{ "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": { "scrolled": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "Acyclic:\n", "substructures : {'non linear', 'linear'}\n", "node_labeled : True\n", "edge_labeled : False\n", "is_directed : False\n", "dataset_size : 183\n", "ave_node_num : 8.153005464480874\n", "min_node_num : 3\n", "max_node_num : 11\n", "ave_edge_num : 7.1530054644808745\n", "min_edge_num : 2\n", "max_edge_num : 10\n", "ave_node_degree : 2.80327868852459\n", "min_node_degree : 2\n", "max_node_degree : 4\n", "node_label_num : 3\n", "edge_label_num : 1\n", "node_attr_dim : 0\n", "edge_attr_dim : 0\n", "class_number : 148\n", "\n", "\n", "Alkane:\n", "substructures : {'non linear', 'linear'}\n", "node_labeled : True\n", "edge_labeled : False\n", "is_directed : False\n", "dataset_size : 150\n", "ave_node_num : 8.873333333333333\n", "min_node_num : 1\n", "max_node_num : 10\n", "ave_edge_num : 7.873333333333333\n", "min_edge_num : 0\n", "max_edge_num : 9\n", "ave_node_degree : 3.36\n", "min_node_degree : 0\n", "max_node_degree : 4\n", "node_label_num : 2\n", "edge_label_num : 1\n", "node_attr_dim : 0\n", "edge_attr_dim : 0\n", "class_number : 123\n", "\n", "\n", "MAO:\n", "substructures : {'non linear', 'linear'}\n", "node_labeled : True\n", "edge_labeled : True\n", "is_directed : False\n", "dataset_size : 68\n", "ave_node_num : 18.38235294117647\n", "min_node_num : 11\n", "max_node_num : 27\n", "ave_edge_num : 19.63235294117647\n", "min_edge_num : 12\n", "max_edge_num : 29\n", "ave_node_degree : 3.0\n", "min_node_degree : 3\n", "max_node_degree : 3\n", "node_label_num : 3\n", "edge_label_num : 4\n", "node_attr_dim : 0\n", "edge_attr_dim : 0\n", "class_number : 2\n", "\n", "\n", "PAH:\n", "substructures : {'non linear', 'linear'}\n", "node_labeled : False\n", "edge_labeled : False\n", "is_directed : False\n", "dataset_size : 94\n", "ave_node_num : 20.70212765957447\n", "min_node_num : 10\n", "max_node_num : 28\n", "ave_edge_num : 24.425531914893618\n", "min_edge_num : 11\n", "max_edge_num : 34\n", "ave_node_degree : 3.0106382978723403\n", "min_node_degree : 3\n", "max_node_degree : 4\n", "node_label_num : 1\n", "edge_label_num : 1\n", "node_attr_dim : 0\n", "edge_attr_dim : 0\n", "class_number : 2\n", "\n", "\n", "MUTAG:\n", "substructures : {'non linear', 'linear'}\n", "node_labeled : True\n", "edge_labeled : True\n", "is_directed : False\n", "dataset_size : 188\n", "ave_node_num : 17.930851063829788\n", "min_node_num : 10\n", "max_node_num : 28\n", "ave_edge_num : 19.79255319148936\n", "min_edge_num : 10\n", "max_edge_num : 33\n", "ave_node_degree : 3.00531914893617\n", "min_node_degree : 3\n", "max_node_degree : 4\n", "node_label_num : 7\n", "edge_label_num : 11\n", "node_attr_dim : 0\n", "edge_attr_dim : 0\n", "class_number : 2\n", "\n", "\n", "Letter-med:\n", "substructures : {'non linear', 'linear'}\n", "node_labeled : False\n", "edge_labeled : False\n", "is_directed : False\n", "dataset_size : 2250\n", "ave_node_num : 4.674666666666667\n", "min_node_num : 1\n", "max_node_num : 9\n", "ave_edge_num : 