frederikkemarin / BENDLinks
Benchmarking DNA Language Models on Biologically Meaningful Tasks
☆123Updated 9 months ago
Alternatives and similar repositories for BEND
Users that are interested in BEND are comparing it to the libraries listed below
Sorting:
- Primary RNA sequence model☆38Updated last year
- Benchmarks for classification of genomic sequences☆153Updated 2 weeks ago
- Repository for mRNA Paper and CodonBERT publication.☆134Updated last year
- Orthrus is a mature RNA model for RNA property prediction. It uses a mamba encoder backbone, a variant of state-space models specifical…☆76Updated 3 weeks ago
- Explore a comprehensive collection of basic theories, applications, papers, and best practices about Large Language Models (LLMs) in geno…☆79Updated 2 weeks ago
- The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)☆36Updated 2 years ago
- ☆77Updated last year
- Inference and numerics for multi-hybrid AI model architectures☆73Updated last week
- Official repository for the paper "Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning". Jo…☆178Updated last year
- RNA-seq prediction with deep convolutional neural networks.☆189Updated 2 months ago
- Genomic Pre-trained Network☆276Updated 3 weeks ago
- Deep networks for protein functional inference☆176Updated 2 months ago
- ☆39Updated last month
- Neural Networks for Protein Sequence Alignment☆125Updated 9 months ago
- CodonTransformer: The ultimate tool for codon optimization, optimizing DNA sequences for heterologous protein expression across 164 speci…☆172Updated last month
- ☆43Updated last year
- gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.☆269Updated this week
- Using Transformer protein embeddings with a linear attention mechanism to make SOTA de-novo predictions for the subcellular location of p…☆66Updated last year
- Evolutionary velocity with protein language models☆94Updated last year
- AI-Driven Digital Organism (AIDO) is a system of multiscale foundation models for predicting, simulating and programming biology at all l…☆121Updated last month
- ☆90Updated 10 months ago
- This repository contains the code for our manuscript - 'The evolution, evolvability, and engineering gene regulatory DNA'☆95Updated 2 years ago
- RiboNucleic Acid (RNA) Language Model☆122Updated 2 months ago
- Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences.☆46Updated 10 months ago
- Genomic language model predicts protein co-regulation and function☆81Updated 5 months ago
- Language modeling of viral evolution☆144Updated 2 years ago
- Official release of the ProGen models☆34Updated 7 months ago
- Code repository for study ''Evaluating the representational power of pre-trained DNA language models for regulatory genomics"☆20Updated last year
- A framework for state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities.☆145Updated last week
- MXfold2: RNA secondary structure prediction using deep learning with thermodynamic integration☆140Updated 2 months ago