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<p class="caption"><span class="caption-text">Importance Function</span></p>





  
  

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<h1>Drug/Target Encoder<a class="headerlink" href="#drug-target-encoder" title="Permalink to this headline">¶</a></h1>





  
  

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<div class="section" id="drug-encoding">





  
  

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<h2>Drug encoding<a class="headerlink" href="#drug-encoding" title="Permalink to this headline">¶</a></h2>





  
  

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<tr class="row-odd"><th class="head"><p>Drug Encodings</p></th>





  
  

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<th class="head"><p>Description</p></th>





  
  

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<tr class="row-even"><td><p>Morgan</p></td>





  
  

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<td><p>Extended-Connectivity Fingerprints</p></td>





  
  

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<tr class="row-odd"><td><p>Pubchem</p></td>





  
  

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<td><p>Pubchem Substructure-based Fingerprints</p></td>





  
  

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</tr>





  
  

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<tr class="row-even"><td><p>Daylight</p></td>





  
  

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<td><p>Daylight-type fingerprints</p></td>





  
  

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</tr>





  
  

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<tr class="row-odd"><td><p>rdkit_2d_normalized</p></td>





  
  

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<td><p>Normalized Descriptastorus</p></td>





  
  

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</tr>





  
  

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<tr class="row-even"><td><p>CNN</p></td>





  
  

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<td><p>Convolutional Neural Network on SMILES</p></td>





  
  

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</tr>





  
  

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<tr class="row-odd"><td><p>CNN_RNN</p></td>





  
  

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<td><p>A GRU/LSTM on top of a CNN on SMILES</p></td>





  
  

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</tr>





  
  

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<tr class="row-even"><td><p>Transformer</p></td>





  
  

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<td><p>Transformer Encoder on ESPF</p></td>





  
  

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</tr>





  
  

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<tr class="row-odd"><td><p>MPNN</p></td>





  
  

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<td><p>Message-passing neural network</p></td>





  
  

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</tr>





  
  

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</tbody>





  
  

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</table>





  
  

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</div>





  
  

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<div class="section" id="target-encoding">





  
  

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<h2>Target encoding<a class="headerlink" href="#target-encoding" title="Permalink to this headline">¶</a></h2>





  
  

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<table class="docutils align-default">





  
  

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<colgroup>





  
  

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<col style="width: 28%" />





  
  

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<col style="width: 72%" />





  
  

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</colgroup>





  
  

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<thead>





  
  

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<tr class="row-odd"><th class="head"><p>Target Encodings</p></th>





  
  

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<th class="head"><p>Description</p></th>





  
  

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</tr>





  
  

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</thead>





  
  

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<tbody>





  
  

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<tr class="row-even"><td><p>AAC</p></td>





  
  

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<td><p>Amino acid composition up to 3-mers</p></td>





  
  

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</tr>





  
  

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<tr class="row-odd"><td><p>PseudoAAC</p></td>





  
  

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<td><p>Pseudo amino acid composition</p></td>





  
  

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</tr>





  
  

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<tr class="row-even"><td><p>Conjoint_triad</p></td>





  
  

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<td><p>Conjoint triad features</p></td>





  
  

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</tr>





  
  

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<tr class="row-odd"><td><p>Quasi-seq</p></td>





  
  

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<td><p>Quasi-sequence order descriptor</p></td>





  
  

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</tr>





  
  

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<tr class="row-even"><td><p>CNN</p></td>





  
  

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<td><p>Convolutional Neural Network on target seq</p></td>





  
  

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</tr>





  
  

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<tr class="row-odd"><td><p>CNN_RNN</p></td>





  
  

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<td><p>A GRU/LSTM on top of a CNN on target seq</p></td>





  
  

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</tr>





  
  

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<tr class="row-even"><td><p>Transformer</p></td>





  
  

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<td><p>Transformer Encoder on ESPF</p></td>





  
  

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</tr>





  
  

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</tbody>





  
  

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</table>





  
  

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</div>





  
  

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<div class="section" id="encoder-model">





  
  

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<h2>Encoder Model<a class="headerlink" href="#encoder-model" title="Permalink to this headline">¶</a></h2>





  
  

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<table class="docutils align-default">





  
  

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<colgroup>





  
  

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<col style="width: 23%" />





  
  

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<col style="width: 77%" />





  
  

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</colgroup>





  
  

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<thead>





  
  

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<tr class="row-odd"><th class="head"><p>Encoder Model</p></th>





  
  

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<th class="head"><p>Description</p></th>





  
  

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</tr>





  
  

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</thead>





  
  

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<tbody>





  
  

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<tr class="row-even"><td><p>CNN</p></td>





  
  

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<td><p>Convolutional Neural Network on SMILES</p></td>





  
  

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</tr>





  
  

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<tr class="row-odd"><td><p>CNN_RNN</p></td>





  
  

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<td><p>A GRU/LSTM on top of a CNN on SMILES</p></td>





  
  

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</tr>





  
  

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<tr class="row-even"><td><p>Transformer</p></td>





  
  

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<td><p>Transformer Encoder on SMILES</p></td>





  
  

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</tr>





  
  

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<tr class="row-odd"><td><p>MPNN</p></td>





  
  

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<td><p>Message Passing Neural Network on Molecular Graph</p></td>





  
  

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</tr>





  
  

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<tr class="row-even"><td><p>MLP</p></td>





  
  

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<td><p>MultiLayer Perceptron on fix-dim feature vector</p></td>





  
  

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</tr>





  
  

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</tbody>





  
  

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</table>





  
  

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</div>





  
  

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<div class="section" id="technical-details">





  
  

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<h2>Technical Details<a class="headerlink" href="#technical-details" title="Permalink to this headline">¶</a></h2>





  
  

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<p>First, we describe the common modules we import in DeepPurpose.</p>





  
  

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<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">torch</span>





  
  

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<span class="kn">from</span> <span class="nn">torch.autograd</span> <span class="kn">import</span> <span class="n">Variable</span>





  
  

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<span class="kn">import</span> <span class="nn">torch.nn.functional</span> <span class="k">as</span> <span class="nn">F</span>





  
  

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<span class="kn">from</span> <span class="nn">torch</span> <span class="kn">import</span> <span class="n">nn</span>





  
  

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<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>





  
  

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<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>





  
  

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</pre></div>





  
  

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</div>





  
  

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<div class="toctree-wrapper compound">





  
  

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<p class="caption"><span class="caption-text">Links of details of various encoders</span></p>





  
  

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<ul>





  
  

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<li class="toctree-l1"><a class="reference internal" href="encoders/transformer.html">Transformer</a></li>





  
  

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<li class="toctree-l1"><a class="reference internal" href="encoders/mpnn.html">Message Passing Neural Network (MPNN)</a></li>





  
  

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<li class="toctree-l1"><a class="reference internal" href="encoders/cnnrnn.html">CNN+RNN</a></li>





  
  

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<li class="toctree-l1"><a class="reference internal" href="encoders/cnn.html">CNN</a></li>





  
  

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<li class="toctree-l1"><a class="reference internal" href="encoders/mlp.html">MLP</a></li>





  
  

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</ul>





  
  

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</div>





  
  

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</div>





  
  

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