graphkit-learn/notebooks/test_marginalizedkernel.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 229,
   "metadata": {},
   "outputs": [],
   "source": [
    "import sys\n",
    "import pathlib\n",
    "sys.path.insert(0, \"../py-graph/\")\n",
    "\n",
    "\n",
    "import networkx as nx\n",
    "import numpy as np\n",
    "import time\n",
    "\n",
    "from utils.utils import getSPGraph\n",
    "\n",
    "\n",
    "def marginalizedkernel(*args):\n",
    "    \"\"\"Calculate marginalized graph kernels between graphs.\n",
    "    \n",
    "    Parameters\n",
    "    ----------\n",
    "    Gn : List of NetworkX graph\n",
    "        List of graphs between which the kernels are calculated.\n",
    "    /\n",
    "    G1, G2 : NetworkX graphs\n",
    "        2 graphs between which the kernel is calculated.\n",
    "        \n",
    "    Return\n",
    "    ------\n",
    "    Kmatrix/Kernel : Numpy matrix/int\n",
    "        Kernel matrix, each element of which is the sp kernel between 2 praphs. / SP Kernel between 2 graphs.\n",
    "        \n",
    "    References\n",
    "    ----------\n",
    "    [1] H. Kashima, K. Tsuda, and A. Inokuchi. Marginalized kernels between labeled graphs. In Proceedings of the 20th International Conference on Machine Learning, Washington, DC, United States, 2003.\n",
    "    \"\"\"\n",
    "    if len(args) == 3: # for a list of graphs\n",
    "        Gn = args[0]\n",
    "\n",
    "        Kmatrix = np.zeros((len(Gn), len(Gn)))\n",
    "\n",
    "        start_time = time.time()\n",
    "        for i in range(0, len(Gn)):\n",
    "            for j in range(i, len(Gn)):\n",
    "                print('\\n --- under the realm of G%d G%d ---' % (i, j))\n",
    "                Kmatrix[i][j] = marginalizedkernel(Gn[i], Gn[j], args[1], args[2])\n",
    "                Kmatrix[j][i] = Kmatrix[i][j]\n",
    "                print(Kmatrix[i][j])\n",
    "\n",
    "            print(\"--- marginalized kernel matrix of size %d built in %s seconds ---\" % (len(Gn), (time.time() - start_time)))\n",
    "        \n",
    "        return Kmatrix\n",
    "        \n",
    "    else: # for only 2 graphs\n",
    "        \n",
    "        # init parameters\n",
    "        G1 = args[0]\n",
    "        G2 = args[1]\n",
    "        p_quit = args[2] # the termination probability in the random walks generating step\n",
    "        itr = args[3] # time of iterations to calculate R_inf\n",
    "        \n",
    "        kernel = 0\n",
    "        num_nodes_G1 = nx.number_of_nodes(G1)\n",
    "        num_nodes_G2 = nx.number_of_nodes(G2)\n",
    "        p_init_G1 = 1 / num_nodes_G1 # the initial probability distribution in the random walks generating step (uniform distribution over |G|)\n",
    "        p_init_G2 = 1 / num_nodes_G2\n",
    "        \n",
    "        q = p_quit * p_quit\n",
    "        r1 = q\n",
    "        \n",
    "        # initial R_inf\n",
    "        R_inf = np.zeros([num_nodes_G1, num_nodes_G2]) # matrix to save all the R_inf for all pairs of nodes\n",
    "#         print(R_inf)\n",
    "        \n",
    "        # calculate R_inf with a simple interative method\n",
    "#         print('\\n --- part I: calculating R_inf ---')\n",
    "        for i in range(1, itr):\n",
    "#             print('\\n --- iterating the %dth time ---' % (i + 1))\n",
    "            R_inf_new = np.zeros([num_nodes_G1, num_nodes_G2])\n",
    "            R_inf_new.fill(r1)\n",
    "#             print(R_inf_new)\n",
    "\n",
    "            for node1 in G1.nodes(data = True):\n",
    "                neighbor_n1 = G1[node1[0]]\n",
    "                p_trans_n1 = (1 - p_quit) / len(neighbor_n1) # the transition probability distribution in the random walks generating step (uniform distribution over the vertices adjacent to the current vertex)\n",
    "                for node2 in G2.nodes(data = True):\n",
    "                    neighbor_n2 = G2[node2[0]]\n",
    "                    p_trans_n2 = (1 - p_quit) / len(neighbor_n2)    \n",
    "#                     print('\\n --- under the realm of node %d in G1 and node %d in G2 ---' % (node1[0], node2[0]))\n",
    "\n",
    "                    for neighbor1 in neighbor_n1:\n",
    "                        for neighbor2 in neighbor_n2:\n",
    "#                             print('\\n --- for neighbors %d in G1 and %d in G2 ---' % (neighbor1, neighbor2))\n",
    "                            \n",
    "                            t = p_trans_n1 * p_trans_n2 * \\\n",
    "                                deltaKernel(G1.node[neighbor1]['label'] == G2.node[neighbor2]['label']) * \\\n",
    "                                deltaKernel(neighbor_n1[neighbor1]['label'] == neighbor_n2[neighbor2]['label'])\n",
    "                            R_inf_new[node1[0]][node2[0]] += t * R_inf[neighbor1][neighbor2]\n",
    "#                             print(R_inf_new)\n",
    "\n",
    "            R_inf[:] = R_inf_new\n",
    "#             print(R_inf)\n",
    "        \n",
    "        # calculate kernel\n",
    "#         print('\\n --- part II: calculating kernel ---')\n",
    "        for node1 in G1.nodes(data = True):\n",
    "            for node2 in G2.nodes(data = True):\n",
    "#                 print('\\n --- under the realm of node %d in G1 and node %d in G2 ---' % (node1[0], node2[0]))\n",
    "                \n",
    "                s = p_init_G1 * p_init_G2 * deltaKernel(node1[1]['label'] == node2[1]['label'])\n",
    "#                 print(s)\n",
    "                kernel += s * R_inf[node1[0]][node2[0]]\n",
    "#                 print(kernel)\n",
    "\n",
    "#         print('\\n --- marginalized kernel built in %s seconds ---' % (time.time() - start_time))\n",
    "        \n",
    "        return kernel\n",
    "    \n",
    "def deltaKernel(condition):\n",
    "    \"\"\"Return 1 if condition holds, 0 otherwise.\n",
    "    \n",
    "    Parameters\n",
    "    ----------\n",
    "    condition : Boolean\n",
    "        List of graphs between which the kernels are calculated.\n",
    "        \n",
    "    Return\n",
    "    ------\n",
    "    Kmatrix/Kernel : Numpy matrix/int\n",
    "        Kernel matrix, each element of which is the sp kernel between 2 praphs. / SP Kernel between 2 graphs.\n",
    "        \n",
    "    References\n",
    "    ----------\n",
    "    [1] H. Kashima, K. Tsuda, and A. Inokuchi. Marginalized kernels between labeled graphs. In Proceedings of the 20th International Conference on Machine Learning, Washington, DC, United States, 2003.\n",
    "    \"\"\"\n",
    "    return (1 if condition else 0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 230,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
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      "text/plain": [
       "<matplotlib.figure.Figure at 0x7f6810a3ad68>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      " --- under the realm of G0 G0 ---\n",
      "0.185185185185\n",
      "\n",
      " --- under the realm of G0 G1 ---\n",
      "0.155913978495\n",
      "\n",
      " --- under the realm of G0 G2 ---\n",
      "0.111111111111\n",
      "\n",
      " --- under the realm of G0 G3 ---\n",
      "0.0833333333333\n",
      "\n",
      " --- under the realm of G0 G4 ---\n",
      "0.17281420765\n",
      "\n",
      " --- under the realm of G0 G5 ---\n",
      "0.152841781874\n",
      "\n",
      " --- under the realm of G0 G6 ---\n",
      "0.177777777777\n",
      "\n",
      " --- under the realm of G0 G7 ---\n",
      "0.125\n",
      "\n",
      " --- under the realm of G0 G8 ---\n",
      "0.1\n",
      "\n",
      " --- under the realm of G0 G9 ---\n",
      "0.1\n",
      "\n",
      " --- under the realm of G0 G10 ---\n",
      "0.171584699454\n",
      "\n",
      " --- under the realm of G0 G11 ---\n",
      "0.165591397849\n",
      "\n",
      " --- under the realm of G0 G12 ---\n",
      "0.169565217391\n",
      "\n",
      " --- under the realm of G0 G13 ---\n",
      "0.150793650794\n",
      "\n",
      " --- under the realm of G0 G14 ---\n",
      "0.15372571213\n",
      "\n",
      " --- under the realm of G0 G15 ---\n",
      "0.165886026542\n",
      "\n",
      " --- under the realm of G0 G16 ---\n",
      "0.172161172161\n",
      "\n",
      " --- under the realm of G0 G17 ---\n",
      "0.174863387978\n",
      "\n",
      " --- under the realm of G0 G18 ---\n",
      "0.133333333333\n",
      "\n",
      " --- under the realm of G0 G19 ---\n",
      "0.133333333333\n",
      "\n",
      " --- under the realm of G0 G20 ---\n",
      "0.133333333333\n",
      "\n",
      " --- under the realm of G0 G21 ---\n",
      "0.111111111111\n",
      "\n",
      " --- under the realm of G0 G22 ---\n",
      "0.111111111111\n",
      "\n",
      " --- under the realm of G0 G23 ---\n",
      "0.111111111111\n",
      "\n",
      " --- under the realm of G0 G24 ---\n",
      "0.111111111111\n",
      "\n",
      " --- under the realm of G0 G25 ---\n",
      "0.170765027322\n",
      "\n",
      " --- under the realm of G0 G26 ---\n",
      "0.165770609319\n",
      "\n",
      " --- under the realm of G0 G27 ---\n",
      "0.164141414141\n",
      "\n",
      " --- under the realm of G0 G28 ---\n",
      "0.170765027322\n",
      "\n",
      " --- under the realm of G0 G29 ---\n",
      "0.169082125604\n",
      "\n",
      " --- under the realm of G0 G30 ---\n",
      "0.168247515808\n",
      "\n",
      " --- under the realm of G0 G31 ---\n",
      "0.165886026542\n",
      "\n",
      " --- under the realm of G0 G32 ---\n",
      "0.169789227166\n",
      "\n",
      " --- under the realm of G0 G33 ---\n",
      "0.173692427791\n",
      "\n",
      " --- under the realm of G0 G34 ---\n",
      "0.169411498074\n",
      "\n",
      " --- under the realm of G0 G35 ---\n",
      "0.172249940603\n",
      "\n",
      " --- under the realm of G0 G36 ---\n",
      "0.138888888889\n",
      "\n",
      " --- under the realm of G0 G37 ---\n",
      "0.138888888889\n",
      "\n",
      " --- under the realm of G0 G38 ---\n",
      "0.138888888889\n",
      "\n",
      " --- under the realm of G0 G39 ---\n",
      "0.138888888889\n",
      "\n",
      " --- under the realm of G0 G40 ---\n",
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      "--- marginalized kernel matrix of size 185 built in 10.833643674850464 seconds ---\n",
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    {
