apply_models.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "bf82531c-032e-4dc9-98d2-d6e1ddeb2d47",
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import numpy as np\n",
    "import json\n",
    "import torch\n",
    "from torch.autograd import Variable\n",
    "from rdkit.Chem import PandasTools\n",
    "from rdkit import Chem\n",
    "from rdkit.Chem.MolStandardize.standardize import Standardizer\n",
    "from models.model_mtnn import MultiTaskNN"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "f186c05e-d3dc-47ca-bba1-519bde34f67b",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Endpoint list\n",
    "ASSAYS_TASKS = ['BSEPi', 'BSEPs', 'PGPi', 'PGPs', 'MRP4i', 'MRP3i', 'MRP3s', 'MRP2i', 'MRP2s', 'BCRPi', 'BCRPs', 'OATP1B1i', \n",
    "               'OATP1B3i', 'NRF2', 'LXR', 'AHR', 'PPARa', 'PPARg', 'PXR', 'FXR', 'MTX_MP', 'MTX_RC', 'MTX_FOM', 'PLD', 'PLD_HTS', 'HTX', 'ERS', 'ARE']\n",
    "DILI_TASKS = ['DILI_majority', 'DILI_sensitive', 'DILI_secure']"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "e8c76f7e-3860-4e18-a37f-80fafc9ab189",
   "metadata": {},
   "source": [
    "# Helper functions"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "2b3e2027-4820-4ef1-873d-3dd912513ac4",
   "metadata": {},
   "source": [
    "## SMILES preparation and descriptor calculation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "52a96632-c640-4c63-95b6-9c12a501ad1f",
   "metadata": {},
   "outputs": [],
   "source": [
    "standardizer = Standardizer(max_tautomers=10)\n",
    "include_stereoinfo = False\n",
    "def standardizeMol(mol):\n",
    "    \"\"\"\n",
    "    Standardizer inspired by MELLODDY consortium\n",
    "    :param mol: rdkit molecule object\n",
    "    :return: cleaned rdkit molecule object\n",
    "    \"\"\"\n",
    "    if mol is None:\n",
    "        return mol\n",
    "    try:\n",
    "        mol = standardizer.charge_parent(mol)\n",
    "        mol = standardizer.isotope_parent(mol)\n",
    "        if include_stereoinfo is False:\n",
    "            mol = standardizer.stereo_parent(mol)\n",
    "        mol = standardizer.tautomer_parent(mol)\n",
    "        return standardizer.standardize(mol)\n",
    "    except Chem.rdchem.AtomValenceException:\n",
    "        return None\n",
    "    \n",
    "def prepare_structures(input_df, smiles_col='smiles'):\n",
    "    '''\n",
    "    Standardize compounds, get canonical smiles and deduplicate structures based on canonical smiles\n",
    "    '''\n",
    "    df = input_df.copy()\n",
    "    PandasTools.AddMoleculeColumnToFrame(df, smiles_col,'molecule', includeFingerprints=False)\n",
    "    len_1 = len(df)\n",
    "    df.dropna(subset=['molecule'], axis=0, inplace=True)\n",
    "    len_2 = len(df)\n",
    "    print(f'No. of missing molecules: {len_1-len_2}')\n",
    "\n",
    "    # Standardize mols and get canonical smiles\n",
    "    for idx in df.index:\n",
    "        try:\n",
    "            stand_mol = standardizeMol(df.loc[idx, 'molecule'])\n",
    "            df.loc[idx, 'canonical_smiles'] = Chem.MolToSmiles(stand_mol, canonical=True)\n",
    "        except:\n",
    "            print(f'Failed to standardize {df.loc[idx, smiles_col]}')\n",
    "            df.loc[idx, 'canonical_smiles'] = None\n",
    "    \n",
    "    df.drop(['molecule'], axis=1, inplace=True)\n",
    "    df.dropna(subset=['canonical_smiles'], inplace=True)\n",
    "    return df"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "07c136c8-48e4-40e5-8e67-f37df0f12ed5",
   "metadata": {},
   "source": [
    "## Inference functions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "3b1114f5",
   "metadata": {},
   "outputs": [],
   "source": [
    "def get_mean_prediction_ensemble(pred_task, tasks):\n",
    "    ### Average predictions and get STD for uncertainty estimation\n",
    "    mean_pred = pd.DataFrame()\n",
    "    for task in tasks:\n",
    "        pred_task_mean = np.mean(pred_task[task], axis=0)\n",
    "        pred_task_std = np.std(pred_task[task], axis=0)\n",
    "        mean_pred[f'{task}_mean'] = pred_task_mean\n",
    "        mean_pred[f'{task}_std'] = pred_task_std\n",
    "        # binary class label\n",
    "        mean_pred[f'{task}_class'] = (pred_task_mean >= 0.5).astype(int)\n",
    "    return mean_pred\n",
    "\n",
    "def make_predictions_with_ensemble(Xtest):\n",
    "    ### apply ensemble model on ONTOX tasks to test set\n",
    "    tasks = DILI_TASKS + ASSAYS_TASKS\n",
    "    # read HPs from json file\n",
    "    with open('models/hyperparameters.json', 'r') as openfile:\n",
    "        hparam_dict = json.load(openfile)\n",
    "\n",
    "        \n",
    "    pred_task = {}\n",
    "    for split_id in range(5): # ensemble with 5 models (one per split)\n",
    "        print(f'Split: {split_id}')\n",
    "        # load models and make predictions\n",
    "        model_file = f'models/model_mtnn_all_tasks_cddd_{split_id}.pth'\n",
    "        hparam = hparam_dict[str(split_id)]\n",
    "\n",
    "        device='cpu'\n",
    "        model = MultiTaskNN(input_size=512, params=hparam, n_tasks=len(tasks))\n",
    "        model.load_state_dict(torch.load(model_file, map_location=device))\n",
    "        model.to(device)\n",
    "        model.eval()\n",
    "\n",
    "        # get predictions from single model\n",
    "        test_data = Variable(torch.from_numpy(Xtest).float())\n",
    "        preds_list = model(test_data)\n",
    "        predictions = [torch.Tensor.cpu(p).detach().numpy() for p in preds_list]\n",
    "        predictions = np.array(predictions).squeeze().T\n",
    "\n",
    "        # calculate predictions for all tasks\n",
    "        for i, task in enumerate(tasks):\n",
    "            if split_id == 0:\n",
    "                pred_task[task] = predictions[:,i]\n",
    "            else:\n",
    "                pred_task[task] = np.vstack((pred_task[task], predictions[:,i]))\n",
