VANDAM: Viewing a nucleotide sequence with DNA molecular priors

Excerpt

arXiv:2610.00411v1 Announce Type: new Abstract: Contemporary Genomic Foundation Models (GFMs) rely on a DNA-as-a-string paradigm that employs masked token prediction objectives for pretraining. However, this abstraction does not explicitly model the biochemical, structural, and physical properties essential to biological function. Many molecular properties can be estimated from sequence using established biophysical models, so their utility lies not in providing an independent modality, but in i