Dataset for Modelling.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-10-21T22:36:01.918359Z",
     "start_time": "2019-10-21T22:36:01.612816Z"
    }
   },
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import numpy as np\n",
    "import pickle"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-10-21T22:36:02.215991Z",
     "start_time": "2019-10-21T22:36:01.920402Z"
    }
   },
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>drug_cas</th>\n",
       "      <th>drug_id</th>\n",
       "      <th>drug_name</th>\n",
       "      <th>target_actions</th>\n",
       "      <th>target_amino</th>\n",
       "      <th>target_gene</th>\n",
       "      <th>target_id</th>\n",
       "      <th>target_name</th>\n",
       "      <th>target_organism</th>\n",
       "      <th>pubchem_id</th>\n",
       "      <th>pubchem_name</th>\n",
       "      <th>target_gene_fingerprint</th>\n",
       "      <th>drug_fingerprint</th>\n",
       "      <th>SMILE</th>\n",
       "      <th>target_embd</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>128270-60-0</td>\n",
       "      <td>DB00006</td>\n",
       "      <td>Bivalirudin</td>\n",
       "      <td>[inhibitor]</td>\n",
       "      <td>&gt;lcl|BSEQ0016004|Prothrombin\\nMAHVRGLQLPGCLALA...</td>\n",
       "      <td>&gt;lcl|BSEQ0016005|Prothrombin (F2)\\nATGGCGCACGT...</td>\n",
       "      <td>BE0000048</td>\n",
       "      <td>Prothrombin</td>\n",
       "      <td>Human</td>\n",
       "      <td>16129704</td>\n",
       "      <td>Bivalirudin</td>\n",
       "      <td>[1.2739266e-05 -2.7748918e-05 0.00095751503 0....</td>\n",
       "      <td>[0.10044218 0.18559723 -0.12865402 -0.0650997 ...</td>\n",
       "      <td>CCC(C)C(C(=O)N1CCCC1C(=O)NC(CCC(=O)O)C(=O)NC(C...</td>\n",
       "      <td>0.0011788049 -0.00059948955 0.00048735933 -0.0...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>65807-02-5</td>\n",
       "      <td>DB00014</td>\n",
       "      <td>Goserelin</td>\n",
       "      <td>[agonist]</td>\n",
       "      <td>&gt;lcl|BSEQ0036957|Lutropin-choriogonadotropic h...</td>\n",
       "      <td>&gt;lcl|BSEQ0010174|Lutropin-choriogonadotropic h...</td>\n",
       "      <td>BE0000134</td>\n",
       "      <td>Lutropin-choriogonadotropic hormone receptor</td>\n",
       "      <td>Human</td>\n",
       "      <td>5311128</td>\n",
       "      <td>goserelin</td>\n",
       "      <td>[1.2739266e-05 -2.7748918e-05 0.00095751503 0....</td>\n",
       "      <td>[0.1331214 0.2391842 -0.14361311 -0.14107014 0...</td>\n",
       "      <td>CC(C)CC(C(=O)NC(CCCN=C(N)N)C(=O)N1CCCC1C(=O)NN...</td>\n",
       "      <td>-2.7273058e-05 -0.0014635038 -0.000130956 0.00...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>65807-02-5</td>\n",
       "      <td>DB00014</td>\n",
       "      <td>Goserelin</td>\n",
       "      <td>[agonist]</td>\n",
       "      <td>&gt;lcl|BSEQ0000405|Gonadotropin-releasing hormon...</td>\n",
       "      <td>&gt;lcl|BSEQ0018926|Gonadotropin-releasing hormon...</td>\n",
       "      <td>BE0000203</td>\n",
       "      <td>Gonadotropin-releasing hormone receptor</td>\n",
       "      <td>Human</td>\n",
       "      <td>5311128</td>\n",
       "      <td>goserelin</td>\n",
       "      <td>[1.2739266e-05 -2.7748918e-05 0.00095751503 0....</td>\n",
       "      <td>[0.1331214 0.2391842 -0.14361311 -0.14107014 0...</td>\n",
       "      <td>CC(C)CC(C(=O)NC(CCCN=C(N)N)C(=O)N1CCCC1C(=O)NN...</td>\n",
       "      <td>-0.00060385827 -0.0011927614 -0.00020535699 -0...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>16679-58-6</td>\n",
       "      <td>DB00035</td>\n",
       "      <td>Desmopressin</td>\n",
       "      <td>[agonist]</td>\n",
       "      <td>&gt;lcl|BSEQ0000583|Vasopressin V2 receptor\\nMLMA...</td>\n",
       "      <td>&gt;lcl|BSEQ0010065|Vasopressin V2 receptor (AVPR...</td>\n",
       "      <td>BE0000293</td>\n",
       "      <td>Vasopressin V2 receptor</td>\n",
       "      <td>Human</td>\n",
       "      <td>16051933</td>\n",
       "      <td>DESMOPRESSIN</td>\n",
       "      <td>[1.2739266e-05 -2.7748918e-05 0.00095751503 0....</td>\n",
       "      <td>[0.051722348 0.24374117 -0.16236018 -0.1723347...</td>\n",