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     "output_type": "stream",
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      "0.1921334227\n",
      "--- marginalized kernel matrix of size 185 built in 13.951702117919922 seconds ---\n",
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      "--- marginalized kernel matrix of size 185 built in 29.081072092056274 seconds ---\n",
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      "--- marginalized kernel matrix of size 185 built in 73.01038122177124 seconds ---\n",
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      "--- marginalized kernel matrix of size 185 built in 89.7324891090393 seconds ---\n",
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      "--- marginalized kernel matrix of size 185 built in 94.31654834747314 seconds ---\n",
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      "--- marginalized kernel matrix of size 185 built in 103.35213112831116 seconds ---\n",
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      "--- marginalized kernel matrix of size 185 built in 107.81398153305054 seconds ---\n",
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      "--- marginalized kernel matrix of size 185 built in 136.09660005569458 seconds ---\n",
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      " --- under the realm of G42 G184 ---\n",
      "0.206012498816\n",
      "--- marginalized kernel matrix of size 185 built in 182.58098125457764 seconds ---\n",
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      "--- marginalized kernel matrix of size 185 built in 221.08330917358398 seconds ---\n",
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      "--- marginalized kernel matrix of size 185 built in 225.77538967132568 seconds ---\n",
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      "--- marginalized kernel matrix of size 185 built in 230.45115995407104 seconds ---\n",
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      "--- marginalized kernel matrix of size 185 built in 235.07260656356812 seconds ---\n",
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      "--- marginalized kernel matrix of size 185 built in 294.1052289009094 seconds ---\n",
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      "--- marginalized kernel matrix of size 185 built in 310.9425971508026 seconds ---\n",
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      "--- marginalized kernel matrix of size 185 built in 315.0771472454071 seconds ---\n",
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      "--- marginalized kernel matrix of size 185 built in 319.1687262058258 seconds ---\n",
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      "--- marginalized kernel matrix of size 185 built in 323.2372226715088 seconds ---\n",
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      "--- marginalized kernel matrix of size 185 built in 327.39819073677063 seconds ---\n",
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      "--- marginalized kernel matrix of size 185 built in 345.25114917755127 seconds ---\n",
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      "--- marginalized kernel matrix of size 185 built in 349.77428579330444 seconds ---\n",
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      "--- marginalized kernel matrix of size 185 built in 363.1714186668396 seconds ---\n",
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      "--- marginalized kernel matrix of size 185 built in 367.5749955177307 seconds ---\n",
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      "0.244945042271\n",
      "--- marginalized kernel matrix of size 185 built in 371.98047614097595 seconds ---\n",
      "\n",
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      "--- marginalized kernel matrix of size 185 built in 376.2770917415619 seconds ---\n",
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      "0.245933322175\n",
      "--- marginalized kernel matrix of size 185 built in 380.5485157966614 seconds ---\n",
      "\n",
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      "--- marginalized kernel matrix of size 185 built in 384.83973240852356 seconds ---\n",
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      "--- marginalized kernel matrix of size 185 built in 389.0551223754883 seconds ---\n",
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      "--- marginalized kernel matrix of size 185 built in 397.4121353626251 seconds ---\n",
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      "0.246952359966\n",
      "--- marginalized kernel matrix of size 185 built in 401.51956510543823 seconds ---\n",
      "\n",
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      "\n",
      " --- under the realm of G91 G159 ---\n"
     ]
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    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0.223256553527\n",
      "\n",
      " --- under the realm of G91 G160 ---\n",
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      "\n",
      " --- under the realm of G91 G161 ---\n",
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      "\n",
      " --- under the realm of G91 G184 ---\n",
      "0.245767951009\n",
      "--- marginalized kernel matrix of size 185 built in 405.58402371406555 seconds ---\n",
      "\n",
      " --- under the realm of G92 G92 ---\n",
      "0.24373634953\n",
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      "\n",
      " --- under the realm of G92 G167 ---\n",
      "0.217487931822\n",
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      "0.218967742098\n",
      "\n",
      " --- under the realm of G92 G169 ---\n",
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      "\n",
      " --- under the realm of G92 G172 ---\n",
      "0.254278640978\n",
      "\n",
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      "0.247457194866\n",
      "\n",
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      "0.253112632307\n",
      "\n",
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      "0.253099806544\n",
      "\n",
      " --- under the realm of G92 G176 ---\n",
      "0.253541498244\n",
      "\n",
      " --- under the realm of G92 G177 ---\n",
      "0.253070866138\n",
      "\n",
      " --- under the realm of G92 G178 ---\n",
      "0.253106219425\n",
      "\n",
      " --- under the realm of G92 G179 ---\n",
      "0.251508860254\n",
      "\n",
      " --- under the realm of G92 G180 ---\n",
      "0.250476954782\n",
      "\n",
      " --- under the realm of G92 G181 ---\n",
      "0.248597667658\n",
      "\n",
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      "0.248611480582\n",
      "\n",
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      "0.248654128041\n",
      "\n",
      " --- under the realm of G92 G184 ---\n",
      "0.246164853283\n",
      "--- marginalized kernel matrix of size 185 built in 409.6086723804474 seconds ---\n",
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      "--- marginalized kernel matrix of size 185 built in 413.58516812324524 seconds ---\n",
      "\n",
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      "0.246005722232\n",
      "--- marginalized kernel matrix of size 185 built in 417.537716627121 seconds ---\n",
      "\n",
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      "--- marginalized kernel matrix of size 185 built in 421.99995851516724 seconds ---\n",
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    {
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      "--- marginalized kernel matrix of size 185 built in 426.4072690010071 seconds ---\n",
      "\n",
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      "--- marginalized kernel matrix of size 185 built in 430.79289865493774 seconds ---\n",
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      "--- marginalized kernel matrix of size 185 built in 435.10396933555603 seconds ---\n",
      "\n",
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      "--- marginalized kernel matrix of size 185 built in 439.4360194206238 seconds ---\n",
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      "--- marginalized kernel matrix of size 185 built in 451.99212622642517 seconds ---\n",
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      "--- marginalized kernel matrix of size 185 built in 456.09091877937317 seconds ---\n",
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      "--- marginalized kernel matrix of size 185 built in 459.65062379837036 seconds ---\n",
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      "0.250445511363\n",
      "--- marginalized kernel matrix of size 185 built in 463.17454624176025 seconds ---\n",
      "\n",
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      "--- marginalized kernel matrix of size 185 built in 466.66933584213257 seconds ---\n",
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      " --- under the realm of G107 G184 ---\n",
      "0.250882509359\n",
      "--- marginalized kernel matrix of size 185 built in 470.08134388923645 seconds ---\n",
      "\n",
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      "0.250153382814\n",
      "--- marginalized kernel matrix of size 185 built in 473.48286533355713 seconds ---\n",
      "\n",
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      "0.251130576939\n",
      "--- marginalized kernel matrix of size 185 built in 476.85581970214844 seconds ---\n",
      "\n",
      " --- under the realm of G110 G110 ---\n",
      "0.244759231959\n",
      "\n",
      " --- under the realm of G110 G111 ---\n",
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      "0.213279336679\n",
      "\n"
     ]
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    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
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      "\n",
      " --- under the realm of G110 G184 ---\n",
      "0.251361719517\n",
      "--- marginalized kernel matrix of size 185 built in 480.1689510345459 seconds ---\n",
      "\n",
      " --- under the realm of G111 G111 ---\n",
      "0.241548846339\n",
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      "0.250048291941\n",
      "--- marginalized kernel matrix of size 185 built in 483.49760341644287 seconds ---\n",
      "\n",
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      "0.250793338285\n",
      "--- marginalized kernel matrix of size 185 built in 486.7736485004425 seconds ---\n",
