├── .gitignore ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── docs ├── Makefile ├── make.bat └── source │ ├── conf.py │ ├── getting_started │ ├── CompleteDR.png │ ├── dataformatting.rst │ ├── decomposition.rst │ ├── downstream.rst │ ├── geo_v3.png │ ├── installation.rst │ ├── introduction.rst │ ├── learning.rst │ └── understandingdrg.rst │ ├── index.rst │ ├── license.rst │ ├── modules.rst │ └── modules │ ├── geometric2dr.data.rst │ ├── geometric2dr.decomposition.rst │ └── geometric2dr.embedding_methods.rst ├── examples ├── anon_walk_mle_kernel.py ├── awe_dd.py ├── data │ ├── MUTAG.Labels │ └── MUTAG │ │ ├── 1.gexf │ │ ├── 10.gexf │ │ ├── 100.gexf │ │ ├── 101.gexf │ │ ├── 102.gexf │ │ ├── 103.gexf │ │ ├── 104.gexf │ │ ├── 105.gexf │ │ ├── 106.gexf │ │ ├── 107.gexf │ │ ├── 108.gexf │ │ ├── 109.gexf │ │ ├── 11.gexf │ │ ├── 110.gexf │ │ ├── 111.gexf │ │ ├── 112.gexf │ │ ├── 113.gexf │ │ ├── 114.gexf │ │ ├── 115.gexf │ │ ├── 116.gexf │ │ ├── 117.gexf │ │ ├── 118.gexf │ │ ├── 119.gexf │ │ ├── 12.gexf │ │ ├── 120.gexf │ │ ├── 121.gexf │ │ ├── 122.gexf │ │ ├── 123.gexf │ │ ├── 124.gexf │ │ ├── 125.gexf │ │ ├── 126.gexf │ │ ├── 127.gexf │ │ ├── 128.gexf │ │ ├── 129.gexf │ │ ├── 13.gexf │ │ ├── 130.gexf │ │ ├── 131.gexf │ │ ├── 132.gexf │ │ ├── 133.gexf │ │ ├── 134.gexf │ │ ├── 135.gexf │ │ ├── 136.gexf │ │ ├── 137.gexf │ │ ├── 138.gexf │ │ ├── 139.gexf │ │ ├── 14.gexf │ │ ├── 140.gexf │ │ ├── 141.gexf │ │ ├── 142.gexf │ │ ├── 143.gexf │ │ ├── 144.gexf │ │ ├── 145.gexf │ │ ├── 146.gexf │ │ ├── 147.gexf │ │ ├── 148.gexf │ │ ├── 149.gexf │ │ ├── 15.gexf │ │ ├── 150.gexf │ │ ├── 151.gexf │ │ ├── 152.gexf │ │ ├── 153.gexf │ │ ├── 154.gexf │ │ ├── 155.gexf │ │ ├── 156.gexf │ │ ├── 157.gexf │ │ ├── 158.gexf │ │ ├── 159.gexf │ │ ├── 16.gexf │ │ ├── 160.gexf │ │ ├── 161.gexf │ │ ├── 162.gexf │ │ ├── 163.gexf │ │ ├── 164.gexf │ │ ├── 165.gexf │ │ ├── 166.gexf │ │ ├── 167.gexf │ │ ├── 168.gexf │ │ ├── 169.gexf │ │ ├── 17.gexf │ │ ├── 170.gexf │ │ ├── 171.gexf │ │ ├── 172.gexf │ │ ├── 173.gexf │ │ ├── 174.gexf │ │ ├── 175.gexf │ │ ├── 176.gexf │ │ ├── 177.gexf │ │ ├── 178.gexf │ │ ├── 179.gexf │ │ ├── 18.gexf │ │ ├── 180.gexf │ │ ├── 181.gexf │ │ ├── 182.gexf │ │ ├── 183.gexf │ │ ├── 184.gexf │ │ ├── 185.gexf │ │ ├── 186.gexf │ │ ├── 187.gexf │ │ ├── 188.gexf │ │ ├── 19.gexf │ │ ├── 2.gexf │ │ ├── 20.gexf │ │ ├── 21.gexf │ │ ├── 22.gexf │ │ ├── 23.gexf │ │ ├── 24.gexf │ │ ├── 25.gexf │ │ ├── 26.gexf │ │ ├── 27.gexf │ │ ├── 28.gexf │ │ ├── 29.gexf │ │ ├── 3.gexf │ │ ├── 30.gexf │ │ ├── 31.gexf │ │ ├── 32.gexf │ │ ├── 33.gexf │ │ ├── 34.gexf │ │ ├── 35.gexf │ │ ├── 36.gexf │ │ ├── 37.gexf │ │ ├── 38.gexf │ │ ├── 39.gexf │ │ ├── 4.gexf │ │ ├── 40.gexf │ │ ├── 41.gexf │ │ ├── 42.gexf │ │ ├── 43.gexf │ │ ├── 44.gexf │ │ ├── 45.gexf │ │ ├── 46.gexf │ │ ├── 47.gexf │ │ ├── 48.gexf │ │ ├── 49.gexf │ │ ├── 5.gexf │ │ ├── 50.gexf │ │ ├── 51.gexf │ │ ├── 52.gexf │ │ ├── 53.gexf │ │ ├── 54.gexf │ │ ├── 55.gexf │ │ ├── 56.gexf │ │ ├── 57.gexf │ │ ├── 58.gexf │ │ ├── 59.gexf │ │ ├── 6.gexf │ │ ├── 60.gexf │ │ ├── 61.gexf │ │ ├── 62.gexf │ │ ├── 63.gexf │ │ ├── 64.gexf │ │ ├── 65.gexf │ │ ├── 66.gexf │ │ ├── 67.gexf │ │ ├── 68.gexf │ │ ├── 69.gexf │ │ ├── 7.gexf │ │ ├── 70.gexf │ │ ├── 71.gexf │ │ ├── 72.gexf │ │ ├── 73.gexf │ │ ├── 74.gexf │ │ ├── 75.gexf │ │ ├── 76.gexf │ │ ├── 77.gexf │ │ ├── 78.gexf │ │ ├── 79.gexf │ │ ├── 8.gexf │ │ ├── 80.gexf │ │ ├── 