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       "      <td>0.0002876672 9.454535e-06 -0.00021410194 -0.00...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>16679-58-6</td>\n",
       "      <td>DB00035</td>\n",
       "      <td>Desmopressin</td>\n",
       "      <td>NaN</td>\n",
       "      <td>&gt;lcl|BSEQ0009979|Vasopressin V1a receptor\\nMRL...</td>\n",
       "      <td>&gt;lcl|BSEQ0009980|Vasopressin V1a receptor (AVP...</td>\n",
       "      <td>BE0000165</td>\n",
       "      <td>Vasopressin V1a receptor</td>\n",
       "      <td>Human</td>\n",
       "      <td>16051933</td>\n",
       "      <td>DESMOPRESSIN</td>\n",
       "      <td>[1.2739266e-05 -2.7748918e-05 0.00095751503 0....</td>\n",
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      ],
      "text/plain": [
       "      drug_cas  drug_id     drug_name target_actions  \\\n",
       "0  128270-60-0  DB00006   Bivalirudin    [inhibitor]   \n",
       "1   65807-02-5  DB00014     Goserelin      [agonist]   \n",
       "2   65807-02-5  DB00014     Goserelin      [agonist]   \n",
       "3   16679-58-6  DB00035  Desmopressin      [agonist]   \n",
       "4   16679-58-6  DB00035  Desmopressin            NaN   \n",
       "\n",
       "                                        target_amino  \\\n",
       "0  >lcl|BSEQ0016004|Prothrombin\\nMAHVRGLQLPGCLALA...   \n",
       "1  >lcl|BSEQ0036957|Lutropin-choriogonadotropic h...   \n",
       "2  >lcl|BSEQ0000405|Gonadotropin-releasing hormon...   \n",
       "3  >lcl|BSEQ0000583|Vasopressin V2 receptor\\nMLMA...   \n",
       "4  >lcl|BSEQ0009979|Vasopressin V1a receptor\\nMRL...   \n",
       "\n",
       "                                         target_gene  target_id  \\\n",
       "0  >lcl|BSEQ0016005|Prothrombin (F2)\\nATGGCGCACGT...  BE0000048   \n",
       "1  >lcl|BSEQ0010174|Lutropin-choriogonadotropic h...  BE0000134   \n",
       "2  >lcl|BSEQ0018926|Gonadotropin-releasing hormon...  BE0000203   \n",
       "3  >lcl|BSEQ0010065|Vasopressin V2 receptor (AVPR...  BE0000293   \n",
       "4  >lcl|BSEQ0009980|Vasopressin V1a receptor (AVP...  BE0000165   \n",
       "\n",
       "                                    target_name target_organism  pubchem_id  \\\n",
       "0                                   Prothrombin           Human    16129704   \n",
       "1  Lutropin-choriogonadotropic hormone receptor           Human     5311128   \n",
       "2       Gonadotropin-releasing hormone receptor           Human     5311128   \n",
       "3                       Vasopressin V2 receptor           Human    16051933   \n",
       "4                      Vasopressin V1a receptor           Human    16051933   \n",
       "\n",
       "   pubchem_name                            target_gene_fingerprint  \\\n",
       "0   Bivalirudin  [1.2739266e-05 -2.7748918e-05 0.00095751503 0....   \n",
       "1     goserelin  [1.2739266e-05 -2.7748918e-05 0.00095751503 0....   \n",
       "2     goserelin  [1.2739266e-05 -2.7748918e-05 0.00095751503 0....   \n",
       "3  DESMOPRESSIN  [1.2739266e-05 -2.7748918e-05 0.00095751503 0....   \n",
       "4  DESMOPRESSIN  [1.2739266e-05 -2.7748918e-05 0.00095751503 0....   \n",
       "\n",
       "                                    drug_fingerprint  \\\n",
       "0  [0.10044218 0.18559723 -0.12865402 -0.0650997 ...   \n",
       "1  [0.1331214 0.2391842 -0.14361311 -0.14107014 0...   \n",
       "2  [0.1331214 0.2391842 -0.14361311 -0.14107014 0...   \n",
       "3  [0.051722348 0.24374117 -0.16236018 -0.1723347...   \n",
       "4  [0.051722348 0.24374117 -0.16236018 -0.1723347...   \n",
       "\n",
       "                                               SMILE  \\\n",
       "0  CCC(C)C(C(=O)N1CCCC1C(=O)NC(CCC(=O)O)C(=O)NC(C...   \n",
       "1  CC(C)CC(C(=O)NC(CCCN=C(N)N)C(=O)N1CCCC1C(=O)NN...   \n",
       "2  CC(C)CC(C(=O)NC(CCCN=C(N)N)C(=O)N1CCCC1C(=O)NN...   \n",
       "3  C1CC(N(C1)C(=O)C2CSSCCC(=O)NC(C(=O)NC(C(=O)NC(...   \n",
       "4  C1CC(N(C1)C(=O)C2CSSCCC(=O)NC(C(=O)NC(C(=O)NC(...   \n",
       "\n",
       "                                         target_embd  \n",
       "0  0.0011788049 -0.00059948955 0.00048735933 -0.0...  \n",
       "1  -2.7273058e-05 -0.0014635038 -0.000130956 0.00...  \n",
       "2  -0.00060385827 -0.0011927614 -0.00020535699 -0...  \n",
       "3  0.0002876672 9.454535e-06 -0.00021410194 -0.00...  \n",
