A repository with exploration into using transformers to predict DNA ↔ transcription factor binding
☆88Jun 2, 2022Updated 3 years ago
Alternatives and similar repositories for tf-bind-transformer
Users that are interested in tf-bind-transformer are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- The full training script for Enformer - Tensorflow Sonnet☆18Apr 18, 2022Updated 4 years ago
- Implementation of Tranception, an attention network, paired with retrieval, that is SOTA for protein fitness prediction☆32Jun 19, 2022Updated 3 years ago
- To be a next-generation DL-based phenotype prediction from genome mutations.☆19May 17, 2021Updated 5 years ago
- Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch☆564Jul 7, 2025Updated 10 months ago
- My own attempt at a long context genomics model, leveraging recent advances in long context attention modeling (Flash Attention + other h…☆54Jul 2, 2023Updated 2 years ago
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- Implementation of Geometric Vector Perceptron, a simple circuit for 3d rotation equivariance for learning over large biomolecules, in Pyt…☆77Jun 8, 2021Updated 4 years ago
- Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.☆96Nov 13, 2025Updated 6 months ago
- Deep learning multi-label classifier of non-coding DNA sequences☆11Mar 3, 2020Updated 6 years ago
- Machine learning methods for DNA sequence analysis.☆63Feb 27, 2026Updated 3 months ago
- A denoising diffusion probabilistic model (DDPM) tailored for conditional generation of protein distograms☆144Apr 20, 2022Updated 4 years ago
- Implementation of an Attention layer where each head can attend to more than just one token, using coordinate descent to pick topk☆47Jul 16, 2023Updated 2 years ago
- ☆10Sep 13, 2021Updated 4 years ago
- Implementation of the Triangle Multiplicative module, used in Alphafold2 as an efficient way to mix rows or columns of a 2d feature map, …☆39Aug 3, 2021Updated 4 years ago
- Implementation of Nvidia's NeuralPlexer, for end-to-end differentiable design of functional small-molecules and ligand-binding proteins, …☆52Nov 20, 2023Updated 2 years ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Graph-based community clustering approach to extract protein domains from a predicted aligned error matrix☆36Jul 28, 2022Updated 3 years ago
- PyTorch implementation of Basenji2.☆21Apr 29, 2025Updated last year
- A simple cross attention that updates both the source and target in one step☆196Jul 29, 2025Updated 10 months ago
- Implementation of COCO-LM, Correcting and Contrasting Text Sequences for Language Model Pretraining, in Pytorch☆46Mar 3, 2021Updated 5 years ago
- Implementation of Invariant Point Attention, used for coordinate refinement in the structure module of Alphafold2, as a standalone Pytorc…☆171Nov 25, 2022Updated 3 years ago
- Implementation and replication of ProGen, Language Modeling for Protein Generation, in Jax☆114Sep 8, 2021Updated 4 years ago
- A command line tool for rapid visualisation of AlphaFold2 and AlphaFold3 predictions.☆14Oct 21, 2025Updated 7 months ago
- An attempt to merge ESBN with Transformers, to endow Transformers with the ability to emergently bind symbols☆16Aug 3, 2021Updated 4 years ago
- A python library for highly configurable transformers - easing model architecture search and experimentation.☆48Nov 30, 2021Updated 4 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Annotated sequence data☆11Feb 2, 2025Updated last year
- ☆13Nov 19, 2021Updated 4 years ago
- A command-line tool to mitigate homology-based data leakage in sequence-to-expression models☆20Mar 29, 2026Updated last month
- ☆19Oct 21, 2024Updated last year
- Contrastive Language-Audio Pretraining☆88Mar 6, 2022Updated 4 years ago
- Sequential regulatory activity predictions with deep convolutional neural networks.☆470Jan 15, 2026Updated 4 months ago
- Local Attention - Flax module for Jax☆22May 26, 2021Updated 5 years ago
- TMol☆75Updated this week
- Code repository for the manuscript: Nucleotide dependency analysis of DNA language models reveals genomic functional elements☆28Mar 13, 2025Updated last year
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Implementation of the Equiformer, SE3/E3 equivariant attention network that reaches new SOTA, and adopted for use by EquiFold for protein…☆289Dec 17, 2024Updated last year
- A simple Transformer where the softmax has been replaced with normalization☆20Sep 11, 2020Updated 5 years ago
- Code for reproducing the Sei manuscript results☆17Jan 25, 2022Updated 4 years ago
- A python package and collection of scripts for computing protein surface meshes, chemical, electrostatic, geometric features, and buildin …☆27Jul 15, 2025Updated 10 months ago
- Implementation of Cross Transformer for spatially-aware few-shot transfer, in Pytorch☆54Mar 30, 2021Updated 5 years ago
- Toolkit for single-cell DNA methylation analysis.☆48May 18, 2026Updated last week
- Implementation of a Transformer using ReLA (Rectified Linear Attention) from https://arxiv.org/abs/2104.07012☆49Apr 6, 2022Updated 4 years ago