├── .gitignore ├── GPSE.png ├── LICENSE ├── README.md ├── configs ├── er-GIN+AllPSE.yaml ├── er-GIN+GPSE.yaml ├── er-GIN+LapPE.yaml ├── er-GIN+RWSE.yaml ├── er-GIN+none.yaml ├── mol_bench │ ├── molhiv-GPS+AllPSE.yaml │ ├── molhiv-GPS+GPSE.yaml │ ├── molhiv-GPS+LapPE+RWSE.yaml │ ├── molhiv-GPS+LapPE.yaml │ ├── molhiv-GPS+RWSE.yaml │ ├── molhiv-GPS+none.yaml │ ├── molhiv-GPS+rand.yaml │ ├── molpcba-GPS+AllPSE.yaml │ ├── molpcba-GPS+GPSE.yaml │ ├── molpcba-GPS+LapPE+RWSE.yaml │ ├── molpcba-GPS+LapPE.yaml │ ├── molpcba-GPS+RWSE.yaml │ ├── molpcba-GPS+none.yaml │ ├── molpcba-GPS+rand.yaml │ ├── pcqm4mfull-GPS+AllPSE.yaml │ ├── pcqm4mfull-GPS+GPSE.yaml │ ├── pcqm4mfull-GPS+LapPE+RWSE.yaml │ ├── pcqm4msubset-GCN+AllPSE.yaml │ ├── pcqm4msubset-GCN+GPSE.yaml │ ├── pcqm4msubset-GCN+LapPE+RWSE.yaml │ ├── pcqm4msubset-GCN+LapPE.yaml │ ├── pcqm4msubset-GCN+RWSE.yaml │ ├── pcqm4msubset-GCN+none.yaml │ ├── pcqm4msubset-GCN+rand.yaml │ ├── pcqm4msubset-GIN+AllPSE.yaml │ ├── pcqm4msubset-GIN+GPSE.yaml │ ├── pcqm4msubset-GIN+LapPE+RWSE.yaml │ ├── pcqm4msubset-GIN+LapPE.yaml │ ├── pcqm4msubset-GIN+RWSE.yaml │ ├── pcqm4msubset-GIN+none.yaml │ ├── pcqm4msubset-GIN+rand.yaml │ ├── pcqm4msubset-GINE+AllPSE.yaml │ ├── pcqm4msubset-GINE+GPSE.yaml │ ├── pcqm4msubset-GINE+LapPE+RWSE.yaml │ ├── pcqm4msubset-GINE+LapPE.yaml │ ├── pcqm4msubset-GINE+RWSE.yaml │ ├── pcqm4msubset-GINE+none.yaml │ ├── pcqm4msubset-GINE+rand.yaml │ ├── pcqm4msubset-GPS+AllPSE.yaml │ ├── pcqm4msubset-GPS+GPSE.yaml │ ├── pcqm4msubset-GPS+LapPE+RWSE.yaml │ ├── pcqm4msubset-GPS+LapPE.yaml │ ├── pcqm4msubset-GPS+RWSE.yaml │ ├── pcqm4msubset-GPS+none.yaml │ ├── pcqm4msubset-GPS+rand.yaml │ ├── pcqm4msubset-GatedGCN+AllPSE.yaml │ ├── pcqm4msubset-GatedGCN+GPSE.yaml │ ├── pcqm4msubset-GatedGCN+LapPE+RWSE.yaml │ ├── pcqm4msubset-GatedGCN+LapPE.yaml │ ├── pcqm4msubset-GatedGCN+RWSE.yaml │ ├── pcqm4msubset-GatedGCN+none.yaml │ ├── pcqm4msubset-GatedGCN+rand.yaml │ ├── pcqm4msubset-Transformer+AllPSE.yaml │ ├── pcqm4msubset-Transformer+GPSE.yaml │ ├── pcqm4msubset-Transformer+LapPE+RWSE.yaml │ ├── pcqm4msubset-Transformer+LapPE.yaml │ ├── pcqm4msubset-Transformer+RWSE.yaml │ ├── pcqm4msubset-Transformer+none.yaml │ ├── pcqm4msubset-Transformer+rand.yaml │ ├── zinc-GCN+AllPSE.yaml │ ├── zinc-GCN+GPSE.yaml │ ├── zinc-GCN+LapPE+RWSE.yaml │ ├── zinc-GCN+LapPE.yaml │ ├── zinc-GCN+RWSE.yaml │ ├── zinc-GCN+none.yaml │ ├── zinc-GCN+rand.yaml │ ├── zinc-GIN+AllPSE.yaml │ ├── zinc-GIN+GPSE.yaml │ ├── zinc-GIN+LapPE+RWSE.yaml │ ├── zinc-GIN+LapPE.yaml │ ├── zinc-GIN+RWSE.yaml │ ├── zinc-GIN+none.yaml │ ├── zinc-GIN+rand.yaml │ ├── zinc-GPS+AllPSE.yaml │ ├── zinc-GPS+GPSE.yaml │ ├── zinc-GPS+LapPE+RWSE.yaml │ ├── zinc-GPS+LapPE.yaml │ ├── zinc-GPS+RWSE.yaml │ ├── zinc-GPS+none.yaml │ ├── zinc-GPS+rand.yaml │ ├── zinc-GatedGCN+AllPSE.yaml │ ├── zinc-GatedGCN+GPSE.yaml │ ├── zinc-GatedGCN+LapPE+RWSE.yaml │ ├── zinc-GatedGCN+LapPE.yaml │ ├── zinc-GatedGCN+RWSE.yaml │ ├── zinc-GatedGCN+none.yaml │ ├── zinc-GatedGCN+rand.yaml │ ├── zinc-Transformer+AllPSE.yaml │ ├── zinc-Transformer+GPSE.yaml │ ├── zinc-Transformer+LapPE+RWSE.yaml │ ├── zinc-Transformer+LapPE.yaml │ ├── zinc-Transformer+RWSE.yaml │ ├── zinc-Transformer+none.yaml │ └── zinc-Transformer+rand.yaml ├── molnet_bench │ ├── bace-GINE+AllPSE.yaml │ ├── bace-GINE+GPSE.yaml │ ├── bace-GINE+GraphLog.yaml │ ├── bace-GINE+LapPE+RWSE.yaml │ ├── bace-GINE+LapPE.yaml │ ├── bace-GINE+RWSE.yaml │ ├── bbbp-GINE+AllPSE.yaml │ ├── bbbp-GINE+GPSE.yaml │ ├── bbbp-GINE+GraphLog.yaml │ ├── bbbp-GINE+LapPE+RWSE.yaml │ ├── bbbp-GINE+LapPE.yaml │ ├── bbbp-GINE+RWSE.yaml │ ├── clintox-GINE+AllPSE.yaml │ ├── clintox-GINE+GPSE.yaml │ ├── clintox-GINE+GraphLog.yaml │ ├── clintox-GINE+LapPE+RWSE.yaml │ ├── clintox-GINE+LapPE.yaml │ ├── clintox-GINE+RWSE.yaml │ ├── hiv-GINE+AllPSE.yaml │ ├── hiv-GINE+GPSE.yaml │ ├── hiv-GINE+GraphLog.yaml │ ├── hiv-GINE+LapPE+RWSE.yaml │ ├── hiv-GINE+LapPE.yaml │ ├── hiv-GINE+RWSE.yaml │ ├── muv-GINE+AllPSE.yaml │ ├── muv-GINE+GPSE.yaml │ ├── muv-GINE+GraphLog.yaml │ ├── muv-GINE+LapPE+RWSE.yaml │ ├── muv-GINE+LapPE.yaml │ ├── muv-GINE+RWSE.yaml │ ├── sider-GINE+AllPSE.yaml │ ├── sider-GINE+GPSE.yaml │ ├── sider-GINE+GraphLog.yaml │ ├── sider-GINE+LapPE+RWSE.yaml │ ├── sider-GINE+LapPE.yaml │ ├── sider-GINE+RWSE.yaml │ ├── tox21-GINE+AllPSE.yaml │ ├── tox21-GINE+GPSE.yaml │ ├── tox21-GINE+GraphLog.yaml │ ├── tox21-GINE+LapPE+RWSE.yaml │ ├── tox21-GINE+LapPE.yaml │ ├── tox21-GINE+RWSE.yaml │ ├── toxcast-GINE+AllPSE.yaml │ ├── toxcast-GINE+GPSE.yaml │ ├── toxcast-GINE+GraphLog.yaml │ ├── toxcast-GINE+LapPE+RWSE.yaml │ ├── toxcast-GINE+LapPE.yaml │ └── toxcast-GINE+RWSE.yaml ├── node_bench │ ├── arxiv-GNN+GPSE.yaml │ ├── arxiv-GNN+LapPE.yaml │ ├── arxiv-GNN+none.yaml │ ├── arxiv-GPS+GPSE.yaml │ ├── arxiv-GPS+LapPE.yaml │ ├── arxiv-GPS+none.yaml │ ├── arxiv-Transformer+GPSE.yaml │ ├── arxiv-Transformer+LapPE.yaml │ ├── arxiv-Transformer+none.yaml │ ├── proteins-GNN+GPSE.yaml │ ├── proteins-GNN+LapPE.yaml │ ├── proteins-GNN+none.yaml │ ├── proteins-GPS+GPSE.yaml │ ├── proteins-GPS+LapPE.yaml │ ├── proteins-GPS+none.yaml │ ├── proteins-Transformer+GPSE.yaml │ ├── proteins-Transformer+LapPE.yaml │ └── proteins-Transformer+none.yaml ├── pretrain │ ├── gpse_chembl.yaml │ ├── gpse_cifar10.yaml │ ├── gpse_geom.yaml │ ├── gpse_mnist.yaml │ ├── gpse_molpcba.yaml │ ├── gpse_molpcba_ablation_template.yaml │ ├── gpse_pcqm4mv2.yaml │ └── gpse_zinc.yaml ├── transfer_bench │ ├── cifar10-GPS+AllPSE.yaml │ ├── cifar10-GPS+GPSE.yaml │ ├── cifar10-GPS+LapPE+RWSE.yaml │ ├── cifar10-GPS+none.yaml │ ├── mnist-GPS+AllPSE.yaml │ ├── mnist-GPS+GPSE.yaml │ ├── mnist-GPS+LapPE+RWSE.yaml │ ├── mnist-GPS+none.yaml │ ├── peptides-func-GCN+AllPSE.yaml │ ├── peptides-func-GCN+GPSE.yaml │ ├── peptides-func-GCN+LapPE.yaml │ ├── peptides-func-GCN+RWSE.yaml │ ├── peptides-func-GPS+AllPSE.yaml │ ├── peptides-func-GPS+GPSE.yaml │ ├── peptides-func-GPS+LapPE+RWSE.yaml │ ├── peptides-func-GPS+none.yaml │ ├── peptides-struct-GCN+AllPSE.yaml │ ├── peptides-struct-GCN+GPSE.yaml │ ├── peptides-struct-GCN+LapPE.yaml │ ├── peptides-struct-GCN+RWSE.yaml │ ├── peptides-struct-GPS+AllPSE.yaml │ ├── peptides-struct-GPS+GPSE.yaml │ ├── peptides-struct-GPS+LapPE+RWSE.yaml │ └── peptides-struct-GPS+none.yaml └── wl_bench │ ├── csl-GIN+GPSE.yaml │ ├── csl-GIN+LapPE.yaml │ ├── csl-GIN+RWSE.yaml │ ├── csl-GIN+none.yaml │ ├── csl-GIN+rand.yaml │ ├── exp-GIN+GPSE.yaml │ ├── exp-GIN+LapPE.yaml │ ├── exp-GIN+RWSE.yaml │ ├── exp-GIN+none.yaml │ ├── exp-GIN+rand.yaml │ └── toywl-GPS+GPSE_v9.yaml ├── data └── Abboud2020 │ ├── CEXP │ └── GRAPHSAT.txt │ ├── EXP │ └── GRAPHSAT.txt │ └── README.md ├── graphgym ├── __init__.py ├── act │ ├── __init__.py │ └── example.py ├── agg_runs.py ├── config │ ├── __init__.py │ ├── custom_gnn_config.py │ ├── dataset_config.py │ ├── defaults_config.py │ ├── example.py │ ├── gt_config.py │ ├── hash_feat.py │ ├── optimizers_config.py │ ├── posenc_config.py │ ├── pretrained_config.py │ ├── split_config.py │ ├── ssl_config.py │ └── wandb_config.py ├── encoder │ ├── __init__.py │ ├── ast_encoder.py │ ├── combined_encoder.py │ ├── composed_encoders.py │ ├── dummy_edge_encoder.py │ ├── equivstable_laplace_pos_encoder.py │ ├── example.py │ ├── gnn_encoder.py │ ├── graphlog_encoder.py │ ├── kernel_pos_encoder.py │ ├── laplace_pos_encoder.py │ ├── linear_edge_encoder.py │ ├── linear_node_encoder.py │ ├── ppa_encoder.py │ ├── random_encoder.py │ ├── signnet_pos_encoder.py │ ├── type_dict_encoder.py │ └── voc_superpixels_encoder.py ├── finetuning.py ├── head │ ├── __init__.py │ ├── example.py │ ├── identity.py │ ├── inductive_edge.py │ ├── inductive_hybrid.py │ ├── inductive_node.py │ ├── ogb_code_graph.py │ └── san_graph.py ├── layer │ ├── __init__.py │ ├── bigbird_layer.py │ ├── example.py │ ├── gatconv.py │ ├── gatedgcn_layer.py │ ├── gatv2conv.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 │ │ ├── er_dataset.py │ │ ├── malnet_tiny.py │ │ ├── open_mol_graph.py │ │ ├── pcqm4mv2_contact.py │ │ ├── peptides_functional.py │ │ ├── peptides_structural.py │ │ ├── spectre.py │ │ ├── synthetic_wl.py │ │ └── voc_superpixels.py │ ├── master_loader.py │ ├── ogbg_code2_utils.py │ └── split_generator.py ├── logger.py ├── loss │ ├── __init__.py │ ├── cosim.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 ├── patches.py ├── pooling │ ├── __init__.py │ └── example.py ├── pretrained_config.py ├── stage │ ├── __init__.py │ └── example.py ├── train │ ├── __init__.py │ ├── custom_train.py │ └── example.py ├── transform │ ├── __init__.py │ ├── cycle_counts.py │ ├── gnn_hash.py │ ├── posenc_stats.py │ └── transforms.py ├── utils.py └── wl_dataset.py ├── main.py ├── requirements.txt ├── run ├── cancel_all.sh ├── mol_bench.sh ├── molnet_bench.sh ├── node_bench.sh ├── pretrain_ablation_architectures.sh ├── pretrain_ablation_petasks.sh ├── pretrain_ablation_train_size.sh ├── transfer_bench.sh ├── wl_bench.sh ├── wrapper.sb ├── wrapper_mila.sb ├── wrapper_mila_large.sb └── wrapper_msuicer.sb ├── unittests ├── __init__.py ├── test_cycle_counts.py ├── test_eigvecs.py └── test_negate_edge_index.py └── viz ├── wl_test.py └── wl_viz.ipynb /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/G-Taxonomy-Workgroup/GPSE/HEAD/.gitignore -------------------------------------------------------------------------------- /GPSE.png: 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