       "4  -0.00047414153 -0.00063484476 0.00041864807 -0...  "
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df = pickle.load(open('drugbank_embds.pkl', 'rb'))\n",
    "df = df[~pd.isna(df['target_embd'])]\n",
    "df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-10-21T22:36:03.253876Z",
     "start_time": "2019-10-21T22:36:02.218092Z"
    }
   },
   "outputs": [],
   "source": [
    "ndf = pd.read_csv('negative_samples/negative_samples_thrsh:12')[['node_0','node_1','shortest_path']]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-10-21T22:36:03.260803Z",
     "start_time": "2019-10-21T22:36:03.256364Z"
    }
   },
   "outputs": [],
   "source": [
    "def getData(x):\n",
    "    if type(x) == list:\n",
    "        return [float(i) for i in x[0].split(' ')]\n",
    "    else:\n",
    "        return [float(i) for i in x.split(' ')]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-10-21T22:36:03.823973Z",
     "start_time": "2019-10-21T22:36:03.262735Z"
    }
   },
   "outputs": [],
   "source": [
    "df['target_embd'] = df['target_embd'].apply(getData)\n",
    "df['drug_fingerprint'] = df['drug_fingerprint'].apply(getData)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-10-21T22:36:03.850519Z",
     "start_time": "2019-10-21T22:36:03.825801Z"
    }
   },
   "outputs": [
    {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>drug_cas</th>\n",
       "      <th>drug_id</th>\n",
       "      <th>drug_name</th>\n",
       "      <th>target_actions</th>\n",
       "      <th>target_amino</th>\n",
       "      <th>target_gene</th>\n",
       "      <th>target_id</th>\n",
       "      <th>target_name</th>\n",
       "      <th>target_organism</th>\n",
       "      <th>pubchem_id</th>\n",
       "      <th>pubchem_name</th>\n",
       "      <th>target_gene_fingerprint</th>\n",
       "      <th>drug_fingerprint</th>\n",
       "      <th>SMILE</th>\n",
       "      <th>target_embd</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>128270-60-0</td>\n",
       "      <td>DB00006</td>\n",
       "      <td>Bivalirudin</td>\n",
       "      <td>[inhibitor]</td>\n",
       "      <td>&gt;lcl|BSEQ0016004|Prothrombin\\nMAHVRGLQLPGCLALA...</td>\n",
       "      <td>&gt;lcl|BSEQ0016005|Prothrombin (F2)\\nATGGCGCACGT...</td>\n",
       "      <td>BE0000048</td>\n",
       "      <td>Prothrombin</td>\n",
       "      <td>Human</td>\n",
       "      <td>16129704</td>\n",
       "      <td>Bivalirudin</td>\n",
       "      <td>[1.2739266e-05 -2.7748918e-05 0.00095751503 0....</td>\n",
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       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>65807-02-5</td>\n",
       "      <td>DB00014</td>\n",
       "      <td>Goserelin</td>\n",
       "      <td>[agonist]</td>\n",
       "      <td>&gt;lcl|BSEQ0036957|Lutropin-choriogonadotropic h...</td>\n",
       "      <td>&gt;lcl|BSEQ0010174|Lutropin-choriogonadotropic h...</td>\n",
       "      <td>BE0000134</td>\n",
       "      <td>Lutropin-choriogonadotropic hormone receptor</td>\n",
       "      <td>Human</td>\n",
       "      <td>5311128</td>\n",
       "      <td>goserelin</td>\n",
       "      <td>[1.2739266e-05 -2.7748918e-05 0.00095751503 0....</td>\n",
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       "      <td>CC(C)CC(C(=O)NC(CCCN=C(N)N)C(=O)N1CCCC1C(=O)NN...</td>\n",
       "      <td>[-2.7273058e-05, -0.0014635038, -0.000130956, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>65807-02-5</td>\n",
       "      <td>DB00014</td>\n",
       "      <td>Goserelin</td>\n",
       "      <td>[agonist]</td>\n",
       "      <td>&gt;lcl|BSEQ0000405|Gonadotropin-releasing hormon...</td>\n",
       "      <td>&gt;lcl|BSEQ0018926|Gonadotropin-releasing hormon...</td>\n",
       "      <td>BE0000203</td>\n",
       "      <td>Gonadotropin-releasing hormone receptor</td>\n",
       "      <td>Human</td>\n",
       "      <td>5311128</td>\n",
       "      <td>goserelin</td>\n",
       "      <td>[1.2739266e-05 -2.7748918e-05 0.00095751503 0....</td>\n",
       "      <td>[0.1331214, 0.2391842, -0.14361311, -0.1410701...</td>\n",
       "      <td>CC(C)CC(C(=O)NC(CCCN=C(N)N)C(=O)N1CCCC1C(=O)NN...</td>\n",
