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 3 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 5 years ago
- ☆25Updated 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…☆98Updated 2 years ago
- Predicting protein structure through sequence modeling☆112Updated 5 years ago
- Implementation of trRosetta and trDesign for Pytorch, made into a convenient package, for protein structure prediction and design☆83Updated 4 years ago
- ☆34Updated 5 months ago
- pytorch implementation of trDesign☆45Updated 4 years ago
- Implementation and replication of ProGen, Language Modeling for Protein Generation, in Jax☆112Updated 4 years ago
- Replication attempt for the Protein Folding Model described in https://www.biorxiv.org/content/10.1101/2021.08.02.454840v1☆37Updated 3 years ago
- Pytorch reimplementation of Molecule Attention Transformer, which uses a transformer to tackle the graph-like structure of molecules☆58Updated 4 years ago
- Energy-based models for atomic-resolution protein conformations☆100Updated 3 years ago
- Implementation of Geometric Vector Perceptron, a simple circuit for 3d rotation equivariance for learning over large biomolecules, in Pyt…☆75Updated 4 years ago
- A tool for predicting the effects of missense mutations on protein stability changes upon missense mutation using protein sequence only. …☆23Updated 2 years ago
- Epistatic Net is an algorithm which allows for spectral regularization of deep neural networks to predict biological fitness functions (e…☆18Updated 4 years ago
- Open source code for AlphaFold to extract protein embeddings☆27Updated 4 years ago
- DistilProtBert implementation, a distilled version of ProtBert model.☆15Updated 3 years ago
- ☆81Updated 2 years ago
- ☆17Updated 2 years ago
- Homology reduced UniProt, train-/valid-/testsets for language modeling☆16Updated 3 years ago
- PyTorch library of layers acting on protein representations☆119Updated last year
- Molecular Generation for Desired Transcriptome Changes with Adversarial Autoencoders☆53Updated 5 years ago
- End-to-end RNA Design using deep reinforcement learning☆71Updated 3 years ago
- To be a next-generation DL-based phenotype prediction from genome mutations.☆19Updated 4 years ago
- Protein Language Model☆119Updated last year
- Readings for "A Unified View of Relational Deep Learning for Drug Pair Scoring." (IJCAI 2022)☆96Updated 3 years ago
- Implementation of the DDPM + IPA (invariant point attention) for protein generation, as outlined in the paper "Protein Structure and Sequ…☆89Updated 3 years ago
- Code for Fold2Seq paper from ICML 2021☆50Updated 3 years ago
- Protein sequence classification with self-supervised pretraining☆82Updated 3 years ago
- Implementation of Neural Distance Embeddings for Biological Sequences (NeuroSEED) in PyTorch (NeurIPS 2021)☆73Updated 2 years ago
- PDNET: A fully open-source framework for deep learning protein real-valued distances☆36Updated 4 years ago