songlab/tokenizer-dna-mlm

Foundation models for genomics and transcriptomics pretrained on 3,000+ human genomes and 850+ diverse species, enabling chromatin accessibility prediction, splice site detection, and promoter classification across multiple model scales (InstaDeep, NVIDIA & TUM, Nature Methods 2023)

A PyTorch port of AlphaGenome, the DNA sequence model from Google DeepMind that predicts hundreds of genomic tracks at single base-pair resolution from sequences up to 1M bp.

This repository contains the model presented in D3LM: A Discrete DNA Diffusion Language Model for Bidirectional DNA Understanding and Generation.

HantaBERT fine-tunes DNABERT-2 on hantavirus RNA sequences for three simultaneous classification tasks: species/lineage, host, and geographic origin. A single forward pass produces predictions for all three tasks along with a 768-dimensional embedding suitable for phylogenetic visualization.

This is an version of Evo 2 40B checkpoint compatible with the savanna repo. Please use it for finetuning and continued training.

A DNA annotation model from the Carbon family.