       "      <td>[-0.00060385827, -0.0011927614, -0.00020535699...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>16679-58-6</td>\n",
       "      <td>DB00035</td>\n",
       "      <td>Desmopressin</td>\n",
       "      <td>[agonist]</td>\n",
       "      <td>&gt;lcl|BSEQ0000583|Vasopressin V2 receptor\\nMLMA...</td>\n",
       "      <td>&gt;lcl|BSEQ0010065|Vasopressin V2 receptor (AVPR...</td>\n",
       "      <td>BE0000293</td>\n",
       "      <td>Vasopressin V2 receptor</td>\n",
       "      <td>Human</td>\n",
       "      <td>16051933</td>\n",
       "      <td>DESMOPRESSIN</td>\n",
       "      <td>[1.2739266e-05 -2.7748918e-05 0.00095751503 0....</td>\n",
       "      <td>[0.051722348, 0.24374117, -0.16236018, -0.1723...</td>\n",
       "      <td>C1CC(N(C1)C(=O)C2CSSCCC(=O)NC(C(=O)NC(C(=O)NC(...</td>\n",
       "      <td>[0.0002876672, 9.454535e-06, -0.00021410194, -...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>16679-58-6</td>\n",
       "      <td>DB00035</td>\n",
       "      <td>Desmopressin</td>\n",
       "      <td>NaN</td>\n",
       "      <td>&gt;lcl|BSEQ0009979|Vasopressin V1a receptor\\nMRL...</td>\n",
       "      <td>&gt;lcl|BSEQ0009980|Vasopressin V1a receptor (AVP...</td>\n",
       "      <td>BE0000165</td>\n",
       "      <td>Vasopressin V1a receptor</td>\n",
       "      <td>Human</td>\n",
       "      <td>16051933</td>\n",
       "      <td>DESMOPRESSIN</td>\n",
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      ],
      "text/plain": [
       "      drug_cas  drug_id     drug_name target_actions  \\\n",
       "0  128270-60-0  DB00006   Bivalirudin    [inhibitor]   \n",
       "1   65807-02-5  DB00014     Goserelin      [agonist]   \n",
       "2   65807-02-5  DB00014     Goserelin      [agonist]   \n",
       "3   16679-58-6  DB00035  Desmopressin      [agonist]   \n",
       "4   16679-58-6  DB00035  Desmopressin            NaN   \n",
       "\n",
       "                                        target_amino  \\\n",
       "0  >lcl|BSEQ0016004|Prothrombin\\nMAHVRGLQLPGCLALA...   \n",
       "1  >lcl|BSEQ0036957|Lutropin-choriogonadotropic h...   \n",
       "2  >lcl|BSEQ0000405|Gonadotropin-releasing hormon...   \n",
       "3  >lcl|BSEQ0000583|Vasopressin V2 receptor\\nMLMA...   \n",
       "4  >lcl|BSEQ0009979|Vasopressin V1a receptor\\nMRL...   \n",
       "\n",
       "                                         target_gene  target_id  \\\n",
       "0  >lcl|BSEQ0016005|Prothrombin (F2)\\nATGGCGCACGT...  BE0000048   \n",
       "1  >lcl|BSEQ0010174|Lutropin-choriogonadotropic h...  BE0000134   \n",
       "2  >lcl|BSEQ0018926|Gonadotropin-releasing hormon...  BE0000203   \n",
       "3  >lcl|BSEQ0010065|Vasopressin V2 receptor (AVPR...  BE0000293   \n",
       "4  >lcl|BSEQ0009980|Vasopressin V1a receptor (AVP...  BE0000165   \n",
       "\n",
       "                                    target_name target_organism  pubchem_id  \\\n",
       "0                                   Prothrombin           Human    16129704   \n",
       "1  Lutropin-choriogonadotropic hormone receptor           Human     5311128   \n",
       "2       Gonadotropin-releasing hormone receptor           Human     5311128   \n",
       "3                       Vasopressin V2 receptor           Human    16051933   \n",
       "4                      Vasopressin V1a receptor           Human    16051933   \n",
       "\n",
       "   pubchem_name                            target_gene_fingerprint  \\\n",
       "0   Bivalirudin  [1.2739266e-05 -2.7748918e-05 0.00095751503 0....   \n",
       "1     goserelin  [1.2739266e-05 -2.7748918e-05 0.00095751503 0....   \n",
       "2     goserelin  [1.2739266e-05 -2.7748918e-05 0.00095751503 0....   \n",
       "3  DESMOPRESSIN  [1.2739266e-05 -2.7748918e-05 0.00095751503 0....   \n",
       "4  DESMOPRESSIN  [1.2739266e-05 -2.7748918e-05 0.00095751503 0....   \n",
       "\n",
       "                                    drug_fingerprint  \\\n",
       "0  [0.10044218, 0.18559723, -0.12865402, -0.06509...   \n",
       "1  [0.1331214, 0.2391842, -0.14361311, -0.1410701...   \n",
       "2  [0.1331214, 0.2391842, -0.14361311, -0.1410701...   \n",
       "3  [0.051722348, 0.24374117, -0.16236018, -0.1723...   \n",
       "4  [0.051722348, 0.24374117, -0.16236018, -0.1723...   \n",
       "\n",
