Article

Mut-BPE: A Modified BPE Strategy Improves Variant Effect Prediction

2025-12-01

Abstract excerpt

Byte Pair Encoding (BPE) is widely used in genome foundation models for its ability to compress long DNA sequences into fewer tokens. However, its variable-length tokens often span multiple nucleotides, limiting the model’s sensitivity to single-nucleotide variations—an essential requirement for accurate Variant Effect Prediction (VEP). We introduce Mut-BPE, a training-free, plug-and-play tokenization strategy tha...

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Literature Corpus work: 71c5b2c1-ce86-5209-8928-6022471dc9de
DOI: 10.1101/2025.12.01.691503

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