Caduceus: Bi-Directional Equivariant Long-Range DNA Sequence Modeling
Authors: name: Yair Schiff, name: Chia-Hsiang Kao, name: Aaron Gokaslan, name: Tri Dao, name: Albert Gu, name: Volodymyr Kuleshov

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, and to a MambaDNA block that
additionally supports RC equivariance. We use MambaDNA as the basis of
Caduceus, the first family of RC equivariant bi-directional long-range DNA
language models, and we introduce pre-training and fine-tuning strategies that
yield Caduceus DNA foundation models. Caduceus outperforms previous long-range
models on downstream benchmarks; on a challenging long-range variant effect
prediction task, Caduceus exceeds the performance of 10x larger models that do
not leverage bi-directionality or equivariance.