├── .gitignore ├── LICENSE ├── README.md ├── configs ├── SBMs_GraphTransformer_CLUSTER_500k_full_graph_BN.json ├── SBMs_GraphTransformer_CLUSTER_500k_full_graph_LN.json ├── SBMs_GraphTransformer_CLUSTER_500k_sparse_graph_BN.json ├── SBMs_GraphTransformer_CLUSTER_500k_sparse_graph_LN.json ├── SBMs_GraphTransformer_LapPE_CLUSTER_500k_full_graph_BN.json ├── SBMs_GraphTransformer_LapPE_CLUSTER_500k_full_graph_LN.json ├── SBMs_GraphTransformer_LapPE_CLUSTER_500k_sparse_graph_BN.json ├── SBMs_GraphTransformer_LapPE_CLUSTER_500k_sparse_graph_LN.json ├── SBMs_GraphTransformer_LapPE_PATTERN_500k_full_graph_BN.json ├── SBMs_GraphTransformer_LapPE_PATTERN_500k_full_graph_LN.json ├── SBMs_GraphTransformer_LapPE_PATTERN_500k_sparse_graph_BN.json ├── SBMs_GraphTransformer_LapPE_PATTERN_500k_sparse_graph_LN.json ├── SBMs_GraphTransformer_PATTERN_500k_full_graph_BN.json ├── SBMs_GraphTransformer_PATTERN_500k_full_graph_LN.json ├── SBMs_GraphTransformer_PATTERN_500k_sparse_graph_BN.json ├── SBMs_GraphTransformer_PATTERN_500k_sparse_graph_LN.json ├── ablation_SBMs_GraphTransformer_WLPE_CLUSTER_500k_sparse_graph_BN.json ├── ablation_SBMs_GraphTransformer_WLPE_PATTERN_500k_sparse_graph_BN.json ├── ablation_molecules_GraphTransformer_WLPE_ZINC_500k_sparse_graph_BN.json ├── molecules_GraphTransformer_LapPE_ZINC_500k_full_graph_BN.json ├── molecules_GraphTransformer_LapPE_ZINC_500k_full_graph_LN.json ├── molecules_GraphTransformer_LapPE_ZINC_500k_sparse_graph_BN.json ├── molecules_GraphTransformer_LapPE_ZINC_500k_sparse_graph_LN.json ├── molecules_GraphTransformer_ZINC_500k_full_graph_BN.json ├── molecules_GraphTransformer_ZINC_500k_full_graph_LN.json ├── molecules_GraphTransformer_ZINC_500k_sparse_graph_BN.json └── molecules_GraphTransformer_ZINC_500k_sparse_graph_LN.json ├── data ├── SBMs.py ├── SBMs │ └── meta.txt ├── data.py ├── molecules.py ├── molecules │ ├── test.index │ ├── train.index │ └── val.index ├── script_download_SBMs.sh ├── script_download_all_datasets.sh └── script_download_molecules.sh ├── docs ├── 01_benchmark_installation.md ├── 02_download_datasets.md ├── 03_run_codes.md └── graph_transformer.png ├── environment_cpu.yml ├── environment_gpu.yml ├── layers ├── graph_transformer_edge_layer.py ├── graph_transformer_layer.py └── mlp_readout_layer.py ├── main_SBMs_node_classification.py ├── main_molecules_graph_regression.py ├── nets ├── SBMs_node_classification │ ├── graph_transformer_net.py │ └── load_net.py └── molecules_graph_regression │ ├── graph_transformer_net.py │ └── load_net.py ├── scripts ├── SBMs │ ├── script_main_SBMs_node_classification_CLUSTER_500k.sh │ ├── script_main_SBMs_node_classification_CLUSTER_500k_WL_ablation.sh │ ├── script_main_SBMs_node_classification_PATTERN_500k.sh │ └── script_main_SBMs_node_classification_PATTERN_500k_WL_ablation.sh ├── StatisticalResults │ └── generate_statistics_molecules_graph_regression_ZINC.ipynb ├── TensorBoard │ └── script_tensorboard.sh └── ZINC │ ├── script_main_molecules_graph_regression_ZINC_500k.sh │ └── script_main_molecules_graph_regression_ZINC_500k_WL_ablation.sh └── train ├── metrics.py ├── train_SBMs_node_classification.py └── train_molecules_graph_regression.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/graphdeeplearning/graphtransformer/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/graphdeeplearning/graphtransformer/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/graphdeeplearning/graphtransformer/HEAD/README.md -------------------------------------------------------------------------------- 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