      "\n",
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      "0.218159979886\n",
      "--- marginalized kernel matrix of size 185 built in 490.4966449737549 seconds ---\n",
      "\n",
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      "0.225322508066\n",
      "\n"
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      "0.250488986765\n",
      "--- marginalized kernel matrix of size 185 built in 494.14681458473206 seconds ---\n",
      "\n",
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      "\n",
      " --- under the realm of G115 G184 ---\n",
      "0.250457487867\n",
      "--- marginalized kernel matrix of size 185 built in 497.7129626274109 seconds ---\n",
      "\n",
      " --- under the realm of G116 G116 ---\n",
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      "\n",
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      "\n"
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      " --- under the realm of G116 G142 ---\n",
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      " --- under the realm of G116 G180 ---\n",
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      "\n",
      " --- under the realm of G116 G181 ---\n",
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      "0.253085894956\n",
      "\n",
      " --- under the realm of G116 G184 ---\n",
      "0.250570498385\n",
      "--- marginalized kernel matrix of size 185 built in 501.2381286621094 seconds ---\n",
      "\n",
      " --- under the realm of G117 G117 ---\n",
      "0.252010368837\n",
      "\n",
      " --- under the realm of G117 G118 ---\n",
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      "--- marginalized kernel matrix of size 185 built in 504.7114350795746 seconds ---\n",
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      "--- marginalized kernel matrix of size 185 built in 508.18280148506165 seconds ---\n",
      "\n",
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      "--- marginalized kernel matrix of size 185 built in 511.57191157341003 seconds ---\n",
      "\n",
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      "\n",
      " --- under the realm of G120 G182 ---\n",
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      "0.250650260558\n",
      "\n",
      " --- under the realm of G120 G184 ---\n",
      "0.248263153866\n",
      "--- marginalized kernel matrix of size 185 built in 514.9148395061493 seconds ---\n",
      "\n",
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      " --- under the realm of G121 G184 ---\n",
      "0.250652010004\n",
      "--- marginalized kernel matrix of size 185 built in 518.195853471756 seconds ---\n",
      "\n",
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      " --- under the realm of G122 G184 ---\n",
      "0.251476309754\n",
      "--- marginalized kernel matrix of size 185 built in 521.4442369937897 seconds ---\n",
      "\n",
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      "0.244412740271\n"
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      "0.252300609504\n",
      "--- marginalized kernel matrix of size 185 built in 524.6475987434387 seconds ---\n",
      "\n",
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      "0.252035999966\n",
      "--- marginalized kernel matrix of size 185 built in 527.7936069965363 seconds ---\n",
      "\n",
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      " --- under the realm of G125 G172 ---\n"
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    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
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      " --- under the realm of G125 G173 ---\n",
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      "0.249856639845\n",
      "\n",
      " --- under the realm of G125 G184 ---\n",
      "0.247518958177\n",
      "--- marginalized kernel matrix of size 185 built in 530.9512453079224 seconds ---\n",
      "\n",
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      "0.253959735344\n",
      "\n",
      " --- under the realm of G126 G184 ---\n",
      "0.251390006131\n",
      "--- marginalized kernel matrix of size 185 built in 534.0428178310394 seconds ---\n",
      "\n",
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      "0.227070548553\n",
      "--- marginalized kernel matrix of size 185 built in 537.4397251605988 seconds ---\n",
      "\n",
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      "0.220872963859\n",
      "--- marginalized kernel matrix of size 185 built in 540.7779405117035 seconds ---\n",
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      "0.219964784638\n",
      "--- marginalized kernel matrix of size 185 built in 544.0505743026733 seconds ---\n",
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      "0.21518380199\n",
      "--- marginalized kernel matrix of size 185 built in 547.2725028991699 seconds ---\n",
      "\n",
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      "0.216103935015\n",
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      " --- under the realm of G131 G184 ---\n",
      "0.214383762891\n",
      "--- marginalized kernel matrix of size 185 built in 550.4463684558868 seconds ---\n",
      "\n",
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      "\n",
      " --- under the realm of G132 G184 ---\n",
      "0.217288198934\n",
      "--- marginalized kernel matrix of size 185 built in 553.5616719722748 seconds ---\n",
      "\n",
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      "0.250751893004\n",
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      "\n",
      " --- under the realm of G133 G178 ---\n"
     ]
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    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0.252944736288\n",
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      "0.257135318254\n",
      "\n",
      " --- under the realm of G133 G184 ---\n",
      "0.255002878658\n",
      "--- marginalized kernel matrix of size 185 built in 556.2920248508453 seconds ---\n",
      "\n",
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      "0.25107068714\n",
      "\n",
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      "\n",
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      "\n",
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      "0.25730510037\n",
      "\n",
      " --- under the realm of G134 G184 ---\n",
      "0.255161396849\n",
      "--- marginalized kernel matrix of size 185 built in 558.9690165519714 seconds ---\n",
      "\n",
      " --- under the realm of G135 G135 ---\n",
      "0.25090576593\n",
      "\n",
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      "\n",
      " --- under the realm of G135 G167 ---\n",
      "0.229496336256\n",
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      "0.251184222827\n",
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      " --- under the realm of G135 G180 ---\n",
      "0.258633895984\n",
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      " --- under the realm of G135 G181 ---\n",
      "0.257157542769\n",
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      "0.257170732536\n",
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      "0.257220209351\n",
      "\n",
      " --- under the realm of G135 G184 ---\n",
      "0.255082137778\n",
      "--- marginalized kernel matrix of size 185 built in 561.5971233844757 seconds ---\n",
      "\n",
      " --- under the realm of G136 G136 ---\n",
      "0.254572688177\n",
      "\n",
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      "0.254854851945\n",
      "\n"
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    {
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     "text": [
      " --- under the realm of G136 G178 ---\n",
      "0.254897765618\n",
      "\n",
      " --- under the realm of G136 G179 ---\n",
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      " --- under the realm of G136 G180 ---\n",
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      "\n",
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      "\n",
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      "0.258759695492\n",
      "\n",
      " --- under the realm of G136 G184 ---\n",
      "0.25622318862\n",
      "--- marginalized kernel matrix of size 185 built in 564.2041752338409 seconds ---\n",
      "\n",
      " --- under the realm of G137 G137 ---\n",
      "0.253415157327\n",
      "\n",
      " --- under the realm of G137 G138 ---\n",
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      "\n",
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      "\n",
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      "\n",
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      "\n",
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      "0.258423480869\n",
      "\n",
      " --- under the realm of G137 G184 ---\n",
      "0.2560122763\n",
      "--- marginalized kernel matrix of size 185 built in 566.7219944000244 seconds ---\n",
      "\n",
      " --- under the realm of G138 G138 ---\n",
      "0.252010368837\n",
      "\n",
      " --- under the realm of G138 G139 ---\n",
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      "\n",
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      "0.254956652394\n",
      "\n",
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      "0.246886734459\n",
      "\n",
      " --- under the realm of G138 G174 ---\n",
      "0.2537078042\n",
      "\n",
      " --- under the realm of G138 G175 ---\n",
      "0.253692447539\n",
      "\n",
      " --- under the realm of G138 G176 ---\n",
      "0.254111230888\n",
      "\n",
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      "0.253654895265\n",
      "\n",
      " --- under the realm of G138 G178 ---\n",
      "0.25370012587\n",
      "\n",
      " --- under the realm of G138 G179 ---\n",
      "0.251828769201\n",
      "\n",
      " --- under the realm of G138 G180 ---\n",
      "0.259394690184\n",
      "\n",
      " --- under the realm of G138 G181 ---\n",
      "0.257725088396\n",
      "\n",
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      "0.257739046918\n",
      "\n",
      " --- under the realm of G138 G183 ---\n",
      "0.25777940249\n",
      "\n",
      " --- under the realm of G138 G184 ---\n",
      "0.255507032476\n",
