notebooks/05_use_model.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import sys\n",
    "sys.path.insert(0, '../rudeus')\n",
    "from machine_learning.use_model import UseModel\n",
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th></th>\n",
       "      <th>p_0</th>\n",
       "      <th>p_1</th>\n",
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       "      <th>p_4</th>\n",
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       "      <th>p_1014</th>\n",
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       "      <th>0</th>\n",
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       "      <td>0.032868</td>\n",
       "      <td>-0.001494</td>\n",
       "      <td>-0.062018</td>\n",
       "      <td>-0.003778</td>\n",
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       "      <td>0.050821</td>\n",
       "      <td>-0.025730</td>\n",
       "      <td>-0.073800</td>\n",
       "      <td>0.018048</td>\n",
       "      <td>-0.039436</td>\n",
       "      <td>0.028100</td>\n",
       "      <td>-0.076365</td>\n",
       "      <td>-0.003436</td>\n",
       "      <td>0.035041</td>\n",
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       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>0.001137</td>\n",
       "      <td>-0.036371</td>\n",
       "      <td>-0.001316</td>\n",
       "      <td>0.012051</td>\n",
       "      <td>-0.003318</td>\n",
       "      <td>-0.082171</td>\n",
       "      <td>0.031120</td>\n",
       "      <td>-0.180047</td>\n",
       "      <td>0.021112</td>\n",
       "      <td>0.035762</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.005131</td>\n",
       "      <td>-0.085110</td>\n",
       "      <td>0.058340</td>\n",
       "      <td>-0.188974</td>\n",
       "      <td>0.033570</td>\n",
       "      <td>-0.023494</td>\n",
       "      <td>0.026138</td>\n",
       "      <td>0.042009</td>\n",
       "      <td>0.023032</td>\n",
       "      <td>-0.025148</td>\n",
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       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>0.000475</td>\n",
       "      <td>0.011274</td>\n",
       "      <td>0.059589</td>\n",
       "      <td>-0.044880</td>\n",
       "      <td>0.042818</td>\n",
       "      <td>-0.000329</td>\n",
       "      <td>-0.011344</td>\n",
       "      <td>-0.122034</td>\n",
       "      <td>0.135050</td>\n",
       "      <td>0.086361</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.031992</td>\n",
       "      <td>0.009314</td>\n",
       "      <td>0.073134</td>\n",
       "      <td>-0.035469</td>\n",
       "      <td>-0.045812</td>\n",
       "      <td>-0.007914</td>\n",
       "      <td>0.026620</td>\n",
       "      <td>0.038053</td>\n",
       "      <td>0.000449</td>\n",
       "      <td>-0.034294</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>0.059392</td>\n",
       "      <td>0.048355</td>\n",
       "      <td>-0.012270</td>\n",
       "      <td>0.023485</td>\n",
       "      <td>0.030040</td>\n",
       "      <td>0.052105</td>\n",
       "      <td>0.020916</td>\n",
       "      <td>-0.073574</td>\n",
       "      <td>0.091505</td>\n",
       "      <td>0.024898</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.023088</td>\n",
       "      <td>0.047880</td>\n",
       "      <td>0.006481</td>\n",
       "      <td>-0.051059</td>\n",
       "      <td>0.020307</td>\n",
       "      <td>-0.018227</td>\n",
       "      <td>-0.037605</td>\n",
       "      <td>-0.044686</td>\n",
       "      <td>-0.069450</td>\n",
       "      <td>0.026355</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>0.009994</td>\n",
       "      <td>0.045471</td>\n",
       "      <td>0.057952</td>\n",
       "      <td>0.003034</td>\n",
       "      <td>-0.006978</td>\n",
       "      <td>0.021273</td>\n",
       "      <td>-0.013984</td>\n",
       "      <td>-0.094211</td>\n",
       "      <td>-0.088434</td>\n",
       "      <td>0.029190</td>\n",
       "      <td>...</td>\n",
       "      <td>0.039743</td>\n",
       "      <td>-0.066216</td>\n",
       "      <td>-0.012646</td>\n",
       "      <td>-0.114583</td>\n",
       "      <td>-0.008175</td>\n",
