Junior B.
3417f85eb1
Post-hoc improvement after the pre-registered v1 recovery test failed. Two changes, diagnosing v1's failure: - score on the full 12,328-gene LINCS space (week2_lincs_extract.py), lifting signature overlap from 12% to 85% (brings erythroid markers in) - src/scoring.py: KS connectivity + per-drug specificity z-score (spec_z = SDs below a 1,000 random-query null). Primary ranking is now spec_z. (Textbook tau saturated at +/-100 for a coherent query — documented; needs a reference-signature library, a v2 item.) - week3_scoring.py: spec_z primary + WTCS reference + prior-blended - tests: tau/spec_z calibration test; 19 passing - scripts/exp_genespace.py: the BING vs all-12,328 comparison Result: hydroxyurea recovers (rank 40 -> 18, top 6%, passes top-10%), confirming the v1 failure was the landmark bottleneck not the algorithm. Overall STILL FAILS: L-glutamine does not reverse (rank 213, metabolite), and negative controls (norethindrone, ciprofloxacin) rank top-3 — connectivity != therapeutic relatedness. v1.1 is post-hoc/exploratory, not a confirmatory test; reported as such in recovery_test_report.md. 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.