      "--- marginalized kernel matrix of size 185 built in 569.2255895137787 seconds ---\n",
      "\n",
      " --- under the realm of G139 G139 ---\n",
      "0.252154238505\n",
      "\n",
      " --- under the realm of G139 G140 ---\n",
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      "\n",
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      "\n",
      " --- under the realm of G139 G144 ---\n",
      "0.225924629043\n",
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      "0.248964270702\n",
      "\n",
      " --- under the realm of G139 G146 ---\n",
      "0.250139176153\n",
      "\n",
      " --- under the realm of G139 G147 ---\n",
      "0.250508345411\n",
      "\n",
      " --- under the realm of G139 G148 ---\n",
      "0.25138686052\n",
      "\n",
      " --- under the realm of G139 G149 ---\n",
      "0.250500073892\n",
      "\n",
      " --- under the realm of G139 G150 ---\n",
      "0.248449770916\n",
      "\n",
      " --- under the realm of G139 G151 ---\n",
      "0.250581307754\n",
      "\n",
      " --- under the realm of G139 G152 ---\n",
      "0.248449698304\n",
      "\n",
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      "0.247752538553\n",
      "\n",
      " --- under the realm of G139 G154 ---\n",
      "0.247871402324\n",
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      " --- under the realm of G139 G155 ---\n",
      "0.248805475301\n",
      "\n",
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      "0.24776348231\n",
      "\n",
      " --- under the realm of G139 G157 ---\n",
      "0.251195564234\n",
      "\n",
      " --- under the realm of G139 G158 ---\n",
      "0.22946393541\n",
      "\n",
      " --- under the realm of G139 G159 ---\n",
      "0.218454759766\n",
      "\n",
      " --- under the realm of G139 G160 ---\n",
      "0.222629445735\n",
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      "0.224076239379\n",
      "\n",
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      "\n",
      " --- under the realm of G139 G166 ---\n",
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      "\n",
      " --- under the realm of G139 G167 ---\n",
      "0.229824201401\n",
      "\n",
      " --- under the realm of G139 G168 ---\n",
      "0.23108895312\n",
      "\n",
      " --- under the realm of G139 G169 ---\n",
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      "\n",
      " --- under the realm of G139 G170 ---\n",
      "0.254408648381\n",
      "\n",
      " --- under the realm of G139 G171 ---\n",
      "0.255373897318\n",
      "\n",
      " --- under the realm of G139 G172 ---\n",
      "0.255039989541\n",
      "\n",
      " --- under the realm of G139 G173 ---\n",
      "0.2469708746\n",
      "\n",
      " --- under the realm of G139 G174 ---\n",
      "0.253792413824\n",
      "\n",
      " --- under the realm of G139 G175 ---\n",
      "0.253777374698\n",
      "\n",
      " --- under the realm of G139 G176 ---\n",
      "0.254193612958\n",
      "\n",
      " --- under the realm of G139 G177 ---\n",
      "0.253740255993\n",
      "\n",
      " --- under the realm of G139 G178 ---\n",
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      "\n",
      " --- under the realm of G139 G179 ---\n",
      "0.251909491924\n",
      "\n",
      " --- under the realm of G139 G180 ---\n",
      "0.259460063171\n",
      "\n",
      " --- under the realm of G139 G181 ---\n",
      "0.257805532901\n",
      "\n",
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      "\n",
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      "0.257864290554\n",
      "\n",
      " --- under the realm of G139 G184 ---\n",
      "0.255586295542\n",
      "--- marginalized kernel matrix of size 185 built in 571.6811184883118 seconds ---\n",
      "\n",
      " --- under the realm of G140 G140 ---\n",
      "0.246228205794\n",
      "\n",
      " --- under the realm of G140 G141 ---\n",
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      "\n",
      " --- under the realm of G140 G142 ---\n",
      "0.226146215776\n",
      "\n",
      " --- under the realm of G140 G143 ---\n"
     ]
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    {
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     "output_type": "stream",
     "text": [
      "0.226975954879\n",
      "\n",
      " --- under the realm of G140 G144 ---\n",
      "0.223290305532\n",
      "\n",
      " --- under the realm of G140 G145 ---\n",
      "0.245198385287\n",
      "\n",
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      "\n",
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      "\n",
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      "\n",
      " --- under the realm of G140 G172 ---\n",
      "0.250919901496\n",
      "\n",
      " --- under the realm of G140 G173 ---\n",
      "0.242924089166\n",
      "\n",
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      "0.249813059669\n",
      "\n",
      " --- under the realm of G140 G175 ---\n",
      "0.249797564097\n",
      "\n",
      " --- under the realm of G140 G176 ---\n",
      "0.250147390778\n",
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      "0.249805311883\n",
      "\n",
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      "0.24808290512\n",
      "\n",
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      "\n",
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      "0.254325944816\n",
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      "0.254368096164\n",
      "\n",
      " --- under the realm of G140 G184 ---\n",
      "0.252668219374\n",
      "--- marginalized kernel matrix of size 185 built in 574.0798966884613 seconds ---\n",
      "\n",
      " --- under the realm of G141 G141 ---\n",
      "0.211218500749\n",
      "\n",
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      "0.22874462882\n",
      "\n",
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      "\n",
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      "0.227657340597\n",
      "\n",
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      "0.227643184722\n",
      "\n",
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      "0.227998544967\n",
      "\n",
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      "\n",
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      "0.23492520964\n",
      "\n",
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      "\n",
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      "\n",
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      "0.233599764141\n",
      "\n",
      " --- under the realm of G141 G184 ---\n",
      "0.231638845106\n",
      "--- marginalized kernel matrix of size 185 built in 576.7751498222351 seconds ---\n",
      "\n",
      " --- under the realm of G142 G142 ---\n",
      "0.211477463478\n",
      "\n",
      " --- under the realm of G142 G143 ---\n",
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      "\n",
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      "0.22485729439\n",
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      "0.196189603131\n",
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      "0.221654604616\n",
      "\n",
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      "0.227809637921\n",
      "\n",
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      "0.227802845764\n",
      "\n",
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      "0.226138450995\n",
      "\n",
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      "\n",
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      "0.233752872551\n",
      "\n",
      " --- under the realm of G142 G184 ---\n",
      "0.231781974184\n",
      "--- marginalized kernel matrix of size 185 built in 579.3824179172516 seconds ---\n",
      "\n",
      " --- under the realm of G143 G143 ---\n",
      "0.21433791283\n",
      "\n",
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      "0.226436292475\n",
      "\n",
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      "0.22454734653\n",
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      "0.224547285208\n",
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      "0.201268928297\n",
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      "0.199730879647\n",
      "\n",
      " --- under the realm of G143 G164 ---\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0.200652199413\n",
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      "\n",
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      "\n",
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      "\n",
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      "\n",
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      "\n",
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      "\n",
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      "\n",
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      "0.229401119928\n",
      "\n",
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      "0.229407989056\n",
      "\n",
      " --- under the realm of G143 G179 ---\n",
      "0.227680843339\n",
      "\n",
      " --- under the realm of G143 G180 ---\n",
      "0.236928192285\n",
      "\n",
      " --- under the realm of G143 G181 ---\n",
      "0.235063907665\n",
      "\n",
      " --- under the realm of G143 G182 ---\n",
      "0.235078276234\n",
      "\n",
      " --- under the realm of G143 G183 ---\n",
      "0.235097629614\n",
      "\n",
      " --- under the realm of G143 G184 ---\n",
      "0.23280149352\n",
      "--- marginalized kernel matrix of size 185 built in 581.9060389995575 seconds ---\n",
      "\n",
      " --- under the realm of G144 G144 ---\n",
      "0.207087336191\n",
      "\n",
      " --- under the realm of G144 G145 ---\n",
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      "\n",
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      "\n",
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      "\n",
      " --- under the realm of G144 G148 ---\n",
      "0.22094473722\n",
      "\n",
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      "0.218484621402\n",
      "\n",
      " --- under the realm of G144 G151 ---\n",
      "0.220180123137\n",
      "\n",
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      "0.218484584397\n",
      "\n",
      " --- under the realm of G144 G153 ---\n",
      "0.217872378432\n",
      "\n",
