Cross-architecture ensembling of DNA foundation models improves the precision and stability of chimera detection in long-read metagenomic bins

Motivation: Chimeric metagenome-assembled genomes (MAGs) that pool DNA from multiple organisms contaminate downstream analyses. Marker-gene tools such as CheckM2 miss low-level chimerism, and DNA foundation models have been proposed as a sequence-composition alternative, but whether large autoregressive models (Evo2, 7B parameters) outperform smaller contrastive models (DNABERT-S, 117M) has not been rigorously tested.