├── .gitignore ├── .pylintrc ├── LICENSE ├── MANIFEST.in ├── README.rst ├── dist ├── embiggen-0.10.0.dev1.tar.gz ├── embiggen-0.10.0.dev10.tar.gz ├── embiggen-0.10.0.dev11.tar.gz ├── embiggen-0.10.0.dev12.tar.gz ├── embiggen-0.10.0.dev2.tar.gz ├── embiggen-0.10.0.dev3.tar.gz ├── embiggen-0.10.0.dev5.tar.gz ├── embiggen-0.10.0.dev6.tar.gz ├── embiggen-0.10.0.dev7.tar.gz ├── embiggen-0.10.0.dev8.tar.gz ├── embiggen-0.11.0.tar.gz ├── embiggen-0.11.1.tar.gz ├── embiggen-0.11.10.tar.gz ├── embiggen-0.11.11.tar.gz ├── embiggen-0.11.12.tar.gz ├── embiggen-0.11.15.tar.gz ├── embiggen-0.11.16.tar.gz ├── embiggen-0.11.17.tar.gz ├── embiggen-0.11.18.tar.gz ├── embiggen-0.11.19.tar.gz ├── embiggen-0.11.20.tar.gz ├── embiggen-0.11.21.tar.gz ├── embiggen-0.11.22.tar.gz ├── embiggen-0.11.23.tar.gz ├── embiggen-0.11.24.tar.gz ├── embiggen-0.11.25.tar.gz ├── embiggen-0.11.26.tar.gz ├── embiggen-0.11.27.tar.gz ├── embiggen-0.11.28.tar.gz ├── embiggen-0.11.29.tar.gz ├── embiggen-0.11.3.tar.gz ├── 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embiggen-0.8.0.tar.gz ├── embiggen-0.8.1.tar.gz ├── embiggen-0.8.2.tar.gz ├── embiggen-0.8.3.tar.gz ├── embiggen-0.8.4.tar.gz ├── embiggen-0.8.5.tar.gz ├── embiggen-0.9.0.tar.gz ├── embiggen-0.9.1.tar.gz ├── embiggen-0.9.2.tar.gz └── embiggen-0.9.3.tar.gz ├── embiggen ├── __init__.py ├── __version__.py ├── edge_label_prediction │ ├── __init__.py │ ├── edge_label_prediction_catboost │ │ ├── __init__.py │ │ └── catboost_edge_label_prediction.py │ ├── edge_label_prediction_evaluation.py │ ├── edge_label_prediction_lightgbm │ │ ├── __init__.py │ │ └── lgbm_edge_label_prediction.py │ ├── edge_label_prediction_lleaves │ │ ├── __init__.py │ │ └── lleaves_edge_label_prediction.py │ ├── edge_label_prediction_model.py │ ├── edge_label_prediction_sklearn │ │ ├── __init__.py │ │ ├── decision_tree_edge_label_prediction.py │ │ ├── extra_trees_edge_label_prediction.py │ │ ├── gradient_boosting_edge_label_prediction.py │ │ ├── hist_gradient_boosting_edge_label_prediction.py │ │ ├── k_neighbours_edge_label_prediction.py │ │ ├── linear_svc_edge_label_prediction.py │ │ ├── logistic_regression_cv_edge_label_prediction.py │ │ ├── mlp_edge_label_prediction.py │ │ ├── nu_svc_edge_label_prediction.py │ │ ├── radius_neighbours_edge_label_prediction.py │ │ ├── random_forest_edge_label_prediction.py │ │ ├── ridge_classifier_cv_edge_label_prediction.py │ │ ├── ridge_classifier_edge_label_prediction.py │ │ └── sklearn_edge_label_prediction_adapter.py │ ├── edge_label_prediction_tensorflow │ │ ├── __init__.py │ │ ├── gcn.py │ │ ├── gnn.py │ │ ├── graph_sage.py │ │ └── kipf_gcn.py │ ├── edge_label_prediction_xgboost │ │ ├── __init__.py │ │ └── xgboost_edge_label_prediction.py │ └── sklearn_like_edge_label_prediction_adapter.py ├── edge_prediction │ ├── __init__.py │ ├── edge_prediction_catboost │ │ ├── __init__.py │ │ └── catboost_edge_prediction.py │ ├── edge_prediction_ensmallen │ │ ├── __init__.py │ │ └── perceptron.py │ ├── edge_prediction_evaluation.py │ ├── edge_prediction_lightgbm │ │ ├── __init__.py │ │ └── lgbm_edge_prediction.py │ ├── edge_prediction_lleaves │ │ ├── __init__.py │ │ └── lleaves_edge_prediction.py │ ├── edge_prediction_model.py │ ├── edge_prediction_sklearn │ │ ├── __init__.py │ │ ├── decision_tree_edge_prediction.py │ │ ├── extra_trees_edge_prediction.py │ │ ├── gradient_boosting_edge_prediction.py │ │ ├── hist_gradient_boosting_classifier.py │ │ ├── k_neighbours_edge_prediction.py │ │ ├── linear_svc_edge_prediction.py │ │ ├── logistic_regression_cv_edge_prediction.py │ │ ├── mlp_edge_prediction.py │ │ ├── nu_svc_edge_prediction.py │ │ ├── radius_neighbours_edge_prediction.py │ │ ├── random_forest_edge_prediction.py │ │ ├── ridge_classifier_cv_edge_prediction.py │ │ ├── ridge_classifier_edge_prediction.py │ │ └── sklearn_edge_prediction_adapter.py │ ├── edge_prediction_tensorflow │ │ ├── __init__.py │ │ ├── gcn.py │ │ ├── gnn.py │ │ ├── graph_sage.py │ │ └── kipf_gcn.py │ ├── edge_prediction_xgboost │ │ ├── __init__.py │ │ └── xgboost_edge_prediction.py │ └── sklearn_like_edge_prediction_adapter.py ├── embedders │ ├── __init__.py │ ├── ensmallen_embedders │ │ ├── __init__.py │ │ ├── deepwalk_cbow.py │ │ ├── deepwalk_glove.py │ │ ├── deepwalk_skipgram.py │ │ ├── degree_spine.py │ │ ├── degree_wine.py │ │ ├── ensmallen_embedder.py │ │ ├── first_order_line.py │ │ ├── geometric_laplacian_eigenmaps.py │ │ ├── hope.py │ │ ├── hyper_sketching.py │ │ ├── laplacian_eigenmaps.py │ │ ├── node2vec.py │ │ ├── node2vec_cbow.py │ │ ├── node2vec_glove.py │ │ ├── node2vec_skipgram.py │ │ ├── node_label_spine.py │ │ ├── node_label_wine.py │ │ ├── rubicone.py │ │ ├── ruine.py │ │ ├── score_spine.py │ │ ├── score_wine.py │ │ ├── second_order_line.py │ │ ├── siamese_model.py │ │ ├── sociodim.py │ │ ├── structured_embedding.py │ │ ├── transe.py │ │ ├── unstructured.py │ │ ├── walklets.py │ │ ├── walklets_cbow.py │ │ ├── walklets_glove.py │ │ ├── walklets_skipgram.py │ │ └── weighted_spine.py │ ├── fastnode2vec_embedders │ │ ├── __init__.py │ │ └── node2vec.py │ ├── graph_embedding_pipeline.py │ ├── karateclub_embedders │ │ ├── __init__.py │ │ ├── abstract_karateclub_embedder.py │ │ ├── boostne.py │ │ ├── deep_walk.py │ │ ├── geometric_laplacian_eigenmaps.py │ │ ├── grarep.py │ │ ├── hope.py │ │ ├── laplacian_eigenmaps.py │ │ ├── mnmf.py │ │ ├── netmf.py │ │ ├── nmfadmm.py │ │ ├── nnsed.py │ │ ├── node_sketch.py │ │ ├── randne.py │ │ ├── role2vec.py │ │ ├── skipgram.py │ │ ├── sociodim.py │ │ └── walklets.py │ ├── non_existent_embedders │ │ ├── __init__.py │ │ └── non_existent_model.py │ ├── pecanpy_embedders │ │ ├── __init__.py │ │ └── node2vec.py │ ├── pykeen_embedders │ │ ├── __init__.py │ │ ├── auto_sf.py │ │ ├── boxe.py │ │ ├── complex.py │ │ ├── conve.py │ │ ├── crosse.py │ │ ├── distma.py │ │ ├── distmult.py │ │ ├── entity_relation_embedding_model_pykeen.py │ │ ├── ermlp.py │ │ ├── ermlpe.py │ │ ├── hole.py │ │ ├── node_piece.py │ │ ├── pairre.py │ │ ├── proje.py │ │ ├── pykeen_embedder.py │ │ ├── quate.py │ │ ├── rescal.py │ │ ├── rotate.py │ │ ├── toruse.py │ │ ├── transd.py │ │ ├── transe.py │ │ ├── transf.py │ │ ├── transh.py │ │ ├── transr.py │ │ └── tucker.py │ ├── pytorch_geometric │ │ ├── __init__.py │ │ ├── node2vec.py │ │ └── pytorch_geometric_embedder.py │ └── tensorflow_embedders │ │ ├── __init__.py │ │ ├── abstract_random_walked_based_embedder_model.py │ │ ├── cbow.py │ │ ├── edge_prediction_based_tensorflow_embedders.py │ │ ├── first_order_line.py │ │ ├── node2vec.py │ │ ├── second_order_line.py │ │ ├── siamese.py │ │ ├── skipgram.py │ │ ├── structured_embedding.py │ │ ├── tensorflow_embedder.py │ │ ├── transe.py │ │ ├── transh.py │ │ └── unstructured.py ├── embedding_transformers │ ├── __init__.py │ ├── edge_label_prediction_transformer.py │ ├── edge_prediction_transformer.py │ ├── edge_transformer.py │ ├── graph_transformer.py │ ├── node_label_prediction_transformer.py │ └── node_transformer.py ├── feature_preprocessors │ ├── __init__.py │ └── graph_convolution.py ├── layers │ ├── __init__.py │ └── tensorflow │ │ ├── __init__.py │ │ ├── element_wise_l1.py │ │ ├── element_wise_l2.py │ │ ├── embedding_lookup.py │ │ ├── flat_embedding.py │ │ ├── graph_convolution_layer.py │ │ ├── l2_norm.py │ │ ├── noise_contrastive_estimation.py │ │ └── sampled_softmax.py ├── node_label_prediction │ ├── __init__.py │ ├── node_label_prediction_catboost │ │ ├── __init__.py │ │ └── catboost_node_label_prediction.py │ ├── node_label_prediction_evaluation.py │ ├── node_label_prediction_lightgbm │ │ ├── __init__.py │ │ └── lgbm_node_label_prediction.py │ ├── node_label_prediction_lleaves │ │ ├── __init__.py │ │ └── lleaves_node_label_prediction.py │ ├── node_label_prediction_model.py │ ├── node_label_prediction_sklearn │ │ ├── __init__.py │ │ ├── decision_tree_node_label_prediction.py │ │ ├── extra_trees_node_label_prediction.py │ │ ├── gradient_boosting_node_label_prediction.py │ │ ├── hist_gradient_boosting_node_label_prediction.py │ │ ├── k_neighbours_node_label_prediction.py │ │ ├── linear_svc_node_label_prediction.py │ │ ├── logistic_regression_cv_node_label_prediction.py │ │ ├── mlp_node_label_prediction.py │ │ ├── nu_svc_node_label_prediction.py │ │ ├── radius_neighbours_node_label_prediction.py │ │ ├── random_forest_node_label_prediction.py │ │ ├── ridge_classifier_cv_node_label_prediction.py │ │ ├── ridge_classifier_node_label_prediction.py │ │ └── sklearn_node_label_prediction_adapter.py │ ├── node_label_prediction_tensorflow │ │ ├── __init__.py │ │ ├── gcn.py │ │ ├── gnn.py │ │ ├── graph_sage.py │ │ └── kipf_gcn.py │ ├── node_label_prediction_xgboost │ │ ├── __init__.py │ │ └── xgboost_node_label_prediction.py │ └── sklearn_like_node_label_prediction_adapter.py ├── sequences │ ├── __init__.py │ ├── generic_sequences │ │ ├── __init__.py │ │ └── edge_prediction_sequence.py │ └── tensorflow_sequences │ │ ├── __init__.py │ │ ├── edge_prediction_training_sequence.py │ │ ├── gcn_edge_label_prediction_sequence.py │ │ ├── gcn_edge_label_prediction_training_sequence.py │ │ ├── gcn_edge_prediction_sequence.py │ │ ├── gcn_edge_prediction_training_sequence.py │ │ ├── node2vec_sequence.py │ │ └── siamese_sequence.py ├── similarities │ ├── __init__.py │ └── dag_resnik.py ├── utils │ ├── __init__.py │ ├── abstract_edge_feature.py │ ├── abstract_edge_gcn.py │ ├── abstract_feature.py │ ├── abstract_gcn.py │ ├── abstract_models │ │ ├── __init__.py │ │ ├── abstract_classifier_model.py │ │ ├── abstract_embedding_model.py │ │ ├── abstract_feature_preprocessor.py │ │ ├── abstract_model.py │ │ ├── auto_init.py │ │ ├── embedding_result.py │ │ ├── list_formatting.py │ │ └── model_stub.py │ ├── networkx_utils.py │ ├── normalization_schemas.json │ ├── normalize_kwargs.py │ ├── normalize_model_structural_parameters.py │ ├── number_to_ordinal.py │ ├── pipeline.py │ ├── pytorch_utils.py │ ├── sklearn_utils.py │ └── tensorflow_utils.py └── visualizations │ ├── __init__.py │ └── graph_visualizer.py ├── setup.py └── tests ├── __init__.py ├── cached_tests.py ├── data ├── short_bible.txt └── small_ppi.tsv ├── test_abstract_classifier_model.py ├── test_abstract_model.py ├── test_all_imports_are_consistent.py ├── test_catboost.py ├── test_combinatorial_gcn_edge_prediction.py ├── test_edge_features_in_multiple_graph_pipeline.py ├── test_edge_label_gcn.py ├── test_edge_label_prediction_pipeline.py ├── test_edge_prediction_based_tensorflow_embedder.py ├── test_edge_prediction_gcn.py ├── test_edge_prediction_pipeline.py ├── test_embed_graph_pipeline.py ├── test_embedding_result.py ├── test_fastnode2vec.py ├── test_grammar.py ├── test_lightgbm.py ├── test_logistic_regression_cv.py ├── test_node_embedding_pipelines.py ├── test_node_label_gcn.py ├── test_node_label_prediction_pipeline.py ├── test_normalize_kwargs.py ├── test_ordinal.py ├── test_pecanpy.py ├── test_pytorch_utils.py ├── test_resnik.py ├── test_ridge_classifier.py ├── test_ridge_classifier_cv.py ├── test_sklearn_utils.py ├── test_stub_model.py ├── 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