agro-nucleotide-transformer-1b

AgroNT is a DNA language model trained on primarily edible plant genomes. More specifically, AgroNT uses the transformer architecture with self-attention and a masked language modeling objective to leverage highly available genotype data from 48 different plant speices to learn general representations of nucleotide sequences. AgroNT contains 1 billion parameters and has a context window of 1024 tokens. AgroNt uses a non-overlapping 6-mer tokenizer to convert genomic nucletoide sequences to tokens. As a result the 1024 tokens correspond to approximately 6144 base pairs. Our pre-training dataset was built from (mostly) edible plants reference genomes contained in the Ensembl Plants database. The dataset consists of approximately 10.5 million genomic sequences across 48 different species. All reference genomes for each specie were assembled into a single fasta file. In this fasta file, all nucleotides other than A, T, C, G were replaced by N. A tokenizer was used to convert strings of letters into sequences of tokens. The tokenizer's alphabet consisted of the 4 6 = 4096 possible 6-mer combinations obtained by combining A, T, C, G, as well as five additional tokens representing standalone A, T, C, G, and N. It also included three special tokens: the pad [PAD], mask [MASK], and class [CLS] tokens. This resulted in a vocabulary of 4104 tokens. To tokenize an input sequence, the tokenizer started with a class token and then converted the sequence from left to right, matching 6-mer tokens when possible, or using the standalone tokens when necessary (for instance, when the letter N was present or if the sequence length was not a multiple of 6).