tpot_demo.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "0ec8971a-11b3-46aa-971a-420c7f3b192f",
   "metadata": {},
   "outputs": [],
   "source": [
    "from tpot import TPOTClassifier\n",
    "import pandas as pd\n",
    "import numpy as np\n",
    "from sklearn.model_selection import train_test_split"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "1dda7632-4376-4b55-bda5-c2e5d1d08b7d",
   "metadata": {},
   "source": [
    "# Import data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "c4b79c38-8534-4eac-85d5-f6e308d90d80",
   "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>id</th>\n",
       "      <th>diagnosis</th>\n",
       "      <th>radius_mean</th>\n",
       "      <th>texture_mean</th>\n",
       "      <th>perimeter_mean</th>\n",
       "      <th>area_mean</th>\n",
       "      <th>smoothness_mean</th>\n",
       "      <th>compactness_mean</th>\n",
       "      <th>concavity_mean</th>\n",
       "      <th>concave points_mean</th>\n",
       "      <th>symmetry_mean</th>\n",
       "      <th>fractal_dimension_mean</th>\n",
       "      <th>radius_se</th>\n",
       "      <th>texture_se</th>\n",
       "      <th>perimeter_se</th>\n",
       "      <th>area_se</th>\n",
       "      <th>smoothness_se</th>\n",
       "      <th>compactness_se</th>\n",
       "      <th>concavity_se</th>\n",
       "      <th>concave points_se</th>\n",
       "      <th>symmetry_se</th>\n",
       "      <th>fractal_dimension_se</th>\n",
       "      <th>radius_worst</th>\n",
       "      <th>texture_worst</th>\n",
       "      <th>perimeter_worst</th>\n",
       "      <th>area_worst</th>\n",
       "      <th>smoothness_worst</th>\n",
       "      <th>compactness_worst</th>\n",
       "      <th>concavity_worst</th>\n",
       "      <th>concave points_worst</th>\n",
       "      <th>symmetry_worst</th>\n",
       "      <th>fractal_dimension_worst</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>842302</td>\n",
       "      <td>M</td>\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>1.0950</td>\n",
       "      <td>0.9053</td>\n",
       "      <td>8.589</td>\n",
       "      <td>153.40</td>\n",
       "      <td>0.006399</td>\n",
       "      <td>0.04904</td>\n",
       "      <td>0.05373</td>\n",
       "      <td>0.01587</td>\n",
       "      <td>0.03003</td>\n",
       "      <td>0.006193</td>\n",
       "      <td>25.38</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>842517</td>\n",
       "      <td>M</td>\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>0.5435</td>\n",
       "      <td>0.7339</td>\n",
       "      <td>3.398</td>\n",
       "      <td>74.08</td>\n",
       "      <td>0.005225</td>\n",
       "      <td>0.01308</td>\n",
       "      <td>0.01860</td>\n",
       "      <td>0.01340</td>\n",
       "      <td>0.01389</td>\n",
       "      <td>0.003532</td>\n",
       "      <td>24.99</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>84300903</td>\n",
       "      <td>M</td>\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>0.7456</td>\n",
       "      <td>0.7869</td>\n",
       "      <td>4.585</td>\n",
       "      <td>94.03</td>\n",
       "      <td>0.006150</td>\n",
       "      <td>0.04006</td>\n",
       "      <td>0.03832</td>\n",
       "      <td>0.02058</td>\n",
       "      <td>0.02250</td>\n",
       "      <td>0.004571</td>\n",
       "      <td>23.57</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>84348301</td>\n",
       "      <td>M</td>\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>0.4956</td>\n",
       "      <td>1.1560</td>\n",
       "      <td>3.445</td>\n",
       "      <td>27.23</td>\n",
       "      <td>0.009110</td>\n",
       "      <td>0.07458</td>\n",
       "      <td>0.05661</td>\n",
       "      <td>0.01867</td>\n",
       "      <td>0.05963</td>\n",
       "      <td>0.009208</td>\n",
       "      <td>14.91</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>84358402</td>\n",
       "      <td>M</td>\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>0.7572</td>\n",
       "      <td>0.7813</td>\n",
       "      <td>5.438</td>\n",
       "      <td>94.44</td>\n",
       "      <td>0.011490</td>\n",
       "      <td>0.02461</td>\n",
       "      <td>0.05688</td>\n",
       "      <td>0.01885</td>\n",
       "      <td>0.01756</td>\n",
       "      <td>0.005115</td>\n",
       "      <td>22.54</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",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "         id diagnosis  ...  symmetry_worst  fractal_dimension_worst\n",
       "0    842302         M  ...          0.4601                  0.11890\n",
       "1    842517         M  ...          0.2750                  0.08902\n",
