A repository with exploration into using transformers to predict DNA ↔ transcription factor binding
☆88Jun 2, 2022Updated 4 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 4 years ago
- Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch☆575Jun 26, 2026Updated 3 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 3 years ago
- Implementation of Geometric Vector Perceptron, a simple circuit for 3d rotation equivariance for learning over large biomolecules, in Pyt…☆76Jun 8, 2021Updated 5 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.
- Deep learning multi-label classifier of non-coding DNA sequences☆11Mar 3, 2020Updated 6 years ago
- A denoising diffusion probabilistic model (DDPM) tailored for conditional generation of protein distograms☆143Apr 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 3 years ago
- ☆10Sep 13, 2021Updated 5 years ago
- Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.☆99Jun 10, 2026Updated 4 months 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
- 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 5 years ago
- Graph-based community clustering approach to extract protein domains from a predicted aligned error matrix☆39Jul 28, 2022Updated 4 years ago
- Machine learning methods for DNA sequence analysis.☆66Sep 30, 2026Updated 2 weeks ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- PyTorch implementation of Basenji2.☆22Apr 29, 2025Updated last year
- A simple cross attention that updates both the source and target in one step☆200Jul 29, 2025Updated last year
- 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…☆173Nov 25, 2022Updated 3 years ago
- ☆19Oct 21, 2024Updated last year
- [Briefings in Bioinformatics'20] Integrating multi-network topology for gene function prediction using deep neural networks☆14Sep 5, 2019Updated 7 years ago
- Implementation and replication of ProGen, Language Modeling for Protein Generation, in Jax☆114Sep 8, 2021Updated 5 years ago
- A command line tool for rapid visualisation of AlphaFold2 and AlphaFold3 predictions.☆17Oct 21, 2025Updated 11 months ago
- An attempt to merge ESBN with Transformers, to endow Transformers with the ability to emergently bind symbols☆16Aug 3, 2021Updated 5 years ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Code repository for the manuscript: Nucleotide dependency analysis of DNA language models reveals genomic functional elements☆30Aug 3, 2026Updated 2 months ago
- A python library for highly configurable transformers - easing model architecture search and experimentation.☆48Nov 30, 2021Updated 4 years ago
- Sequential regulatory activity predictions with deep convolutional neural networks.☆475Jan 15, 2026Updated 9 months ago
- CpG Transformer for imputation of single-cell methylomes☆39Sep 14, 2023Updated 3 years ago
- ☆13Nov 19, 2021Updated 4 years ago
- ☆33Dec 2, 2022Updated 3 years ago
- Contrastive Language-Audio Pretraining☆88Mar 6, 2022Updated 4 years ago
- Local Attention - Flax module for Jax☆22May 26, 2021Updated 5 years ago
- A simple Transformer where the softmax has been replaced with normalization☆20Sep 11, 2020Updated 6 years ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Implementation of the Equiformer, SE3/E3 equivariant attention network that reaches new SOTA, and adopted for use by EquiFold for protein…☆290Dec 17, 2024Updated last year
- A python package and collection of scripts for computing protein surface meshes, chemical, electrostatic, geometric features, and buildin…☆27Jul 15, 2025Updated last year
- Code for reproducing the Sei manuscript results☆17Jan 25, 2022Updated 4 years ago
- Implementation of Cross Transformer for spatially-aware few-shot transfer, in Pytorch☆54Mar 30, 2021Updated 5 years ago
- Implementation of a Transformer using ReLA (Rectified Linear Attention) from https://arxiv.org/abs/2104.07012☆49Apr 6, 2022Updated 4 years ago
- Implementation of the Remixer Block from the Remixer paper, in Pytorch☆36Sep 27, 2021Updated 5 years ago
- Another attempt at a long-context / efficient transformer by me☆38Apr 11, 2022Updated 4 years ago