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A DNA model does not necessarily process one token per base. The attached diagram shows the same 24 bases represented as 24 single-base tokens, four non-overlapping six-base tokens, or six illustrative variable-length tokens.

DNABERT-2 uses byte-pair encoding, which learns frequent sequence fragments. Its token count therefore depends on the input sequence. The six-token example is an illustration, not a tokenizer measurement.

For a compute comparison, record both the number of DNA bases and the number of model tokens, including any special tokens. Equal token limits do not mean equal biological context, and fewer tokens alone do not establish better accuracy or lower end-to-end runtime.

Primary paper: https://arxiv.org/abs/2306.15006

Guide: https://rewirebio.io/blog/genomic-foundation-models-in-the-diagnostic-lab/

Disclosure: the guide and diagram are from my site, rewirebio.io. This post was prepared with AI assistance. It explains published methods rather than reporting a new experiment.