frederikkemarin / BEND
Benchmarking DNA Language Models on Biologically Meaningful Tasks
☆96Updated last week
Related projects ⓘ
Alternatives and complementary repositories for BEND
- gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.☆224Updated this week
- Genomic Pre-trained Network☆187Updated 3 weeks ago
- Benchmarks for classification of genomic sequences☆116Updated 8 months ago
- Orthrus is a mature RNA model for RNA property prediction. It uses a mamba encoder backbone, a variant of state-space models specifical…☆36Updated last week
- Repository for mRNA Paper and CodonBERT publication.☆112Updated 4 months ago
- RNA-seq prediction with deep convolutional neural networks.☆87Updated 2 weeks ago
- Cell2Sentence turns scRNA-seq data into text for LLM training.☆84Updated 2 months ago
- Official repository for the paper "Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning". Jo…☆155Updated 7 months ago
- Computational Optimization of DNA Activity (CODA)☆32Updated last month
- The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)☆34Updated last year
- Polygraph evaluates and compares groups of nucleic acid sequences based on their sequence and functional content for effective design of …☆27Updated 6 months ago
- Deep networks for protein functional inference☆159Updated 2 weeks ago
- ☆32Updated last year
- ☆66Updated last year
- ☆51Updated 2 months ago
- A repository with exploration into using transformers to predict DNA ↔ transcription factor binding☆81Updated 2 years ago
- A Transformer-based model for read-level DNA methylation pattern identification and tumour deconvolution☆20Updated this week
- Primary RNA sequence model☆29Updated 5 months ago
- Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.☆104Updated 3 months ago
- Evolutionary velocity with protein language models☆83Updated last year
- Stochastic Sequence Propagation - A Keras Model for optimizing DNA, RNA and protein sequences based on a predictor☆42Updated 2 months ago
- code to run EPInformer for gene expression prediction and gene-enhancer links prioritization☆30Updated this week
- This repository contains the python package for Helical☆62Updated this week
- accurate prediction of promoter activity and variant effects from massive parallel reporter assays☆28Updated 2 weeks ago
- Explainable AI for Bioinformatics☆116Updated last year
- DNABERT_S: Learning Species-Aware DNA Embedding with Genome Foundation Models☆73Updated 5 months ago
- RiboNucleic Acid (RNA) Language Model☆67Updated 6 months ago
- Biological sequence analysis for the modern age.☆190Updated last week
- python tools for TCR:peptide-MHC modeling and analysis☆66Updated 6 months ago
- Draw RNA secondary structures in python.☆43Updated 2 months ago