3.2057777777777776\n", "min_edge_num : 0\n", "max_edge_num : 7\n", "ave_node_degree : 2.012888888888889\n", "min_node_degree : 0\n", "max_node_degree : 4\n", "node_label_num : 0\n", "edge_label_num : 0\n", "node_attr_dim : 2\n", "edge_attr_dim : 0\n", "class_number : 15\n", "\n", "\n", "ENZYMES:\n", "substructures : {'non linear', 'linear'}\n", "node_labeled : True\n", "edge_labeled : False\n", "is_directed : False\n", "dataset_size : 600\n", "ave_node_num : 32.63333333333333\n", "min_node_num : 2\n", "max_node_num : 126\n", "ave_edge_num : 62.13666666666666\n", "min_edge_num : 1\n", "max_edge_num : 149\n", "ave_node_degree : 6.086666666666667\n", "min_node_degree : 1\n", "max_node_degree : 9\n", "node_label_num : 3\n", "edge_label_num : 0\n", "node_attr_dim : 18\n", "edge_attr_dim : 0\n", "class_number : 6\n", "\n", "\n", "Mutagenicity:\n", "substructures : {'non linear', 'linear'}\n", "node_labeled : True\n", "edge_labeled : True\n", "is_directed : False\n", "dataset_size : 4337\n", "ave_node_num : 30.317731150564907\n", "min_node_num : 4\n", "max_node_num : 417\n", "ave_edge_num : 30.76942587041734\n", "min_edge_num : 3\n", "max_edge_num : 112\n", "ave_node_degree : 3.75651371916071\n", "min_node_degree : 3\n", "max_node_degree : 4\n", "node_label_num : 14\n", "edge_label_num : 3\n", "node_attr_dim : 0\n", "edge_attr_dim : 0\n", "class_number : 2\n", "\n", "\n", "D&D:\n", "substructures : {'non linear', 'linear'}\n", "node_labeled : True\n", "edge_labeled : False\n", "is_directed : False\n", "dataset_size : 1178\n", "ave_node_num : 284.3166383701188\n", "min_node_num : 30\n", "max_node_num : 5748\n", "ave_edge_num : 715.6587436332767\n", "min_edge_num : 63\n", "max_edge_num : 14267\n", "ave_node_degree : 9.509337860780985\n", "min_node_degree : 6\n", "max_node_degree : 19\n", "node_label_num : 82\n", "edge_label_num : 0\n", "node_attr_dim : 0\n", "edge_attr_dim : 0\n", "class_number : 2\n", "\n", "\n", "AIDS:\n", "substructures : {'non linear', 'linear'}\n", "node_labeled : True\n", "edge_labeled : True\n", "is_directed : False\n", "dataset_size : 2000\n", "ave_node_num : 15.6925\n", "min_node_num : 2\n", "max_node_num : 95\n", "ave_edge_num : 16.195\n", "min_edge_num : 1\n", "max_edge_num : 103\n", "ave_node_degree : 3.322\n", "min_node_degree : 1\n", "max_node_degree : 6\n", "node_label_num : 38\n", "edge_label_num : 3\n", "node_attr_dim : 4\n", "edge_attr_dim : 0\n", "class_number : 2\n", "\n", "\n", "FIRSTMM_DB:\n", "substructures : {'non linear'}\n", "node_labeled : True\n", "edge_labeled : False\n", "is_directed : False\n", "dataset_size : 41\n", "ave_node_num : 1377.2682926829268\n", "min_node_num : 134\n", "max_node_num : 5037\n", "ave_edge_num : 3074.0975609756097\n", "min_edge_num : 320\n", "max_edge_num : 10888\n", "ave_node_degree : 7.853658536585366\n", "min_node_degree : 6\n", "max_node_degree : 10\n", "node_label_num : 5\n", "edge_label_num : 0\n", "node_attr_dim : 1\n", "edge_attr_dim : 2\n", "class_number : 11\n", "\n", "\n", "MSRC9:\n", "substructures : {'non linear', 'linear'}\n", "node_labeled : True\n", "edge_labeled : False\n", "is_directed : False\n", "dataset_size : 221\n", "ave_node_num : 40.57918552036199\n", "min_node_num : 25\n", "max_node_num : 55\n", "ave_edge_num : 97.9366515837104\n", "min_edge_num : 53\n", "max_edge_num : 145\n", "ave_node_degree : 10.158371040723981\n", "min_node_degree : 8\n", "max_node_degree : 16\n", "node_label_num : 10\n", "edge_label_num : 0\n", "node_attr_dim : 0\n", "edge_attr_dim : 0\n", "class_number : 8\n", "\n", "\n", "MSRC21:\n", "substructures : {'non linear', 'linear'}\n", "node_labeled : True\n", "edge_labeled : False\n", "is_directed : False\n", "dataset_size : 563\n", "ave_node_num : 77.52042628774423\n", "min_node_num : 51\n", "max_node_num : 141\n", "ave_edge_num : 198.32326820603907\n", "min_edge_num : 121\n", "max_edge_num : 405\n", "ave_node_degree : 11.41563055062167\n", "min_node_degree : 8\n", "max_node_degree : 23\n", "node_label_num : 22\n", "edge_label_num : 0\n", "node_attr_dim : 0\n", "edge_attr_dim : 0\n", "class_number : 20\n", "\n", "\n", "SYNTHETIC:\n", "substructures : {'non linear', 'linear'}\n", "node_labeled : True\n", "edge_labeled : False\n", "is_directed : False\n", "dataset_size : 300\n", "ave_node_num : 100.0\n", "min_node_num : 100\n", "max_node_num : 100\n", "ave_edge_num : 196.0\n", "min_edge_num : 196\n", "max_edge_num : 196\n", "ave_node_degree : 8.0\n", "min_node_degree : 8\n", "max_node_degree : 8\n", "node_label_num : 8\n", "edge_label_num : 0\n", "node_attr_dim : 1\n", "edge_attr_dim : 0\n", "class_number : 2\n", "\n", "\n", "BZR:\n", "substructures : {'non linear', 'linear'}\n", "node_labeled : True\n", "edge_labeled : False\n", "is_directed : False\n", "dataset_size : 405\n", "ave_node_num : 35.75061728395062\n", "min_node_num : 13\n", "max_node_num : 57\n", "ave_edge_num : 38.358024691358025\n", "min_edge_num : 13\n", "max_edge_num : 60\n", "ave_node_degree : 3.8641975308641974\n", "min_node_degree : 3\n", "max_node_degree : 4\n", "node_label_num : 10\n", "edge_label_num : 0\n", "node_attr_dim : 3\n", "edge_attr_dim : 0\n", "class_number : 2\n", "\n", "\n", "COX2:\n", "substructures : {'non linear', 'linear'}\n", "node_labeled : True\n", "edge_labeled : False\n", "is_directed : False\n", "dataset_size : 467\n", "ave_node_num : 41.224839400428266\n", "min_node_num : 32\n", "max_node_num : 56\n", "ave_edge_num : 43.44539614561028\n", "min_edge_num : 34\n", "max_edge_num : 59\n", "ave_node_degree : 4.0\n", "min_node_degree : 4\n", "max_node_degree : 4\n", "node_label_num : 8\n", "edge_label_num : 0\n", "node_attr_dim : 3\n", "edge_attr_dim : 0\n", "class_number : 2\n", "\n", "\n", "DHFR:\n", "substructures : {'non linear', 'linear'}\n", "node_labeled : True\n", "edge_labeled : False\n", "is_directed : False\n", "dataset_size : 756\n", "ave_node_num : 42.42724867724868\n", "min_node_num : 20\n", "max_node_num : 71\n", "ave_edge_num : 44.544973544973544\n", "min_edge_num : 21\n", "max_edge_num : 73\n", "ave_node_degree : 3.955026455026455\n", "min_node_degree : 3\n", "max_node_degree : 4\n", "node_label_num : 9\n", "edge_label_num : 0\n", "node_attr_dim : 3\n", "edge_attr_dim : 0\n", "class_number : 2\n", "\n", "\n", "PROTEINS:\n", "substructures : {'non linear', 'linear'}\n", "node_labeled : True\n", "edge_labeled : False\n", "is_directed : False\n", "dataset_size : 1113\n", "ave_node_num : 39.05750224618149\n", "min_node_num : 4\n", "max_node_num : 620\n", "ave_edge_num : 72.8158131176999\n", "min_edge_num : 5\n", "max_edge_num : 1049\n", "ave_node_degree : 5.794249775381851\n", "min_node_degree : 3\n", "max_node_degree : 25\n", "node_label_num : 3\n", "edge_label_num : 0\n", "node_attr_dim : 1\n", "edge_attr_dim : 0\n", "class_number : 2\n", "\n", "\n", "PROTEINS_full:\n", "substructures : {'non linear', 'linear'}\n", "node_labeled : True\n", "edge_labeled : False\n", "is_directed : False\n", "dataset_size : 1113\n", "ave_node_num : 39.05750224618149\n", "min_node_num : 4\n", "max_node_num : 620\n", "ave_edge_num : 72.8158131176999\n", "min_edge_num : 5\n", "max_edge_num : 1049\n", "ave_node_degree : 5.794249775381851\n", "min_node_degree : 3\n", "max_node_degree : 25\n", "node_label_num : 3\n", "edge_label_num : 0\n", "node_attr_dim : 29\n", "edge_attr_dim : 0\n", "class_number : 2\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "\n", "NCI1:\n", "substructures : {'non linear', 'linear'}\n", "node_labeled : True\n", "edge_labeled : False\n", "is_directed : False\n", "dataset_size : 4110\n", "ave_node_num : 29.8654501216545\n", "min_node_num : 3\n", "max_node_num : 111\n", "ave_edge_num : 32.3\n", "min_edge_num : 2\n", "max_edge_num : 119\n", "ave_node_degree : 3.3360097323600972\n", "min_node_degree : 2\n", "max_node_degree : 4\n", "node_label_num : 37\n", "edge_label_num : 0\n", "node_attr_dim : 0\n", "edge_attr_dim : 0\n", "class_number : 2\n", "\n", "\n", "NCI109:\n", "substructures : {'non linear', 'linear'}\n", "node_labeled : True\n", "edge_labeled : False\n", "is_directed : False\n", "dataset_size : 4127\n", "ave_node_num : 29.681124303368065\n", "min_node_num : 4\n", "max_node_num : 111\n", "ave_edge_num : 32.13084565059365\n", "min_edge_num : 3\n", "max_edge_num : 119\n", "ave_node_degree : 3.343833292948873\n", "min_node_degree : 2\n", "max_node_degree : 5\n", "node_label_num : 38\n", "edge_label_num : 0\n", "node_attr_dim : 0\n", "edge_attr_dim : 0\n", "class_number : 2\n", "\n", "load SDF: 100%|██████████| 4457424/4457424 [00:10<00:00, 430440.94it/s]\n", "ajust data: 100%|██████████| 42687/42687 [00:09<00:00, 4352.25it/s] \n", "\n", "NCI-HIV:\n", "substructures : {'non linear', 'linear'}\n", "node_labeled : True\n", "edge_labeled : True\n", "is_directed : False\n", "dataset_size : 42682\n", "ave_node_num : 45.70945597675835\n", "min_node_num : 2\n", "max_node_num : 438\n", "ave_edge_num : 47.7137903565906\n", "min_edge_num : 1\n", "max_edge_num : 441\n", "ave_node_degree : 3.9760554800618526\n", "min_node_degree : 1\n", "max_node_degree : 12\n", "node_label_num : 63\n", "edge_label_num : 3\n", "node_attr_dim : 0\n", "edge_attr_dim : 0\n", "class_number : 3\n", "\n" ] } ], "source": [ "import sys\n", "sys.path.insert(0, \"../\")\n", "from pygraph.utils.graphfiles import