Tootfinder

Caduceus: Bi-Directional Equivariant Long-Range DNA Sequence Modeling
Yair Schiff, Chia-Hsiang Kao, Aaron Gokaslan, Tri Dao, Albert Gu, Volodymyr Kuleshov
https://arxiv.org/abs/2403.03234

Caduceus: Bi-Directional Equivariant Long-Range DNA Sequence Modeling
Large-scale sequence modeling has sparked rapid advances that now extend into biology and genomics. However, modeling genomic sequences introduces challenges such as the need to model long-range token interactions, the effects of upstream and downstream regions of the genome, and the reverse complementarity (RC) of DNA. Here, we propose an architecture motivated by these challenges that builds off the long-range Mamba block, and extends it to a BiMamba component that supports bi-directionality,…