      " --- under the realm of G144 G154 ---\n",
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      "\n",
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      "\n",
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      "\n",
      " --- under the realm of G144 G157 ---\n",
      "0.220822925764\n",
      "\n",
      " --- under the realm of G144 G158 ---\n",
      "0.201681542177\n",
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      "0.196275601164\n",
      "\n",
      " --- under the realm of G144 G161 ---\n",
      "0.196623031335\n",
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      "\n",
      " --- under the realm of G144 G167 ---\n",
      "0.209379215857\n",
      "\n",
      " --- under the realm of G144 G168 ---\n",
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      "\n",
      " --- under the realm of G144 G169 ---\n",
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      "\n",
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      "0.223557025845\n",
      "\n",
      " --- under the realm of G144 G171 ---\n",
      "0.224250589891\n",
      "\n",
      " --- under the realm of G144 G172 ---\n",
      "0.224035222491\n",
      "\n",
      " --- under the realm of G144 G173 ---\n",
      "0.216745860551\n",
      "\n",
      " --- under the realm of G144 G174 ---\n",
      "0.222934480092\n",
      "\n",
      " --- under the realm of G144 G175 ---\n",
      "0.22292451693\n",
      "\n",
      " --- under the realm of G144 G176 ---\n",
      "0.223343504243\n",
      "\n",
      " --- under the realm of G144 G177 ---\n",
      "0.22290250482\n",
      "\n",
      " --- under the realm of G144 G178 ---\n",
      "0.222929498511\n",
      "\n",
      " --- under the realm of G144 G179 ---\n",
      "0.221429515964\n",
      "\n",
      " --- under the realm of G144 G180 ---\n",
      "0.231421900622\n",
      "\n",
      " --- under the realm of G144 G181 ---\n",
      "0.229971309432\n",
      "\n",
      " --- under the realm of G144 G182 ---\n",
      "0.229980775751\n",
      "\n",
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      "0.229987173464\n",
      "\n",
      " --- under the realm of G144 G184 ---\n",
      "0.228306400323\n",
      "--- marginalized kernel matrix of size 185 built in 584.3532395362854 seconds ---\n",
      "\n",
      " --- under the realm of G145 G145 ---\n",
      "0.255237881268\n",
      "\n",
      " --- under the realm of G145 G146 ---\n",
      "0.256139390007\n",
      "\n",
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      "0.256492976067\n",
      "\n",
      " --- under the realm of G145 G148 ---\n",
      "0.257118886902\n",
      "\n",
      " --- under the realm of G145 G149 ---\n",
      "0.2564842149\n",
      "\n",
      " --- under the realm of G145 G150 ---\n",
      "0.254819953374\n",
      "\n",
      " --- under the realm of G145 G151 ---\n",
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      "\n",
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      "\n",
      " --- under the realm of G145 G179 ---\n",
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      "\n",
      " --- under the realm of G145 G180 ---\n",
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      " --- under the realm of G145 G181 ---\n",
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      "0.255540431352\n",
      "\n",
      " --- under the realm of G145 G184 ---\n",
      "0.253039278207\n",
      "--- marginalized kernel matrix of size 185 built in 586.8177616596222 seconds ---\n",
      "\n",
      " --- under the realm of G146 G146 ---\n",
      "0.257156859846\n",
      "\n",
      " --- under the realm of G146 G147 ---\n",
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      "\n",
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      "0.25878676316\n",
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      "0.256739552833\n",
      "\n",
      " --- under the realm of G146 G184 ---\n",
      "0.254165885985\n",
      "--- marginalized kernel matrix of size 185 built in 589.1715576648712 seconds ---\n",
      "\n",
      " --- under the realm of G147 G147 ---\n",
      "0.257858295159\n",
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      "0.255570098171\n",
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      "0.256337825217\n"
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    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
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      "\n",
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      "0.257143299584\n",
      "\n",
      " --- under the realm of G147 G184 ---\n",
      "0.254559259039\n",
      "--- marginalized kernel matrix of size 185 built in 591.4724524021149 seconds ---\n",
      "\n",
      " --- under the realm of G148 G148 ---\n",
      "0.259448415334\n",
      "\n",
      " --- under the realm of G148 G149 ---\n",
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      "\n",
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      "\n",
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      "\n",
      " --- under the realm of G148 G176 ---\n",
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      "\n",
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      "0.261553697178\n",
      "\n",
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      "0.259788819629\n",
      "\n",
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      "\n",
      " --- under the realm of G148 G181 ---\n",
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      "\n",
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      "0.25797404634\n",
      "\n",
      " --- under the realm of G148 G183 ---\n",
      "0.258020130044\n",
      "\n",
      " --- under the realm of G148 G184 ---\n",
      "0.255374489272\n",
      "--- marginalized kernel matrix of size 185 built in 593.7085263729095 seconds ---\n",
      "\n",
      " --- under the realm of G149 G149 ---\n",
      "0.257841274964\n",
      "\n",
      " --- under the realm of G149 G150 ---\n",
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      "\n",
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      "\n",
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      "\n",
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      "0.260810544157\n",
      "\n",
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      "0.260795337184\n",
      "\n",
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      "0.261112730013\n",
      "\n",
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      "\n",
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      "\n",
      " --- under the realm of G149 G179 ---\n",
      "0.259143901755\n",
      "\n",
      " --- under the realm of G149 G180 ---\n",
      "0.258930843696\n",
      "\n",
      " --- under the realm of G149 G181 ---\n",
      "0.257069376825\n",
      "\n",
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      "0.257085789115\n",
      "\n",
      " --- under the realm of G149 G183 ---\n",
      "0.257134092351\n",
      "\n",
      " --- under the realm of G149 G184 ---\n",
      "0.254549981508\n",
      "--- marginalized kernel matrix of size 185 built in 595.8861720561981 seconds ---\n",
      "\n",
      " --- under the realm of G150 G150 ---\n",
      "0.254414673425\n",
      "\n",
      " --- under the realm of G150 G151 ---\n",
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      "\n",
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      "\n",
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      "\n",
      " --- under the realm of G150 G182 ---\n",
      "0.254961965879\n",
      "\n",
      " --- under the realm of G150 G183 ---\n",
      "0.25500670409\n",
      "\n",
      " --- under the realm of G150 G184 ---\n",
      "0.252533412138\n",
      "--- marginalized kernel matrix of size 185 built in 597.9962964057922 seconds ---\n",
      "\n",
      " --- under the realm of G151 G151 ---\n",
      "0.258001148328\n",
      "\n",
      " --- under the realm of G151 G152 ---\n",
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      "0.231289931623\n",
      "\n",
      " --- under the realm of G151 G164 ---\n"
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      "\n",
      " --- under the realm of G151 G165 ---\n",
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      "\n",
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      "0.257171436208\n",
      "\n",
      " --- under the realm of G151 G183 ---\n",
      "0.257221014815\n",
      "\n",
      " --- under the realm of G151 G184 ---\n",
      "0.254632619497\n",
      "--- marginalized kernel matrix of size 185 built in 600.0754623413086 seconds ---\n",
      "\n",
      " --- under the realm of G152 G152 ---\n",
      "0.254414498141\n",
      "\n",
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      "\n",
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      "0.257437234188\n",
      "\n",
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      "\n",
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      "0.254961872762\n",
      "\n",
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      "0.255006614921\n",
      "\n",
      " --- under the realm of G152 G184 ---\n",
      "0.252533315384\n",
      "--- marginalized kernel matrix of size 185 built in 602.0894904136658 seconds ---\n",
      "\n",
      " --- under the realm of G153 G153 ---\n",
      "0.253474880557\n",
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      "\n",
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      "\n",
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      "\n",
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      "0.25848740326\n",
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      "\n",
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      "0.258308896489\n",
      "\n",
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      "0.256905699845\n",
      "\n",
      " --- under the realm of G153 G180 ---\n",
      "0.255963570234\n",
      "\n",
      " --- under the realm of G153 G181 ---\n",
      "0.254238845251\n",
      "\n",
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      "0.254255095805\n",
      "\n",
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      "0.254300347972\n",
      "\n",
      " --- under the realm of G153 G184 ---\n",
      "0.251871626437\n",
