4.4_Demo_Feature_Selection_Feature_Shuffling.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import numpy as np\n",
    "# import seaborn as sns\n",
    "# import matplotlib.pyplot as plt\n",
    "import os\n",
    "from sklearn.model_selection import train_test_split\n",
    "from sklearn.feature_selection import SelectFromModel\n",
    "from sklearn.ensemble import RandomForestClassifier\n",
    "# plt.style.use('seaborn-colorblind')\n",
    "# %matplotlib inline\n",
    "from feature_selection import feature_shuffle\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Load Dataset"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from sklearn.datasets import load_breast_cancer\n",
    "data = load_breast_cancer()\n",
    "data = pd.DataFrame(np.c_[data['data'], data['target']],\n",
    "                  columns= np.append(data['feature_names'], ['target']))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>mean radius</th>\n",
       "      <th>mean texture</th>\n",
       "      <th>mean perimeter</th>\n",
       "      <th>mean area</th>\n",
       "      <th>mean smoothness</th>\n",
       "      <th>mean compactness</th>\n",
       "      <th>mean concavity</th>\n",
       "      <th>mean concave points</th>\n",
       "      <th>mean symmetry</th>\n",
       "      <th>mean fractal dimension</th>\n",
       "      <th>...</th>\n",
       "      <th>worst texture</th>\n",
       "      <th>worst perimeter</th>\n",
       "      <th>worst area</th>\n",
       "      <th>worst smoothness</th>\n",
       "      <th>worst compactness</th>\n",
       "      <th>worst concavity</th>\n",
       "      <th>worst concave points</th>\n",
       "      <th>worst symmetry</th>\n",
       "      <th>worst fractal dimension</th>\n",
       "      <th>target</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>17.99</td>\n",
       "      <td>10.38</td>\n",
       "      <td>122.80</td>\n",
       "      <td>1001.0</td>\n",
       "      <td>0.11840</td>\n",
       "      <td>0.27760</td>\n",
       "      <td>0.3001</td>\n",
       "      <td>0.14710</td>\n",
       "      <td>0.2419</td>\n",
       "      <td>0.07871</td>\n",
       "      <td>...</td>\n",
       "      <td>17.33</td>\n",
       "      <td>184.60</td>\n",
       "      <td>2019.0</td>\n",
       "      <td>0.1622</td>\n",
       "      <td>0.6656</td>\n",
       "      <td>0.7119</td>\n",
       "      <td>0.2654</td>\n",
       "      <td>0.4601</td>\n",
       "      <td>0.11890</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>20.57</td>\n",
       "      <td>17.77</td>\n",
       "      <td>132.90</td>\n",
       "      <td>1326.0</td>\n",
       "      <td>0.08474</td>\n",
       "      <td>0.07864</td>\n",
       "      <td>0.0869</td>\n",
       "      <td>0.07017</td>\n",
       "      <td>0.1812</td>\n",
       "      <td>0.05667</td>\n",
       "      <td>...</td>\n",
       "      <td>23.41</td>\n",
       "      <td>158.80</td>\n",
       "      <td>1956.0</td>\n",
       "      <td>0.1238</td>\n",
       "      <td>0.1866</td>\n",
       "      <td>0.2416</td>\n",
       "      <td>0.1860</td>\n",
       "      <td>0.2750</td>\n",
       "      <td>0.08902</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>19.69</td>\n",
       "      <td>21.25</td>\n",
       "      <td>130.00</td>\n",
       "      <td>1203.0</td>\n",
       "      <td>0.10960</td>\n",
       "      <td>0.15990</td>\n",
       "      <td>0.1974</td>\n",
       "      <td>0.12790</td>\n",
       "      <td>0.2069</td>\n",
       "      <td>0.05999</td>\n",
       "      <td>...</td>\n",
       "      <td>25.53</td>\n",
       "      <td>152.50</td>\n",
       "      <td>1709.0</td>\n",
       "      <td>0.1444</td>\n",
       "      <td>0.4245</td>\n",
       "      <td>0.4504</td>\n",
       "      <td>0.2430</td>\n",
       "      <td>0.3613</td>\n",
       "      <td>0.08758</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>11.42</td>\n",
       "      <td>20.38</td>\n",
       "      <td>77.58</td>\n",
       "      <td>386.1</td>\n",
       "      <td>0.14250</td>\n",
       "      <td>0.28390</td>\n",
       "      <td>0.2414</td>\n",
       "      <td>0.10520</td>\n",
       "      <td>0.2597</td>\n",
       "      <td>0.09744</td>\n",
       "      <td>...</td>\n",
       "      <td>26.50</td>\n",
       "      <td>98.87</td>\n",
       "      <td>567.7</td>\n",
       "      <td>0.2098</td>\n",
       "      <td>0.8663</td>\n",
       "      <td>0.6869</td>\n",
       "      <td>0.2575</td>\n",
       "      <td>0.6638</td>\n",
       "      <td>0.17300</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>20.29</td>\n",
       "      <td>14.34</td>\n",
       "      <td>135.10</td>\n",
       "      <td>1297.0</td>\n",
       "      <td>0.10030</td>\n",
       "      <td>0.13280</td>\n",
       "      <td>0.1980</td>\n",
       "      <td>0.10430</td>\n",
       "      <td>0.1809</td>\n",
       "      <td>0.05883</td>\n",
       "      <td>...</td>\n",
       "      <td>16.67</td>\n",
       "      <td>152.20</td>\n",
       "      <td>1575.0</td>\n",
       "      <td>0.1374</td>\n",
       "      <td>0.2050</td>\n",
       "      <td>0.4000</td>\n",
       "      <td>0.1625</td>\n",
       "      <td>0.2364</td>\n",
       "      <td>0.07678</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 31 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "   mean radius  mean texture  mean perimeter  mean area  mean smoothness  \\\n",
       "0        17.99         10.38          122.80     1001.0          0.11840   \n",
       "1        20.57         17.77          132.90     1326.0          0.08474   \n",
       "2        19.69         21.25          130.00     1203.0          0.10960   \n",
       "3        11.42         20.38           77.58      386.1          0.14250   \n",
       "4        20.29         14.34          135.10     1297.0          0.10030   \n",
       "\n",
       "   mean compactness  mean concavity  mean concave points  mean symmetry  \\\n",
       "0           0.27760          0.3001              0.14710         0.2419   \n",
       "1           0.07864          0.0869              0.07017         0.1812   \n",
       "2           0.15990          0.1974              0.12790         0.2069   \n",
       "3           0.28390          0.2414              0.10520         0.2597   \n",
       "4           0.13280          0.1980              0.10430         0.1809   \n",
       "\n",
       "   mean fractal dimension   ...    worst texture  worst perimeter  worst area  \\\n",
       "0                 0.07871   ...            17.33           184.60      2019.0   \n",
       "1                 0.05667   ...            23.41           158.80      1956.0   \n",
       "2                 0.05999   ...            25.53           152.50      1709.0   \n",
       "3                 0.09744   ...            26.50            98.87       567.7   \n",