       "                                               SMILE  \\\n",
       "0  CCC(C)C(C(=O)N1CCCC1C(=O)NC(CCC(=O)O)C(=O)NC(C...   \n",
       "1  CC(C)CC(C(=O)NC(CCCN=C(N)N)C(=O)N1CCCC1C(=O)NN...   \n",
       "2  CC(C)CC(C(=O)NC(CCCN=C(N)N)C(=O)N1CCCC1C(=O)NN...   \n",
       "3  C1CC(N(C1)C(=O)C2CSSCCC(=O)NC(C(=O)NC(C(=O)NC(...   \n",
       "4  C1CC(N(C1)C(=O)C2CSSCCC(=O)NC(C(=O)NC(C(=O)NC(...   \n",
       "\n",
       "                                         target_embd  \n",
       "0  [0.0011788049, -0.00059948955, 0.00048735933, ...  \n",
       "1  [-2.7273058e-05, -0.0014635038, -0.000130956, ...  \n",
       "2  [-0.00060385827, -0.0011927614, -0.00020535699...  \n",
       "3  [0.0002876672, 9.454535e-06, -0.00021410194, -...  \n",
       "4  [-0.00047414153, -0.00063484476, 0.00041864807...  "
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-10-21T22:36:04.094017Z",
     "start_time": "2019-10-21T22:36:03.852521Z"
    }
   },
   "outputs": [],
   "source": [
    "data_1 = pd.concat([pd.DataFrame(df['target_embd'].values.tolist(), columns=['Target_Vec_'+str(i) for i in range(0, 30)]), \n",
    "               pd.DataFrame(df['drug_fingerprint'].values.tolist(), columns=['Drug_Vec_'+str(i) for i in range(0, 100)])], axis=1)\n",
    "data_1['Class'] = 1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-10-21T22:36:18.034260Z",
     "start_time": "2019-10-21T22:36:04.097175Z"
    }
   },
   "outputs": [],
   "source": [
    "d = dict()\n",
    "for item in np.unique(df['drug_id'].values):\n",
    "    try:\n",
    "        _ = d[item]\n",
    "    except:\n",
    "        d.update({item : df[df['drug_id'] == item]['drug_fingerprint'].values[0] })\n",
    "\n",
    "for item in np.unique(df['target_id'].values):\n",
    "    try:\n",
    "        _ = d[item]\n",
    "    except:\n",
    "        d.update({item : df[df['target_id'] == item]['target_embd'].values[0] })"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-10-21T22:36:18.040534Z",
     "start_time": "2019-10-21T22:36:18.036506Z"
    }
   },
   "outputs": [],
   "source": [
    "def getVec(n1, n2):\n",
    "    try:\n",
    "        if n1.startswith('DB'):\n",
    "            drug = d[n1]\n",
    "            target = d[n2]\n",
    "        else:\n",
    "            drug = d[n2]\n",
    "            target = d[n1]\n",
    "        return target, drug\n",
    "    except:\n",
    "        return np.nan, np.nan"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-10-21T22:41:02.952974Z",
     "start_time": "2019-10-21T22:36:18.042799Z"
    }
   },
   "outputs": [],
   "source": [
    "ndf[['target_embd', 'drug_fingerprint']] = ndf.apply(lambda x: getVec(x.node_0, x.node_1), \n",
    "                                                         axis=1, result_type='expand')\n",
    "ndf = ndf[~pd.isna(ndf['target_embd'])]\n",
    "ndf['len'] = ndf['target_embd'].apply(lambda x: len(x))\n",
    "ndf = ndf[ndf['len'] == 30]\n",
    "ndf['len2'] = ndf['drug_fingerprint'].apply(lambda x: len(x))\n",
    "ndf = ndf[ndf['len2'] == 100]\n",
    "ndf = ndf.sample(data_1.shape[0])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-10-21T22:41:03.154461Z",
     "start_time": "2019-10-21T22:41:02.955026Z"
    }
   },
   "outputs": [],
   "source": [
    "data_2 = pd.concat([pd.DataFrame(ndf['target_embd'].values.tolist(), columns=['Target_Vec_'+str(i) for i in range(0, 30)]), \n",
    "               pd.DataFrame(ndf['drug_fingerprint'].values.tolist(), columns=['Drug_Vec_'+str(i) for i in range(0, 100)])], axis=1)\n",
    "\n",
    "data_2['Class'] = 0"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-10-21T22:41:03.176320Z",
     "start_time": "2019-10-21T22:41:03.156511Z"
    }
   },
   "outputs": [],
   "source": [
    "data = pd.concat([data_1, data_2])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-10-21T22:41:03.181263Z",
     "start_time": "2019-10-21T22:41:03.178588Z"
    }
   },
   "outputs": [],
   "source": [
    "pickle.dump(data.open(\"data/dataset_vBalanced.pkl\", \"wb\"))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "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>Target_Vec_0</th>\n",
       "      <th>Target_Vec_1</th>\n",
       "      <th>Target_Vec_2</th>\n",
       "      <th>Target_Vec_3</th>\n",
       "      <th>Target_Vec_4</th>\n",