       "      <td>-0.032120</td>\n",
       "      <td>0.060356</td>\n",
       "      <td>0.046519</td>\n",
       "      <td>-0.020255</td>\n",
       "      <td>0.086085</td>\n",
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       "      <th>...</th>\n",
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       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
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       "    <tr>\n",
       "      <th>1228</th>\n",
       "      <td>0.007045</td>\n",
       "      <td>-0.006162</td>\n",
       "      <td>0.067712</td>\n",
       "      <td>-0.039342</td>\n",
       "      <td>-0.045674</td>\n",
       "      <td>0.038811</td>\n",
       "      <td>-0.056044</td>\n",
       "      <td>-0.054620</td>\n",
       "      <td>0.014197</td>\n",
       "      <td>0.063544</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.049473</td>\n",
       "      <td>0.030314</td>\n",
       "      <td>-0.005808</td>\n",
       "      <td>-0.073638</td>\n",
       "      <td>0.119511</td>\n",
       "      <td>0.045004</td>\n",
       "      <td>-0.008894</td>\n",
       "      <td>0.015136</td>\n",
       "      <td>-0.037982</td>\n",
       "      <td>0.101611</td>\n",
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       "    <tr>\n",
       "      <th>1229</th>\n",
       "      <td>0.037221</td>\n",
       "      <td>0.027043</td>\n",
       "      <td>0.015975</td>\n",
       "      <td>0.076492</td>\n",
       "      <td>-0.003602</td>\n",
       "      <td>0.021602</td>\n",
       "      <td>-0.063808</td>\n",
       "      <td>-0.029782</td>\n",
       "      <td>-0.034291</td>\n",
       "      <td>0.027042</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.048298</td>\n",
       "      <td>-0.003977</td>\n",
       "      <td>-0.076859</td>\n",
       "      <td>-0.065963</td>\n",
       "      <td>0.047613</td>\n",
       "      <td>-0.015720</td>\n",
       "      <td>-0.029573</td>\n",
       "      <td>-0.026455</td>\n",
       "      <td>-0.064972</td>\n",
       "      <td>0.006135</td>\n",
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       "      <th>1230</th>\n",
       "      <td>0.006880</td>\n",
       "      <td>-0.008367</td>\n",
       "      <td>0.024328</td>\n",
       "      <td>0.037605</td>\n",
       "      <td>-0.037526</td>\n",
       "      <td>0.056906</td>\n",
       "      <td>-0.073287</td>\n",
       "      <td>-0.056837</td>\n",
       "      <td>-0.016108</td>\n",
       "      <td>-0.026925</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.015349</td>\n",
       "      <td>-0.022129</td>\n",
       "      <td>0.013645</td>\n",
       "      <td>-0.114597</td>\n",
       "      <td>0.097413</td>\n",
       "      <td>0.020561</td>\n",
       "      <td>-0.004321</td>\n",
       "      <td>-0.043400</td>\n",
       "      <td>0.028065</td>\n",
       "      <td>0.048372</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1231</th>\n",
       "      <td>0.062053</td>\n",
       "      <td>0.036159</td>\n",
       "      <td>0.023534</td>\n",
       "      <td>0.074796</td>\n",
       "      <td>0.039753</td>\n",
       "      <td>0.040898</td>\n",
       "      <td>-0.072007</td>\n",
       "      <td>-0.056739</td>\n",
       "      <td>-0.068124</td>\n",
       "      <td>-0.052774</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.048452</td>\n",
       "      <td>-0.062047</td>\n",
       "      <td>-0.025315</td>\n",
       "      <td>0.026157</td>\n",
       "      <td>0.056093</td>\n",
       "      <td>0.039692</td>\n",
       "      <td>-0.080755</td>\n",
       "      <td>-0.049286</td>\n",
       "      <td>-0.032102</td>\n",
       "      <td>-0.010265</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1232</th>\n",
       "      <td>-0.023281</td>\n",
       "      <td>0.015620</td>\n",
       "      <td>0.058617</td>\n",
       "      <td>-0.070567</td>\n",
       "      <td>0.030250</td>\n",
       "      <td>0.036481</td>\n",
       "      <td>-0.036506</td>\n",
       "      <td>-0.096132</td>\n",
       "      <td>-0.038251</td>\n",
       "      <td>0.012462</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.049110</td>\n",
       "      <td>0.041891</td>\n",
