Awesome-GNN-based-drug-discovery

Graph Neural Networks (GNN) Software and Libraries

General GNN Frameworks

• PyTorch Geometric (PyG)
  • Deep learning on graphs, point clouds, manifolds. GitHub , Tutorial
• Deep Graph Library (DGL)
  • Training/deploying GNNs on PyTorch, TensorFlow, MXNet. GitHub , Tutorial
• Spektral
  • TensorFlow/Keras library for graph deep learning. GitHub , Tutorial
• TensorFlow-GNN
  • TensorFlow library for graph neural networks. GitHub , Paper:TF-GNN: Graph Neural Networks in TensorFlow

Specialized GNN Tools

• Graph Nets by DeepMind
  • TensorFlow library for building graph networks. GitHub
• StellarGraph
  • Machine learning on graphs/networks with TensorFlow 2.x. GitHub , Tutorial
• PyTorch BigGraph (PBG)
  • Graph embeddings for large graphs by Facebook. GitHub , Tutorial

Innovative GNN Libraries

• CogDL
  • Toolkit for graph representation learning on PyTorch. GitHub , Website
• PyTorch Geometric Temporal (PyGT)
  • Temporal graph deep learning on PyTorch Geometric. GitHub , Tutorial
• Dive into Graphs (DIG)
  • Higher-level graph deep learning tasks. GitHub , Documentation , Tutorial

Platform and Toolkits

• GraphGym
  • Platform for GNN design and evaluation. GitHub
• OpenHGNN
  • Toolkit for heterogeneous GNNs on PyTorch and DGL. GitHub

Drug Discovery Tools, Software, and Libraries

Deep Learning and Cheminformatics

• DeepChem
  • Deep learning for life sciences. GitHub
• RDKit
  • Cheminformatics and machine learning. Website , GitHub
• TorchDrug
  • Toolkit for drug discovery on PyTorch. Website , GitHub

Molecular Processing and Prediction

• DataMol
  • Simplifies molecular processing for ML. Website , GitHub
• Chemprop
  • GNNs for molecular property prediction on PyTorch. GitHub

Benchmarks and Datasets

• MoleculeNet
  • Benchmark for molecular machine learning. Website
• Open Graph Benchmark (OGB)
  • Benchmark for graph machine learning. Website , GitHub

Specialized Tools for Drug Discovery

• Chemical Representation Learning for Toxicity Prediction
  • Datasets and models for toxicity prediction on PyTorch. GitHub , Paper
• BioCypher
  • Biomedical knowledge graphs framework. Website , GitHub , Paper

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