       "      <th>Target_Vec_5</th>\n",
       "      <th>Target_Vec_6</th>\n",
       "      <th>Target_Vec_7</th>\n",
       "      <th>Target_Vec_8</th>\n",
       "      <th>Target_Vec_9</th>\n",
       "      <th>...</th>\n",
       "      <th>Drug_Vec_91</th>\n",
       "      <th>Drug_Vec_92</th>\n",
       "      <th>Drug_Vec_93</th>\n",
       "      <th>Drug_Vec_94</th>\n",
       "      <th>Drug_Vec_95</th>\n",
       "      <th>Drug_Vec_96</th>\n",
       "      <th>Drug_Vec_97</th>\n",
       "      <th>Drug_Vec_98</th>\n",
       "      <th>Drug_Vec_99</th>\n",
       "      <th>Class</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>1.178805e-03</td>\n",
       "      <td>-0.000599</td>\n",
       "      <td>0.000487</td>\n",
       "      <td>-0.000306</td>\n",
       "      <td>0.000802</td>\n",
       "      <td>-0.000354</td>\n",
       "      <td>0.001005</td>\n",
       "      <td>-0.000329</td>\n",
       "      <td>-0.000619</td>\n",
       "      <td>-0.000425</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.027773</td>\n",
       "      <td>-0.261224</td>\n",
       "      <td>-0.349108</td>\n",
       "      <td>0.229779</td>\n",
       "      <td>0.161475</td>\n",
       "      <td>0.124695</td>\n",
       "      <td>0.368989</td>\n",
       "      <td>-0.198983</td>\n",
       "      <td>-0.435481</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>-2.727306e-05</td>\n",
       "      <td>-0.001464</td>\n",
       "      <td>-0.000131</td>\n",
       "      <td>0.000246</td>\n",
       "      <td>0.000441</td>\n",
       "      <td>-0.000762</td>\n",
       "      <td>0.000180</td>\n",
       "      <td>-0.000694</td>\n",
       "      <td>-0.000680</td>\n",
       "      <td>-0.000532</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.009263</td>\n",
       "      <td>-0.166779</td>\n",
       "      <td>-0.276308</td>\n",
       "      <td>0.178456</td>\n",
       "      <td>0.128912</td>\n",
       "      <td>0.083457</td>\n",
       "      <td>0.357332</td>\n",
       "      <td>-0.184330</td>\n",
       "      <td>-0.500235</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>-6.038583e-04</td>\n",
       "      <td>-0.001193</td>\n",
       "      <td>-0.000205</td>\n",
       "      <td>-0.000217</td>\n",
       "      <td>0.000200</td>\n",
       "      <td>-0.000553</td>\n",
       "      <td>0.000444</td>\n",
       "      <td>-0.001070</td>\n",
       "      <td>-0.001007</td>\n",
       "      <td>-0.000424</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.009263</td>\n",
       "      <td>-0.166779</td>\n",
       "      <td>-0.276308</td>\n",
       "      <td>0.178456</td>\n",
       "      <td>0.128912</td>\n",
       "      <td>0.083457</td>\n",
       "      <td>0.357332</td>\n",
       "      <td>-0.184330</td>\n",
       "      <td>-0.500235</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>2.876672e-04</td>\n",
       "      <td>0.000009</td>\n",
       "      <td>-0.000214</td>\n",
       "      <td>-0.000342</td>\n",
       "      <td>-0.000452</td>\n",
       "      <td>-0.000095</td>\n",
       "      <td>0.000965</td>\n",
       "      <td>-0.000946</td>\n",
       "      <td>-0.000221</td>\n",
       "      <td>-0.000475</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.197189</td>\n",
       "      <td>-0.190077</td>\n",
       "      <td>-0.227381</td>\n",
       "      <td>0.206817</td>\n",
       "      <td>0.102296</td>\n",
       "      <td>0.015936</td>\n",
       "      <td>0.315439</td>\n",
       "      <td>-0.296255</td>\n",
       "      <td>-0.259058</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>-4.741415e-04</td>\n",
       "      <td>-0.000635</td>\n",
       "      <td>0.000419</td>\n",
       "      <td>-0.000580</td>\n",
       "      <td>-0.000105</td>\n",
       "      <td>-0.000468</td>\n",
       "      <td>0.000574</td>\n",
       "      <td>-0.001202</td>\n",
       "      <td>0.000006</td>\n",
       "      <td>-0.000512</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.197189</td>\n",
       "      <td>-0.190077</td>\n",
       "      <td>-0.227381</td>\n",
       "      <td>0.206817</td>\n",
       "      <td>0.102296</td>\n",
       "      <td>0.015936</td>\n",
       "      <td>0.315439</td>\n",
       "      <td>-0.296255</td>\n",
