Pre-trained Borzoi foundation model (johahi/borzoi-replicate-0) fine-tuned on the silicusPlusCGDCtcfCreExonTEUtr3 synthetic genome with CUT&Tag H3K27me3 and H3K4me3 targets.

Genome: Silicus + CGD + CTCF + CRE + Exon + TE + UTR3 (full)
Base model: johahi/borzoi-replicate-0
Receptive field: 524 kb
Resolution: 32 bp
Paper: Casimov, Lifshitz et al., "Reverse engineering the genomic encodings of the pluripotent epigenome"

See the paper companion repository for full code and configs.

tanaylab/sns-paper-borzoi-fm-silicus-cgdctcfcreexonteutr3

Borzoi FM fine-tuned on silicusPlusCGDCtcfCreExonTEUtr3

tanaylab/
sns-paper-borzoi-fm-silicus-cgdctcfcreexonteutr3