week3_scoring.py: score 300 drugs -> ranked_candidates_v1.csv with a
  raw ranking and a secondary mechanistic-prior-weighted ranking

Preliminary (formal recovery test is Week 4): hydroxyurea raw rank
40/300 (top 13%, just misses pre-registered top-10%), blended rank 7;
L-glutamine WTCS=0 (ambiguous). Notably anti-inflammatory SCD drugs
cluster in the raw top tier — the engine reverses the inflammation axis,
not the erythroid axis, traceable to the 12% landmark-overlap caveat.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

2026-06-23 22:34:56 +02:00

Junior B.

b731478f5d

Scaffold Reverso MVP pipeline structure

Set up the project skeleton per PLAN.md §4:
- src/ package: identifiers, disease, drugs, scoring, provenance
  with pydantic schemas and confidence-tier logic (working);
  data-pull/compute functions stubbed per their build week
- 5 starter notebooks (01-05) with PLAN-referenced steps
- tests/test_scoring.py: tier-assignment tests pass; scoring
  reference test xfail until Week 3
- docs/: recovery_test_report, data_sources, known_limitations skeletons
- pyproject.toml (requires-python >=3.11,<3.14), .gitignore, README
- data/ tree preserved via .gitkeep; raw/processed/results gitignored

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

2026-06-23 20:20:09 +02:00

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