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A lightweight codon-based DNA Transformer for Regulatory Region Identification in the Genome

Karthik, A. S. P.; Das, A. B.

2026-05-07 bioinformatics
10.64898/2026.05.04.722647 bioRxiv
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We developed a lightweight codon-based DNA Transformer equipped with multi-head self-attention and an adaptive classifier head, which achieves exon intron classification with high accuracy and also has moderate accuracy in CDS classification and splice site recognition. We named this model as ExIT (Exon-Intron Transformer). We have implemented codon tokenization for this model. This has been validated on the human genome with external validation from the chimpanzee genome. Further benchmarking has implied that our model is better than the existing models in the above tasks.

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