The Borzoi model from Calico, but ported to Pytorch! Original implementation and weights are here.
We show that the Pytorch version produces the same predictions as the original implementation for all tested notebook examples.

Ported weights (with permission) are uploaded to Huggingface, the model (human or mouse heads) can be loaded with:

from borzoi_pytorch import Borzoi
borzoi = Borzoi.from_pretrained('johahi/borzoi-replicate-0') # 'johahi/borzoi-replicate-[0-3][-mouse]'

pip install git+https://github.com/johahi/borzoi-pytorch.git

Documentation coming soon. The relative shift operation should be faster than in enformer_pytorch or other implementations.

[1] Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation
Johannes Linder, Divyanshi Srivastava, Han Yuan, Vikram Agarwal, David R. Kelley
bioRxiv 2023.08.30.555582; doi: https://doi.org/10.1101/2023.08.30.555582
[2] enformer-pytorch github, Phil Wang lucidrains

Please cite this repository if you used borzoi-pytorch.