{ "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": { "scrolled": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\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_graph_size : 30.3177311506\n", "min_graph_size : 4\n", "max_graph_size : 417\n", "ave_graph_edge_num : 30.7694258704\n", "min_graph_edge_num : 3\n", "max_graph_edge_num : 112\n", "ave_graph_degree : 3.75651371916\n", "min_graph_degree : 3\n", "max_graph_degree : 4\n", "node_label_num : 14\n", "edge_label_num : 3\n", "node_attr_dim : False\n", "edge_attr_dim : False\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_graph_size : 15.6925\n", "min_graph_size : 2\n", "max_graph_size : 95\n", "ave_graph_edge_num : 16.195\n", "min_graph_edge_num : 1\n", "max_graph_edge_num : 103\n", "ave_graph_degree : 3.322\n", "min_graph_degree : 1\n", "max_graph_degree : 6\n", "node_label_num : 38\n", "edge_label_num : 3\n", "node_attr_dim : 4\n", "edge_attr_dim : False\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_graph_size : 1377.26829268\n", "min_graph_size : 134\n", "max_graph_size : 5037\n", "ave_graph_edge_num : 3074.09756098\n", "min_graph_edge_num : 320\n", "max_graph_edge_num : 10888\n", "ave_graph_degree : 7.85365853659\n", "min_graph_degree : 6\n", "max_graph_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_graph_size : 40.5791855204\n", "min_graph_size : 25\n", "max_graph_size : 55\n", "ave_graph_edge_num : 97.9366515837\n", "min_graph_edge_num : 53\n", "max_graph_edge_num : 145\n", "ave_graph_degree : 10.1583710407\n", "min_graph_degree : 8\n", "max_graph_degree : 16\n", "node_label_num : 10\n", "edge_label_num : 0\n", "node_attr_dim : False\n", "edge_attr_dim : False\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_graph_size : 77.5204262877\n", "min_graph_size : 51\n", "max_graph_size : 141\n", "ave_graph_edge_num : 198.323268206\n", "min_graph_edge_num : 121\n", "max_graph_edge_num : 405\n", "ave_graph_degree : 11.4156305506\n", "min_graph_degree : 8\n", "max_graph_degree : 23\n", "node_label_num : 22\n", "edge_label_num : 0\n", "node_attr_dim : False\n", "edge_attr_dim : False\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_graph_size : 100.0\n", "min_graph_size : 100\n", "max_graph_size : 100\n", "ave_graph_edge_num : 196.0\n", "min_graph_edge_num : 196\n", "max_graph_edge_num : 196\n", "ave_graph_degree : 8.0\n", "min_graph_degree : 8\n", "max_graph_degree : 8\n", "node_label_num : 8\n", "edge_label_num : 0\n", "node_attr_dim : 1\n", "edge_attr_dim : False\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_graph_size : 35.750617284\n", "min_graph_size : 13\n", "max_graph_size : 57\n", "ave_graph_edge_num : 38.3580246914\n", "min_graph_edge_num : 13\n", "max_graph_edge_num : 60\n", "ave_graph_degree : 3.86419753086\n", "min_graph_degree : 3\n", "max_graph_degree : 4\n", "node_label_num : 10\n", "edge_label_num : 0\n", "node_attr_dim : 3\n", "edge_attr_dim : False\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_graph_size : 41.2248394004\n", "min_graph_size : 32\n", "max_graph_size : 56\n", "ave_graph_edge_num : 43.4453961456\n", "min_graph_edge_num : 34\n", "max_graph_edge_num : 59\n", "ave_graph_degree : 4.0\n", "min_graph_degree : 4\n", "max_graph_degree : 4\n", "node_label_num : 8\n", "edge_label_num : 0\n", "node_attr_dim : 3\n", "edge_attr_dim : False\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_graph_size : 42.4272486772\n", "min_graph_size : 20\n", "max_graph_size : 71\n", "ave_graph_edge_num : 44.544973545\n", "min_graph_edge_num : 21\n", "max_graph_edge_num : 73\n", "ave_graph_degree : 3.95502645503\n", "min_graph_degree : 3\n", "max_graph_degree : 4\n", "node_label_num : 9\n", "edge_label_num : 0\n", "node_attr_dim : 3\n", "edge_attr_dim : False\n", "class_number : 2\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_graph_size : 32.6333333333\n", "min_graph_size : 2\n", "max_graph_size : 126\n", "ave_graph_edge_num : 62.1366666667\n", "min_graph_edge_num : 1\n", "max_graph_edge_num : 149\n", "ave_graph_degree : 6.08666666667\n", "min_graph_degree : 1\n", "max_graph_degree : 9\n", "node_label_num : 3\n", "edge_label_num : 0\n", "node_attr_dim : 18\n", "edge_attr_dim : False\n", "class_number : 6\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_graph_size : 39.0575022462\n", "min_graph_size : 4\n", "max_graph_size : 620\n", "ave_graph_edge_num : 72.8158131177\n", "min_graph_edge_num : 5\n", "max_graph_edge_num : 1049\n", "ave_graph_degree : 5.79424977538\n", "min_graph_degree : 3\n", "max_graph_degree : 25\n", "node_label_num : 3\n", "edge_label_num : 0\n", "node_attr_dim : 1\n", "edge_attr_dim : False\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_graph_size : 39.0575022462\n", "min_graph_size : 4\n", "max_graph_size : 620\n", "ave_graph_edge_num : 72.8158131177\n", "min_graph_edge_num : 5\n", "max_graph_edge_num : 1049\n", "ave_graph_degree : 5.79424977538\n", "min_graph_degree : 3\n", "max_graph_degree : 25\n", "node_label_num : 3\n", "edge_label_num : 0\n", "node_attr_dim : 29\n", "edge_attr_dim : False\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_graph_size : 284.31663837\n", "min_graph_size : 30\n", "max_graph_size : 5748\n", "ave_graph_edge_num : 715.658743633\n", "min_graph_edge_num : 63\n", "max_graph_edge_num : 14267\n", "ave_graph_degree : 9.50933786078\n", "min_graph_degree : 6\n", "max_graph_degree : 19\n", "node_label_num : 82\n", "edge_label_num : 0\n", "node_attr_dim : False\n", "edge_attr_dim : False\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_graph_size : 17.9308510638\n", "min_graph_size : 10\n", "max_graph_size : 28\n", "ave_graph_edge_num : 19.7925531915\n", "min_graph_edge_num : 10\n", "max_graph_edge_num : 33\n", "ave_graph_degree : 3.00531914894\n", "min_graph_degree : 3\n", "max_graph_degree : 4\n", "node_label_num : 7\n", "edge_label_num : 11\n", "node_attr_dim : False\n", "edge_attr_dim : False\n", "class_number : 2\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_graph_size : 8.87333333333\n", "min_graph_size : 1\n", "max_graph_size : 10\n", "ave_graph_edge_num : 7.87333333333\n", "min_graph_edge_num : 0\n", "max_graph_edge_num : 9\n", "ave_graph_degree : 3.36\n", "min_graph_degree : 0\n", "max_graph_degree : 4\n", "node_label_num : 2\n", "edge_label_num : 1\n", "node_attr_dim : False\n", "edge_attr_dim : False\n", "class_number : 123\n", "\n", "\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_graph_size : 8.15300546448\n", "min_graph_size : 3\n", "max_graph_size : 11\n", "ave_graph_edge_num : 7.15300546448\n", "min_graph_edge_num : 2\n", "max_graph_edge_num : 10\n", "ave_graph_degree : 2.80327868852\n", "min_graph_degree : 2\n", "max_graph_degree : 4\n", "node_label_num : 3\n", "edge_label_num : 1\n", "node_attr_dim : False\n", "edge_attr_dim : False\n", "class_number : 148\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_graph_size : 18.3823529412\n", "min_graph_size : 11\n", "max_graph_size : 27\n", "ave_graph_edge_num : 19.6323529412\n", "min_graph_edge_num : 12\n", "max_graph_edge_num : 29\n", "ave_graph_degree : 3.0\n", "min_graph_degree : 3\n", "max_graph_degree : 3\n", "node_label_num : 3\n", "edge_label_num : 4\n", "node_attr_dim : False\n", "edge_attr_dim : False\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_graph_size : 20.7021276596\n", "min_graph_size : 10\n", "max_graph_size : 28\n", "ave_graph_edge_num : 24.4255319149\n", "min_graph_edge_num : 11\n", "max_graph_edge_num : 34\n", "ave_graph_degree : 3.01063829787\n", "min_graph_degree : 3\n", "max_graph_degree : 4\n", "node_label_num : 1\n", "edge_label_num : 1\n", "node_attr_dim : False\n", "edge_attr_dim : False\n", "class_number : 2\n", "\n", "\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_graph_size : 29.8654501217\n", "min_graph_size : 3\n", "max_graph_size : 111\n", "ave_graph_edge_num : 32.3\n", "min_graph_edge_num : 2\n", "max_graph_edge_num : 119\n", "ave_graph_degree : 3.33600973236\n", "min_graph_degree : 2\n", "max_graph_degree : 4\n", "node_label_num : 37\n", "edge_label_num : 0\n", "node_attr_dim : False\n", "edge_attr_dim : False\n", "class_number : 2\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "\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_graph_size : 29.6811243034\n", "min_graph_size : 4\n", "max_graph_size : 111\n", "ave_graph_edge_num : 32.1308456506\n", "min_graph_edge_num : 3\n", "max_graph_edge_num : 119\n", "ave_graph_degree : 3.34383329295\n", "min_graph_degree : 2\n", "max_graph_degree : 5\n", "node_label_num : 38\n", "edge_label_num : 0\n", "node_attr_dim : False\n", "edge_attr_dim : False\n", "class_number : 2\n", "\n", "load SDF: 100%|██████████| 4457424/4457424 [00:11<00:00, 397248.47it/s]\n", "ajust data: 100%|██████████| 42687/42687 [00:10<00:00, 3939.72it/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_graph_size : 45.7094559768\n", "min_graph_size : 2\n", "max_graph_size : 438\n", "ave_graph_edge_num : 47.7137903566\n", "min_graph_edge_num : 1\n", "max_graph_edge_num : 441\n", "ave_graph_degree : 3.97605548006\n", "min_graph_degree : 1\n", "max_graph_degree : 12\n", "node_label_num : 63\n", "edge_label_num : 3\n", "node_attr_dim : False\n", "edge_attr_dim : False\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': 'Mutagenicity', 'dataset': '../datasets/Mutagenicity/Mutagenicity_A.txt'},\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': 'ENZYMES', 'dataset': '../datasets/ENZYMES_txt/ENZYMES_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': 'D&D', 'dataset': '../datasets/D&D/DD.mat',\n", " 'extra_params': {'am_sp_al_nl_el': [0, 1, 2, 1, -1]}},\n", " {'name': 'MUTAG', 'dataset': '../datasets/MUTAG/MUTAG.mat',\n", " 'extra_params': {'am_sp_al_nl_el': [0, 0, 3, 1, 2]}},\n", " {'name': 'Alkane', 'dataset': '../datasets/Alkane/dataset.ds',\n", " 'dataset_y': '../datasets/Alkane/dataset_boiling_point_names.txt',},\n", " {'name': 'Acyclic', 'dataset': '../datasets/acyclic/dataset_bps.ds',},\n", " {'name': 'MAO', 'dataset': '../datasets/MAO/dataset.ds',},\n", " {'name': 'PAH', 'dataset': '../datasets/PAH/dataset.ds',},\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": "3.5.2" } }, "nbformat": 4, "nbformat_minor": 2 }