       "      <td>-0.259058</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\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",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14076</th>\n",
       "      <td>-3.845415e-05</td>\n",
       "      <td>-0.000653</td>\n",
       "      <td>0.000587</td>\n",
       "      <td>-0.000515</td>\n",
       "      <td>0.000325</td>\n",
       "      <td>-0.001115</td>\n",
       "      <td>0.000875</td>\n",
       "      <td>-0.000988</td>\n",
       "      <td>-0.000410</td>\n",
       "      <td>-0.001185</td>\n",
       "      <td>...</td>\n",
       "      <td>0.165878</td>\n",
       "      <td>-0.106813</td>\n",
       "      <td>-0.177413</td>\n",
       "      <td>-0.068752</td>\n",
       "      <td>-0.020657</td>\n",
       "      <td>0.261743</td>\n",
       "      <td>0.216247</td>\n",
       "      <td>-0.180014</td>\n",
       "      <td>-0.321167</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14077</th>\n",
       "      <td>-5.031932e-07</td>\n",
       "      <td>-0.001942</td>\n",
       "      <td>0.000211</td>\n",
       "      <td>-0.000311</td>\n",
       "      <td>0.001769</td>\n",
       "      <td>-0.001692</td>\n",
       "      <td>0.000943</td>\n",
       "      <td>-0.000321</td>\n",
       "      <td>-0.000433</td>\n",
       "      <td>-0.000134</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.040043</td>\n",
       "      <td>-0.147016</td>\n",
       "      <td>-0.250347</td>\n",
       "      <td>0.031116</td>\n",
       "      <td>0.115812</td>\n",
       "      <td>0.172605</td>\n",
       "      <td>0.182108</td>\n",
       "      <td>-0.112508</td>\n",
       "      <td>-0.388979</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14078</th>\n",
       "      <td>2.341437e-04</td>\n",
       "      <td>-0.001047</td>\n",
       "      <td>0.000316</td>\n",
       "      <td>-0.000212</td>\n",
       "      <td>0.000614</td>\n",
       "      <td>-0.000927</td>\n",
       "      <td>0.000499</td>\n",
       "      <td>-0.000944</td>\n",
       "      <td>-0.000781</td>\n",
       "      <td>-0.000883</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.068147</td>\n",
       "      <td>-0.292997</td>\n",
       "      <td>-0.155505</td>\n",
       "      <td>0.198814</td>\n",
       "      <td>0.048889</td>\n",
       "      <td>0.188944</td>\n",
       "      <td>0.406694</td>\n",
       "      <td>-0.128643</td>\n",
       "      <td>-0.313929</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14079</th>\n",
       "      <td>-4.443420e-05</td>\n",
       "      <td>-0.000221</td>\n",
       "      <td>0.000039</td>\n",
       "      <td>-0.000140</td>\n",
       "      <td>0.000169</td>\n",
       "      <td>-0.000976</td>\n",
       "      <td>0.000579</td>\n",
       "      <td>-0.000595</td>\n",
       "      <td>-0.000039</td>\n",
       "      <td>-0.000564</td>\n",
       "      <td>...</td>\n",
       "      <td>0.045299</td>\n",
       "      <td>-0.187073</td>\n",
       "      <td>-0.099166</td>\n",
       "      <td>0.009447</td>\n",
       "      <td>0.100605</td>\n",
       "      <td>0.215792</td>\n",
       "      <td>0.203580</td>\n",
       "      <td>-0.066847</td>\n",
       "      <td>-0.382959</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14080</th>\n",
       "      <td>-7.125188e-05</td>\n",
       "      <td>-0.001330</td>\n",
       "      <td>-0.000334</td>\n",
       "      <td>-0.000709</td>\n",
       "      <td>0.000394</td>\n",
       "      <td>-0.000490</td>\n",
       "      <td>-0.000104</td>\n",
       "      <td>-0.000448</td>\n",
       "      <td>-0.000504</td>\n",
       "      <td>-0.000058</td>\n",
       "      <td>...</td>\n",
       "      <td>0.060210</td>\n",
       "      <td>-0.125469</td>\n",
       "      <td>-0.023296</td>\n",
       "      <td>0.040318</td>\n",
       "      <td>0.023454</td>\n",
       "      <td>0.093525</td>\n",
       "      <td>0.227268</td>\n",
       "      <td>-0.056917</td>\n",
       "      <td>-0.394649</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>28162 rows × 131 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "       Target_Vec_0  Target_Vec_1  Target_Vec_2  Target_Vec_3  Target_Vec_4  \\\n",