    "        display(pred_task[task].shape)\n",
    "        \n",
    "    # get mean prediction and STD from ensemble\n",
    "    mean_pred = get_mean_prediction_ensemble(pred_task, tasks)\n",
    "    return mean_pred, pred_task"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "391310ab-9fde-4458-86cf-d9804ad730e4",
   "metadata": {},
   "source": [
    "# Make predictions"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "fbb98314-1012-4417-b6de-81cfa4ea3076",
   "metadata": {},
   "source": [
    "## Load test set and prepare SMILES"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "463753bf-59af-48d7-a4a7-9ee6120a37d2",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "data": {
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>compoundName</th>\n",
       "      <th>compoundCas</th>\n",
       "      <th>ID</th>\n",
       "      <th>SMILES</th>\n",
       "      <th>cddd_0</th>\n",
       "      <th>cddd_1</th>\n",
       "      <th>cddd_2</th>\n",
       "      <th>cddd_3</th>\n",
       "      <th>cddd_4</th>\n",
       "      <th>cddd_5</th>\n",
       "      <th>...</th>\n",
       "      <th>cddd_502</th>\n",
       "      <th>cddd_503</th>\n",
       "      <th>cddd_504</th>\n",
       "      <th>cddd_505</th>\n",
       "      <th>cddd_506</th>\n",
       "      <th>cddd_507</th>\n",
       "      <th>cddd_508</th>\n",
       "      <th>cddd_509</th>\n",
       "      <th>cddd_510</th>\n",
       "      <th>cddd_511</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>cefadroxil</td>\n",
       "      <td>50370-12-2</td>\n",
       "      <td>193</td>\n",
       "      <td>O=C(C(c1ccc(cc1)O)N)NC1C(=O)N2C1SCC(=C2C(=O)O)C</td>\n",
       "      <td>-0.345609</td>\n",
       "      <td>0.435677</td>\n",
       "      <td>0.443579</td>\n",
       "      <td>-0.230919</td>\n",
       "      <td>-0.155220</td>\n",
       "      <td>0.435055</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.012822</td>\n",
       "      <td>-0.649319</td>\n",
       "      <td>-0.259375</td>\n",
       "      <td>0.154243</td>\n",
       "      <td>-0.998582</td>\n",
       "      <td>-0.656491</td>\n",
       "      <td>-0.047186</td>\n",
       "      <td>-0.139226</td>\n",
       "      <td>0.290642</td>\n",
       "      <td>0.249692</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>cefalexin</td>\n",
       "      <td>15686-71-2</td>\n",
       "      <td>194</td>\n",
       "      <td>NC(c1ccccc1)C(=O)NC1C(=O)N2C1SCC(=C2C(=O)O)C</td>\n",
       "      <td>-0.206731</td>\n",
       "      <td>0.223643</td>\n",
       "      <td>0.343376</td>\n",
       "      <td>-0.291107</td>\n",
       "      <td>-0.530366</td>\n",
       "      <td>0.471886</td>\n",
       "      <td>...</td>\n",
       "      <td>0.337684</td>\n",
       "      <td>-0.777834</td>\n",
       "      <td>-0.483351</td>\n",
       "      <td>0.022820</td>\n",
       "      <td>-0.997673</td>\n",
       "      <td>-0.656915</td>\n",
       "      <td>-0.076998</td>\n",
       "      <td>0.225208</td>\n",
       "      <td>0.507705</td>\n",
       "      <td>0.675936</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>cefroxadine</td>\n",
       "      <td>51762-05-1</td>\n",
       "      <td>195</td>\n",
       "      <td>COC1=C(C(=O)O)N2C(SC1)C(C2=O)NC(=O)C(C1=CCC=CC1)N</td>\n",
       "      <td>0.280529</td>\n",
       "      <td>0.379214</td>\n",
       "      <td>-0.035095</td>\n",
       "      <td>-0.207573</td>\n",
       "      <td>-0.135618</td>\n",
       "      <td>0.873147</td>\n",
       "      <td>...</td>\n",
       "      <td>0.612471</td>\n",
       "      <td>-0.527370</td>\n",
       "      <td>-0.742913</td>\n",
       "      <td>0.255554</td>\n",
       "      <td>-0.999407</td>\n",
       "      <td>0.026243</td>\n",
       "      <td>-0.243761</td>\n",
       "      <td>0.219092</td>\n",
       "      <td>0.144513</td>\n",
       "      <td>0.274512</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>cefaclor</td>\n",
       "      <td>53994-73-3</td>\n",
       "      <td>196</td>\n",
       "      <td>NC(c1ccccc1)C(=O)NC1C(=O)N2C1SCC(=C2C(=O)O)Cl</td>\n",
       "      <td>-0.463277</td>\n",
       "      <td>0.523447</td>\n",
       "      <td>0.274103</td>\n",
       "      <td>-0.004757</td>\n",
       "      <td>0.219428</td>\n",
       "      <td>-0.110411</td>\n",
       "      <td>...</td>\n",
       "      <td>0.632502</td>\n",
       "      <td>-0.643733</td>\n",
       "      <td>-0.514364</td>\n",
       "      <td>0.199848</td>\n",
       "      <td>-0.998535</td>\n",
       "      <td>-0.372263</td>\n",
       "      <td>-0.219406</td>\n",
       "      <td>0.443599</td>\n",
       "      <td>0.693524</td>\n",
       "      <td>0.614740</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>cidofovir</td>\n",
       "      <td>113852-37-2</td>\n",
       "      <td>197</td>\n",
       "      <td>OCC(Cn1ccc(nc1=O)N)OCP(=O)(O)O</td>\n",
       "      <td>0.827905</td>\n",
       "      <td>0.151661</td>\n",
       "      <td>-0.634442</td>\n",
       "      <td>-0.624787</td>\n",
       "      <td>-0.288666</td>\n",
       "      <td>-0.424812</td>\n",
       "      <td>...</td>\n",
       "      <td>0.073548</td>\n",
       "      <td>-0.340514</td>\n",
       "      <td>0.626049</td>\n",
       "      <td>-0.161234</td>\n",
       "      <td>-0.997134</td>\n",
       "      <td>0.118878</td>\n",
       "      <td>-0.430494</td>\n",
       "      <td>-0.616421</td>\n",
       "      <td>-0.406417</td>\n",
       "      <td>0.623281</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>adefovir</td>\n",
       "      <td>106941-25-7</td>\n",
       "      <td>198</td>\n",
       "      <td>Nc1ncnc2c1ncn2CCOCP(=O)(O)O</td>\n",
       "      <td>0.878535</td>\n",
       "      <td>0.225458</td>\n",
       "      <td>-0.857043</td>\n",
       "      <td>-0.529709</td>\n",
       "      <td>-0.536128</td>\n",