       "4                 0.05883   ...            16.67           152.20      1575.0   \n",
       "\n",
       "   worst smoothness  worst compactness  worst concavity  worst concave points  \\\n",
       "0            0.1622             0.6656           0.7119                0.2654   \n",
       "1            0.1238             0.1866           0.2416                0.1860   \n",
       "2            0.1444             0.4245           0.4504                0.2430   \n",
       "3            0.2098             0.8663           0.6869                0.2575   \n",
       "4            0.1374             0.2050           0.4000                0.1625   \n",
       "\n",
       "   worst symmetry  worst fractal dimension  target  \n",
       "0          0.4601                  0.11890     0.0  \n",
       "1          0.2750                  0.08902     0.0  \n",
       "2          0.3613                  0.08758     0.0  \n",
       "3          0.6638                  0.17300     0.0  \n",
       "4          0.2364                  0.07678     0.0  \n",
       "\n",
       "[5 rows x 31 columns]"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "data.head(5)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "((455, 30), (114, 30))"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "X_train, X_test, y_train, y_test = train_test_split(data.drop(labels=['target'], axis=1), \n",
    "                                                    data.target, test_size=0.2,\n",
    "                                                    random_state=0)\n",
    "X_train.shape, X_test.shape"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "##  Feature Shuffling\n",
    "permute the values of each feature, one at the time, and measure how much the permutation decreases the accuracy, or the roc_auc, or the mse of the machine learning model.\n",
    "If the variables are important, this is, highly predictive, a random permutation of their values will decrease dramatically any of these metrics."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [],
   "source": [
    "auc_drop, selected_features = feature_shuffle.feature_shuffle_rf(X_train=X_train,\n",
    "                                                                 y_train=y_train,\n",
    "                                                                 random_state=0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>feature</th>\n",
       "      <th>auc_drop</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>worst perimeter</td>\n",
       "      <td>8.359457e-05</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>worst concave points</td>\n",
       "      <td>3.134796e-05</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>worst area</td>\n",
       "      <td>1.110223e-16</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>perimeter error</td>\n",
       "      <td>1.110223e-16</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>mean radius</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>concavity error</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>worst symmetry</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>worst concavity</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>worst compactness</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>worst smoothness</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>worst texture</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>worst radius</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>fractal dimension error</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>symmetry error</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>concave points error</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>compactness error</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>mean texture</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>smoothness error</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>area error</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>texture error</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>radius error</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>mean fractal dimension</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>mean symmetry</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>mean concave points</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>mean concavity</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>mean compactness</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>mean smoothness</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>mean area</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>mean perimeter</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>worst fractal dimension</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                    feature      auc_drop\n",
       "22          worst perimeter  8.359457e-05\n",
       "27     worst concave points  3.134796e-05\n",
       "23               worst area  1.110223e-16\n",
       "12          perimeter error  1.110223e-16\n",
       "0               mean radius  0.000000e+00\n",
       "16          concavity error  0.000000e+00\n",
       "28           worst symmetry  0.000000e+00\n",
       "26          worst concavity  0.000000e+00\n",
       "25        worst compactness  0.000000e+00\n",
       "24         worst smoothness  0.000000e+00\n",
       "21            worst texture  0.000000e+00\n",
       "20             worst radius  0.000000e+00\n",
       "19  fractal dimension error  0.000000e+00\n",
       "18           symmetry error  0.000000e+00\n",
       "17     concave points error  0.000000e+00\n",
       "15        compactness error  0.000000e+00\n",
       "1              mean texture  0.000000e+00\n",
       "14         smoothness error  0.000000e+00\n",
       "13               area error  0.000000e+00\n",
       "11            texture error  0.000000e+00\n",
       "10             radius error  0.000000e+00\n",
       "9    mean fractal dimension  0.000000e+00\n",
       "8             mean symmetry  0.000000e+00\n",
       "7       mean concave points  0.000000e+00\n",
       "6            mean concavity  0.000000e+00\n",
       "5          mean compactness  0.000000e+00\n",
       "4           mean smoothness  0.000000e+00\n",
       "3                 mean area  0.000000e+00\n",
       "2            mean perimeter  0.000000e+00\n",
       "29  worst fractal dimension  0.000000e+00"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#  we select features that have auc_drop > 0\n",
    "auc_drop"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "22         worst perimeter\n",
       "27    worst concave points\n",
       "23              worst area\n",
       "12         perimeter error\n",
       "Name: feature, dtype: object"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "selected_features"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
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