brennanaba / AbData
☆10Updated 3 years ago
Alternatives and similar repositories for AbData:
Users that are interested in AbData are comparing it to the libraries listed below
- pytorch implementation of trDesign☆45Updated 4 years ago
- To be a next-generation DL-based phenotype prediction from genome mutations.☆19Updated 3 years ago
- Replication attempt for the Protein Folding Model described in https://www.biorxiv.org/content/10.1101/2021.08.02.454840v1☆37Updated 2 years ago
- ☆33Updated 3 years ago
- Implementation of Geometric Vector Perceptron, a simple circuit for 3d rotation equivariance for learning over large biomolecules, in Pyt…☆72Updated 3 years ago
- Implementation of Tranception, an attention network, paired with retrieval, that is SOTA for protein fitness prediction☆31Updated 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, …☆29Updated 3 years ago
- Implementation of Denoising Diffusion for protein design, but using the new Equiformer (successor to SE3 Transformers) with some addition…☆56Updated 2 years ago
- ☆25Updated 2 years ago
- A tool for predicting the effects of missense mutations on protein stability changes upon missense mutation using protein sequence only. …☆22Updated last year
- A Modular Architecture for Deep Learning Systems☆40Updated 5 months ago
- This repository contains code for reproducing results in our paper Interpreting Potts and Transformer Protein Models Through the Lens of …☆58Updated 2 years ago
- Source code for ICLR 2021 paper: "Molecule Optimization by Explainable Evolution"☆28Updated 3 years ago
- A repository with exploration into using transformers to predict DNA ↔ transcription factor binding☆84Updated 2 years ago
- ☆34Updated 4 years ago
- RITA is a family of autoregressive protein models, developed by LightOn in collaboration with the OATML group at Oxford and the Debora Ma…☆96Updated 2 years ago
- Pytorch reimplementation of Molecule Attention Transformer, which uses a transformer to tackle the graph-like structure of molecules☆58Updated 4 years ago
- Universal Transforming Geometric Network for protein structure prediction.☆8Updated 4 years ago
- Unofficially Implements https://arxiv.org/abs/2112.05682 to get Linear Memory Cost on Attention for PyTorch☆12Updated 3 years ago
- My own attempt at a long context genomics model, leveraging recent advances in long context attention modeling (Flash Attention + other h…☆52Updated last year
- Implementation of the DDPM + IPA (invariant point attention) for protein generation, as outlined in the paper "Protein Structure and Sequ…☆88Updated 2 years ago
- Code for Fold2Seq paper from ICML 2021☆50Updated 2 years ago
- Implementation and replication of ProGen, Language Modeling for Protein Generation, in Jax☆112Updated 3 years ago
- Homology reduced UniProt, train-/valid-/testsets for language modeling☆16Updated 2 years ago
- Epistatic Net is an algorithm which allows for spectral regularization of deep neural networks to predict biological fitness functions (e…☆18Updated 3 years ago
- Implementation of trRosetta and trDesign for Pytorch, made into a convenient package, for protein structure prediction and design☆80Updated 3 years ago
- ☆131Updated 2 years ago
- Experiments in protein folding through language modeling☆10Updated 3 years ago
- Open source code for AlphaFold to extract protein embeddings☆26Updated 3 years ago