       "      <td>-0.627331</td>\n",
       "      <td>...</td>\n",
       "      <td>0.289310</td>\n",
       "      <td>0.145662</td>\n",
       "      <td>0.324091</td>\n",
       "      <td>0.730698</td>\n",
       "      <td>-0.994450</td>\n",
       "      <td>0.764640</td>\n",
       "      <td>-0.707223</td>\n",
       "      <td>-0.717028</td>\n",
       "      <td>-0.842849</td>\n",
       "      <td>0.807021</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>tenidap</td>\n",
       "      <td>120210-48-2</td>\n",
       "      <td>199</td>\n",
       "      <td>Clc1ccc2c(c1)c(C(=O)c1cccs1)c(n2C(=O)N)O</td>\n",
       "      <td>0.546082</td>\n",
       "      <td>0.275444</td>\n",
       "      <td>0.562035</td>\n",
       "      <td>-0.475908</td>\n",
       "      <td>0.142944</td>\n",
       "      <td>0.121655</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.527007</td>\n",
       "      <td>0.749456</td>\n",
       "      <td>0.639992</td>\n",
       "      <td>-0.275460</td>\n",
       "      <td>-0.990277</td>\n",
       "      <td>-0.758119</td>\n",
       "      <td>0.439286</td>\n",
       "      <td>0.140462</td>\n",
       "      <td>0.040768</td>\n",
       "      <td>0.497276</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>vinorelbine</td>\n",
       "      <td>71486-22-1</td>\n",
       "      <td>200</td>\n",
       "      <td>CCC1=CC2CN(C1)Cc1c3ccccc3[nH]c1C(C2)(C(=O)OC)c...</td>\n",
       "      <td>0.565227</td>\n",
       "      <td>-0.215023</td>\n",
       "      <td>0.411864</td>\n",
       "      <td>0.035846</td>\n",
       "      <td>-0.514231</td>\n",
       "      <td>0.323490</td>\n",
       "      <td>...</td>\n",
       "      <td>0.437771</td>\n",
       "      <td>-0.251952</td>\n",
       "      <td>-0.039950</td>\n",
       "      <td>0.711807</td>\n",
       "      <td>-0.997629</td>\n",
       "      <td>-0.760012</td>\n",
       "      <td>0.284355</td>\n",
       "      <td>0.895465</td>\n",
       "      <td>0.377786</td>\n",
       "      <td>-0.275700</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>2-(phosphonomethyl)pentanedioic acid</td>\n",
       "      <td>173039-10-6</td>\n",
       "      <td>201</td>\n",
       "      <td>OC(=O)CCC(C(=O)O)CP(=O)(O)O</td>\n",
       "      <td>-0.267367</td>\n",
       "      <td>0.143161</td>\n",
       "      <td>-0.960844</td>\n",
       "      <td>0.161823</td>\n",
       "      <td>-0.619050</td>\n",
       "      <td>-0.629508</td>\n",
       "      <td>...</td>\n",
       "      <td>0.007566</td>\n",
       "      <td>-0.600597</td>\n",
       "      <td>-0.514969</td>\n",
       "      <td>-0.079095</td>\n",
       "      <td>-0.958287</td>\n",
       "      <td>-0.522038</td>\n",
       "      <td>-0.223990</td>\n",
       "      <td>-0.554607</td>\n",
       "      <td>0.661822</td>\n",
       "      <td>0.335066</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>sulfadiazine</td>\n",
       "      <td>68-35-9</td>\n",
       "      <td>202</td>\n",
       "      <td>Nc1ccc(cc1)S(=O)(=O)Nc1ncccn1</td>\n",
       "      <td>-0.411361</td>\n",
       "      <td>-0.235456</td>\n",
       "      <td>-0.189376</td>\n",
       "      <td>-0.089840</td>\n",
       "      <td>0.002908</td>\n",
       "      <td>-0.296240</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.280758</td>\n",
       "      <td>-0.214666</td>\n",
       "      <td>-0.109768</td>\n",
       "      <td>-0.581410</td>\n",
       "      <td>-0.935882</td>\n",
       "      <td>-0.124828</td>\n",
       "      <td>0.327465</td>\n",
       "      <td>-0.676434</td>\n",
       "      <td>-0.438199</td>\n",
       "      <td>0.238666</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>ketamine</td>\n",
       "      <td>6740-88-1</td>\n",
       "      <td>203</td>\n",
       "      <td>CNC1(CCCCC1=O)c1ccccc1Cl</td>\n",
       "      <td>0.263739</td>\n",
       "      <td>0.229217</td>\n",
       "      <td>0.144718</td>\n",
       "      <td>-0.529496</td>\n",
       "      <td>-0.429607</td>\n",
       "      <td>-0.482378</td>\n",
       "      <td>...</td>\n",
       "      <td>0.071402</td>\n",
       "      <td>0.557034</td>\n",
       "      <td>0.515500</td>\n",
       "      <td>-0.148030</td>\n",
       "      <td>-0.847870</td>\n",
       "      <td>0.130376</td>\n",
       "      <td>0.251666</td>\n",
       "      <td>0.278704</td>\n",
       "      <td>0.538239</td>\n",
       "      <td>0.269551</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>voriconazole</td>\n",
       "      <td>137234-62-9</td>\n",
       "      <td>204</td>\n",
       "      <td>Fc1ccc(c(c1)F)C(C(c1ncncc1F)C)(Cn1cncn1)O</td>\n",
       "      <td>-0.341490</td>\n",
       "      <td>0.016214</td>\n",
       "      <td>0.544691</td>\n",
       "      <td>-0.593738</td>\n",
       "      <td>0.605177</td>\n",
       "      <td>0.250180</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.216274</td>\n",
       "      <td>-0.270445</td>\n",
       "      <td>0.566601</td>\n",
       "      <td>0.463743</td>\n",
       "      <td>-0.998390</td>\n",
       "      <td>0.071954</td>\n",
       "      <td>-0.026053</td>\n",
       "      <td>-0.143775</td>\n",
       "      <td>-0.494848</td>\n",
       "      <td>0.241437</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>carmustine</td>\n",
       "      <td>154-93-8</td>\n",
       "      <td>205</td>\n",
       "      <td>ClCCNC(=O)N(CCCl)N=O</td>\n",
       "      <td>-0.425694</td>\n",
       "      <td>-0.266368</td>\n",
       "      <td>0.062939</td>\n",
       "      <td>0.520326</td>\n",
       "      <td>-0.255197</td>\n",
       "      <td>-0.006745</td>\n",
       "      <td>...</td>\n",
       "      <td>0.413419</td>\n",
       "      <td>-0.654950</td>\n",
       "      <td>-0.241833</td>\n",
       "      <td>0.528662</td>\n",
       "      <td>-0.633870</td>\n",
       "      <td>0.148116</td>\n",
