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tanaylab/
sns-paper-borzoi-finetuned-rf2k

Name: sns-paper-borzoi-finetuned-rf2k
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Borzoi Fine-tuned RF 2k — Foundation Model

Pre-trained Borzoi model (johahi/borzoi-replicate-0) fine-tuned on mouse ESC-derived CUT&Tag H3K27me3 and H3K4me3 tracks via two-stage training (linear probe then full fine-tuning).

Receptive field: 2k
Base model: johahi/borzoi-replicate-0
Resolution: 32 bp
Training data: Normalized CUT&Tag from mouse ESC-derived embryoid bodies
Paper: Casimov, Lifshitz et al., "Reverse engineering the genomic encodings of the pluripotent epigenome"

Usage

bash

torchrun --nproc_per_node=8 infer_borzoi_pytorch.py \
    --config config.yaml \
    --checkpoint model.safetensors \
    --genome_fasta mm10.fa \
    --output_dir predictions/

See the paper companion repository for full code and configs.

tanaylab/sns-paper-borzoi-finetuned-rf2k

Borzoi Fine-tuned RF 2k — Foundation Model

Usage

tanaylab/
sns-paper-borzoi-finetuned-rf2k