ML-Bioinfo-CEITEC / genomic_benchmarksLinks
Benchmarks for classification of genomic sequences
☆171Updated 5 months ago
Alternatives and similar repositories for genomic_benchmarks
Users that are interested in genomic_benchmarks are comparing it to the libraries listed below
Sorting:
- RNA-seq prediction with deep convolutional neural networks.☆225Updated 5 months ago
- gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.☆314Updated 2 weeks ago
- Explore a comprehensive collection of basic theories, applications, papers, and best practices about Large Language Models (LLMs) in geno…☆123Updated this week
- Benchmarking DNA Language Models on Biologically Meaningful Tasks☆129Updated last year
- Genomic Pre-trained Network☆321Updated this week
- [ISMB 2025] DNABERT_S: Learning Species-Aware DNA Embedding with Genome Foundation Models☆122Updated last month
- [ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome☆453Updated last month
- Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.☆94Updated 2 months ago
- Biological sequence analysis for the modern age.☆261Updated 3 weeks ago
- Inference and numerics for multi-hybrid AI model architectures☆91Updated last month
- Official repository for the paper "Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning". Jo…☆191Updated last year
- A framework for state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities.☆189Updated this week
- ☆42Updated 2 weeks ago
- The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)☆37Updated 2 years ago
- ☆45Updated 2 years ago
- Primary RNA sequence model☆42Updated 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…☆87Updated 2 months ago
- UCE is a zero-shot foundation model for single-cell gene expression data☆242Updated 11 months ago
- Comprehensive suite for evaluating perturbation prediction models☆122Updated 3 weeks ago
- Evaluating genomic sequence models for explaining personalized expression variation☆19Updated 2 years ago
- Computational Optimization of DNA Activity (CODA)☆67Updated 10 months ago
- ☆34Updated last year
- Code repository for study ''Evaluating the representational power of pre-trained DNA language models for regulatory genomics"☆24Updated last year
- Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences.☆50Updated last year
- deep learning-inspired explainable sequence model for transcription initiation☆100Updated 11 months ago
- ☆15Updated this week
- ☆92Updated 5 months ago
- ☆33Updated this week
- Knowledge distillation on DNABERT (DistilBERT and MiniLM techniques) for promoter identification.☆24Updated 3 years ago
- Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them☆174Updated 4 months ago