       "      <td>-0.800904</td>\n",
       "      <td>-0.118718</td>\n",
       "      <td>0.003625</td>\n",
       "      <td>0.433747</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>acarbose</td>\n",
       "      <td>56180-94-0</td>\n",
       "      <td>206</td>\n",
       "      <td>CC1C(C(C(C(O1)OC2C(OC(C(C2O)O)OC3C(OC(C(C3O)O)...</td>\n",
       "      <td>-0.611535</td>\n",
       "      <td>-0.189840</td>\n",
       "      <td>0.650048</td>\n",
       "      <td>-0.142314</td>\n",
       "      <td>0.667809</td>\n",
       "      <td>0.097717</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.656676</td>\n",
       "      <td>-0.612773</td>\n",
       "      <td>-0.478983</td>\n",
       "      <td>-0.882060</td>\n",
       "      <td>-0.999834</td>\n",
       "      <td>-0.677430</td>\n",
       "      <td>-0.058677</td>\n",
       "      <td>-0.965948</td>\n",
       "      <td>-0.723834</td>\n",
       "      <td>-0.771724</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>imatinib</td>\n",
       "      <td>152459-95-5</td>\n",
       "      <td>207</td>\n",
       "      <td>CN1CCN(CC1)Cc1ccc(cc1)C(=O)Nc1ccc(c(c1)Nc1nccc...</td>\n",
       "      <td>-0.743269</td>\n",
       "      <td>-0.382688</td>\n",
       "      <td>0.396285</td>\n",
       "      <td>-0.561093</td>\n",
       "      <td>-0.461451</td>\n",
       "      <td>-0.335652</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.150412</td>\n",
       "      <td>-0.355470</td>\n",
       "      <td>0.064715</td>\n",
       "      <td>0.094740</td>\n",
       "      <td>-0.999090</td>\n",
       "      <td>0.112300</td>\n",
       "      <td>0.008749</td>\n",
       "      <td>-0.021251</td>\n",
       "      <td>-0.236708</td>\n",
       "      <td>0.029252</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>tacrolimus</td>\n",
       "      <td>104987-11-3</td>\n",
       "      <td>208</td>\n",
       "      <td>C=CCC1C=C(C)CC(C)CC(OC)C2OC(O)(C(CC2OC)C)C(=O)...</td>\n",
       "      <td>0.730178</td>\n",
       "      <td>0.120244</td>\n",
       "      <td>-0.165683</td>\n",
       "      <td>0.154953</td>\n",
       "      <td>-0.162697</td>\n",
       "      <td>0.438203</td>\n",
       "      <td>...</td>\n",
       "      <td>0.295740</td>\n",
       "      <td>0.583257</td>\n",
       "      <td>0.446116</td>\n",
       "      <td>-0.590984</td>\n",
       "      <td>-0.999152</td>\n",
       "      <td>-0.744923</td>\n",
       "      <td>0.677472</td>\n",
       "      <td>0.443931</td>\n",
       "      <td>0.702394</td>\n",
       "      <td>-0.597210</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>16 rows × 516 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                            compoundName  compoundCas   ID  \\\n",
       "0                             cefadroxil   50370-12-2  193   \n",
       "1                              cefalexin   15686-71-2  194   \n",
       "2                            cefroxadine   51762-05-1  195   \n",
       "3                               cefaclor   53994-73-3  196   \n",
       "4                              cidofovir  113852-37-2  197   \n",
       "5                               adefovir  106941-25-7  198   \n",
       "6                                tenidap  120210-48-2  199   \n",
       "7                            vinorelbine   71486-22-1  200   \n",
       "8   2-(phosphonomethyl)pentanedioic acid  173039-10-6  201   \n",
       "9                           sulfadiazine      68-35-9  202   \n",
       "10                              ketamine    6740-88-1  203   \n",
       "11                          voriconazole  137234-62-9  204   \n",
       "12                            carmustine     154-93-8  205   \n",
       "13                              acarbose   56180-94-0  206   \n",
       "14                              imatinib  152459-95-5  207   \n",
       "15                            tacrolimus  104987-11-3  208   \n",
       "\n",
       "                                               SMILES    cddd_0    cddd_1  \\\n",
       "0     O=C(C(c1ccc(cc1)O)N)NC1C(=O)N2C1SCC(=C2C(=O)O)C -0.345609  0.435677   \n",
       "1        NC(c1ccccc1)C(=O)NC1C(=O)N2C1SCC(=C2C(=O)O)C -0.206731  0.223643   \n",
       "2   COC1=C(C(=O)O)N2C(SC1)C(C2=O)NC(=O)C(C1=CCC=CC1)N  0.280529  0.379214   \n",
       "3       NC(c1ccccc1)C(=O)NC1C(=O)N2C1SCC(=C2C(=O)O)Cl -0.463277  0.523447   \n",
       "4                      OCC(Cn1ccc(nc1=O)N)OCP(=O)(O)O  0.827905  0.151661   \n",
       "5                         Nc1ncnc2c1ncn2CCOCP(=O)(O)O  0.878535  0.225458   \n",
       "6            Clc1ccc2c(c1)c(C(=O)c1cccs1)c(n2C(=O)N)O  0.546082  0.275444   \n",
       "7   CCC1=CC2CN(C1)Cc1c3ccccc3[nH]c1C(C2)(C(=O)OC)c...  0.565227 -0.215023   \n",
       "8                         OC(=O)CCC(C(=O)O)CP(=O)(O)O -0.267367  0.143161   \n",
       "9                       Nc1ccc(cc1)S(=O)(=O)Nc1ncccn1 -0.411361 -0.235456   \n",
       "10                           CNC1(CCCCC1=O)c1ccccc1Cl  0.263739  0.229217   \n",
       "11          Fc1ccc(c(c1)F)C(C(c1ncncc1F)C)(Cn1cncn1)O -0.341490  0.016214   \n",
       "12                               ClCCNC(=O)N(CCCl)N=O -0.425694 -0.266368   \n",
       "13  CC1C(C(C(C(O1)OC2C(OC(C(C2O)O)OC3C(OC(C(C3O)O)... -0.611535 -0.189840   \n",
       "14  CN1CCN(CC1)Cc1ccc(cc1)C(=O)Nc1ccc(c(c1)Nc1nccc... -0.743269 -0.382688   \n",
       "15  C=CCC1C=C(C)CC(C)CC(OC)C2OC(O)(C(CC2OC)C)C(=O)...  0.730178  0.120244   \n",
       "\n",
       "      cddd_2    cddd_3    cddd_4    cddd_5  ...  cddd_502  cddd_503  cddd_504  \\\n",
       "0   0.443579 -0.230919 -0.155220  0.435055  ... -0.012822 -0.649319 -0.259375   \n",
       "1   0.343376 -0.291107 -0.530366  0.471886  ...  0.337684 -0.777834 -0.483351   \n",
       "2  -0.035095 -0.207573 -0.135618  0.873147  ...  0.612471 -0.527370 -0.742913   \n",
       "3   0.274103 -0.004757  0.219428 -0.110411  ...  0.632502 -0.643733 -0.514364   \n",
