alex-hh

deep-protein-generation

eDICE

Epigenomic Data Imputation via Contextualised Embeddings

batchbald_redux

Reusable BatchBALD implementation

deep-active-learning

An implementation of the state-of-the-art Deep Active Learning algorithms

PoET

Inference code for PoET: A generative model of protein families as sequences-of-sequences

accelerate

🚀 A simple way to train and use PyTorch models with multi-GPU, TPU, mixed-precision

ArDCA.jl

Autoregressive networks for protein

biopython

Official git repository for Biopython (originally converted from CVS)

bayesian-torch

A library for Bayesian neural network layers and uncertainty estimation in Deep Learning extending the core of PyTorch

ByProt

ColabFold

Making Protein folding accessible to all!

cryptic

DSMBind

edice-pytorch

encode-imputation

Code for entry into ENCODE imputation challenge (team imp)

esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

fitness_data

Protein fitness datasets

kotsu

Lightweight framework for structured and repeatable model validation

Laplace

Laplace approximations for Deep Learning.

lolbo

MI_IPA

Matlab code for the MI-IPA described in "Inferring interaction partners from protein sequences using mutual information", by Anne-Florence Bitbol, DOI: 10.1101/378042.

MMDGS_NeurIPS

openfold

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

progen

Official release of the ProGen models

programming-notes

ProteinMPNN

Code for the ProteinMPNN paper

prototorch

Lightweight framework for accelerating PyTorch research projects

proximal-exploration

PyTorch implementation for our paper "Proximal Exploration for Model-guided Protein Sequence Design"

template

Tranception

Official repository for the paper "Tranception: Protein Fitness Prediction with Autoregressive Transformers and Inference-time Retrieval"