├── .gitignore ├── .readthedocs.yaml ├── .travis.yml ├── LICENSE ├── MANIFEST.in ├── README.md ├── benchmarks └── xgraph │ ├── RandomSelection.py │ ├── Readme.md │ ├── config │ ├── config.yaml │ ├── datasets │ │ ├── ba_2motifs.yaml │ │ ├── ba_community.yaml │ │ ├── ba_lrp.yaml │ │ ├── ba_shapes.yaml │ │ ├── bace.yaml │ │ ├── bbbp.yaml │ │ ├── clintox.yaml │ │ ├── graph_sst2.yaml │ │ ├── graph_sst5.yaml │ │ ├── tox21.yaml │ │ ├── tree_cycle.yaml │ │ ├── tree_grid.yaml │ │ └── twitter.yaml │ ├── explainers │ │ ├── deep_lift.yaml │ │ ├── gnn_explainer.yaml │ │ ├── gnn_gi.yaml │ │ ├── gnn_lrp.yaml │ │ ├── grad_cam.yaml │ │ ├── pgexplainer.yaml │ │ ├── random_explainer.yaml │ │ └── subgraphx.yaml │ └── models │ │ └── gcn.yaml │ ├── dataset.py │ ├── deep_lift.py │ ├── gnnNets.py │ ├── gnn_explainer.py │ ├── gnn_gi.py │ ├── gnn_lrp.py │ ├── grad_cam.py │ ├── imgs │ ├── fidelity.png │ ├── fidelity_inv.png │ └── xgraph.jpg │ ├── pgexplainer_edges.py │ ├── random_explain.py │ ├── subgraphx.py │ ├── train_gnns.py │ └── utils.py ├── dig ├── __init__.py ├── auggraph │ ├── __init__.py │ ├── dataset │ │ ├── __init__.py │ │ └── aug_dataset.py │ └── method │ │ ├── GraphAug │ │ ├── __init__.py │ │ ├── aug │ │ │ ├── __init__.py │ │ │ ├── aug_encoder.py │ │ │ ├── aug_utils.py │ │ │ ├── augmenter.py │ │ │ ├── edge_per.py │ │ │ ├── node_drop.py │ │ │ └── node_fm.py │ │ ├── constants │ │ │ ├── __init__.py │ │ │ ├── conf_params.py │ │ │ └── enums.py │ │ ├── model │ │ │ ├── __init__.py │ │ │ ├── classifier.py │ │ │ ├── genet.py │ │ │ ├── gmnet.py │ │ │ └── reward_generator.py │ │ ├── runner_aug_cls.py │ │ ├── runner_generator.py │ │ └── runner_reward_gen.py │ │ ├── SMixup │ │ ├── __init__.py │ │ ├── model │ │ │ ├── GCN.py │ │ │ ├── GIN.py │ │ │ ├── GMNET.py │ │ │ ├── GraphMatching.py │ │ │ └── __init__.py │ │ ├── smixup.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── sinkhorn.py │ │ │ └── utils.py │ │ └── __init__.py ├── fairgraph │ ├── __init__.py │ ├── dataset │ │ ├── __init__.py │ │ └── fairgraph_dataset.py │ ├── method │ │ ├── Graphair │ │ │ ├── GCN.py │ │ │ ├── __init__.py │ │ │ ├── aug_module.py │ │ │ ├── classifier.py │ │ │ └── graphair.py │ │ ├── __init__.py │ │ └── run.py │ └── utils │ │ ├── __init__.py │ │ └── utils.py ├── ggraph │ ├── __init__.py │ ├── dataset │ │ ├── PygDataset.py │ │ ├── __init__.py │ │ ├── config.csv │ │ └── ggraph_dataset.py │ ├── evaluation │ │ ├── __init__.py │ │ └── metric.py │ ├── method │ │ ├── GraphAF │ │ │ ├── __init__.py │ │ │ ├── graphaf.py │ │ │ ├── model │ │ │ │ ├── __init__.py │ │ │ │ ├── graphaf.py │ │ │ │ ├── graphflow.py │ │ │ │ ├── graphflow_con_rl.py │ │ │ │ ├── graphflow_rl.py │ │ │ │ ├── model_utils.py │ │ │ │ ├── rgcn.py │ │ │ │ └── st_net.py │ │ │ └── train_utils.py │ │ ├── GraphDF │ │ │ ├── __init__.py │ │ │ ├── graphdf.py │ │ │ ├── model │ │ │ │ ├── __init__.py │ │ │ │ ├── df_utils.py │ │ │ │ ├── disgraphaf.py │ │ │ │ ├── graphflow.py │ │ │ │ ├── graphflow_con_rl.py │ │ │ │ ├── graphflow_rl.py │ │ │ │ ├── rgcn.py │ │ │ │ └── st_net.py │ │ │ └── train_utils.py │ │ ├── GraphEBM │ │ │ ├── __init__.py │ │ │ ├── energy_func.py │ │ │ ├── graphebm.py │ │ │ └── util.py │ │ ├── JTVAE │ │ │ ├── __init__.py │ │ │ ├── fast_jtnn │ │ │ │ ├── __init__.py │ │ │ │ ├── chemutils.py │ │ │ │ ├── datautils.py │ │ │ │ ├── jtmpn.py │ │ │ │ ├── jtmpn_bo.py │ │ │ │ ├── jtnn_dec.py │ │ │ │ ├── jtnn_enc.py │ │ │ │ ├── jtnn_enc_bo.py │ │ │ │ ├── jtnn_vae.py │ │ │ │ ├── jtnn_vae_bo.py │ │ │ │ ├── jtprop_vae.py │ │ │ │ ├── mol_tree.py │ │ │ │ ├── mpn.py │ │ │ │ ├── nnutils.py │ │ │ │ ├── sascorer.py │ │ │ │ └── vocab.py │ │ │ └── jtvae.py │ │ ├── __init__.py │ │ └── generator.py │ └── utils │ │ ├── __init__.py │ │ ├── environment.py │ │ ├── fpscores.pkl.gz │ │ ├── gen_mol_from_one_shot_tensor.py │ │ └── sascorer.py ├── ggraph3D │ ├── __init__.py │ ├── dataset │ │ ├── __init__.py │ │ └── ggraph3D_dataset.py │ ├── evaluation │ │ ├── __init__.py │ │ └── metric.py │ ├── method │ │ ├── G_SphereNet │ │ │ ├── __init__.py │ │ │ ├── gspherenet.py │ │ │ └── model │ │ │ │ ├── __init__.py │ │ │ │ ├── att.py │ │ │ │ ├── features.py │ │ │ │ ├── geometric_computing.py │ │ │ │ ├── net_utils.py │ │ │ │ ├── spherenet.py │ │ │ │ └── sphgen.py │ │ └── __init__.py │ └── utils │ │ ├── __init__.py │ │ ├── eval_bond_mmd_utils.py │ │ ├── eval_prop_utils.py │ │ └── eval_validity_utils.py ├── lsgraph │ ├── __init__.py │ ├── dataset │ │ ├── __init__.py │ │ ├── get_data.py │ │ └── loader.py │ └── method │ │ ├── FM.py │ │ ├── GraphFMOB │ │ ├── __init__.py │ │ ├── csrc │ │ │ ├── cpu │ │ │ │ ├── relabel_cpu.cpp │ │ │ │ └── relabel_cpu.h │ │ │ ├── cuda │ │ │ │ ├── sync_cuda.cu │ │ │ │ └── sync_cuda.h │ │ │ ├── relabel.cpp │ │ │ ├── sync.cpp │ │ │ └── thread.h │ │ ├── history.py │ │ ├── loader.py │ │ ├── metis.py │ │ ├── models │ │ │ ├── __init__.py │ │ │ ├── base.py │ │ │ ├── gcn.py │ │ │ ├── gcn2.py │ │ │ ├── pna.py │ │ │ └── pna_jk.py │ │ ├── pool.py │ │ └── utils.py │ │ └── __init__.py ├── oodgraph │ ├── __init__.py │ ├── good_arxiv.py │ ├── good_cbas.py │ ├── good_cmnist.py │ ├── good_cora.py │ ├── good_hiv.py │ ├── good_motif.py │ ├── good_pcba.py │ └── good_zinc.py ├── sslgraph │ ├── __init__.py │ ├── dataset │ │ ├── TUDataset.py │ │ ├── __init__.py │ │ ├── datasets.py │ │ └── feat_expansion.py │ ├── evaluation │ │ ├── __init__.py │ │ ├── eval_graph.py │ │ └── eval_node.py │ ├── method │ │ ├── __init__.py │ │ └── contrastive │ │ │ ├── __init__.py │ │ │ ├── model │ │ │ ├── __init__.py │ │ │ ├── contrastive.py │ │ │ ├── grace.py │ │ │ ├── graphcl.py │ │ │ ├── infograph.py │ │ │ ├── mvgrl.py │ │ │ └── pgrace.py │ │ │ ├── objectives │ │ │ ├── __init__.py │ │ │ ├── infonce.py │ │ │ └── jse.py │ │ │ └── views_fn │ │ │ ├── __init__.py │ │ │ ├── combination.py │ │ │ ├── feature.py │ │ │ ├── sample.py │ │ │ └── structure.py │ └── utils │ │ ├── __init__.py │ │ ├── adaptive.py │ │ ├── encoders.py │ │ └── seed.py ├── threedgraph │ ├── __init__.py │ ├── dataset │ │ ├── ECdataset.py │ │ ├── FOLDdataset.py │ │ ├── PygMD17.py │ │ ├── PygQM93D.py │ │ ├── README.md │ │ └── __init__.py │ ├── evaluation │ │ ├── __init__.py │ │ └── eval.py │ ├── method │ │ ├── __init__.py │ │ ├── comenet │ │ │ ├── __init__.py │ │ │ ├── comenet.py │ │ │ ├── features.py │ │ │ └── ocp │ │ │ │ ├── ComENetIS2REResults.jpg │ │ │ │ ├── IS2RETrainedModelWeights.pt │ │ │ │ ├── README.md │ │ │ │ ├── comenet-ocp.py │ │ │ │ ├── comenet.yml │ │ │ │ └── utils.py │ │ ├── dimenetpp │ │ │ ├── __init__.py │ │ │ ├── dimenetpp.py │ │ │ └── features.py │ │ ├── pronet │ │ │ ├── __init__.py │ │ │ ├── features.py │ │ │ └── pronet.py │ │ ├── run.py │ │ ├── schnet │ │ │ ├── __init__.py │ │ │ └── schnet.py │ │ └── spherenet │ │ │ ├── __init__.py │ │ │ ├── features.py │ │ │ └── spherenet.py │ └── utils │ │ ├── __init__.py │ │ └── geometric_computing.py ├── version.py └── xgraph │ ├── __init__.py │ ├── dataset │ ├── __init__.py │ ├── mol_dataset.py │ ├── nlp_dataset.py │ ├── syn_dataset.py │ └── utils_dataset.py │ ├── evaluation │ ├── Readme.md │ ├── __init__.py │ ├── defi.py │ └── metrics.py │ ├── method │ ├── __init__.py │ ├── base_explainer.py │ ├── deeplift.py │ ├── flowx.py │ ├── gnn_gi.py │ ├── gnn_lrp.py │ ├── gnnexplainer.py │ ├── gradcam.py │ ├── pgexplainer.py │ ├── shapley.py │ ├── subgraphx.py │ └── utils │ │ ├── __init__.py │ │ └── symmetric_edge_mask.py │ ├── models │ ├── __init__.py │ ├── ext │ │ ├── __init__.py │ │ └── deeplift │ │ │ ├── __init__.py │ │ │ ├── deep_lift.py │ │ │ └── layer_deep_lift.py │ ├── gradient_utils.py │ ├── model_manager.py │ ├── models.py │ └── utils.py │ └── utils │ ├── __init__.py │ ├── compatibility.py │ └── init.py ├── docs ├── .DS_Store ├── Makefile ├── environment.yaml ├── imgs │ ├── DIG-logo.jpg │ ├── DIG-overview.png │ └── GOOD-datasets.png ├── make.bat └── source │ ├── 3dgraph │ ├── dataset.rst │ ├── evaluation.rst │ ├── method.rst │ └── utils.rst │ ├── auggraph │ ├── dataset.rst │ └── method.rst │ ├── conf.py │ ├── contribution │ └── instruction.rst │ ├── fairgraph │ ├── dataset.rst │ └── method.rst │ ├── ggraph │ ├── dataset.rst │ ├── evaluation.rst │ ├── method.rst │ └── utils.rst │ ├── ggraph3d │ ├── dataset.rst │ ├── evaluation.rst │ ├── method.rst │ └── utils.rst │ ├── index.rst │ ├── intro │ ├── installation.rst │ └── introduction.rst │ ├── oodgraph │ └── good.rst │ ├── sslgraph │ ├── dataset.rst │ ├── evaluation.rst │ ├── method.rst │ └── utils.rst │ ├── tutorials │ ├── fairgraph.rst │ ├── graphdf.rst │ ├── imgs │ │ ├── subgraphx_explanation.png │ │ └── subgraphx_ori_graph.png │ ├── oodgraph.rst │ ├── sslgraph.rst │ ├── subgraphx.rst │ └── threedgraph.rst │ └── xgraph │ ├── dataset.rst │ ├── evaluation.rst │ ├── method.rst │ └── utils.rst ├── examples ├── README.md ├── auggraph │ ├── GraphAug │ │ ├── conf │ │ │ ├── aug_cls_conf.py │ │ │ ├── generator_conf.py │ │ │ └── reward_gen_conf.py │ │ ├── run_aug_cls.py │ │ ├── run_generator.py │ │ └── run_reward_gen.py │ └── SMixup │ │ └── run.py ├── fairgraph │ └── Graphair │ │ ├── run_graphair_nba.py │ │ └── run_graphair_pokec.py ├── ggraph │ ├── GraphAF │ │ ├── README.md │ │ ├── config │ │ │ ├── const_prop_opt_graphaf_config_dict.json │ │ │ ├── prop_opt_plogp_config_dict.json │ │ │ ├── prop_opt_qed_config_dict.json │ │ │ ├── rand_gen_qm9_config_dict.json │ │ │ └── rand_gen_zinc250k_config_dict.json │ │ ├── figs │ │ │ └── graphaf.png │ │ ├── run_const_prop_opt.py │ │ ├── run_prop_opt.py │ │ └── run_rand_gen.py │ ├── GraphDF │ │ ├── README.md │ │ ├── config │ │ │ ├── const_prop_opt_graphaf_config_dict.json │ │ │ ├── const_prop_opt_jt_config_dict.json │ │ │ ├── prop_opt_plogp_config_dict.json │ │ │ ├── prop_opt_qed_config_dict.json │ │ │ ├── rand_gen_moses_config_dict.json │ │ │ ├── rand_gen_qm9_config_dict.json │ │ │ └── rand_gen_zinc250k_config_dict.json │ │ ├── figs │ │ │ ├── .DS_Store │ │ │ └── graphdf.png │ │ ├── run_const_prop_opt.py │ │ ├── run_prop_opt.py │ │ └── run_rand_gen.py │ ├── GraphEBM │ │ ├── README.md │ │ ├── compositional_gen.ipynb │ │ ├── figs │ │ │ └── graphebm_training.png │ │ ├── goal-directed_gen.ipynb │ │ └── randn_gen.ipynb │ └── JTVAE │ │ ├── cons_optim.ipynb │ │ └── rand_gen.ipynb ├── ggraph3D │ └── G_SphereNet │ │ ├── README.md │ │ ├── config_dict.json │ │ ├── figs │ │ └── gspherenet.png │ │ ├── run_prop_opt.py │ │ ├── run_rand_gen.py │ │ └── target_bond_lengths.dict ├── lsgraph │ ├── GraphFMIB │ │ └── reddit_example.py │ └── GraphFMOB │ │ ├── GraphFMOB.py │ │ └── conf │ │ ├── config.yaml │ │ ├── dataset │ │ ├── amazon.yaml │ │ ├── arxiv.yaml │ │ ├── flickr.yaml │ │ ├── ppi.yaml │ │ ├── products.yaml │ │ ├── reddit.yaml │ │ └── yelp.yaml │ │ └── model │ │ ├── gcn.yaml │ │ ├── gcn2.yaml │ │ ├── pna.yaml │ │ └── pna_jk.yaml ├── oodgraph │ └── good_datasets.ipynb ├── sslgraph │ ├── example_gca.ipynb │ ├── example_grace.ipynb │ ├── example_graphcl.ipynb │ ├── example_graphcl_grid_search.ipynb │ ├── example_infograph.ipynb │ └── example_mvgrl.ipynb ├── threedgraph │ ├── run_ProNet.py │ ├── threedgraph.ipynb │ └── xyz_to_dat.ipynb └── xgraph │ ├── deeplift.ipynb │ ├── flowx.ipynb │ ├── gnn_lrp.ipynb │ ├── gnnexplainer.ipynb │ ├── gradcam.ipynb │ ├── pgexplainer.ipynb │ └── subgraphx.ipynb ├── imgs ├── DIG-logo.jpg └── DIG-overview.png ├── script └── conda.sh ├── setup.cfg ├── setup.py ├── test ├── ggraph │ ├── dataset │ │ ├── test_QM9.py │ │ ├── test_ZINC250k.py │ │ └── test_ZINC800.py │ ├── evaluation │ │ ├── test_ConstPropOptEvaluator.py │ │ ├── test_PropOptEvaluator.py │ │ └── test_RandGenEvaluator.py │ └── utils │ │ ├── test_environment.py │ │ └── test_gen_mol_from_one_shot_tensor.py ├── oodgraph │ └── test_good_datasets.py ├── sslgraph │ ├── dataset │ │ ├── test_TUDatasetExt.py │ │ ├── test_get_dataset.py │ │ └── test_get_node_dataset.py │ └── evaluation │ │ ├── test_GraphSemisupervised.py │ │ ├── test_GraphUnsupervised.py │ │ ├── test_NodeUnsupervised.py │ │ └── test_nce_more_view.py ├── threedgraph │ ├── dataset │ │ ├── test_MD17.py │ │ └── test_QM93D.py │ └── evaluation │ │ └── test_ThreeDEvaluator.py └── xgraph │ ├── dataset │ ├── test_BA_LRP.py │ ├── test_MarginalDataset.py │ ├── test_MoleculeDataset.py │ └── test_SynGraphDataset.py │ └── evaluation │ └── test_metrics.py └── tutorials └── KDD2022 ├── 3dgraph_code_tutorial.ipynb ├── DIG-Tutorial-KDD22.pdf ├── README.md ├── ggraph_code_tutorial.ipynb ├── sslgraph_code_tutorial.ipynb └── xgraph_code_tutorial.ipynb /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/divelab/DIG/HEAD/.gitignore -------------------------------------------------------------------------------- /.readthedocs.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/divelab/DIG/HEAD/.readthedocs.yaml -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- 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