       "2  84300903         M  ...          0.3613                  0.08758\n",
       "3  84348301         M  ...          0.6638                  0.17300\n",
       "4  84358402         M  ...          0.2364                  0.07678\n",
       "\n",
       "[5 rows x 32 columns]"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# NOTE: Make sure that the outcome column is labeled 'target' in the data file\n",
    "tpot_data = pd.read_csv('00_datasets/breast_cancer_classification/wdbc_data.csv', \n",
    "                        sep=',')\n",
    "tpot_data.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "38ee1cbd-e899-479b-bd7d-b3294c8ee8c4",
   "metadata": {},
   "source": [
    "## Rename target column"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "3e7e1109-afa0-43ab-a456-7881e9644e47",
   "metadata": {},
   "outputs": [],
   "source": [
    "tpot_data = tpot_data.drop('id', axis=1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "3ce66ba3-d425-4079-a5d6-15ed5e943019",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>target</th>\n",
       "      <th>radius_mean</th>\n",
       "      <th>texture_mean</th>\n",
       "      <th>perimeter_mean</th>\n",
       "      <th>area_mean</th>\n",
       "      <th>smoothness_mean</th>\n",
       "      <th>compactness_mean</th>\n",
       "      <th>concavity_mean</th>\n",
       "      <th>concave points_mean</th>\n",
       "      <th>symmetry_mean</th>\n",
       "      <th>fractal_dimension_mean</th>\n",
       "      <th>radius_se</th>\n",
       "      <th>texture_se</th>\n",
       "      <th>perimeter_se</th>\n",
       "      <th>area_se</th>\n",
       "      <th>smoothness_se</th>\n",
       "      <th>compactness_se</th>\n",
       "      <th>concavity_se</th>\n",
       "      <th>concave points_se</th>\n",
       "      <th>symmetry_se</th>\n",
       "      <th>fractal_dimension_se</th>\n",
       "      <th>radius_worst</th>\n",
       "      <th>texture_worst</th>\n",
       "      <th>perimeter_worst</th>\n",
       "      <th>area_worst</th>\n",
       "      <th>smoothness_worst</th>\n",
       "      <th>compactness_worst</th>\n",
       "      <th>concavity_worst</th>\n",
       "      <th>concave points_worst</th>\n",
       "      <th>symmetry_worst</th>\n",
       "      <th>fractal_dimension_worst</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>M</td>\n",
       "      <td>17.99</td>\n",
       "      <td>10.38</td>\n",
       "      <td>122.80</td>\n",
       "      <td>1001.0</td>\n",
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       "      <td>8.589</td>\n",
       "      <td>153.40</td>\n",
       "      <td>0.006399</td>\n",
       "      <td>0.04904</td>\n",
       "      <td>0.05373</td>\n",
       "      <td>0.01587</td>\n",
       "      <td>0.03003</td>\n",
       "      <td>0.006193</td>\n",
       "      <td>25.38</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>M</td>\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>0.5435</td>\n",
       "      <td>0.7339</td>\n",
       "      <td>3.398</td>\n",
       "      <td>74.08</td>\n",
       "      <td>0.005225</td>\n",
       "      <td>0.01308</td>\n",
       "      <td>0.01860</td>\n",
       "      <td>0.01340</td>\n",
       "      <td>0.01389</td>\n",
       "      <td>0.003532</td>\n",
       "      <td>24.99</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>M</td>\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>0.7456</td>\n",
       "      <td>0.7869</td>\n",
       "      <td>4.585</td>\n",
       "      <td>94.03</td>\n",
       "      <td>0.006150</td>\n",
       "      <td>0.04006</td>\n",
       "      <td>0.03832</td>\n",
       "      <td>0.02058</td>\n",
       "      <td>0.02250</td>\n",
       "      <td>0.004571</td>\n",
       "      <td>23.57</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>M</td>\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>0.4956</td>\n",
       "      <td>1.1560</td>\n",
       "      <td>3.445</td>\n",
       "      <td>27.23</td>\n",
       "      <td>0.009110</td>\n",
       "      <td>0.07458</td>\n",
       "      <td>0.05661</td>\n",
       "      <td>0.01867</td>\n",
       "      <td>0.05963</td>\n",
       "      <td>0.009208</td>\n",
       "      <td>14.91</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>M</td>\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>0.7572</td>\n",
       "      <td>0.7813</td>\n",
       "      <td>5.438</td>\n",
       "      <td>94.44</td>\n",
       "      <td>0.011490</td>\n",
       "      <td>0.02461</td>\n",
       "      <td>0.05688</td>\n",
       "      <td>0.01885</td>\n",
       "      <td>0.01756</td>\n",
       "      <td>0.005115</td>\n",
