Author

Wouter Boomsma

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#machine learning Preprint Nov 2026

BEND 2.0: Benchmarking the Capabilities Needed to Design DNA

Genomic foundation models are increasingly used to propose DNA sequences and edits. But successful design requires capabilities that current benchmarks do not measure. Here we introduce BEND 2.0 (BENchmark for DNA language models), which tests how well models predict the effects of DNA changes and whether these predict...

Andreas Bjerregaard, Rachael DeVries, Dionysia Danai Brilli et al. · 0 citations

#machine learning Preprint Oct 2026

RAGenome: Scaling Retrieval-Based Genomic Language Models to Long Contexts

The genome holds the blueprint that governs the biological properties of the cell. Consequently, advancing our knowledge of genomic function is crucial both for a broader understanding of biology and for continued biomedical advances. The success of large language models on natural language and protein sequences has mo...

F. I. Marin, Panagiotis Antoniadis, Dionysia Danai Brilli et al. · 0 citations