       "      <td>0.047380</td>\n",
       "      <td>-0.091642</td>\n",
       "      <td>0.041190</td>\n",
       "      <td>-0.076618</td>\n",
       "      <td>-0.048200</td>\n",
       "      <td>0.031701</td>\n",
       "      <td>0.022359</td>\n",
       "      <td>0.079386</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1233 rows × 1024 columns</p>\n",
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      ],
      "text/plain": [
       "           p_0       p_1       p_2       p_3       p_4       p_5       p_6  \\\n",
       "0     0.048092  0.032868 -0.001494 -0.062018 -0.003778  0.011553 -0.003336   \n",
       "1     0.001137 -0.036371 -0.001316  0.012051 -0.003318 -0.082171  0.031120   \n",
       "2     0.000475  0.011274  0.059589 -0.044880  0.042818 -0.000329 -0.011344   \n",
       "3     0.059392  0.048355 -0.012270  0.023485  0.030040  0.052105  0.020916   \n",
       "4     0.009994  0.045471  0.057952  0.003034 -0.006978  0.021273 -0.013984   \n",
       "...        ...       ...       ...       ...       ...       ...       ...   \n",
       "1228  0.007045 -0.006162  0.067712 -0.039342 -0.045674  0.038811 -0.056044   \n",
       "1229  0.037221  0.027043  0.015975  0.076492 -0.003602  0.021602 -0.063808   \n",
       "1230  0.006880 -0.008367  0.024328  0.037605 -0.037526  0.056906 -0.073287   \n",
       "1231  0.062053  0.036159  0.023534  0.074796  0.039753  0.040898 -0.072007   \n",
       "1232 -0.023281  0.015620  0.058617 -0.070567  0.030250  0.036481 -0.036506   \n",
       "\n",
       "           p_7       p_8       p_9  ...    p_1014    p_1015    p_1016  \\\n",
       "0    -0.081583  0.036913 -0.059285  ... -0.006735  0.050821 -0.025730   \n",
       "1    -0.180047  0.021112  0.035762  ... -0.005131 -0.085110  0.058340   \n",
       "2    -0.122034  0.135050  0.086361  ... -0.031992  0.009314  0.073134   \n",
       "3    -0.073574  0.091505  0.024898  ... -0.023088  0.047880  0.006481   \n",
       "4    -0.094211 -0.088434  0.029190  ...  0.039743 -0.066216 -0.012646   \n",
       "...        ...       ...       ...  ...       ...       ...       ...   \n",
       "1228 -0.054620  0.014197  0.063544  ... -0.049473  0.030314 -0.005808   \n",
       "1229 -0.029782 -0.034291  0.027042  ... -0.048298 -0.003977 -0.076859   \n",
       "1230 -0.056837 -0.016108 -0.026925  ... -0.015349 -0.022129  0.013645   \n",
       "1231 -0.056739 -0.068124 -0.052774  ... -0.048452 -0.062047 -0.025315   \n",
       "1232 -0.096132 -0.038251  0.012462  ... -0.049110  0.041891  0.047380   \n",
       "\n",
       "        p_1017    p_1018    p_1019    p_1020    p_1021    p_1022    p_1023  \n",
       "0    -0.073800  0.018048 -0.039436  0.028100 -0.076365 -0.003436  0.035041  \n",
       "1    -0.188974  0.033570 -0.023494  0.026138  0.042009  0.023032 -0.025148  \n",
       "2    -0.035469 -0.045812 -0.007914  0.026620  0.038053  0.000449 -0.034294  \n",
       "3    -0.051059  0.020307 -0.018227 -0.037605 -0.044686 -0.069450  0.026355  \n",
       "4    -0.114583 -0.008175 -0.032120  0.060356  0.046519 -0.020255  0.086085  \n",
       "...        ...       ...       ...       ...       ...       ...       ...  \n",
       "1228 -0.073638  0.119511  0.045004 -0.008894  0.015136 -0.037982  0.101611  \n",
       "1229 -0.065963  0.047613 -0.015720 -0.029573 -0.026455 -0.064972  0.006135  \n",
       "1230 -0.114597  0.097413  0.020561 -0.004321 -0.043400  0.028065  0.048372  \n",
       "1231  0.026157  0.056093  0.039692 -0.080755 -0.049286 -0.032102 -0.010265  \n",
       "1232 -0.091642  0.041190 -0.076618 -0.048200  0.031701  0.022359  0.079386  \n",
       "\n",
       "[1233 rows x 1024 columns]"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df = pd.read_csv(\"../rudeus_data/encoded_data/single_double/prottrans_t5_uniref.csv\")\n",
    "df = df.drop(columns=[\"type_interaction\"])\n",
    "df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([1, 1, 0, ..., 0, 0, 0])"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "use_model = UseModel(\"../trained_models/single_double/ExtraTreesClassifier_prottrans_t5_uniref.joblib\", df)\n",
    "use_model.predict()"
   ]
  }
 ],
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