Inference code for scalable emulation of protein equilibrium ensembles with generative deep learning

https://deepgraphlearning.github.io/ProteinTutorial_AAAI2025/

verl: Volcano Engine Reinforcement Learning for LLMs

Simple Guidance Mechanisms for Discrete Diffusion Models

AlphaFold 3 inference pipeline.

A trainable PyTorch reproduction of AlphaFold 3.

High-Resolution Image Synthesis with Latent Diffusion Models

Pytorch implementation of Transfusion, "Predict the Next Token and Diffuse Images with One Multi-Modal Model", from MetaAI

Simple and Effective Masked Diffusion Language Model

DDPO for finetuning diffusion models, implemented in PyTorch with LoRA support

code for "Diffusion Forcing: Next-token Prediction Meets Full-Sequence Diffusion"

An implementation of local windowed attention for language modeling

Implementation of Alphafold 3 from Google Deepmind in Pytorch

Equivariant Scalar Fields for Molecular Docking with Fast Fourier Transforms

code for "Riemannian Flow Matching on General Geometries".

A concise but complete full-attention transformer with a set of promising experimental features from various papers

Skipping the replica exchange ladder with normalizing flows

Timewarp is a research project using deep learning to accelerate molecular dynamics simulation.

Code for the paper Iterated Denoising Energy Matching for Sampling from Boltzmann Densities.

Mamba SSM architecture

PyTorch Lightning + Hydra. A very user-friendly template for ML experimentation. ⚡🔥⚡

Code and Pre-Trained Models for "AttnPacker: An end-to-end deep learning method for protein side-chain packing"

A generative model for programmable protein design