Article

Benchmarking DNA Foundation Models: Biological Blind Spots in Evo2 Variant-Effect Prediction

2026-03-11

Abstract excerpt

DNA foundation models such as Evo and DNABERT-2 have generated considerable interest for clinically relevant genomics applications, particularly variant-effect prediction (VEP). However, rigorous benchmarks tailored to assessing their understanding of known biological constraints remain limited. Here, we develop controlled evaluation metrics based on well-characterized nuclear and mitochondrial sequence features a...

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Literature Corpus work: 165515cc-df11-5e1b-8d2a-0946028efdd8
DOI: 10.64898/2026.03.10.710786

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