       "4  -0.634442 -0.624787 -0.288666 -0.424812  ...  0.073548 -0.340514  0.626049   \n",
       "5  -0.857043 -0.529709 -0.536128 -0.627331  ...  0.289310  0.145662  0.324091   \n",
       "6   0.562035 -0.475908  0.142944  0.121655  ... -0.527007  0.749456  0.639992   \n",
       "7   0.411864  0.035846 -0.514231  0.323490  ...  0.437771 -0.251952 -0.039950   \n",
       "8  -0.960844  0.161823 -0.619050 -0.629508  ...  0.007566 -0.600597 -0.514969   \n",
       "9  -0.189376 -0.089840  0.002908 -0.296240  ... -0.280758 -0.214666 -0.109768   \n",
       "10  0.144718 -0.529496 -0.429607 -0.482378  ...  0.071402  0.557034  0.515500   \n",
       "11  0.544691 -0.593738  0.605177  0.250180  ... -0.216274 -0.270445  0.566601   \n",
       "12  0.062939  0.520326 -0.255197 -0.006745  ...  0.413419 -0.654950 -0.241833   \n",
       "13  0.650048 -0.142314  0.667809  0.097717  ... -0.656676 -0.612773 -0.478983   \n",
       "14  0.396285 -0.561093 -0.461451 -0.335652  ... -0.150412 -0.355470  0.064715   \n",
       "15 -0.165683  0.154953 -0.162697  0.438203  ...  0.295740  0.583257  0.446116   \n",
       "\n",
       "    cddd_505  cddd_506  cddd_507  cddd_508  cddd_509  cddd_510  cddd_511  \n",
       "0   0.154243 -0.998582 -0.656491 -0.047186 -0.139226  0.290642  0.249692  \n",
       "1   0.022820 -0.997673 -0.656915 -0.076998  0.225208  0.507705  0.675936  \n",
       "2   0.255554 -0.999407  0.026243 -0.243761  0.219092  0.144513  0.274512  \n",
       "3   0.199848 -0.998535 -0.372263 -0.219406  0.443599  0.693524  0.614740  \n",
       "4  -0.161234 -0.997134  0.118878 -0.430494 -0.616421 -0.406417  0.623281  \n",
       "5   0.730698 -0.994450  0.764640 -0.707223 -0.717028 -0.842849  0.807021  \n",
       "6  -0.275460 -0.990277 -0.758119  0.439286  0.140462  0.040768  0.497276  \n",
       "7   0.711807 -0.997629 -0.760012  0.284355  0.895465  0.377786 -0.275700  \n",
       "8  -0.079095 -0.958287 -0.522038 -0.223990 -0.554607  0.661822  0.335066  \n",
       "9  -0.581410 -0.935882 -0.124828  0.327465 -0.676434 -0.438199  0.238666  \n",
       "10 -0.148030 -0.847870  0.130376  0.251666  0.278704  0.538239  0.269551  \n",
       "11  0.463743 -0.998390  0.071954 -0.026053 -0.143775 -0.494848  0.241437  \n",
       "12  0.528662 -0.633870  0.148116 -0.800904 -0.118718  0.003625  0.433747  \n",
       "13 -0.882060 -0.999834 -0.677430 -0.058677 -0.965948 -0.723834 -0.771724  \n",
       "14  0.094740 -0.999090  0.112300  0.008749 -0.021251 -0.236708  0.029252  \n",
       "15 -0.590984 -0.999152 -0.744923  0.677472  0.443931  0.702394 -0.597210  \n",
       "\n",
       "[16 rows x 516 columns]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "test_df = pd.read_csv('example_data_with_CDDD.csv')\n",
    "test_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "ed745d52-59e0-46fd-95fe-64548bcba094",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "No. of missing molecules: 0\n",
      "16\n"
     ]
    }
   ],
   "source": [
    "test_df = prepare_structures(test_df, smiles_col='SMILES')\n",
    "print(len(test_df))"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "c7dc707b-d208-4390-a7b0-438a024e60c7",
   "metadata": {},
   "source": [
    "### Note: in this example the CDDD descriptors used as input for the model are already calculated. For new compounds, the CDDD descriptors need to be calculated at this step as described here: https://github.com/jrwnter/cddd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "dd61de95-d6c9-49eb-983f-cbfcec1db316",
   "metadata": {},
   "outputs": [],
   "source": [
    "Xtest = test_df[[c for c in test_df if 'cddd' in c]].values"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "eb80dd0e-d1a2-4fe1-bc08-fd43df99d076",
   "metadata": {},
   "source": [
    "## Make predictions for all tasks with the 10 models in the ensemble"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "b8e43778",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Split: 0\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "(16,)"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Split: 1\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "(2, 16)"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Split: 2\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "(3, 16)"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Split: 3\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "(4, 16)"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Split: 4\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "(5, 16)"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
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       "    }\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>compoundName</th>\n",
       "      <th>compoundCas</th>\n",
       "      <th>ID</th>\n",
       "      <th>SMILES</th>\n",
       "      <th>cddd_0</th>\n",
       "      <th>cddd_1</th>\n",
       "      <th>cddd_2</th>\n",
       "      <th>cddd_3</th>\n",
       "      <th>cddd_4</th>\n",
       "      <th>cddd_5</th>\n",
       "      <th>...</th>\n",
       "      <th>PLD_HTS_class</th>\n",
       "      <th>HTX_mean</th>\n",
       "      <th>HTX_std</th>\n",
       "      <th>HTX_class</th>\n",
       "      <th>ERS_mean</th>\n",
       "      <th>ERS_std</th>\n",
       "      <th>ERS_class</th>\n",
       "      <th>ARE_mean</th>\n",
       "      <th>ARE_std</th>\n",
       "      <th>ARE_class</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>cefadroxil</td>\n",
       "      <td>50370-12-2</td>\n",
       "      <td>193</td>\n",
       "      <td>O=C(C(c1ccc(cc1)O)N)NC1C(=O)N2C1SCC(=C2C(=O)O)C</td>\n",
       "      <td>-0.345609</td>\n",
       "      <td>0.435677</td>\n",
       "      <td>0.443579</td>\n",
       "      <td>-0.230919</td>\n",
       "      <td>-0.155220</td>\n",
       "      <td>0.435055</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0.000360</td>\n",
