daiki-ko

Graph-Mamba

Graph-Mamba: Towards Long-Range Graph Sequence Modelling with Selective State Spaces

diffusion_models

A series of tutorial notebooks on denoising diffusion probabilistic models in PyTorch

foldingdiff

Diffusion models of protein structure; trigonometry and attention are all you need!

Smooth-Diffusion

Smooth Diffusion: Crafting Smooth Latent Spaces in Diffusion Models arXiv 2023 / CVPR 2024

naist-thesis-tmpl

NAIST情報科学研究科向けのやや現代的な修士論文用LaTeXテンプレート

GPSE

Graph Positional and Structural Encoder

cheminfotutorial1023

material for cheminfo tutorial

MolCLR

Implementation of MolCLR: "Molecular Contrastive Learning of Representations via Graph Neural Networks" in PyG.

NPVAE

FlowSite

Implementation of FlowSite and HarmonicFlow from the paper "Harmonic Self-Conditioned Flow Matching for Multi-Ligand Docking and Binding Site Design"

pytorch_flows

Implementation and tutorials of normalizing flows with the novel distributions module

DiffDock

Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking

torsional-diffusion

Implementation of Torsional Diffusion for Molecular Conformer Generation (NeurIPS 2022)

3DInfomax

Making self-supervised learning work on molecules by using their 3D geometry to pre-train GNNs. Implemented in DGL and Pytorch Geometric.

GraphMVP

Pre-training Molecular Graph Representation with 3D Geometry, ICLR'22 (https://openreview.net/forum?id=xQUe1pOKPam)

LSGM

The Official PyTorch Implementation of "LSGM: Score-based Generative Modeling in Latent Space" (NeurIPS 2021)

pytorch_MCMC

Lightweight MCMC sampling for PyTorch Models aka My Corona Project

ChEMBL_Structure_Pipeline

ChEMBL database structure pipelines

FreeSolv

Experimental and calculated small molecule hydration free energies

Graphormer

Graphormer is a general-purpose deep learning backbone for molecular modeling.

e3nn

A modular framework for neural networks with Euclidean symmetry

benchmarking-gnns

Repository for benchmarking graph neural networks

graph_neural_network_drug_response

GeoDiff

Implementation of GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation (ICLR 2022).

DL-schrodinger

GeoLDM

Geometric Latent Diffusion Models for 3D Molecule Generation

e3_diffusion_for_molecules

DiffFlow

[Neurips 2021]Diffusion Normalizing Flow (DiffFlow)

CARD

Official PyTorch implementation for the paper "CARD: Classification and Regression Diffusion Models"

ddpm-torch

Unofficial PyTorch Implementation of Denoising Diffusion Probabilistic Models (DDPM)