├── .gitignore ├── LICENSE ├── LPE ├── README.md ├── configs │ ├── CLUSTER │ │ └── optimized │ ├── MOLHIV │ │ ├── optimized │ │ ├── optimized_spectral_full_1 │ │ └── optimized_spectral_sparse_1 │ ├── PATTERN │ │ ├── ablation │ │ │ ├── full │ │ │ │ ├── 1e-1 │ │ │ │ │ └── node │ │ │ │ ├── 1e-2 │ │ │ │ │ └── node │ │ │ │ ├── 1e-3 │ │ │ │ │ └── node │ │ │ │ ├── 1e-4 │ │ │ │ │ └── node │ │ │ │ ├── 1e-5 │ │ │ │ │ └── node │ │ │ │ ├── 1e-6 │ │ │ │ │ └── node │ │ │ │ ├── 1e-7 │ │ │ │ │ └── node │ │ │ │ ├── 1e-8 │ │ │ │ │ └── node │ │ │ │ └── none │ │ │ └── sparse │ │ │ │ ├── node │ │ │ │ └── none │ │ ├── optimized │ │ ├── optimized_spectral_full_1 │ │ └── optimized_spectral_sparse_1 │ └── ZINC │ │ ├── ablation │ │ ├── full │ │ │ ├── 1e-2 │ │ │ │ └── node │ │ │ ├── 1e-3 │ │ │ │ └── node │ │ │ ├── 1e-4 │ │ │ │ └── node │ │ │ ├── 1e-5 │ │ │ │ └── node │ │ │ ├── 1e-6 │ │ │ │ └── node │ │ │ ├── 1e-7 │ │ │ │ └── node │ │ │ ├── 1e-8 │ │ │ │ └── node │ │ │ └── none │ │ └── sparse │ │ │ ├── node │ │ │ └── none │ │ ├── optimized │ │ ├── optimized_gat_1 │ │ ├── optimized_gat_feta_1 │ │ └── optimized_gat_feta_alllayers_1 ├── data │ ├── SBMs.py │ ├── data.py │ ├── molecules.py │ ├── molhiv.py │ ├── script_download_SBMs.sh │ ├── script_download_all_datasets.sh │ ├── script_download_molecules.sh │ ├── transformer_spectrum.py │ └── tudatasets.py ├── layers │ ├── GT_layer_bkp.py │ ├── gat_feta_layer.py │ ├── gat_layer.py │ ├── graph_transformer_layer.py │ ├── graph_transformer_spectra_layer.py │ └── mlp_readout_layer.py ├── main_SBMs_node_classification.py ├── main_TU_graph_classification.py ├── main_ZINC_graph_regression.py ├── main_molhiv.py ├── misc │ ├── download_datasets.md │ └── env_installation.md ├── nets │ ├── SBMs_node_classification │ │ ├── SAN.py │ │ ├── SAN_EdgeLPE.py │ │ ├── SAN_NodeLPE.py │ │ ├── SAN_NodeSpectra.py │ │ └── load_net.py │ ├── TU_graph_classification │ │ ├── SAN.py │ │ ├── SAN_EdgeLPE.py │ │ ├── SAN_NodeLPE.py │ │ ├── SAN_NodeSpectra.py │ │ └── load_net.py │ ├── ZINC_graph_regression │ │ ├── SAN.py │ │ ├── SAN_EdgeLPE.py │ │ ├── SAN_NodeLPE.py │ │ ├── SAN_NodeSpectra.py │ │ ├── gat_feta_net.py │ │ ├── gat_net.py │ │ └── load_net.py │ └── molhiv_graph_regression │ │ ├── SAN.py │ │ ├── SAN_EdgeLPE.py │ │ ├── SAN_NodeLPE.py │ │ ├── SAN_NodeSpectra.py │ │ └── load_net.py ├── requirements.txt ├── train │ ├── metrics.py │ ├── train_SBMs_node_classification.py │ ├── train_TU_graph_classification.py │ ├── train_ZINC_graph_regression.py │ └── train_molhiv.py └── utils.py ├── LSPE ├── .gitignore ├── configs │ ├── GatedGCN_MOLPCBA_LSPE.json │ ├── GatedGCN_MOLPCBA_LapPE.json │ ├── GatedGCN_MOLPCBA_NoPE.json │ ├── GatedGCN_MOLTOX21_LSPE.json │ ├── GatedGCN_MOLTOX21_LapPE.json │ ├── GatedGCN_MOLTOX21_NoPE.json │ ├── GatedGCN_ZINC_LSPE.json │ ├── GatedGCN_ZINC_LSPE_withLapEigLoss.json │ ├── GatedGCN_ZINC_LapPE.json │ ├── GatedGCN_ZINC_NoPE.json │ ├── GraphiT_MOLTOX21_LSPE.json │ ├── GraphiT_MOLTOX21_NoPE.json │ ├── GraphiT_SBM_PATTERN_LSPE.json │ ├── GraphiT_ZINC_LSPE.json │ ├── GraphiT_ZINC_NoPE.json │ ├── PNA_MOLPCBA_LSPE.json │ ├── PNA_MOLPCBA_NoPE.json │ ├── PNA_MOLTOX21_LSPE.json │ ├── PNA_MOLTOX21_LSPE_withLapEigLoss.json │ ├── PNA_MOLTOX21_NoPE.json │ ├── PNA_ZINC_LSPE.json │ ├── PNA_ZINC_NoPE.json │ ├── SAN_MOLTOX21_LSPE.json │ ├── SAN_MOLTOX21_NoPE.json │ ├── SAN_ZINC_LSPE.json │ └── SAN_ZINC_NoPE.json ├── data │ ├── SBMs.py │ ├── data.py │ ├── molecules.py │ ├── ogb_mol.py │ ├── script_download_ZINC.sh │ └── tudatasets.py ├── environment_cpu.yml ├── environment_gpu.yml ├── layers │ ├── gatedgcn_layer.py │ ├── gatedgcn_lspe_layer.py │ ├── graphit_gt_layer.py │ ├── graphit_gt_lspe_layer.py │ ├── graphit_spectra_lspe_layer.py │ ├── mlp_readout_layer.py │ ├── pna_layer.py │ ├── pna_lspe_layer.py │ ├── pna_utils.py │ ├── san_gt_layer.py │ └── san_gt_lspe_layer.py ├── main_OGBMOL_graph_classification.py ├── main_SBM_node_classification.py ├── main_TU_graph_classification.py ├── main_ZINC_graph_regression.py ├── nets │ ├── OGBMOL_graph_classification │ │ ├── gatedgcn_net.py │ │ ├── graphit_net.py │ │ ├── graphit_spectra_net.py │ │ ├── load_net.py │ │ ├── pna_net.py │ │ └── san_net.py │ ├── SBM_node_classification │ │ ├── graphit_net.py │ │ ├── graphit_spectra_net.py │ │ └── load_net.py │ ├── TU_graph_classification │ │ ├── graphit_net.py │ │ ├── graphit_spectra_net.py │ │ └── load_net.py │ └── ZINC_graph_regression │ │ ├── gatedgcn_net.py │ │ ├── graphit_net.py │ │ ├── graphit_spectra_net.py │ │ ├── load_net.py │ │ ├── pna_net.py │ │ └── san_net.py ├── train │ ├── _train_TU_graph_classification.py │ ├── metrics.py │ ├── train_OGBMOL_graph_classification.py │ ├── train_SBM_node_classification.py │ ├── train_ZINC_graph_regression.py │ └── train_tu_graph_classification.py └── utils │ ├── cleaner_main.py │ ├── plot_util.py │ └── visualize_RWPE_studies.ipynb ├── Makefile ├── README.md ├── experiments ├── data_utils.py ├── gckn_sup.py ├── gckn_sup_cv.py ├── run_transformer.py ├── run_transformer_SBM_cv.py ├── run_transformer_cv.py ├── run_transformer_gckn.py ├── run_transformer_gckn_SBM_cv.py ├── run_transformer_gckn_cv.py ├── run_transformer_gckn_gengcn.py ├── run_transformer_gckn_gengcn_SBM_cv.py ├── run_transformer_gckn_gengcn_cv.py ├── run_transformer_gckn_gengcn_molpcba.py ├── run_transformer_gckn_molhiv.py ├── run_transformer_gcn.py ├── run_transformer_gcn_cv.py ├── run_transformer_gengcn.py ├── run_transformer_gengcn_SBM_cv.py ├── run_transformer_gengcn_cv.py ├── run_transformer_gengcn_molhiv.py ├── run_transformer_gengcn_molpcba.py ├── run_transformer_gengcn_pcqm4m.py ├── run_transformer_molhiv.py └── visu_attention.py ├── figures ├── FeTA.png └── gatv2_spectral_response.png ├── gckn ├── __init__.py ├── data.py ├── data_io.py ├── dynamic_pooling │ ├── __init__.py │ ├── pooling.cpp │ ├── pooling.py │ ├── pooling_cuda.cpp │ └── pooling_cuda_kernel.cu ├── gckn_fast │ ├── __init__.py │ ├── gckn_fast.cpp │ ├── gckn_fast.py │ ├── gckn_fast_cuda.cpp │ └── gckn_fast_cuda_kernel.cu ├── graphs │ ├── __init__.py │ ├── graphs_fast.pyx │ └── setup.py ├── kernels.py ├── layers.py ├── loss.py ├── models.py ├── ops.py ├── path_conv_agg.py ├── path_kernel.py ├── setup.py └── utils.py ├── s_env ├── setup.py ├── setup_torch.py └── transformer ├── ChebNetDynamic.py ├── GenGCN.py ├── __init__.py ├── data.py ├── gckn_pe.py ├── layers.py ├── models.py ├── position_encoding.py └── utils.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ansonb/FeTA_TMLR/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ansonb/FeTA_TMLR/HEAD/LICENSE -------------------------------------------------------------------------------- /LPE/README.md: -------------------------------------------------------------------------------- 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