wangwei
/
graphkit-learn

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "Acyclic\n",
      "\n",
      "--- This is a regression problem ---\n",
      "\n",
      "1. Loading dataset from file...\n",
      "\n",
      "2. Calculating gram matrices. This could take a while...\n",
      "\n",
      "calculating kernels:   1%|          | 87/16836.0 [00:00<00:37, 451.37it/s]"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "../pygraph/kernels/commonWalkKernel.py:170: ComplexWarning: Casting complex values to real discards the imaginary part\n",
      "  D[i][i] = np.exp(beta * ew[i])\n",
      "../pygraph/kernels/commonWalkKernel.py:81: ComplexWarning: Casting complex values to real discards the imaginary part\n",
      "  edge_label, weight)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "calculating kernels:   5%|▍         | 795/16836.0 [00:01<00:42, 374.66it/s]"
     ]
    },
    {
     "ename": "LinAlgError",
     "evalue": "singular matrix",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mLinAlgError\u001b[0m                               Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-1-bdaea04c845f>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m     58\u001b[0m         \u001b[0;34m(\u001b[0m\u001b[0mds\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'task'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0;34m'task'\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mds\u001b[0m \u001b[0;32melse\u001b[0m \u001b[0;34m'classification'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mNUM_TRIALS\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m30\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     59\u001b[0m         \u001b[0mdatafile_y\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mds\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'dataset_y'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0;34m'dataset_y'\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mds\u001b[0m \u001b[0;32melse\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 60\u001b[0;31m         extra_params=(ds['extra_params'] if 'extra_params' in ds else None))\n\u001b[0m\u001b[1;32m     61\u001b[0m     \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/media/ljia/DATA/research-repo/codes/Linlin/py-graph/pygraph/utils/model_selection_precomputed.py\u001b[0m in \u001b[0;36mmodel_selection_for_precomputed_kernel\u001b[0;34m(datafile, estimator, param_grid_precomputed, param_grid, model_type, NUM_TRIALS, datafile_y, extra_params)\u001b[0m\n\u001b[1;32m     99\u001b[0m             \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'gram matrix with parameters'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mparams_out\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'is: '\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    100\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 101\u001b[0;31m         \u001b[0mKmatrix\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcurrent_run_time\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mestimator\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdataset\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mparams_out\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    102\u001b[0m         \u001b[0mKmatrix_diag\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mKmatrix\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdiagonal\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcopy\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    103\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/media/ljia/DATA/research-repo/codes/Linlin/py-graph/pygraph/kernels/commonWalkKernel.py\u001b[0m in \u001b[0;36mcommonwalkkernel\u001b[0;34m(node_label, edge_label, n, weight, compute_method, *args)\u001b[0m\n\u001b[1;32m     79\u001b[0m             \u001b[0;32mfor\u001b[0m \u001b[0mj\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mrange\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mi\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mGn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     80\u001b[0m                 Kmatrix[i][j] = _untilnwalkkernel_exp(Gn[i], Gn[j], node_label,\n\u001b[0;32m---> 81\u001b[0;31m                                                       edge_label, weight)\n\u001b[0m\u001b[1;32m     82\u001b[0m                 \u001b[0mKmatrix\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mj\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mi\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mKmatrix\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mi\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mj\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     83\u001b[0m                 \u001b[0mpbar\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mupdate\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/media/ljia/DATA/research-repo/codes/Linlin/py-graph/pygraph/kernels/commonWalkKernel.py\u001b[0m in \u001b[0;36m_untilnwalkkernel_exp\u001b[0;34m(G1, G2, node_label, edge_label, beta)\u001b[0m\n\u001b[1;32m    177\u001b[0m     \u001b[0;31m# print(ev)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    178\u001b[0m     \u001b[0;31m# print(np.linalg.inv(ev))\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 179\u001b[0;31m     \u001b[0mexp_D\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mev\u001b[0m \u001b[0;34m*\u001b[0m \u001b[0mD\u001b[0m \u001b[0;34m*\u001b[0m \u001b[0mev\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mI\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    180\u001b[0m     \u001b[0;31m# print(exp_D)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    181\u001b[0m     \u001b[0;31m# print(np.exp(weight * A))\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/usr/local/lib/python3.5/dist-packages/numpy/matrixlib/defmatrix.py\u001b[0m in \u001b[0;36mgetI\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m    936\u001b[0m         \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    937\u001b[0m             \u001b[0;32mfrom\u001b[0m \u001b[0mnumpy\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdual\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mpinv\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mfunc\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 938\u001b[0;31m         \u001b[0;32mreturn\u001b[0m \u001b[0masmatrix\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfunc\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    939\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    940\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mgetA\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.local/lib/python3.5/site-packages/scipy/linalg/basic.py\u001b[0m in \u001b[0;36minv\u001b[0;34m(a, overwrite_a, check_finite)\u001b[0m\n\u001b[1;32m    974\u001b[0m         \u001b[0minv_a\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0minfo\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mgetri\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlu\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mpiv\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mlwork\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mlwork\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0moverwrite_lu\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    975\u001b[0m     \u001b[0;32mif\u001b[0m \u001b[0minfo\u001b[0m \u001b[0;34m>\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 976\u001b[0;31m         \u001b[0;32mraise\u001b[0m \u001b[0mLinAlgError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"singular matrix\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    977\u001b[0m     \u001b[0;32mif\u001b[0m \u001b[0minfo\u001b[0m \u001b[0;34m<\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    978\u001b[0m         raise ValueError('illegal value in %d-th argument of internal '\n",
      "\u001b[0;31mLinAlgError\u001b[0m: singular matrix"
     ]
    }
   ],
   "source": [
    "%load_ext line_profiler\n",
    "%matplotlib inline\n",
    "import numpy as np\n",
    "import sys\n",
    "sys.path.insert(0, \"../\")\n",
    "from pygraph.utils.model_selection_precomputed import model_selection_for_precomputed_kernel\n",
    "from pygraph.kernels.commonWalkKernel import commonwalkkernel\n",
    "\n",
    "dslist = [   \n",
    "    {'name': 'Acyclic', 'dataset': '../datasets/acyclic/dataset_bps.ds', 'task': 'regression'}, # node_labeled\n",
    "#     {'name': 'COIL-DEL', 'dataset': '../datasets/COIL-DEL/COIL-DEL_A.txt'}, # edge_labeled\n",
    "#     {'name': 'PAH', 'dataset': '../datasets/PAH/dataset.ds',}, # unlabeled\n",
    "#     {'name': 'Mutagenicity', 'dataset': '../datasets/Mutagenicity/Mutagenicity_A.txt'}, # fully_labeled\n",
    "    {'name': 'MAO', 'dataset': '../datasets/MAO/dataset.ds',},\n",
    "\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', 'task': 'regression', \n",
    "#         'dataset_y': '../datasets/Alkane/dataset_boiling_point_names.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': 'ENZYMES', 'dataset': '../datasets/ENZYMES_txt/ENZYMES_A_sparse.txt'},\n",
    "#     {'name': 'DHFR', 'dataset': '../datasets/DHFR_txt/DHFR_A_sparse.txt'},\n",
    "#     {'name': 'SYNTHETIC', 'dataset': '../datasets/SYNTHETIC_txt/SYNTHETIC_A_sparse.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': 'FIRSTMM_DB', 'dataset': '../datasets/FIRSTMM_DB/FIRSTMM_DB_A.txt'},\n",
    "\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': 'AIDS', 'dataset': '../datasets/AIDS/AIDS_A.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",
    "estimator = commonwalkkernel\n",
    "param_grid_precomputed = {}\n",
    "param_grid = [{'C': np.logspace(-10, 10, num = 41, base = 10)}, \n",
    "              {'alpha': np.logspace(-10, 10, num = 41, base = 10)}]\n",
    "\n",
    "for ds in dslist:\n",
    "    print()\n",
    "    print(ds['name'])\n",
    "    model_selection_for_precomputed_kernel(\n",
    "        ds['dataset'], estimator, param_grid_precomputed, \n",
    "        (param_grid[1] if ('task' in ds and ds['task'] == 'regression') else param_grid[0]), \n",
    "        (ds['task'] if 'task' in ds else 'classification'), NUM_TRIALS=30,\n",
    "        datafile_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",
    "    print()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "--- This is a regression problem ---\n",
      "\n",
      "1. Loading dataset from file...\n",
      "\n",
      "2. Calculating gram matrices. This could take a while...\n",
      "\n",
      "gram matrix with parameters {'n': 0.0} is: \n"
     ]
    },
    {
     "ename": "IndexError",
     "evalue": "index 1 is out of bounds for axis 0 with size 1",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mIndexError\u001b[0m                                Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-1-2b1121e86472>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m     13\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     14\u001b[0m model_selection_for_precomputed_kernel(datafile, estimator, param_grid_precomputed, param_grid, \n\u001b[0;32m---> 15\u001b[0;31m                                        'regression', NUM_TRIALS=30)\n\u001b[0m",
      "\u001b[0;32m/media/ljia/DATA/research-repo/codes/Linlin/py-graph/pygraph/utils/model_selection_precomputed.py\u001b[0m in \u001b[0;36mmodel_selection_for_precomputed_kernel\u001b[0;34m(datafile, estimator, param_grid_precomputed, param_grid, model_type, NUM_TRIALS, datafile_y)\u001b[0m\n\u001b[1;32m     94\u001b[0m         \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'gram matrix with parameters'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mparams_out\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'is: '\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     95\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 96\u001b[0;31m         \u001b[0mKmatrix\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcurrent_run_time\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mestimator\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdataset\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mparams_out\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     97\u001b[0m         \u001b[0mKmatrix_diag\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mKmatrix\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdiagonal\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcopy\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     98\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/media/ljia/DATA/research-repo/codes/Linlin/py-graph/pygraph/kernels/untilnWalkKernel.py\u001b[0m in \u001b[0;36muntilnwalkkernel\u001b[0;34m(node_label, edge_label, labeled, n, weight, compute_method, *args)\u001b[0m\n\u001b[1;32m     65\u001b[0m             \u001b[0;32mfor\u001b[0m \u001b[0mj\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mrange\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mi\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mGn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     66\u001b[0m                 Kmatrix[i][j] = _untilnwalkkernel_direct(\n\u001b[0;32m---> 67\u001b[0;31m                     Gn[i], Gn[j], node_label, edge_label, labeled, weight)\n\u001b[0m\u001b[1;32m     68\u001b[0m                 \u001b[0mKmatrix\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mj\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mi\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mKmatrix\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mi\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mj\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     69\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/media/ljia/DATA/research-repo/codes/Linlin/py-graph/pygraph/kernels/untilnWalkKernel.py\u001b[0m in \u001b[0;36m_untilnwalkkernel_direct\u001b[0;34m(G1, G2, node_label, edge_label, labeled, weight)\u001b[0m\n\u001b[1;32m    129\u001b[0m     \u001b[0;32mfor\u001b[0m \u001b[0mi\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mj\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mproduct\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mgp\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mgp\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    130\u001b[0m         \u001b[0mmat_tmp\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mT\u001b[0m \u001b[0;34m*\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mexp\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mweight\u001b[0m \u001b[0;34m*\u001b[0m \u001b[0mD\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m*\u001b[0m \u001b[0mT\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mI\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 131\u001b[0;31m         \u001b[0mkernel\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mkernel\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0mmat_tmp\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mi\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mj\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    132\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    133\u001b[0m     \u001b[0;31m# from matplotlib import pyplot as plt\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/usr/local/lib/python3.5/dist-packages/numpy/matrixlib/defmatrix.py\u001b[0m in \u001b[0;36m__getitem__\u001b[0;34m(self, index)\u001b[0m\n\u001b[1;32m    282\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    283\u001b[0m         \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 284\u001b[0;31m             \u001b[0mout\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mN\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mndarray\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__getitem__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mindex\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    285\u001b[0m         \u001b[0;32mfinally\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    286\u001b[0m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_getitem\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mIndexError\u001b[0m: index 1 is out of bounds for axis 0 with size 1"
     ]
    }
   ],
   "source": [
    "%load_ext line_profiler\n",
    "%matplotlib inline\n",
    "import numpy as np\n",
    "import sys\n",
    "sys.path.insert(0, \"../\")\n",
    "from pygraph.utils.model_selection_precomputed import model_selection_for_precomputed_kernel\n",
    "from pygraph.kernels.untilnWalkKernel import untilnwalkkernel\n",
    "\n",
    "datafile = '../../../../datasets/acyclic/Acyclic/dataset_bps.ds'\n",
    "estimator = untilnwalkkernel\n",
    "param_grid_precomputed = {'n': np.linspace(0, 10, 11)}\n",
    "param_grid = {'alpha': np.logspace(-10, 10, num = 41, base = 10)}\n",
    "\n",
    "model_selection_for_precomputed_kernel(datafile, estimator, param_grid_precomputed, param_grid, \n",
    "                                       'regression', NUM_TRIALS=30)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# results\n",
    "\n",
    "# untiln kernel when h = 2\n",
    "       lmda    rmse_test    std_test    rmse_train    std_train    k_time\n",
    "-----------  -----------  ----------  ------------  -----------  --------\n",
    "     1e-10       7.46524     1.71862       5.99486     0.356634   38.1447\n",
    "     1e-09       7.37326     1.77195       5.96155     0.374395   37.4921\n",
    "     1e-08       7.35105     1.78349       5.96481     0.378047   37.9971\n",
    "     1e-07       7.35213     1.77903       5.96728     0.382251   38.3182\n",
    "     1e-06       7.3524      1.77992       5.9696      0.3863     39.6428\n",
    "     1e-05       7.34958     1.78141       5.97114     0.39017    37.3711\n",
    "     0.0001      7.3513      1.78136       5.94251     0.331843   37.3967\n",
    "     0.001       7.35822     1.78119       5.9326      0.32534    36.7357\n",
    "     0.01        7.37552     1.79037       5.94089     0.34763    36.8864\n",
    "     0.1         7.32951     1.91346       6.42634     1.29405    36.8382\n",
    "     1           7.27134     2.20774       6.62425     1.2242     37.2425\n",
    "    10           7.49787     2.36815       6.81697     1.50182    37.8286\n",
    "   100           7.42887     2.64789       6.68766     1.34809    36.3701\n",
    "  1000           7.24914     2.65554       6.81906     1.41008    36.1695\n",
    " 10000           7.08183     2.6248        6.93431     1.38441    37.5723\n",
    "100000           8.021       3.43694       8.69813     0.909839   37.8158\n",
    "     1e+06       8.49625     3.6332        9.59333     0.96626    38.4688\n",
    "     1e+07      10.9067      3.17593      11.5642      2.07792    36.9926\n",
    "     1e+08      61.1524     10.4355       65.3527     13.9538     37.1321\n",
    "     1e+09      99.943      13.6994       98.8848      5.27014    36.7443\n",
    "     1e+10     100.083      13.8503       97.9168      3.22768    37.096\n"
   ]
  }
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