       "      <td>0.000606</td>\n",
       "      <td>0</td>\n",
       "      <td>0.000211</td>\n",
       "      <td>0.000422</td>\n",
       "      <td>0</td>\n",
       "      <td>0.002386</td>\n",
       "      <td>0.003650</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>cefalexin</td>\n",
       "      <td>15686-71-2</td>\n",
       "      <td>194</td>\n",
       "      <td>NC(c1ccccc1)C(=O)NC1C(=O)N2C1SCC(=C2C(=O)O)C</td>\n",
       "      <td>-0.206731</td>\n",
       "      <td>0.223643</td>\n",
       "      <td>0.343376</td>\n",
       "      <td>-0.291107</td>\n",
       "      <td>-0.530366</td>\n",
       "      <td>0.471886</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0.000211</td>\n",
       "      <td>0.000363</td>\n",
       "      <td>0</td>\n",
       "      <td>0.000022</td>\n",
       "      <td>0.000044</td>\n",
       "      <td>0</td>\n",
       "      <td>0.000227</td>\n",
       "      <td>0.000303</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>cefroxadine</td>\n",
       "      <td>51762-05-1</td>\n",
       "      <td>195</td>\n",
       "      <td>COC1=C(C(=O)O)N2C(SC1)C(C2=O)NC(=O)C(C1=CCC=CC1)N</td>\n",
       "      <td>0.280529</td>\n",
       "      <td>0.379214</td>\n",
       "      <td>-0.035095</td>\n",
       "      <td>-0.207573</td>\n",
       "      <td>-0.135618</td>\n",
       "      <td>0.873147</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0.000293</td>\n",
       "      <td>0.000506</td>\n",
       "      <td>0</td>\n",
       "      <td>0.000024</td>\n",
       "      <td>0.000047</td>\n",
       "      <td>0</td>\n",
       "      <td>0.002713</td>\n",
       "      <td>0.003312</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>cefaclor</td>\n",
       "      <td>53994-73-3</td>\n",
       "      <td>196</td>\n",
       "      <td>NC(c1ccccc1)C(=O)NC1C(=O)N2C1SCC(=C2C(=O)O)Cl</td>\n",
       "      <td>-0.463277</td>\n",
       "      <td>0.523447</td>\n",
       "      <td>0.274103</td>\n",
       "      <td>-0.004757</td>\n",
       "      <td>0.219428</td>\n",
       "      <td>-0.110411</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0.001413</td>\n",
       "      <td>0.002644</td>\n",
       "      <td>0</td>\n",
       "      <td>0.000030</td>\n",
       "      <td>0.000060</td>\n",
       "      <td>0</td>\n",
       "      <td>0.006670</td>\n",
       "      <td>0.011748</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>cidofovir</td>\n",
       "      <td>113852-37-2</td>\n",
       "      <td>197</td>\n",
       "      <td>OCC(Cn1ccc(nc1=O)N)OCP(=O)(O)O</td>\n",
       "      <td>0.827905</td>\n",
       "      <td>0.151661</td>\n",
       "      <td>-0.634442</td>\n",
       "      <td>-0.624787</td>\n",
       "      <td>-0.288666</td>\n",
       "      <td>-0.424812</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0.000269</td>\n",
       "      <td>0.000501</td>\n",
       "      <td>0</td>\n",
       "      <td>0.000194</td>\n",
       "      <td>0.000387</td>\n",
       "      <td>0</td>\n",
       "      <td>0.034363</td>\n",
       "      <td>0.030649</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>adefovir</td>\n",
       "      <td>106941-25-7</td>\n",
       "      <td>198</td>\n",
       "      <td>Nc1ncnc2c1ncn2CCOCP(=O)(O)O</td>\n",
       "      <td>0.878535</td>\n",
       "      <td>0.225458</td>\n",
       "      <td>-0.857043</td>\n",
       "      <td>-0.529709</td>\n",
       "      <td>-0.536128</td>\n",
       "      <td>-0.627331</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0.000548</td>\n",
       "      <td>0.000889</td>\n",
       "      <td>0</td>\n",
       "      <td>0.000445</td>\n",
       "      <td>0.000888</td>\n",
       "      <td>0</td>\n",
       "      <td>0.031498</td>\n",
       "      <td>0.018437</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>tenidap</td>\n",
       "      <td>120210-48-2</td>\n",
       "      <td>199</td>\n",
       "      <td>Clc1ccc2c(c1)c(C(=O)c1cccs1)c(n2C(=O)N)O</td>\n",
       "      <td>0.546082</td>\n",
       "      <td>0.275444</td>\n",
       "      <td>0.562035</td>\n",
       "      <td>-0.475908</td>\n",
       "      <td>0.142944</td>\n",
       "      <td>0.121655</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0.057262</td>\n",
       "      <td>0.099890</td>\n",
       "      <td>0</td>\n",
       "      <td>0.015813</td>\n",
       "      <td>0.017492</td>\n",
       "      <td>0</td>\n",
       "      <td>0.382610</td>\n",
       "      <td>0.305057</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>vinorelbine</td>\n",
       "      <td>71486-22-1</td>\n",
       "      <td>200</td>\n",
       "      <td>CCC1=CC2CN(C1)Cc1c3ccccc3[nH]c1C(C2)(C(=O)OC)c...</td>\n",
       "      <td>0.565227</td>\n",
       "      <td>-0.215023</td>\n",
       "      <td>0.411864</td>\n",
       "      <td>0.035846</td>\n",
       "      <td>-0.514231</td>\n",
       "      <td>0.323490</td>\n",
       "      <td>...</td>\n",
       "      <td>1</td>\n",
       "      <td>0.262759</td>\n",
       "      <td>0.304819</td>\n",
       "      <td>0</td>\n",
       "      <td>0.013343</td>\n",
       "      <td>0.015159</td>\n",
       "      <td>0</td>\n",
       "      <td>0.195870</td>\n",
       "      <td>0.280803</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>2-(phosphonomethyl)pentanedioic acid</td>\n",
       "      <td>173039-10-6</td>\n",
       "      <td>201</td>\n",
       "      <td>OC(=O)CCC(C(=O)O)CP(=O)(O)O</td>\n",
       "      <td>-0.267367</td>\n",
       "      <td>0.143161</td>\n",
       "      <td>-0.960844</td>\n",
       "      <td>0.161823</td>\n",
       "      <td>-0.619050</td>\n",
       "      <td>-0.629508</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0.000258</td>\n",
       "      <td>0.000516</td>\n",
       "      <td>0</td>\n",
       "      <td>0.000343</td>\n",
       "      <td>0.000683</td>\n",
