In Search of Lost DNA Sequence Pretraining
DNA sequence encoding is fundamental to gene function prediction, protein synthesis, and diverse downstream biological tasks. Despite the substantial progress achieved by large-scale DNA sequence pretraining, existing studies have overwhelmingly emphasized pretraining scale and custom downstream evaluation datasets, while neglecting some essential components of the pretraining paradigm. In this paper, we reveal three critical yet heretofore overlooked problems in DNA pretraining: inappropriate downstream datasets, inherent flaws in the neighbor-masking strategy, and the lack of detailed discussion on vocabulary. Therefore, we undertake comprehensive investigations and propose principled g...
| Authors | Zhijiang Tang, Jiaxin Qi, Yan Cui et al. |
|---|---|
| Primary category | cs.LG |
| Published | 17 April 2026 |
| Last updated at source | 17 April 2026 |
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