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1. geometric-rna-design geometric-rna-design Public

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

   Jupyter Notebook 292 25

2. geometric-gnn-dojo geometric-gnn-dojo Public

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

   Jupyter Notebook 522 51

3. facebookresearch/all-atom-diffusion-transformer facebookresearch/all-atom-diffusion-transformer Public

   Official implementation of All Atom Diffusion Transformers (ICML 2025)

   Python 297 36

4. a-r-j/ProteinWorkshop a-r-j/ProteinWorkshop Public

   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 267 22

5. graphdeeplearning/benchmarking-gnns graphdeeplearning/benchmarking-gnns Public

   Repository for benchmarking graph neural networks (JMLR 2023)

   Jupyter Notebook 2.7k 458

6. graph-convnet-tsp graph-convnet-tsp Public archive

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

   Python 329 66