       "      <td>0</td>\n",
       "      <td>0.047065</td>\n",
       "      <td>0.071224</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>sulfadiazine</td>\n",
       "      <td>68-35-9</td>\n",
       "      <td>202</td>\n",
       "      <td>Nc1ccc(cc1)S(=O)(=O)Nc1ncccn1</td>\n",
       "      <td>-0.411361</td>\n",
       "      <td>-0.235456</td>\n",
       "      <td>-0.189376</td>\n",
       "      <td>-0.089840</td>\n",
       "      <td>0.002908</td>\n",
       "      <td>-0.296240</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0.000591</td>\n",
       "      <td>0.000728</td>\n",
       "      <td>0</td>\n",
       "      <td>0.000036</td>\n",
       "      <td>0.000071</td>\n",
       "      <td>0</td>\n",
       "      <td>0.008832</td>\n",
       "      <td>0.008288</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>ketamine</td>\n",
       "      <td>6740-88-1</td>\n",
       "      <td>203</td>\n",
       "      <td>CNC1(CCCCC1=O)c1ccccc1Cl</td>\n",
       "      <td>0.263739</td>\n",
       "      <td>0.229217</td>\n",
       "      <td>0.144718</td>\n",
       "      <td>-0.529496</td>\n",
       "      <td>-0.429607</td>\n",
       "      <td>-0.482378</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0.034784</td>\n",
       "      <td>0.059985</td>\n",
       "      <td>0</td>\n",
       "      <td>0.000167</td>\n",
       "      <td>0.000333</td>\n",
       "      <td>0</td>\n",
       "      <td>0.000534</td>\n",
       "      <td>0.000442</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>voriconazole</td>\n",
       "      <td>137234-62-9</td>\n",
       "      <td>204</td>\n",
       "      <td>Fc1ccc(c(c1)F)C(C(c1ncncc1F)C)(Cn1cncn1)O</td>\n",
       "      <td>-0.341490</td>\n",
       "      <td>0.016214</td>\n",
       "      <td>0.544691</td>\n",
       "      <td>-0.593738</td>\n",
       "      <td>0.605177</td>\n",
       "      <td>0.250180</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0.001159</td>\n",
       "      <td>0.001835</td>\n",
       "      <td>0</td>\n",
       "      <td>0.000146</td>\n",
       "      <td>0.000293</td>\n",
       "      <td>0</td>\n",
       "      <td>0.037190</td>\n",
       "      <td>0.055694</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>carmustine</td>\n",
       "      <td>154-93-8</td>\n",
       "      <td>205</td>\n",
       "      <td>ClCCNC(=O)N(CCCl)N=O</td>\n",
       "      <td>-0.425694</td>\n",
       "      <td>-0.266368</td>\n",
       "      <td>0.062939</td>\n",
       "      <td>0.520326</td>\n",
       "      <td>-0.255197</td>\n",
       "      <td>-0.006745</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0.006465</td>\n",
       "      <td>0.008015</td>\n",
       "      <td>0</td>\n",
       "      <td>0.000175</td>\n",
       "      <td>0.000351</td>\n",
       "      <td>0</td>\n",
       "      <td>0.182184</td>\n",
       "      <td>0.231458</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>acarbose</td>\n",
       "      <td>56180-94-0</td>\n",
       "      <td>206</td>\n",
       "      <td>CC1C(C(C(C(O1)OC2C(OC(C(C2O)O)OC3C(OC(C(C3O)O)...</td>\n",
       "      <td>-0.611535</td>\n",
       "      <td>-0.189840</td>\n",
       "      <td>0.650048</td>\n",
       "      <td>-0.142314</td>\n",
       "      <td>0.667809</td>\n",
       "      <td>0.097717</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0.014476</td>\n",
       "      <td>0.028948</td>\n",
       "      <td>0</td>\n",
       "      <td>0.000596</td>\n",
       "      <td>0.001192</td>\n",
       "      <td>0</td>\n",
       "      <td>0.038357</td>\n",
       "      <td>0.063377</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>imatinib</td>\n",
       "      <td>152459-95-5</td>\n",
       "      <td>207</td>\n",
       "      <td>CN1CCN(CC1)Cc1ccc(cc1)C(=O)Nc1ccc(c(c1)Nc1nccc...</td>\n",
       "      <td>-0.743269</td>\n",
       "      <td>-0.382688</td>\n",
       "      <td>0.396285</td>\n",
       "      <td>-0.561093</td>\n",
       "      <td>-0.461451</td>\n",
       "      <td>-0.335652</td>\n",
       "      <td>...</td>\n",
       "      <td>1</td>\n",
       "      <td>0.115280</td>\n",
       "      <td>0.138552</td>\n",
       "      <td>0</td>\n",
       "      <td>0.002517</td>\n",
       "      <td>0.003172</td>\n",
       "      <td>0</td>\n",
       "      <td>0.255158</td>\n",
       "      <td>0.338649</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>tacrolimus</td>\n",
       "      <td>104987-11-3</td>\n",
       "      <td>208</td>\n",
       "      <td>C=CCC1C=C(C)CC(C)CC(OC)C2OC(O)(C(CC2OC)C)C(=O)...</td>\n",
       "      <td>0.730178</td>\n",
       "      <td>0.120244</td>\n",
       "      <td>-0.165683</td>\n",
       "      <td>0.154953</td>\n",
       "      <td>-0.162697</td>\n",
       "      <td>0.438203</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0.214226</td>\n",
       "      <td>0.273211</td>\n",
       "      <td>0</td>\n",
       "      <td>0.004570</td>\n",
       "      <td>0.008083</td>\n",
       "      <td>0</td>\n",
       "      <td>0.117277</td>\n",
       "      <td>0.128432</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>16 rows × 610 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                            compoundName  compoundCas   ID  \\\n",
       "0                             cefadroxil   50370-12-2  193   \n",
       "1                              cefalexin   15686-71-2  194   \n",
       "2                            cefroxadine   51762-05-1  195   \n",
       "3                               cefaclor   53994-73-3  196   \n",
       "4                              cidofovir  113852-37-2  197   \n",
       "5                               adefovir  106941-25-7  198   \n",
       "6                                tenidap  120210-48-2  199   \n",
       "7                            vinorelbine   71486-22-1  200   \n",
