songlab-cal / factored-attentionLinks
This repository contains code for reproducing results in our paper Interpreting Potts and Transformer Protein Models Through the Lens of Simplified Attention
☆58Updated 2 years ago
Alternatives and similar repositories for factored-attention
Users that are interested in factored-attention are comparing it to the libraries listed below
Sorting:
- ☆34Updated 4 years ago
- Implementation of trRosetta and trDesign for Pytorch, made into a convenient package, for protein structure prediction and design☆82Updated 3 years ago
- pytorch implementation of trDesign☆45Updated 4 years ago
- ☆25Updated 3 years ago
- ☆34Updated last month
- Replication attempt for the Protein Folding Model described in https://www.biorxiv.org/content/10.1101/2021.08.02.454840v1☆37Updated 3 years ago
- Universal Transforming Geometric Network for protein structure prediction.☆8Updated 4 years ago
- Code for Fold2Seq paper from ICML 2021☆50Updated 3 years ago
- Pytorch reimplementation of Molecule Attention Transformer, which uses a transformer to tackle the graph-like structure of molecules☆59Updated 4 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
- Predicting protein structure through sequence modeling☆111Updated 5 years ago
- PDNET: A fully open-source framework for deep learning protein real-valued distances☆35Updated 4 years ago
- Energy-based models for atomic-resolution protein conformations☆97Updated 3 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…☆97Updated 2 years ago
- Molecular Generation for Desired Transcriptome Changes with Adversarial Autoencoders☆53Updated 4 years ago
- Implementation of Geometric Vector Perceptron, a simple circuit for 3d rotation equivariance for learning over large biomolecules, in Pyt…☆74Updated 4 years ago
- DistilProtBert implementation, a distilled version of ProtBert model.☆15Updated 2 years ago
- A tool for predicting the effects of missense mutations on protein stability changes upon missense mutation using protein sequence only. …☆22Updated 2 years ago
- Source code for ICLR 2021 paper: "Molecule Optimization by Explainable Evolution"☆30Updated 4 years ago
- To be a next-generation DL-based phenotype prediction from genome mutations.☆19Updated 4 years ago
- A Python package for extracting protein sequence features☆59Updated 2 years ago
- De novo protein structure prediction using iteratively predicted structural constraints☆58Updated 3 years ago
- NLP for Proteins - A paper collection☆13Updated 4 years ago
- Code associated with "Biophysical prediction of protein-peptide interactions and signaling networks using machine learning."☆70Updated last year
- PyTorch library of layers acting on protein representations☆118Updated 11 months ago
- A repository with exploration into using transformers to predict DNA ↔ transcription factor binding☆85Updated 3 years ago
- Open source code for AlphaFold to extract protein embeddings☆26Updated 3 years ago
- Implementation of Nvidia's NeuralPlexer, for end-to-end differentiable design of functional small-molecules and ligand-binding proteins, …☆51Updated last year
- ☆131Updated 2 years ago
- Implementation and replication of ProGen, Language Modeling for Protein Generation, in Jax☆113Updated 3 years ago