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

   gRNAde: Geometric Deep Learning for 3D RNA inverse design (ICLR 2025 Spotlight)

   Jupyter Notebook 218 22

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 508 48

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

   Official implementation of All Atom Diffusion Transformers (ICML 2025)

   Python 264 30

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 253 22

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

   Repository for benchmarking graph neural networks (JMLR 2023)

   Jupyter Notebook 2.6k 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 323 67