Alternatives and similar repositories for genomic_benchmarks

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

• frederikkemarin / BEND
  Benchmarking DNA Language Models on Biologically Meaningful Tasks
  ☆115Updated 7 months ago
• MAGICS-LAB / DNABERT_S
  [ISMB 2025] DNABERT_S: Learning Species-Aware DNA Embedding with Genome Foundation Models
  ☆101Updated 3 months ago
• ychuest / Awesome-LLMs-meet-genomes
  Explore a comprehensive collection of basic theories, applications, papers, and best practices about Large Language Models (LLMs) in geno…
  ☆59Updated last week
• songlab-cal / gpn
  Genomic Pre-trained Network
  ☆268Updated 2 months ago
• calico / borzoi
  RNA-seq prediction with deep convolutional neural networks.
  ☆152Updated 2 months ago
• Genentech / gReLU
  gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.
  ☆263Updated this week
• MAGICS-LAB / DNABERT_2
  [ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome
  ☆382Updated 5 months ago
• kundajelab / DART-Eval
  ☆34Updated last month
• lbcb-sci / RiNALMo
  RiboNucleic Acid (RNA) Language Model
  ☆102Updated 2 weeks ago
• jmschrei / tangermeme
  Biological sequence analysis for the modern age.
  ☆223Updated 3 weeks ago
• FunctionLab / sei-framework
  code to run sei and obtain sei and sequence class predictions
  ☆105Updated 2 years ago
• TencentAILabHealthcare / DNAGPT
  ☆39Updated last year
• OATML-Markslab / EVE
  Official repository for the paper "Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning". Jo…
  ☆174Updated last year
• ntranoslab / esm-variants
  ☆74Updated last year
• johahi / borzoi-pytorch
  Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.
  ☆56Updated 2 weeks ago
• deweihu96 / SPACE
  Repository for the manuscript: "SPACE: STRING proteins as complementary embeddings"
  ☆18Updated last week
• jzhoulab / puffin
  deep learning-inspired explainable sequence model for transcription initiation
  ☆94Updated 3 months ago
• jkobject / geneformer
  ☆68Updated last week
• a96123155 / UTR-LM
  ☆85Updated 7 months ago
• dohlee / chromoformer
  The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)
  ☆35Updated last year
• jimmylihui / GenBench
  ☆21Updated 3 months ago
• theislab / single-cell-transformer-papers
  ☆315Updated last week
• snap-stanford / GEARS
  GEARS is a geometric deep learning model that predicts outcomes of novel multi-gene perturbations
  ☆258Updated 4 months ago
• Zymrael / vortex
  Inference and numerics for multi-hybrid AI model architectures
  ☆61Updated this week
• amberT15 / LLM_eval
  Code repository for study ''Evaluating the representational power of pre-trained DNA language models for regulatory genomics"
  ☆19Updated 11 months ago
• sjgosai / boda2
  Computational Optimization of DNA Activity (CODA)
  ☆59Updated 2 months ago
• Sanofi-Public / CodonBERT
  Repository for mRNA Paper and CodonBERT publication.
  ☆130Updated 11 months ago
• ml4bio / RNA-FM
  Nature Methods: RNA foundation model (together with RhoFold)
  ☆276Updated last week
• Genentech / BRAID
  BRAID is a department within Genentech dedicated to advancing biological and clinical sciences through artificial intelligence.
  ☆197Updated this week
• google-research / proteinfer
  Deep networks for protein functional inference
  ☆172Updated 2 months ago