macwiatrak/bacformer-large-masked-complete-genomes

- 2025-05-15: We identified a bug in the Bacformer Large code on HuggingFace which resulted in a significant drop in the quality of the output embeddings. This is now fixed, but if you downloaded or cached the model before this date, re-download and use the latest model revision before running…

The Nucleotide Transformers are a collection of foundational language models that were pre-trained on DNA sequences from whole-genomes. Compared to other approaches, our models do not only integrate information from single reference genomes, but leverage DNA sequences from over 3,200 diverse human…

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

Minimal HuggingFace repackage of the large variant of ModernGENA -- a ModernBERT DNA encoder pretrained on vertebrate genomes with masked language modeling.

The Nucleotide Transformers are a collection of foundational language models that were pre-trained on DNA sequences from whole-genomes. Compared to other approaches, our models do not only integrate information from single reference genomes, but leverage DNA sequences from over 3,200 diverse human…