README.md

metadata

title: Genome Firewall Inference
emoji: 🧬
colorFrom: blue
colorTo: green
sdk: docker
app_port: 8000
pinned: false

Genome Firewall inference service

FASTA → antibiotic-response prediction. This is the service the Convex action (convex/analysis.ts) calls. It runs the real trained E. coli models from Darkroom4364/genome-firewall-ecoli.

Pipeline

1. POST /predict receives an assembled genome FASTA + a target antibiotic.
2. AMRFinderPlus 4.2.7 (NCBI) detects resistance genes / point mutations.
3. Hits become a 600-dim binary feature vector (features/build_feature_matrix.py).
4. The per-drug calibrated elastic-net model gives p_fail (probability of resistance).
5. No-call bands (models/<drug>/nocall_bands.json) decide work / fail / abstain.
6. Evidence genes are mapped per drug (features/map_evidence.py + drug_class_map.yaml).

Response score = 1 − p_fail (probability the drug is effective). Contract: see ../convex/README.md.

Supported drugs: ciprofloxacin, gentamicin, ampicillin, cefotaxime, trimethoprim_sulfamethoxazole (UI labels are mapped in gf_infer.py:LABEL_TO_KEY).

Contents

Path	What
serve.py	FastAPI service (/health, /predict)
gf_infer.py	Inference core: TSV/features → model → app contract
features/	build_feature_matrix.py, map_evidence.py, drug_class_map.yaml, feature_columns.json, metadata.json (reused from branch sprint/baseline)
models/<drug>/	model.skops + nocall_bands.json (from Hugging Face)
requirements.txt, Dockerfile, .dockerignore	packaging

Deploy (recommended — container has AMRFinderPlus + DB baked in)

cd inference
docker build --platform linux/amd64 -t genome-firewall-api .
docker run --platform linux/amd64 -p 8000:8000 \
  -e INFERENCE_API_TOKEN=<optional-shared-secret> \
  genome-firewall-api

Then set INFERENCE_API_URL (the public URL of this host) in the Convex dashboard. Host needs an amd64 runtime with enough RAM/CPU for AMRFinderPlus (a genome takes ~1–3 min).

Local dev (host Python; AMRFinderPlus via Docker)

cd inference
uv venv --python 3.13 .venv
uv pip install --python .venv/bin/python -r requirements.txt
./.venv/bin/uvicorn serve:app --host 0.0.0.0 --port 8000

When the amrfinder binary is not on PATH, serve.py runs AMRFinderPlus via docker run staphb/ncbi-amrfinderplus:4.2.7-2026-03-24.1 automatically. GET /health reports "amrfinder": "binary" or "docker" accordingly.

curl -s localhost:8000/health | jq
curl -s localhost:8000/predict -H 'content-type: application/json' \
  -d "{\"fasta\": \"$(sed ':a;N;$!ba;s/\n/\\n/g' genome.fna)\", \"antibiotic\": \"Ampicillin\"}" | jq

Research prototype. All predictions must be confirmed with standard laboratory susceptibility testing. Not a medical device.