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1. geometric-rna-designgeometric-rna-designPublic

   gRNAde is a Generative AI framework for inverse design of 3D RNA structure and function

   Jupyter Notebook 287 26

2. geometric-gnn-dojogeometric-gnn-dojoPublic

   Geometric GNN Dojo provides unified implementations and experiments to explore the design space of Geometric Graph Neural Networks (ICML 2023)

   Jupyter Notebook 518 51

3. facebookresearch/all-atom-diffusion-transformerfacebookresearch/all-atom-diffusion-transformerPublic

   Official implementation of All Atom Diffusion Transformers (ICML 2025)

   Python 293 37

4. a-r-j/ProteinWorkshopa-r-j/ProteinWorkshopPublic

   Benchmarking framework for protein representation learning. Includes a large number of pre-training and downstream task datasets, models and training/task utilities. (ICLR 2024)

   Python 266 22

5. graphdeeplearning/benchmarking-gnnsgraphdeeplearning/benchmarking-gnnsPublic

   Repository for benchmarking graph neural networks (JMLR 2023)

   Jupyter Notebook 2.6k 459

6. graph-convnet-tspgraph-convnet-tspPublic archive

   Code for the paper 'An Efficient Graph Convolutional Network Technique for the Travelling Salesman Problem' (INFORMS Annual Meeting Session 2019)

   Python 331 67