      "--- marginalized kernel matrix of size 185 built in 604.0442929267883 seconds ---\n",
      "\n",
      " --- under the realm of G154 G154 ---\n",
      "0.253713311145\n",
      "\n",
      " --- under the realm of G154 G155 ---\n",
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      "0.235559717087\n",
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      "\n",
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      "0.230224254752\n",
      "\n",
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      "0.250725836446\n",
      "\n",
      " --- under the realm of G154 G166 ---\n",
      "0.248499015598\n",
      "\n",
      " --- under the realm of G154 G167 ---\n",
      "0.222633737188\n",
      "\n",
      " --- under the realm of G154 G168 ---\n",
      "0.223874536272\n",
      "\n",
      " --- under the realm of G154 G169 ---\n",
      "0.258084623746\n",
      "\n",
      " --- under the realm of G154 G170 ---\n",
      "0.258694905432\n",
      "\n",
      " --- under the realm of G154 G171 ---\n",
      "0.259545808358\n",
      "\n",
      " --- under the realm of G154 G172 ---\n",
      "0.25921343594\n",
      "\n",
      " --- under the realm of G154 G173 ---\n",
      "0.251966299484\n",
      "\n",
      " --- under the realm of G154 G174 ---\n",
      "0.258438597689\n",
      "\n",
      " --- under the realm of G154 G175 ---\n",
      "0.258422760596\n",
      "\n",
      " --- under the realm of G154 G176 ---\n",
      "0.258598875259\n",
      "\n",
      " --- under the realm of G154 G177 ---\n",
      "0.258382186609\n",
      "\n",
      " --- under the realm of G154 G178 ---\n",
      "0.258430679142\n",
      "\n",
      " --- under the realm of G154 G179 ---\n",
      "0.257023061824\n",
      "\n",
      " --- under the realm of G154 G180 ---\n",
      "0.256088234248\n",
      "\n",
      " --- under the realm of G154 G181 ---\n",
      "0.254367922005\n",
      "\n",
      " --- under the realm of G154 G182 ---\n",
      "0.254384380498\n",
      "\n",
      " --- under the realm of G154 G183 ---\n",
      "0.254430145103\n",
      "\n",
      " --- under the realm of G154 G184 ---\n",
      "0.251997874709\n",
      "--- marginalized kernel matrix of size 185 built in 605.9348838329315 seconds ---\n",
      "\n",
      " --- under the realm of G155 G155 ---\n",
      "0.254944936492\n",
      "\n",
      " --- under the realm of G155 G156 ---\n",
      "0.254154042246\n",
      "\n",
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      "0.256804190302\n",
      "\n",
      " --- under the realm of G155 G158 ---\n",
      "0.236523767752\n",
      "\n",
      " --- under the realm of G155 G159 ---\n",
      "0.228406018224\n",
      "\n",
      " --- under the realm of G155 G160 ---\n",
      "0.231632033039\n",
      "\n",
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      "0.232114074986\n",
      "\n",
      " --- under the realm of G155 G162 ---\n",
      "0.232757681649\n",
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      "0.230275983388\n",
      "\n",
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      "\n",
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      "0.251659178571\n",
      "\n",
      " --- under the realm of G155 G166 ---\n",
      "0.249349515682\n",
      "\n",
      " --- under the realm of G155 G167 ---\n",
      "0.223371303261\n",
      "\n",
      " --- under the realm of G155 G168 ---\n",
      "0.224711527675\n",
      "\n",
      " --- under the realm of G155 G169 ---\n",
      "0.258914554589\n",
      "\n",
      " --- under the realm of G155 G170 ---\n",
      "0.259652332757\n",
      "\n",
      " --- under the realm of G155 G171 ---\n",
      "0.260475697521\n",
      "\n",
      " --- under the realm of G155 G172 ---\n",
      "0.260182105567\n",
      "\n",
      " --- under the realm of G155 G173 ---\n",
      "0.252915466197\n",
      "\n",
      " --- under the realm of G155 G174 ---\n",
      "0.259237418491\n",
      "\n",
      " --- under the realm of G155 G175 ---\n",
      "0.259221245246\n",
      "\n",
      " --- under the realm of G155 G176 ---\n",
      "0.259503686618\n",
      "\n",
      " --- under the realm of G155 G177 ---\n",
      "0.259181931504\n",
      "\n",
      " --- under the realm of G155 G178 ---\n",
      "0.259229331869\n",
      "\n",
      " --- under the realm of G155 G179 ---\n",
      "0.257711062175\n",
      "\n",
      " --- under the realm of G155 G180 ---\n",
      "0.257112438834\n",
      "\n",
      " --- under the realm of G155 G181 ---\n",
      "0.255307272177\n",
      "\n",
      " --- under the realm of G155 G182 ---\n",
      "0.255323484638\n",
      "\n",
      " --- under the realm of G155 G183 ---\n",
      "0.255367789375\n",
      "\n",
      " --- under the realm of G155 G184 ---\n",
      "0.252872240694\n",
      "--- marginalized kernel matrix of size 185 built in 607.8047144412994 seconds ---\n",
      "\n",
      " --- under the realm of G156 G156 ---\n",
      "0.253498355786\n",
      "\n",
      " --- under the realm of G156 G157 ---\n",
      "0.255773029158\n",
      "\n",
      " --- under the realm of G156 G158 ---\n"
     ]
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    {
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     "text": [
      "0.235480269887\n",
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      "\n",
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      "\n",
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      "\n",
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      "\n",
      " --- under the realm of G156 G172 ---\n",
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      "\n",
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      "\n",
      " --- under the realm of G156 G174 ---\n",
      "0.258328797101\n",
      "\n",
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      "0.2583128064\n",
      "\n",
      " --- under the realm of G156 G176 ---\n",
      "0.258498941918\n",
      "\n",
      " --- under the realm of G156 G177 ---\n",
      "0.258272240323\n",
      "\n",
      " --- under the realm of G156 G178 ---\n",
      "0.25832080175\n",
      "\n",
      " --- under the realm of G156 G179 ---\n",
      "0.256917785285\n",
      "\n",
      " --- under the realm of G156 G180 ---\n",
      "0.255975548156\n",
      "\n",
      " --- under the realm of G156 G181 ---\n",
      "0.254251370829\n",
      "\n",
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      "0.254267752777\n",
      "\n",
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      "0.254312734994\n",
      "\n",
      " --- under the realm of G156 G184 ---\n",
      "0.251884193405\n",
      "--- marginalized kernel matrix of size 185 built in 609.5871107578278 seconds ---\n",
      "\n",
      " --- under the realm of G157 G157 ---\n",
      "0.259115165326\n",
      "\n",
      " --- under the realm of G157 G158 ---\n",
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      "0.233585893804\n",
      "\n",
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      "\n",
      " --- under the realm of G157 G171 ---\n",
      "0.262864422412\n",
      "\n",
      " --- under the realm of G157 G172 ---\n",
      "0.262598043277\n",
      "\n",
      " --- under the realm of G157 G173 ---\n",
      "0.255326933631\n",
      "\n",
      " --- under the realm of G157 G174 ---\n",
      "0.261364671567\n",
      "\n",
      " --- under the realm of G157 G175 ---\n",
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      "\n",
      " --- under the realm of G157 G176 ---\n",
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      "\n",
      " --- under the realm of G157 G177 ---\n",
      "0.261313024872\n",
      "\n",
      " --- under the realm of G157 G178 ---\n",
      "0.261356897323\n",
      "\n",
      " --- under the realm of G157 G179 ---\n",
      "0.259598376248\n",
      "\n",
      " --- under the realm of G157 G180 ---\n",
      "0.259705026098\n",
      "\n",
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      "\n",
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      "0.257810779523\n",
      "\n",
      " --- under the realm of G157 G184 ---\n",
      "0.255170290258\n",
      "--- marginalized kernel matrix of size 185 built in 611.3457882404327 seconds ---\n",
      "\n",
      " --- under the realm of G158 G158 ---\n",
      "0.222909074266\n",
      "\n",
      " --- under the realm of G158 G159 ---\n",
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      "\n",
      " --- under the realm of G158 G165 ---\n",
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      " --- under the realm of G158 G166 ---\n",
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      "\n",
      " --- under the realm of G158 G167 ---\n",
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      "\n",
      " --- under the realm of G158 G168 ---\n",
      "0.207111197713\n",
      "\n",
      " --- under the realm of G158 G169 ---\n",
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      "\n",
      " --- under the realm of G158 G170 ---\n",
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      "\n",
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      "\n",
      " --- under the realm of G158 G173 ---\n",
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      "\n",
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      "0.240602405627\n",
      "\n",
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      " --- under the realm of G158 G176 ---\n",
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      "\n",
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      "0.240595086797\n",
      "\n",
      " --- under the realm of G158 G179 ---\n",
      "0.238877806472\n",
      "\n",
      " --- under the realm of G158 G180 ---\n",
      "0.237293601632\n",
      "\n",
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      "0.235447505183\n",
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      "0.235462076898\n",
      "\n",
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      "0.235503707552\n",
      "\n",
      " --- under the realm of G158 G184 ---\n",
      "0.233037327773\n",
      "--- marginalized kernel matrix of size 185 built in 613.1899893283844 seconds ---\n",
      "\n",
      " --- under the realm of G159 G159 ---\n",
      "0.209990144495\n",
      "\n",