       "0      1.178805e-03     -0.000599      0.000487     -0.000306      0.000802   \n",
       "1     -2.727306e-05     -0.001464     -0.000131      0.000246      0.000441   \n",
       "2     -6.038583e-04     -0.001193     -0.000205     -0.000217      0.000200   \n",
       "3      2.876672e-04      0.000009     -0.000214     -0.000342     -0.000452   \n",
       "4     -4.741415e-04     -0.000635      0.000419     -0.000580     -0.000105   \n",
       "...             ...           ...           ...           ...           ...   \n",
       "14076 -3.845415e-05     -0.000653      0.000587     -0.000515      0.000325   \n",
       "14077 -5.031932e-07     -0.001942      0.000211     -0.000311      0.001769   \n",
       "14078  2.341437e-04     -0.001047      0.000316     -0.000212      0.000614   \n",
       "14079 -4.443420e-05     -0.000221      0.000039     -0.000140      0.000169   \n",
       "14080 -7.125188e-05     -0.001330     -0.000334     -0.000709      0.000394   \n",
       "\n",
       "       Target_Vec_5  Target_Vec_6  Target_Vec_7  Target_Vec_8  Target_Vec_9  \\\n",
       "0         -0.000354      0.001005     -0.000329     -0.000619     -0.000425   \n",
       "1         -0.000762      0.000180     -0.000694     -0.000680     -0.000532   \n",
       "2         -0.000553      0.000444     -0.001070     -0.001007     -0.000424   \n",
       "3         -0.000095      0.000965     -0.000946     -0.000221     -0.000475   \n",
       "4         -0.000468      0.000574     -0.001202      0.000006     -0.000512   \n",
       "...             ...           ...           ...           ...           ...   \n",
       "14076     -0.001115      0.000875     -0.000988     -0.000410     -0.001185   \n",
       "14077     -0.001692      0.000943     -0.000321     -0.000433     -0.000134   \n",
       "14078     -0.000927      0.000499     -0.000944     -0.000781     -0.000883   \n",
       "14079     -0.000976      0.000579     -0.000595     -0.000039     -0.000564   \n",
       "14080     -0.000490     -0.000104     -0.000448     -0.000504     -0.000058   \n",
       "\n",
       "       ...  Drug_Vec_91  Drug_Vec_92  Drug_Vec_93  Drug_Vec_94  Drug_Vec_95  \\\n",
       "0      ...    -0.027773    -0.261224    -0.349108     0.229779     0.161475   \n",
       "1      ...    -0.009263    -0.166779    -0.276308     0.178456     0.128912   \n",
       "2      ...    -0.009263    -0.166779    -0.276308     0.178456     0.128912   \n",
       "3      ...    -0.197189    -0.190077    -0.227381     0.206817     0.102296   \n",
       "4      ...    -0.197189    -0.190077    -0.227381     0.206817     0.102296   \n",
       "...    ...          ...          ...          ...          ...          ...   \n",
       "14076  ...     0.165878    -0.106813    -0.177413    -0.068752    -0.020657   \n",
       "14077  ...    -0.040043    -0.147016    -0.250347     0.031116     0.115812   \n",
       "14078  ...    -0.068147    -0.292997    -0.155505     0.198814     0.048889   \n",
       "14079  ...     0.045299    -0.187073    -0.099166     0.009447     0.100605   \n",
       "14080  ...     0.060210    -0.125469    -0.023296     0.040318     0.023454   \n",
       "\n",
       "       Drug_Vec_96  Drug_Vec_97  Drug_Vec_98  Drug_Vec_99  Class  \n",
       "0         0.124695     0.368989    -0.198983    -0.435481      1  \n",
       "1         0.083457     0.357332    -0.184330    -0.500235      1  \n",
       "2         0.083457     0.357332    -0.184330    -0.500235      1  \n",
       "3         0.015936     0.315439    -0.296255    -0.259058      1  \n",
       "4         0.015936     0.315439    -0.296255    -0.259058      1  \n",
       "...            ...          ...          ...          ...    ...  \n",
       "14076     0.261743     0.216247    -0.180014    -0.321167      0  \n",
       "14077     0.172605     0.182108    -0.112508    -0.388979      0  \n",
       "14078     0.188944     0.406694    -0.128643    -0.313929      0  \n",
       "14079     0.215792     0.203580    -0.066847    -0.382959      0  \n",
       "14080     0.093525     0.227268    -0.056917    -0.394649      0  \n",
       "\n",
       "[28162 rows x 131 columns]"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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