       "      <td>22.54</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",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  target  radius_mean  ...  symmetry_worst  fractal_dimension_worst\n",
       "0      M        17.99  ...          0.4601                  0.11890\n",
       "1      M        20.57  ...          0.2750                  0.08902\n",
       "2      M        19.69  ...          0.3613                  0.08758\n",
       "3      M        11.42  ...          0.6638                  0.17300\n",
       "4      M        20.29  ...          0.2364                  0.07678\n",
       "\n",
       "[5 rows x 31 columns]"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "tpot_data.rename(columns={'diagnosis':'target'}, inplace=True)\n",
    "tpot_data.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "6deae176-c4b6-4004-832f-e7324679734d",
   "metadata": {},
   "source": [
    "## Extract features"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "id": "46603e16-6fdb-4444-9550-3d08fa9241c9",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>radius_mean</th>\n",
       "      <th>texture_mean</th>\n",
       "      <th>perimeter_mean</th>\n",
       "      <th>area_mean</th>\n",
       "      <th>smoothness_mean</th>\n",
       "      <th>compactness_mean</th>\n",
       "      <th>concavity_mean</th>\n",
       "      <th>concave points_mean</th>\n",
       "      <th>symmetry_mean</th>\n",
       "      <th>fractal_dimension_mean</th>\n",
       "      <th>radius_se</th>\n",
       "      <th>texture_se</th>\n",
       "      <th>perimeter_se</th>\n",
       "      <th>area_se</th>\n",
       "      <th>smoothness_se</th>\n",
       "      <th>compactness_se</th>\n",
       "      <th>concavity_se</th>\n",
       "      <th>concave points_se</th>\n",
       "      <th>symmetry_se</th>\n",
       "      <th>fractal_dimension_se</th>\n",
       "      <th>radius_worst</th>\n",
       "      <th>texture_worst</th>\n",
       "      <th>perimeter_worst</th>\n",
       "      <th>area_worst</th>\n",
       "      <th>smoothness_worst</th>\n",
       "      <th>compactness_worst</th>\n",
       "      <th>concavity_worst</th>\n",
       "      <th>concave points_worst</th>\n",
       "      <th>symmetry_worst</th>\n",
       "      <th>fractal_dimension_worst</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>1.0950</td>\n",
       "      <td>0.9053</td>\n",
       "      <td>8.589</td>\n",
       "      <td>153.40</td>\n",
       "      <td>0.006399</td>\n",
       "      <td>0.04904</td>\n",
       "      <td>0.05373</td>\n",
       "      <td>0.01587</td>\n",
       "      <td>0.03003</td>\n",
       "      <td>0.006193</td>\n",
       "      <td>25.38</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",
       "    </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>0.5435</td>\n",
       "      <td>0.7339</td>\n",
       "      <td>3.398</td>\n",
       "      <td>74.08</td>\n",
       "      <td>0.005225</td>\n",
       "      <td>0.01308</td>\n",
       "      <td>0.01860</td>\n",
       "      <td>0.01340</td>\n",
       "      <td>0.01389</td>\n",
       "      <td>0.003532</td>\n",
       "      <td>24.99</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",
       "    </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>0.7456</td>\n",
       "      <td>0.7869</td>\n",
       "      <td>4.585</td>\n",
       "      <td>94.03</td>\n",
       "      <td>0.006150</td>\n",
       "      <td>0.04006</td>\n",
       "      <td>0.03832</td>\n",
       "      <td>0.02058</td>\n",
       "      <td>0.02250</td>\n",
       "      <td>0.004571</td>\n",
       "      <td>23.57</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",
       "    </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>0.4956</td>\n",
       "      <td>1.1560</td>\n",
       "      <td>3.445</td>\n",
       "      <td>27.23</td>\n",
       "      <td>0.009110</td>\n",
       "      <td>0.07458</td>\n",
       "      <td>0.05661</td>\n",
       "      <td>0.01867</td>\n",
       "      <td>0.05963</td>\n",
       "      <td>0.009208</td>\n",
       "      <td>14.91</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",
       "    </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>0.7572</td>\n",
       "      <td>0.7813</td>\n",
       "      <td>5.438</td>\n",
       "      <td>94.44</td>\n",
       "      <td>0.011490</td>\n",
       "      <td>0.02461</td>\n",
       "      <td>0.05688</td>\n",
       "      <td>0.01885</td>\n",
       "      <td>0.01756</td>\n",
       "      <td>0.005115</td>\n",
       "      <td>22.54</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",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   radius_mean  texture_mean  ...  symmetry_worst  fractal_dimension_worst\n",
