Junior B.
fd4591949c
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>
Reverso MVP — Sickle Cell Repurposing Pipeline
A minimum viable drug repurposing pipeline for sickle cell disease: build a disease signature from public transcriptomic data, build drug profiles for ~300 small molecules, and rank them by CMap-style connectivity scoring. Validated by a recovery test — do the two known sickle cell drugs (hydroxyurea, L-glutamine) rank near the top?
See PLAN.md for the full specification, locked decisions, and week-by-week build plan.
Quickstart
# Requires Python >=3.11,<3.13 (see note below)
pip install -e . # or: pip install -e ".[dev]" for test/lint tooling
pytest # run unit tests
Python version note: use Python 3.11–3.13 (
python3.13 -m venv .venv). Python 3.14 is not yet supported by all pipeline dependencies (pydeseq2,cmapPy).
Project layout
data/ raw (downloaded, never edited) / processed / results — gitignored
notebooks/ 01..05, run end-to-end in order
src/ identifiers, disease, drugs, scoring, provenance
tests/ scoring unit tests
docs/ recovery_test_report.md, data_sources.md, known_limitations.md
The deliverable
When complete, the artifact to share is three files:
docs/recovery_test_report.md— the 2-page write-updata/results/ranked_candidates_v1.csv— the ranked drug list- The signature + drug profile files with provenance
Pipeline
| Notebook | Stage | Output |
|---|---|---|
01_setup_identifiers.ipynb |
Pin disease/gene IDs | data/processed/identifiers.json |
02_disease_signature.ipynb |
GEO + differential expression | sickle_cell_signature_v1.json |
03_drug_profiles.ipynb |
ChEMBL + LINCS | drug_profiles_v1.parquet |
04_connectivity_scoring.ipynb |
CMap scoring | ranked_candidates_v1.csv |
05_recovery_test.ipynb |
Validation | docs/recovery_test_report.md |
Every persisted artifact carries a confidence tier (A/B/C) and provenance. See PLAN.md §3.