Code for the paper Progressive Inference-Time Annealing of Diffusion Models for Sampling from Boltzmann Densities.

MMseqs2: ultra fast and sensitive search and clustering suite

code for "Adjoint Sampling: Highly Scalable Diffusion Samplers via Adjoint Matching"

Research Project Template Repository

Let LLM run your MDs.

Python package for P2 (Path Planning), a masked diffusion model sampling method for sequence generation (protein, text, etc.).

Official PyTorch implementation for "Large Language Diffusion Models"

Triton Implementation of Flash Attention with Bias.

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

(Unofficial) FoldFlow 1 / 2 repo

A standardized protein design benchmark for motif-scaffolding problems

Implementation of Trajectory Inference in Wasserstein Space

Collecting research materials on neural samplers with diffusion/flow models

Boltzmann-ranked alternative protein conformations from reduced-MSA AlphaFold2

A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.

Official implementation of MatterGen -- a generative model for inorganic materials design across the periodic table that can be fine-tuned to steer the generation towards a wide range of property c…

User-friendly AI Interface (Supports Ollama, OpenAI API, ...)

The Superposition of Diffusion Models Using the Itô Density Estimator

Official PyTorch implementation for ICLR2025 paper "Scaling up Masked Diffusion Models on Text"

Official Jax Implementation of MD4 Masked Diffusion Models

A 15TB Collection of Physics Simulation Datasets

FAPLM: A Drop-in Efficient Pytorch Implementation of Protein Language Models

Geometric Generative Model Tutorial at LoG 2024

$100K or 100 Days: Trade-offs when Pre-Training with Academic Resources

AlphaFold 3 inference pipeline.

A trainable PyTorch reproduction of AlphaFold 3.