Borzoi — DNA → Functional Track Prediction
Prerequisites
| Requirement | Minimum | Recommended |
|---|---|---|
| Python | 3.10+ | 3.11 |
| CUDA | 12.1+ | 12.4+ |
| GPU VRAM | 16 GB | 24 GB+ |
How to run
pythonfrom borzoi_pytorch import Borzoi model = Borzoi.from_pretrained("johahi/borzoi-replicate-0").cuda().eval() # input: (batch, 4, 524288) one-hot DNA → output: (batch, tracks, 6144) bins
Borzoi consumes ~524 kb one-hot windows and emits binned predictions across
7,611 human tracks (the separate 2,608-track mouse head is off by default;
enable via enable_mouse_head=True and select with
forward(..., is_human=False)). For variant scoring, run ref/alt windows
centred on the variant and compare per-track output.
Output format
(B, T, L) tensor — T tracks × L 32-bp bins. Track metadata (assay,
biosample) is in borzoi_pytorch.pytorch_borzoi_model.TRACKS_DF (or model.tracks_df when using the AnnotatedBorzoi subclass) — the base Borzoi model has no targets attribute.
Remote compute
Needs ≥24 GB VRAM and either pre-cached HF weights or egress to
huggingface.co. Read compute_details({provider, mode:'read'}) for an
environment with borzoi-pytorch, then:
pythonc = host.compute.create(provider) job = c.submit_job( intent="Borzoi track prediction for 1 locus — 1×GPU, ~2 min", inputs=[{"src": "borzoi_run.py", "dst_filename": "borzoi_run.py"}], command="python3 borzoi_run.py", # env selection is host-specific — see compute_details for your provider outputs=["tracks.npz"], timeout_seconds=1800, ) print(job.job_id) # cell ends here — kernel never blocks on compute
Then call the wait_for_notification brain-tool. When the
compute_done notification arrives, act on its payload:
pythonsave_artifacts(payload["featured_files"]) # paths under hpc/<job_id>/
For the full result dict (output_files, remote_workdir, …), re-enter the
kernel: c.attach_job(job_id).result() then c.close(). See the
remote-compute-ssh / remote-compute-modal skill for the orchestration
details.
If the provider exposes a weight-cache mount, point HF_HOME at it inside
borzoi_run.py (path is in compute_details).
Troubleshooting
| Symptom | Cause | Fix |
|---|---|---|
module has no __version__ | Package exposes no attr | Use importlib.metadata.version("borzoi-pytorch") |
| Shape mismatch on input | Wrong window length | Pad/crop to 524288 bp (fixed; not exposed as a model attribute) |
Next: combine track deltas with evo2 likelihood deltas for a
two-axis variant prioritisation.
