Fig. 4: Mechanistic interpretability of Evo 2 reveals DNA, RNA, protein and organism-level features.

a, SAEs were trained on Evo 2 to extract SAE features associated with interpretable biological function that can be used for annotation, discovery and steering of sequence generations. b, Phage-associated feature activates preferentially on RefSeq-annotated prophages (left and top right) in the E. coli K12 MG1655 genome and fires on phage-derived spacer sequences within CRISPR arrays (bottom right). c, Activations of features associated with ORFs, intergenic loci, tRNAs and rRNAs, in a 100-kb region in E. coli K12 MG1655. d, Activations of features associated with α-helices, β-sheets and tRNAs at an E. coli K12 MG1655 locus containing tufB and a tRNA array ending with thrT (left) and the rpoB–rpoC locus (right). AlphaFold 3 (AF3) structure predictions with feature activations overlaid, of EF–Tu in complex with the tRNA (left) and of RpoB and RpoC in complex (right). e, A feature in the human genome with preferential activation immediately after frameshift mutations over other less deleterious mutation types. f, Features with activation on DNA motifs in the human genome that correspond to transcription factor-binding motifs. g, Features associated with exons, introns and their boundaries in the human genome generalize to a segment of the woolly mammoth genome.