       "0        17.99         10.38  ...          0.4601                  0.11890\n",
       "1        20.57         17.77  ...          0.2750                  0.08902\n",
       "2        19.69         21.25  ...          0.3613                  0.08758\n",
       "3        11.42         20.38  ...          0.6638                  0.17300\n",
       "4        20.29         14.34  ...          0.2364                  0.07678\n",
       "\n",
       "[5 rows x 30 columns]"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "features = tpot_data.drop('target', axis=1)\n",
    "features = features.astype(np.float64) # to avoid warning message during optimization\n",
    "features.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "id": "a7f7d45a-5186-4169-921c-04bf1d1930bd",
   "metadata": {},
   "outputs": [],
   "source": [
    "training_features, testing_features, training_target, testing_target = \\\n",
    "            train_test_split(features, tpot_data['target'], random_state=42)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "853e0986-9266-4808-a3c5-c470ab854736",
   "metadata": {},
   "source": [
    "# Perform AutoML with TPOT\n",
    "See the documentation for complete set of parameters:  \n",
    "https://epistasislab.github.io/tpot/api/"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "id": "78bb265c-8381-47de-b20e-ebef91e75b3a",
   "metadata": {},
   "outputs": [],
   "source": [
    "pipeline_optimizer = TPOTClassifier(generations=5,\n",
    "                                    population_size=20,\n",
    "                                    cv=5,                  # cross validation\n",
    "                                    random_state=42,\n",
    "                                    verbosity=2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "id": "56a10e5c-efb8-474e-adf9-193ea3627262",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "                                                                                                       \n",
      "Generation 1 - Current best internal CV score: 0.9694938440492477\n",
      "                                                                                                       \n",
      "Generation 2 - Current best internal CV score: 0.9694938440492477\n",
      "                                                                                                       \n",
      "Generation 3 - Current best internal CV score: 0.9718467852257182\n",
      "                                                                                                       \n",
      "Generation 4 - Current best internal CV score: 0.9718467852257182\n",
      "                                                                                                       \n",
      "Generation 5 - Current best internal CV score: 0.9718467852257182\n",
      "                                                                                                       \n",
      "Best pipeline: MLPClassifier(RobustScaler(input_matrix), alpha=0.01, learning_rate_init=0.01)\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "TPOTClassifier(generations=5, population_size=20, random_state=42, verbosity=2)"
      ]
     },
     "execution_count": 28,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pipeline_optimizer.fit(features=training_features, target=training_target)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "2daa5c15-845e-4381-a677-9a6793ff199c",
   "metadata": {},
   "source": [
    "# Questions "
   ]
  },
  {
   "cell_type": "markdown",
   "id": "67e49742-8b3c-415d-b228-bdb8dd42904d",
   "metadata": {},
   "source": [
    "By changing the value of the `max_time_mins` argument in the `TPOTClassifier`, answer the following question:\n",
    "\n",
    "1. What is the best accuracy score after:\n",
    "    - One minute?\n",
    "    - Two minutes?\n",
    "    - Five minutes?"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "a8579b78-90c6-493e-a564-19af4a193f34",
   "metadata": {},
   "source": [
    "2. How does the accuracy changes with the number of generations? Try 1, 2 up to 5 generations and make a plot. "
   ]
  },
  {
   "cell_type": "markdown",
   "id": "33e7af85-e566-4222-95bb-3f0923d34151",
   "metadata": {},
   "source": [
    "3. Is the population size parameter a strong modifier of the final accuracy?"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "cf03efbb-a332-4bc5-a82a-f9a451fa4e2b",
   "metadata": {},
   "source": [
    "4. Find the best model for the regression problem based on the `00_datasets/student_regression/student-mat.csv` dataset. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "945b29b8-990d-4dd2-9075-c864d564ec22",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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