      " --- under the realm of G159 G160 ---\n",
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      "0.231175608618\n",
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      "0.231208996726\n",
      "\n",
      " --- under the realm of G159 G179 ---\n",
      "0.230476349449\n",
      "\n",
      " --- under the realm of G159 G180 ---\n",
      "0.225396852104\n",
      "\n",
      " --- under the realm of G159 G181 ---\n",
      "0.224069260106\n",
      "\n",
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      "0.224081265354\n",
      "\n",
      " --- under the realm of G159 G183 ---\n",
      "0.224117742485\n",
      "\n",
      " --- under the realm of G159 G184 ---\n",
      "0.222249586527\n",
      "--- marginalized kernel matrix of size 185 built in 614.9664504528046 seconds ---\n",
      "\n",
      " --- under the realm of G160 G160 ---\n",
      "0.213720620852\n",
      "\n",
      " --- under the realm of G160 G161 ---\n",
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      "\n",
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      "\n",
      " --- under the realm of G160 G173 ---\n",
      "0.229990155423\n",
      "\n",
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      "0.234910138769\n",
      "\n",
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      "0.234900371292\n",
      "\n",
      " --- under the realm of G160 G176 ---\n",
      "0.235181557847\n",
      "\n",
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      "\n",
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      "\n",
      " --- under the realm of G160 G179 ---\n",
      "0.233740032784\n",
      "\n",
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      "\n",
      " --- under the realm of G160 G181 ---\n",
      "0.228326676846\n",
      "\n",
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      "0.228338038392\n",
      "\n",
      " --- under the realm of G160 G183 ---\n",
      "0.228375203492\n",
      "\n",
      " --- under the realm of G160 G184 ---\n",
      "0.226250924688\n",
      "--- marginalized kernel matrix of size 185 built in 616.6813824176788 seconds ---\n",
      "\n",
      " --- under the realm of G161 G161 ---\n",
      "0.214421920755\n",
      "\n",
      " --- under the realm of G161 G162 ---\n",
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      "0.236206140749\n",
      "\n",
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      "0.230518061443\n",
      "\n",
      " --- under the realm of G161 G174 ---\n",
      "0.235455560296\n",
      "\n",
      " --- under the realm of G161 G175 ---\n",
      "0.235447535593\n",
      "\n",
      " --- under the realm of G161 G176 ---\n",
      "0.235675764902\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      " --- under the realm of G161 G177 ---\n",
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      "\n",
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      "\n",
      " --- under the realm of G161 G179 ---\n",
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      "\n",
      " --- under the realm of G161 G180 ---\n",
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      "\n",
      " --- under the realm of G161 G181 ---\n",
      "0.228906448087\n",
      "\n",
      " --- under the realm of G161 G182 ---\n",
      "0.228917882288\n",
      "\n",
      " --- under the realm of G161 G183 ---\n",
      "0.228960178246\n",
      "\n",
      " --- under the realm of G161 G184 ---\n",
      "0.226814609573\n",
      "--- marginalized kernel matrix of size 185 built in 618.3072783946991 seconds ---\n",
      "\n",
      " --- under the realm of G162 G162 ---\n",
      "0.215724126815\n",
      "\n",
      " --- under the realm of G162 G163 ---\n",
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      "\n",
      " --- under the realm of G162 G169 ---\n",
      "0.236010592954\n",
      "\n",
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      "0.236761549614\n",
      "\n",
      " --- under the realm of G162 G171 ---\n",
      "0.237348030699\n",
      "\n",
      " --- under the realm of G162 G172 ---\n",
      "0.237175739003\n",
      "\n",
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      "\n",
      " --- under the realm of G162 G174 ---\n",
      "0.236197528185\n",
      "\n",
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      "\n",
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      "\n",
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      "\n",
      " --- under the realm of G162 G178 ---\n",
      "0.236192494115\n",
      "\n",
      " --- under the realm of G162 G179 ---\n",
      "0.234881844633\n",
      "\n",
      " --- under the realm of G162 G180 ---\n",
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      "\n",
      " --- under the realm of G162 G181 ---\n",
      "0.22980378401\n",
      "\n",
      " --- under the realm of G162 G182 ---\n",
      "0.22981515744\n",
      "\n",
      " --- under the realm of G162 G183 ---\n",
      "0.229852921564\n",
      "\n",
      " --- under the realm of G162 G184 ---\n",
      "0.227640227048\n",
      "--- marginalized kernel matrix of size 185 built in 619.8694264888763 seconds ---\n",
      "\n",
      " --- under the realm of G163 G163 ---\n",
      "0.211774903859\n",
      "\n",
      " --- under the realm of G163 G164 ---\n",
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      "\n",
      " --- under the realm of G163 G165 ---\n",
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      "\n",
      " --- under the realm of G163 G166 ---\n",
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      "\n",
      " --- under the realm of G163 G167 ---\n",
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      "\n",
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      " --- under the realm of G163 G169 ---\n",
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      "\n",
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      "\n",
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      "0.234283146342\n",
      "\n",
      " --- under the realm of G163 G172 ---\n",
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      "\n",
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      "0.22833542611\n",
      "\n",
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      "0.233403556172\n",
      "\n",
      " --- under the realm of G163 G175 ---\n",
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      "\n",
      " --- under the realm of G163 G176 ---\n",
      "0.233599525022\n",
      "\n",
      " --- under the realm of G163 G177 ---\n",
      "0.233378747521\n",
      "\n",
      " --- under the realm of G163 G178 ---\n",
      "0.233400180615\n",
      "\n",
      " --- under the realm of G163 G179 ---\n",
      "0.232351380483\n",
      "\n",
      " --- under the realm of G163 G180 ---\n",
      "0.228148217227\n",
      "\n",
      " --- under the realm of G163 G181 ---\n",
      "0.22661864079\n",
      "\n",
      " --- under the realm of G163 G182 ---\n",
      "0.226628929396\n",
      "\n",
      " --- under the realm of G163 G183 ---\n",
      "0.226668751016\n",
      "\n",
      " --- under the realm of G163 G184 ---\n",
      "0.224627458708\n",
      "--- marginalized kernel matrix of size 185 built in 621.3790225982666 seconds ---\n",
      "\n",
      " --- under the realm of G164 G164 ---\n",
      "0.212961914143\n",
      "\n",
      " --- under the realm of G164 G165 ---\n",
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      "\n",
      " --- under the realm of G164 G166 ---\n",
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      "\n",
      " --- under the realm of G164 G167 ---\n",
      "0.199557064097\n",
      "\n",
      " --- under the realm of G164 G168 ---\n",
      "0.200898642992\n",
      "\n",
      " --- under the realm of G164 G169 ---\n",
      "0.233989266109\n",
      "\n",
      " --- under the realm of G164 G170 ---\n",
      "0.234672051458\n",
      "\n",
      " --- under the realm of G164 G171 ---\n",
      "0.235178527967\n",
      "\n",
      " --- under the realm of G164 G172 ---\n",
      "0.235035842844\n",
      "\n",
      " --- under the realm of G164 G173 ---\n",
      "0.229267012457\n",
      "\n",
      " --- under the realm of G164 G174 ---\n",
      "0.234145527358\n",
      "\n",
      " --- under the realm of G164 G175 ---\n",
      "0.234136732862\n",
      "\n",
      " --- under the realm of G164 G176 ---\n",
      "0.234491483302\n",
      "\n",
      " --- under the realm of G164 G177 ---\n",
      "0.234118763125\n",
      "\n",
      " --- under the realm of G164 G178 ---\n",
      "0.23414113011\n",
      "\n",
      " --- under the realm of G164 G179 ---\n",
      "0.232972625619\n",
      "\n",
      " --- under the realm of G164 G180 ---\n",
      "0.229156017567\n",
      "\n",
      " --- under the realm of G164 G181 ---\n",
      "0.227515976713\n",
      "\n",
      " --- under the realm of G164 G182 ---\n",
      "0.227526204548\n",
      "\n",
      " --- under the realm of G164 G183 ---\n",
      "0.227561494335\n",
      "\n",
      " --- under the realm of G164 G184 ---\n",
      "0.225453076182\n",
      "--- marginalized kernel matrix of size 185 built in 622.8127200603485 seconds ---\n",
      "\n",
      " --- under the realm of G165 G165 ---\n",
      "0.257156859846\n",
      "\n",
      " --- under the realm of G165 G166 ---\n",
      "0.255086098063\n",
      "\n",
      " --- under the realm of G165 G167 ---\n",
      "0.231851581867\n",
      "\n",
      " --- under the realm of G165 G168 ---\n",
      "0.233047078496\n",
      "\n",
      " --- under the realm of G165 G169 ---\n",
      "0.256339130242\n",
      "\n",
      " --- under the realm of G165 G170 ---\n",
      "0.257303777288\n",
      "\n",
      " --- under the realm of G165 G171 ---\n",
      "0.258274678615\n",
      "\n",
      " --- under the realm of G165 G172 ---\n",
      "0.257940093103\n",
      "\n",
      " --- under the realm of G165 G173 ---\n",
      "0.249781707497\n",
      "\n",
      " --- under the realm of G165 G174 ---\n",
      "0.256692809944\n",
      "\n",
      " --- under the realm of G165 G175 ---\n",
      "0.256676973349\n",
      "\n",
      " --- under the realm of G165 G176 ---\n",
      "0.257089907714\n",
      "\n",
      " --- under the realm of G165 G177 ---\n",
      "0.256637363941\n",
