John newton's starred repositories
alphafold3-pytorch
Implementation of Alphafold 3 in Pytorch
Linux-Bash-Commands
:godmode: Ultimate list of Linux bash commands, cheatsheets and resources
Contour-Stochastic-Gradient-Langevin-Dynamics
An elegant adaptive importance sampling algorithms for simulations of multi-modal distributions (NeurIPS'20)
tr-rosetta-pytorch
Implementation of trRosetta and trDesign for Pytorch, made into a convenient package, for protein structure prediction and design
torchmd-protein-thermodynamics
Tutorials and data necessary to reproduce the results of publication Machine Learning Coarse-Grained Potentials of Protein Thermodynamics
flash-attention
Fast and memory-efficient exact attention
awesome-protein-representation-learning
Awesome Protein Representation Learning
Awesome-Diffusion-Models
A collection of resources and papers on Diffusion Models
DiffDock-PP
Implementation of DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models in PyTorch (ICLR 2023 - MLDD Workshop)
alphafold_finetune
Python code for fine-tuning AlphaFold to perform protein-peptide binding predictions
PyTorchStepByStep
Official repository of my book: "Deep Learning with PyTorch Step-by-Step: A Beginner's Guide"
pytorch-accelerated
A lightweight library designed to accelerate the process of training PyTorch models by providing a minimal, but extensible training loop which is flexible enough to handle the majority of use cases, and capable of utilizing different hardware options with no code changes required. Docs: https://pytorch-accelerated.readthedocs.io/en/latest/
accelerate
🚀 A simple way to launch, train, and use PyTorch models on almost any device and distributed configuration, automatic mixed precision (including fp8), and easy-to-configure FSDP and DeepSpeed support
bio-diffusion
A geometry-complete diffusion generative model (GCDM) for 3D molecule generation and optimization (Nature CommsChem)
denoising-diffusion-pytorch
Implementation of Denoising Diffusion Probabilistic Model in Pytorch
BayesianOptimization
A Python implementation of global optimization with gaussian processes.
scribble-diffusion
Turn your rough sketch into a refined image using AI
denoising-diffusion-model
A simple guide to diffusion models. Helpful in understanding the concept and practicing with the method.
foldingdiff
Diffusion models of protein structure; trigonometry and attention are all you need!
gpt-pytorch
PyTorch Implementation of OpenAI GPT