81.gexf │ │ ├── 82.gexf │ │ ├── 83.gexf │ │ ├── 84.gexf │ │ ├── 85.gexf │ │ ├── 86.gexf │ │ ├── 87.gexf │ │ ├── 88.gexf │ │ ├── 89.gexf │ │ ├── 9.gexf │ │ ├── 90.gexf │ │ ├── 91.gexf │ │ ├── 92.gexf │ │ ├── 93.gexf │ │ ├── 94.gexf │ │ ├── 95.gexf │ │ ├── 96.gexf │ │ ├── 97.gexf │ │ ├── 98.gexf │ │ └── 99.gexf ├── dgk_graphlets.py ├── dgk_shortest_paths.py ├── dgk_wl.py ├── dgk_wl_cbow.py ├── graph2vec.py ├── graphlet_mle_kernel.py ├── random_walk_mle_kernel.py ├── shortest_path_mle_kernel.py ├── sp_pvdm.py └── wl_mle_kernel.py ├── geometric2dr ├── __init__.py ├── data │ ├── __init__.py │ ├── dortmund_formatter.py │ └── tu_gexifier.py ├── decomposition │ ├── __init__.py │ ├── anonymous_walk_patterns.py │ ├── canonical_maps │ │ ├── canonical_map_n2.p │ │ ├── canonical_map_n3.p │ │ ├── canonical_map_n4.p │ │ ├── canonical_map_n5.p │ │ ├── canonical_map_n6.p │ │ ├── canonical_map_n7.p │ │ └── canonical_map_n8.p │ ├── graphlet_counter_maps │ │ ├── graphlet_counter_nodebased_n2.p │ │ ├── graphlet_counter_nodebased_n3.p │ │ ├── graphlet_counter_nodebased_n4.p │ │ ├── graphlet_counter_nodebased_n5.p │ │ ├── graphlet_counter_nodebased_n6.p │ │ ├── graphlet_counter_nodebased_n7.p │ │ └── graphlet_counter_nodebased_n8.p │ ├── graphlet_patterns.py │ ├── random_walk_patterns.py │ ├── shortest_path_patterns.py │ ├── utils.py │ └── weisfeiler_lehman_patterns.py └── embedding_methods │ ├── __init__.py │ ├── cbow.py │ ├── cbow_data_reader.py │ ├── cbow_trainer.py │ ├── classify.py │ ├── dev_noclass_trainer.py │ ├── pvdbow_data_reader.py │ ├── pvdbow_trainer.py │ ├── pvdm.py │ ├── pvdm_data_reader.py │ ├── pvdm_trainer.py │ ├── skipgram.py │ ├── skipgram_data_reader.py │ ├── skipgram_trainer.py │ └── utils.py ├── replication ├── anon_walk_mle_kernel.py ├── awe_all.py ├── data_format_script_with_geo2dr.py ├── dgk_gk_all.py ├── dgk_sp_all.py ├── dgk_wl_all.py ├── graph2vec_all.py ├── graphlet_mle_kernel.py ├── gridsearch_svmrbf_method_dataset.py ├── readme.md ├── reverse_gexf_to_dgk_format.py ├── runtime_analysis_graph2vec_geo2dr.py ├── runtime_dgk_gensim.py ├── shortest_path_mle_kernel.py ├── summary_results.py └── wl_mle_kernel.py ├── setup.py ├── tests ├── __init__.py ├── data │ ├── __init__.py │ └── test_dortmund_formatter.py ├── decomposition │ ├── __init__.py │ ├── test_anonymous_walk_patterns.py │ ├── test_graphlet_patterns.py │ ├── test_random_walk_patterns.py │ ├── test_shortest_path_patterns.py │ ├── test_utils.py │ └── test_weisfeiler_lehman_patterns.py └── embedding_methods │ ├── __init__.py │ ├── test_cbow.py │ ├── test_cbow_trainer.py │ ├── test_classify.py │ ├── test_data_readers.py │ ├── test_pvdbow_trainer.py │ ├── test_pvdm.py │ ├── test_pvdm_trainer.py │ ├── test_skipgram.py │ ├── test_skipgram_trainer.py │ └── test_utils.py └── update_log.md /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/paulmorio/geo2dr/HEAD/.gitignore -------------------------------------------------------------------------------- /CODE_OF_CONDUCT.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/paulmorio/geo2dr/HEAD/CODE_OF_CONDUCT.md -------------------------------------------------------------------------------- /CONTRIBUTING.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/paulmorio/geo2dr/HEAD/CONTRIBUTING.md -------------------------------------------------------------------------------- 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