      "\n",
      " --- under the realm of G165 G178 ---\n",
      "0.256684891646\n",
      "\n",
      " --- under the realm of G165 G179 ---\n",
      "0.254800149478\n",
      "\n",
      " --- under the realm of G165 G180 ---\n",
      "0.262041693067\n",
      "\n",
      " --- under the realm of G165 G181 ---\n",
      "0.26042545023\n",
      "\n",
      " --- under the realm of G165 G182 ---\n",
      "0.260440111061\n",
      "\n",
      " --- under the realm of G165 G183 ---\n",
      "0.260480198342\n",
      "\n",
      " --- under the realm of G165 G184 ---\n",
      "0.258239520109\n",
      "--- marginalized kernel matrix of size 185 built in 624.0437519550323 seconds ---\n",
      "\n",
      " --- under the realm of G166 G166 ---\n",
      "0.253474880557\n",
      "\n",
      " --- under the realm of G166 G167 ---\n",
      "0.230695893488\n",
      "\n",
      " --- under the realm of G166 G168 ---\n",
      "0.231383574285\n",
      "\n",
      " --- under the realm of G166 G169 ---\n",
      "0.253897078083\n",
      "\n",
      " --- under the realm of G166 G170 ---\n",
      "0.254787671411\n",
      "\n",
      " --- under the realm of G166 G171 ---\n",
      "0.255736582381\n",
      "\n",
      " --- under the realm of G166 G172 ---\n",
      "0.255402223599\n",
      "\n",
      " --- under the realm of G166 G173 ---\n",
      "0.247298079517\n",
      "\n",
      " --- under the realm of G166 G174 ---\n",
      "0.254255095805\n",
      "\n",
      " --- under the realm of G166 G175 ---\n",
      "0.254238845251\n",
      "\n",
      " --- under the realm of G166 G176 ---\n",
      "0.254599531224\n",
      "\n",
      " --- under the realm of G166 G177 ---\n",
      "0.254197278525\n",
      "\n",
      " --- under the realm of G166 G178 ---\n",
      "0.254246970528\n",
      "\n",
      " --- under the realm of G166 G179 ---\n",
      "0.252456249641\n",
      "\n",
      " --- under the realm of G166 G180 ---\n",
      "0.259484362217\n",
      "\n",
      " --- under the realm of G166 G181 ---\n",
      "0.258301100819\n",
      "\n",
      " --- under the realm of G166 G182 ---\n",
      "0.258316692158\n",
      "\n",
      " --- under the realm of G166 G183 ---\n",
      "0.258360657926\n",
      "\n",
      " --- under the realm of G166 G184 ---\n",
      "0.256505961298\n",
      "--- marginalized kernel matrix of size 185 built in 625.2099053859711 seconds ---\n",
      "\n",
      " --- under the realm of G167 G167 ---\n",
      "0.213088391707\n",
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      "0.234377044121\n",
      "\n",
      " --- under the realm of G167 G184 ---\n",
      "0.233025152127\n",
      "--- marginalized kernel matrix of size 185 built in 626.4377243518829 seconds ---\n",
      "\n",
      " --- under the realm of G168 G168 ---\n",
      "0.214622113165\n",
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      "0.233796003463\n"
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    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "--- marginalized kernel matrix of size 185 built in 627.5980844497681 seconds ---\n",
      "\n",
      " --- under the realm of G169 G169 ---\n",
      "0.263177651713\n",
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      "\n",
      " --- under the realm of G169 G184 ---\n",
      "0.257518590966\n",
      "--- marginalized kernel matrix of size 185 built in 628.6881618499756 seconds ---\n",
      "\n",
      " --- under the realm of G170 G170 ---\n",
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      "\n",
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      "0.261130740836\n",
      "\n",
      " --- under the realm of G170 G184 ---\n",
      "0.258435083955\n",
      "--- marginalized kernel matrix of size 185 built in 629.7222907543182 seconds ---\n",
      "\n",
      " --- under the realm of G171 G171 ---\n",
      "0.2668738448\n",
      "\n",
      " --- under the realm of G171 G172 ---\n",
      "0.26653261021\n",
      "\n",
      " --- under the realm of G171 G173 ---\n",
      "0.259136127692\n",
      "\n",
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      "0.262155561478\n",
      "\n",
      " --- under the realm of G171 G184 ---\n",
      "0.259415420787\n",
      "--- marginalized kernel matrix of size 185 built in 630.6808168888092 seconds ---\n",
      "\n",
      " --- under the realm of G172 G172 ---\n",
      "0.266231778001\n",
      "\n",
      " --- under the realm of G172 G173 ---\n",
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      "0.261795126173\n",
      "\n",
      " --- under the realm of G172 G184 ---\n",
      "0.259069571735\n",
      "--- marginalized kernel matrix of size 185 built in 631.5739166736603 seconds ---\n",
      "\n",
      " --- under the realm of G173 G173 ---\n",
      "0.252134698274\n",
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      "\n",
      " --- under the realm of G173 G184 ---\n",
      "0.250876791346\n",
      "--- marginalized kernel matrix of size 185 built in 632.1531755924225 seconds ---\n",
      "\n",
      " --- under the realm of G174 G174 ---\n",
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      "\n",
      " --- under the realm of G174 G184 ---\n",
      "0.257889481809\n",
      "--- marginalized kernel matrix of size 185 built in 632.9248306751251 seconds ---\n",
      "\n",
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      "0.260516904067\n",
      "\n",
      " --- under the realm of G175 G184 ---\n",
      "0.25787261357\n",
      "--- marginalized kernel matrix of size 185 built in 633.6153528690338 seconds ---\n",
      "\n",
      " --- under the realm of G176 G176 ---\n",
      "0.264574418575\n",
      "\n",
      " --- under the realm of G176 G177 ---\n",
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      "0.260873008897\n",
      "\n",
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      "0.260920831777\n",
      "\n",
      " --- under the realm of G176 G184 ---\n",
      "0.258242184844\n",
      "--- marginalized kernel matrix of size 185 built in 634.2469310760498 seconds ---\n",
      "\n",
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      "0.26375843941\n",
      "\n",
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      "0.260474460118\n",
      "\n",
      " --- under the realm of G177 G184 ---\n",
      "0.257829376107\n",
      "--- marginalized kernel matrix of size 185 built in 634.8114056587219 seconds ---\n",
      "\n",
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      "0.263853522237\n",
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      "\n",
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      "0.260525274278\n",
      "\n",
      " --- under the realm of G178 G184 ---\n",
      "0.25788104769\n",
      "--- marginalized kernel matrix of size 185 built in 635.2957293987274 seconds ---\n",
      "\n",
      " --- under the realm of G179 G179 ---\n",
      "0.26056260539\n",
      "\n",
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      "\n",
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      "0.25853201087\n",
      "\n",
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      "0.258578167467\n",
      "\n",
      " --- under the realm of G179 G184 ---\n",
      "0.256034432868\n",
      "--- marginalized kernel matrix of size 185 built in 635.7093262672424 seconds ---\n",
      "\n",
      " --- under the realm of G180 G180 ---\n",
      "0.267536917007\n",
      "\n",
      " --- under the realm of G180 G181 ---\n",
      "0.265468597784\n",
      "\n",
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      "0.265484754318\n",
      "\n",
      " --- under the realm of G180 G183 ---\n",
      "0.265519772667\n",
      "\n",
      " --- under the realm of G180 G184 ---\n",
      "0.262847604027\n",
      "--- marginalized kernel matrix of size 185 built in 636.0648431777954 seconds ---\n",
      "\n",
      " --- under the realm of G181 G181 ---\n",
      "0.263837534785\n",
      "\n",
      " --- under the realm of G181 G182 ---\n",
      "0.263853280481\n",
      "\n",
      " --- under the realm of G181 G183 ---\n",
      "0.263900400911\n",
      "\n",
      " --- under the realm of G181 G184 ---\n",
      "0.261565573137\n",
      "--- marginalized kernel matrix of size 185 built in 636.3432593345642 seconds ---\n",
      "\n",
      " --- under the realm of G182 G182 ---\n",
      "0.263869993201\n",
      "\n",
      " --- under the realm of G182 G183 ---\n",
      "0.263915149254\n",
      "\n",
      " --- under the realm of G182 G184 ---\n",
      "0.261581842053\n",
      "--- marginalized kernel matrix of size 185 built in 636.5545530319214 seconds ---\n",
      "\n",
      " --- under the realm of G183 G183 ---\n",
      "0.263966877902\n",
      "\n",
      " --- under the realm of G183 G184 ---\n",
      "0.261627293059\n",
      "--- marginalized kernel matrix of size 185 built in 636.6913950443268 seconds ---\n",
      "\n",
      " --- under the realm of G184 G184 ---\n",
      "0.259645923991\n",
      "--- marginalized kernel matrix of size 185 built in 636.7594740390778 seconds ---\n",
      "--- behold, the kernel presented ---\n",
      "[[ 0.18518519  0.15591398  0.11111111 ...,  0.15151515  0.15151515\n",
      "   0.15151515]\n",
      " [ 0.          0.15254237  0.08333333 ...,  0.11363636  0.11363636\n",
      "   0.11363636]\n",
      " [ 0.          0.          0.18518519 ...,  0.16617791  0.16617791\n",
      "   0.16890214]\n",
      " ..., \n",
      " [ 0.          0.          0.         ...,  0.26386999  0.26391515\n",
      "   0.26158184]\n",
      " [ 0.          0.          0.         ...,  0.          0.26396688\n",
      "   0.26162729]\n",
      " [ 0.          0.          0.         ...,  0.          0.          0.25964592]]\n"
     ]
    }
   ],
   "source": [
    "import matplotlib.pyplot as plt\n",
    "from utils.graphfiles import loadDataset\n",
    "\n",
    "dataset, y = loadDataset(\"/home/ljia/Documents/research-repo/datasets/acyclic/Acyclic/dataset_bps.ds\")\n",
    "G1 = dataset[12]\n",
    "G2 = dataset[20]\n",
    "nx.draw_networkx(G1)\n",
    "plt.show()\n",
    "Kmatrix = marginalizedkernel(dataset, 0.5, 20)\n",
    "\n",
    "print('--- behold, the kernel presented ---')\n",
    "print(Kmatrix)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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