Genomic prediction and design now require models that connect local motifs with megabase scale regulatory context and that operate across many organisms. Nucleotide Transformer v3, or NTv3, is InstaDeep’s new multi species genomics foundation model for this setting. It unifies representation learning, functional track and genome annotation prediction, and controllable sequence generation in a single backbone that runs on 1 Mb contexts at single nucleotide resolution. Earlier Nucleotide Transformer models already showed that self supervised pretraining on thousands of genomes yields strong features for molecular phenotype prediction. The original series included models from 50M to 2.5B parameters trained on 3,200…