       "8   2-(phosphonomethyl)pentanedioic acid  173039-10-6  201   \n",
       "9                           sulfadiazine      68-35-9  202   \n",
       "10                              ketamine    6740-88-1  203   \n",
       "11                          voriconazole  137234-62-9  204   \n",
       "12                            carmustine     154-93-8  205   \n",
       "13                              acarbose   56180-94-0  206   \n",
       "14                              imatinib  152459-95-5  207   \n",
       "15                            tacrolimus  104987-11-3  208   \n",
       "\n",
       "                                               SMILES    cddd_0    cddd_1  \\\n",
       "0     O=C(C(c1ccc(cc1)O)N)NC1C(=O)N2C1SCC(=C2C(=O)O)C -0.345609  0.435677   \n",
       "1        NC(c1ccccc1)C(=O)NC1C(=O)N2C1SCC(=C2C(=O)O)C -0.206731  0.223643   \n",
       "2   COC1=C(C(=O)O)N2C(SC1)C(C2=O)NC(=O)C(C1=CCC=CC1)N  0.280529  0.379214   \n",
       "3       NC(c1ccccc1)C(=O)NC1C(=O)N2C1SCC(=C2C(=O)O)Cl -0.463277  0.523447   \n",
       "4                      OCC(Cn1ccc(nc1=O)N)OCP(=O)(O)O  0.827905  0.151661   \n",
       "5                         Nc1ncnc2c1ncn2CCOCP(=O)(O)O  0.878535  0.225458   \n",
       "6            Clc1ccc2c(c1)c(C(=O)c1cccs1)c(n2C(=O)N)O  0.546082  0.275444   \n",
       "7   CCC1=CC2CN(C1)Cc1c3ccccc3[nH]c1C(C2)(C(=O)OC)c...  0.565227 -0.215023   \n",
       "8                         OC(=O)CCC(C(=O)O)CP(=O)(O)O -0.267367  0.143161   \n",
       "9                       Nc1ccc(cc1)S(=O)(=O)Nc1ncccn1 -0.411361 -0.235456   \n",
       "10                           CNC1(CCCCC1=O)c1ccccc1Cl  0.263739  0.229217   \n",
       "11          Fc1ccc(c(c1)F)C(C(c1ncncc1F)C)(Cn1cncn1)O -0.341490  0.016214   \n",
       "12                               ClCCNC(=O)N(CCCl)N=O -0.425694 -0.266368   \n",
       "13  CC1C(C(C(C(O1)OC2C(OC(C(C2O)O)OC3C(OC(C(C3O)O)... -0.611535 -0.189840   \n",
       "14  CN1CCN(CC1)Cc1ccc(cc1)C(=O)Nc1ccc(c(c1)Nc1nccc... -0.743269 -0.382688   \n",
       "15  C=CCC1C=C(C)CC(C)CC(OC)C2OC(O)(C(CC2OC)C)C(=O)...  0.730178  0.120244   \n",
       "\n",
       "      cddd_2    cddd_3    cddd_4    cddd_5  ...  PLD_HTS_class  HTX_mean  \\\n",
       "0   0.443579 -0.230919 -0.155220  0.435055  ...              0  0.000360   \n",
       "1   0.343376 -0.291107 -0.530366  0.471886  ...              0  0.000211   \n",
       "2  -0.035095 -0.207573 -0.135618  0.873147  ...              0  0.000293   \n",
       "3   0.274103 -0.004757  0.219428 -0.110411  ...              0  0.001413   \n",
       "4  -0.634442 -0.624787 -0.288666 -0.424812  ...              0  0.000269   \n",
       "5  -0.857043 -0.529709 -0.536128 -0.627331  ...              0  0.000548   \n",
       "6   0.562035 -0.475908  0.142944  0.121655  ...              0  0.057262   \n",
       "7   0.411864  0.035846 -0.514231  0.323490  ...              1  0.262759   \n",
       "8  -0.960844  0.161823 -0.619050 -0.629508  ...              0  0.000258   \n",
       "9  -0.189376 -0.089840  0.002908 -0.296240  ...              0  0.000591   \n",
       "10  0.144718 -0.529496 -0.429607 -0.482378  ...              0  0.034784   \n",
       "11  0.544691 -0.593738  0.605177  0.250180  ...              0  0.001159   \n",
       "12  0.062939  0.520326 -0.255197 -0.006745  ...              0  0.006465   \n",
       "13  0.650048 -0.142314  0.667809  0.097717  ...              0  0.014476   \n",
       "14  0.396285 -0.561093 -0.461451 -0.335652  ...              1  0.115280   \n",
       "15 -0.165683  0.154953 -0.162697  0.438203  ...              0  0.214226   \n",
       "\n",
       "     HTX_std  HTX_class  ERS_mean   ERS_std  ERS_class  ARE_mean   ARE_std  \\\n",
       "0   0.000606          0  0.000211  0.000422          0  0.002386  0.003650   \n",
       "1   0.000363          0  0.000022  0.000044          0  0.000227  0.000303   \n",
       "2   0.000506          0  0.000024  0.000047          0  0.002713  0.003312   \n",
       "3   0.002644          0  0.000030  0.000060          0  0.006670  0.011748   \n",
       "4   0.000501          0  0.000194  0.000387          0  0.034363  0.030649   \n",
       "5   0.000889          0  0.000445  0.000888          0  0.031498  0.018437   \n",
       "6   0.099890          0  0.015813  0.017492          0  0.382610  0.305057   \n",
       "7   0.304819          0  0.013343  0.015159          0  0.195870  0.280803   \n",
       "8   0.000516          0  0.000343  0.000683          0  0.047065  0.071224   \n",
       "9   0.000728          0  0.000036  0.000071          0  0.008832  0.008288   \n",
       "10  0.059985          0  0.000167  0.000333          0  0.000534  0.000442   \n",
       "11  0.001835          0  0.000146  0.000293          0  0.037190  0.055694   \n",
       "12  0.008015          0  0.000175  0.000351          0  0.182184  0.231458   \n",
       "13  0.028948          0  0.000596  0.001192          0  0.038357  0.063377   \n",
       "14  0.138552          0  0.002517  0.003172          0  0.255158  0.338649   \n",
       "15  0.273211          0  0.004570  0.008083          0  0.117277  0.128432   \n",
       "\n",
       "    ARE_class  \n",
       "0           0  \n",
       "1           0  \n",
       "2           0  \n",
       "3           0  \n",
       "4           0  \n",
       "5           0  \n",
       "6           0  \n",
       "7           0  \n",
       "8           0  \n",
       "9           0  \n",
       "10          0  \n",
       "11          0  \n",
       "12          0  \n",
       "13          0  \n",
       "14          0  \n",
       "15          0  \n",
       "\n",
       "[16 rows x 610 columns]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mean_pred, pred_task = make_predictions_with_ensemble(Xtest)\n",
    "test_pred = test_df.merge(mean_pred, right_index=True, left_index=True)\n",
    "test_pred"
   ]
  }
 ],
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