Alternatives and similar repositories for DNABERT_2

Users that are interested in DNABERT_2 are comparing it to the libraries listed below

• jerryji1993 / DNABERT
  DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
  ☆724Updated 5 months ago
• songlab-cal / gpn
  Genomic Pre-trained Network
  ☆316Updated last week
• instadeepai / nucleotide-transformer
  Foundation Models for Genomics & Transcriptomics
  ☆789Updated this week
• MAGICS-LAB / DNABERT_S
  [ISMB 2025] DNABERT_S: Learning Species-Aware DNA Embedding with Genome Foundation Models
  ☆118Updated 10 months ago
• ML-Bioinfo-CEITEC / genomic_benchmarks
  Benchmarks for classification of genomic sequences
  ☆167Updated 4 months ago
• ml4bio / RNA-FM
  Nature Methods: RNA foundation model (together with RhoFold)
  ☆333Updated 7 months ago
• calico / borzoi
  RNA-seq prediction with deep convolutional neural networks.
  ☆216Updated 4 months ago
• Genentech / gReLU
  gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.
  ☆312Updated 3 weeks ago
• TencentAILabHealthcare / DNAGPT
  ☆45Updated 2 years ago
• calico / basenji
  Sequential regulatory activity predictions with deep convolutional neural networks.
  ☆461Updated 7 months ago
• theislab / single-cell-transformer-papers
  ☆335Updated 7 months ago
• ArcInstitute / state
  State is a machine learning model that predicts cellular perturbation response across diverse contexts
  ☆479Updated this week
• biomap-research / scFoundation
  ☆380Updated last month
• TencentAILabHealthcare / scBERT
  ☆341Updated 2 years ago
• ArcInstitute / arc-virtual-cell-atlas
  Arc Virtual Cell Atlas
  ☆473Updated last week
• apeterswu / Awesome-Bio-Foundation-Models
  A collection of awesome bio-foundation models, including protein, RNA, DNA, gene, single-cell, and so on.
  ☆279Updated 7 months ago
• google-deepmind / alphamissense
  ☆597Updated last year
• LucaOne / LucaOne
  The resources of LucaOne, including: the model code, training scripts, embedding inference code, and trained checkpoints.
  ☆350Updated last month
• OATML-Markslab / EVE
  Official repository for the paper "Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning". Jo…
  ☆187Updated last year
• ychuest / Awesome-LLMs-meet-genomes
  Explore a comprehensive collection of basic theories, applications, papers, and best practices about Large Language Models (LLMs) in geno…
  ☆112Updated this week
• frederikkemarin / BEND
  Benchmarking DNA Language Models on Biologically Meaningful Tasks
  ☆127Updated last year
• snap-stanford / GEARS
  GEARS is a geometric deep learning model that predicts outcomes of novel multi-gene perturbations
  ☆322Updated 10 months ago
• JoshuaChou2018 / AutoBA
  An AI Agent for Fully Automated Multi-omic Analyses
  ☆202Updated last year
• LinearDesignSoftware / LinearDesign
  The LinearDesign mRNA design software.
  ☆197Updated last year
• OmicsML / awesome-deep-learning-single-cell-papers
  ☆828Updated 8 months ago
• yiqunchen / GenePT
  ☆298Updated last year
• lucidrains / enformer-pytorch
  Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch
  ☆550Updated 5 months ago
• ViennaRNA / ViennaRNA
  The ViennaRNA Package
  ☆376Updated 3 weeks ago
• Illumina / SpliceAI
  A deep learning-based tool to identify splice variants
  ☆475Updated 5 months ago
• HazyResearch / hyena-dna
  Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena
  ☆743Updated 8 months ago