loadDataset\n", "from pygraph.utils.graphdataset import get_dataset_attributes\n", "\n", "dslist = [\n", " {'name': 'Acyclic', 'dataset': '../datasets/acyclic/dataset_bps.ds',},\n", " {'name': 'Alkane', 'dataset': '../datasets/Alkane/dataset.ds',\n", " 'dataset_y': '../datasets/Alkane/dataset_boiling_point_names.txt',},\n", " {'name': 'MAO', 'dataset': '../datasets/MAO/dataset.ds',},\n", " {'name': 'PAH', 'dataset': '../datasets/PAH/dataset.ds',},\n", " {'name': 'MUTAG', 'dataset': '../datasets/MUTAG/MUTAG.mat',\n", " 'extra_params': {'am_sp_al_nl_el': [0, 0, 3, 1, 2]}},\n", " {'name': 'Letter-med', 'dataset': '../datasets/Letter-med/Letter-med_A.txt'},\n", " {'name': 'ENZYMES', 'dataset': '../datasets/ENZYMES_txt/ENZYMES_A_sparse.txt'},\n", " {'name': 'Mutagenicity', 'dataset': '../datasets/Mutagenicity/Mutagenicity_A.txt'},\n", " {'name': 'D&D', 'dataset': '../datasets/D&D/DD.mat',\n", " 'extra_params': {'am_sp_al_nl_el': [0, 1, 2, 1, -1]}},\n", " {'name': 'AIDS', 'dataset': '../datasets/AIDS/AIDS_A.txt'},\n", " {'name': 'FIRSTMM_DB', 'dataset': '../datasets/FIRSTMM_DB/FIRSTMM_DB_A.txt'},\n", " {'name': 'MSRC9', 'dataset': '../datasets/MSRC_9_txt/MSRC_9_A.txt'},\n", " {'name': 'MSRC21', 'dataset': '../datasets/MSRC_21_txt/MSRC_21_A.txt'},\n", " {'name': 'SYNTHETIC', 'dataset': '../datasets/SYNTHETIC_txt/SYNTHETIC_A_sparse.txt'},\n", " {'name': 'BZR', 'dataset': '../datasets/BZR_txt/BZR_A_sparse.txt'},\n", " {'name': 'COX2', 'dataset': '../datasets/COX2_txt/COX2_A_sparse.txt'},\n", " {'name': 'DHFR', 'dataset': '../datasets/DHFR_txt/DHFR_A_sparse.txt'}, \n", " {'name': 'PROTEINS', 'dataset': '../datasets/PROTEINS_txt/PROTEINS_A_sparse.txt'},\n", " {'name': 'PROTEINS_full', 'dataset': '../datasets/PROTEINS_full_txt/PROTEINS_full_A_sparse.txt'}, \n", " {'name': 'NCI1', 'dataset': '../datasets/NCI1/NCI1.mat',\n", " 'extra_params': {'am_sp_al_nl_el': [1, 1, 2, 0, -1]}},\n", " {'name': 'NCI109', 'dataset': '../datasets/NCI109/NCI109.mat',\n", " 'extra_params': {'am_sp_al_nl_el': [1, 1, 2, 0, -1]}},\n", " {'name': 'NCI-HIV', 'dataset': '../datasets/NCI-HIV/AIDO99SD.sdf',\n", " 'dataset_y': '../datasets/NCI-HIV/aids_conc_may04.txt',},\n", "\n", "# # not working below\n", "# {'name': 'PTC_FM', 'dataset': '../datasets/PTC/Train/FM.ds',},\n", "# {'name': 'PTC_FR', 'dataset': '../datasets/PTC/Train/FR.ds',},\n", "# {'name': 'PTC_MM', 'dataset': '../datasets/PTC/Train/MM.ds',},\n", "# {'name': 'PTC_MR', 'dataset': '../datasets/PTC/Train/MR.ds',},\n", "]\n", "\n", "for ds in dslist:\n", " dataset, y = loadDataset(\n", " ds['dataset'],\n", " filename_y=(ds['dataset_y'] if 'dataset_y' in ds else None),\n", " extra_params=(ds['extra_params'] if 'extra_params' in ds else None))\n", " attrs = get_dataset_attributes(\n", " dataset, target=y, node_label='atom', edge_label='bond_type')\n", " print()\n", " print(ds['name'] + ':')\n", " for atr in attrs:\n", " print(atr, ':', attrs[atr])\n", " print()" ] } ], "metadata": { "kernelspec": { "display_name": "Python 3", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.6.5" } }, "nbformat": 4, "nbformat_minor": 2 }