├── .gitattributes ├── .gitignore ├── CSA_network.png ├── LICENSE ├── LICENSE_GraphGPS ├── README.md ├── configs └── CSA │ ├── cifar10-CSA.yaml │ ├── cluster-CSA.yaml │ ├── mnist-CSA.yaml │ ├── pattern-CSA.yaml │ ├── pcqm4m-CSA+RWSE-Rings.yaml │ ├── pcqm4m-CSA+RWSE-shared-e150.yaml │ ├── pcqm4m-CSA+RWSE-shared-e300.yaml │ ├── pcqm4m-CSA+RWSE.yaml │ ├── pcqm4m-CSADeep+RWSE-shared-e150.yaml │ ├── pcqm4m-CSADeep+SPDE-Rings-e150.yaml │ ├── pcqm4m_full-CSA+RWSE-shared-Rings.yaml │ ├── pcqm4m_full-CSA+RWSE-shared.yaml │ ├── pcqm4m_subset-CSA+RWSE-Rings.yaml │ ├── pcqm4m_subset-CSA+RWSE.yaml │ ├── pcqm4m_subset-CSA+SPDE-Rings.yaml │ ├── pcqm4m_subset-CSA+SPDE.yaml │ ├── pcqm4m_subset-CSAnoPE+SPDE.yaml │ ├── zinc-CSA+GINE.yaml │ ├── zinc-CSA+RWSE.yaml │ ├── zinc-CSA+Rings.yaml │ ├── zinc-CSA+SPDE-Rings.yaml │ ├── zinc-CSA+SPDE.yaml │ ├── zinc-CSA+noRPE-Rings.yaml │ ├── zinc-CSA+noRPE.yaml │ ├── zinc-CSA-RWSE-SPDE.yaml │ ├── zinc-CSA-RWSE-noPE.yaml │ ├── zinc-CSA-noPE-RWSE16.yaml │ ├── zinc-CSA-noPE-RWSE2.yaml │ ├── zinc-CSA-noPE-RWSE20.yaml │ ├── zinc-CSA-noPE-RWSE4.yaml │ ├── zinc-CSA-noPE-RWSE8.yaml │ ├── zinc-CSA-noPE-SPDE.yaml │ ├── zinc-CSA-noPE-noPE.yaml │ └── zinc-CSA.yaml ├── graphgps ├── __init__.py ├── act │ ├── __init__.py │ └── example.py ├── config │ ├── __init__.py │ ├── custom_gnn_config.py │ ├── dataset_config.py │ ├── defaults_config.py │ ├── example.py │ ├── gt_config.py │ ├── optimizers_config.py │ ├── posenc_config.py │ ├── pretrained_config.py │ ├── split_config.py │ └── wandb_config.py ├── encoder │ ├── __init__.py │ ├── ast_encoder.py │ ├── composed_edge_encoders.py │ ├── composed_encoders.py │ ├── dense_edge_encoder.py │ ├── dummy_edge_encoder.py │ ├── equivstable_laplace_pos_encoder.py │ ├── example.py │ ├── kernel_pos_encoder.py │ ├── laplace_pos_encoder.py │ ├── linear_edge_encoder.py │ ├── linear_node_encoder.py │ ├── ogb_encoder.py │ ├── ppa_encoder.py │ ├── relative_pe_encoder.py │ ├── signnet_pos_encoder.py │ ├── topology_edge_encoder.py │ ├── type_dict_encoder.py │ └── voc_superpixels_encoder.py ├── finetuning.py ├── head │ ├── __init__.py │ ├── example.py │ ├── inductive_edge.py │ ├── inductive_node.py │ ├── ogb_code_graph.py │ └── san_graph.py ├── layer │ ├── __init__.py │ ├── bigbird_layer.py │ ├── csa_layer.py │ ├── example.py │ ├── gatedgcn_layer.py │ ├── gine_conv_layer.py │ ├── gps_layer.py │ ├── performer_layer.py │ ├── san2_layer.py │ └── san_layer.py ├── loader │ ├── __init__.py │ ├── dataset │ │ ├── __init__.py │ │ ├── aqsol_molecules.py │ │ ├── coco_superpixels.py │ │ ├── malnet_tiny.py │ │ ├── pcqm4mv2_contact.py │ │ ├── peptides_functional.py │ │ ├── peptides_structural.py │ │ └── voc_superpixels.py │ ├── master_loader.py │ ├── ogbg_code2_utils.py │ └── split_generator.py ├── logger.py ├── loss │ ├── __init__.py │ ├── l1.py │ ├── multilabel_classification_loss.py │ ├── subtoken_prediction_loss.py │ └── weighted_cross_entropy.py ├── metric_wrapper.py ├── metrics_ogb.py ├── network │ ├── __init__.py │ ├── big_bird.py │ ├── custom_gnn.py │ ├── example.py │ ├── gps_model.py │ ├── performer.py │ └── san_transformer.py ├── optimizer │ ├── __init__.py │ └── extra_optimizers.py ├── pooling │ ├── __init__.py │ └── example.py ├── stage │ ├── __init__.py │ └── example.py ├── train │ ├── __init__.py │ ├── custom_train.py │ └── example.py ├── transform │ ├── __init__.py │ ├── posenc_stats.py │ └── transforms.py └── utils.py ├── install.sh ├── main.py ├── run ├── cancel_all.sh ├── run_experiments.sh ├── run_experiments_pcqm.sh └── wrapper.sb ├── setup.py ├── tests ├── configs │ ├── graph │ │ ├── cifar10.yaml │ │ ├── cluster-SAN.yaml │ │ ├── cluster.yaml │ │ ├── collab.yaml │ │ ├── dd.yaml │ │ ├── enzymes.yaml │ │ ├── imdb-binary.yaml │ │ ├── imdb-multi.yaml │ │ ├── malnettiny-GPS+RWSE.yaml │ │ ├── malnettiny-GPS-noPE.yaml │ │ ├── malnettiny-GPS.yaml │ │ ├── malnettiny-LapPE.yaml │ │ ├── malnettiny-SAN-sparse.yaml │ │ ├── malnettiny.yaml │ │ ├── mnist.yaml │ │ ├── nci1-LapPE.yaml │ │ ├── nci1-Performer.yaml │ │ ├── nci1.yaml │ │ ├── ogbg-code2-GPS.yaml │ │ ├── ogbg-code2.yaml │ │ ├── ogbg-molhiv-LapPE.yaml │ │ ├── ogbg-molhiv-RWSE.yaml │ │ ├── ogbg-molhiv-SAN+RWSE.yaml │ │ ├── ogbg-molhiv-SAN.yaml │ │ ├── ogbg-molhiv.yaml │ │ ├── ogbg-molpcba-GPS+RWSE-inference.yaml │ │ ├── ogbg-molpcba-GPS.yaml │ │ ├── ogbg-molpcba-LapPE.yaml │ │ ├── ogbg-molpcba-SAN.yaml │ │ ├── ogbg-molpcba.yaml │ │ ├── ogbg-ppa-GPS.yaml │ │ ├── ogbg-ppa.yaml │ │ ├── ogbl-collab.yaml │ │ ├── pattern-SAN.yaml │ │ ├── pattern.yaml │ │ ├── pcqm4m.yaml │ │ ├── proteins.yaml │ │ ├── zinc-BigBird.yaml │ │ ├── zinc-GPS+SignNet.yaml │ │ ├── zinc-GPS-BigBird.yaml │ │ ├── zinc-GPS-small.yaml │ │ ├── zinc-GPS.yaml │ │ ├── zinc-GPSwLPE.yaml │ │ ├── zinc-LapPE.yaml │ │ ├── zinc-Performer.yaml │ │ ├── zinc-SAN-LapPE+RWSE.yaml │ │ ├── zinc-SAN-small.yaml │ │ ├── zinc-SAN.yaml │ │ ├── zinc-SignNet.yaml │ │ └── zinc.yaml │ ├── node │ │ ├── citeseer.yaml │ │ ├── cora.yaml │ │ ├── default.yaml 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