Abstract:Tokens serve as the basic units of representation in DNA language models (DNALMs), yet their design remains underexplored. Unlike natural language, DNA lacks inherent token boundaries or predefined compositional rules, making tokenization a fundamental modeling decision rather than a naturally specified one. While existing approaches like byte-pair encoding (BPE) excel at capturing token structures that reflect human-generated linguistic regularities, DNA is organized by biological function and evolutionary constraint rather than linguistic convention. We argue that DNA tokenization should prioritize functional sequence patterns like regulatory motifs-short, recurring segments under evolutionary constraint and typically preserved across species. We incorporate evolutionary information directly into the tokenization process through EvoLen, a tokenizer that combines evolutionary stratification with length-aware decoding to better preserve motif-scale functional sequence units. EvoLen uses cross-species evolutionary signals to group DNA sequences, trains separate BPE tokenizers on each group, merges the resulting vocabularies via a rule prioritizing preserved patterns, and applies length-aware decoding with dynamic programming. Through controlled experiments, EvoLen improves the preservation of functional sequence patterns, differentiation across genomic contexts, and alignment with evolutionary constraint, while matching or outperforming standard BPE across diverse DNALM benchmarks. These results demonstrate that tokenization introduces a critical inductive bias and that incorporating evolutionary information yields more biologically meaningful and interpretable sequence representations.
| Subjects: | Machine Learning (cs.LG); Genomics (q-bio.GN) |
| Cite as: | arXiv:2604.08698 [cs.LG] |
| (or arXiv:2604.08698v1 [cs.LG] for this version) | |
| https://doi.org/10.48550/arXiv.2604.08698 arXiv-issued DOI via DataCite |
From: Nan Huang [view email]
[v1]
Thu, 9 Apr 2026 18:41:28 UTC (472 KB)
此内容由惯性聚合(RSS阅读器)自动聚合整理，仅供阅读参考。 原文来自 — 版权归原作者所有。