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--- a +++ b/docs/build/html/notes/mpnn.html @@ -0,0 +1,151 @@ + +<!DOCTYPE html> + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta charset="utf-8" /> + <title>Message Passing Neural Network (MPNN) — DeepPurpose 0.0.1 documentation</title> + <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> + <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> + <script id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> + <script src="../_static/jquery.js"></script> + <script src="../_static/underscore.js"></script> + <script src="../_static/doctools.js"></script> + <script src="../_static/language_data.js"></script> + <link rel="index" title="Index" href="../genindex.html" /> + <link rel="search" title="Search" href="../search.html" /> + <link rel="next" title="CNN+RNN" href="cnnrnn.html" /> + <link rel="prev" title="Transformer" href="transformer.html" /> + + <link rel="stylesheet" href="../_static/custom.css" type="text/css" /> + + + <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" /> + + </head><body> + + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + + + <div class="body" role="main"> + + <div class="section" id="message-passing-neural-network-mpnn"> +<h1>Message Passing Neural Network (MPNN)<a class="headerlink" href="#message-passing-neural-network-mpnn" title="Permalink to this headline">¶</a></h1> +<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="k">class</span> <span class="nc">DeepPurpose</span><span class="o">.</span><span class="n">models</span><span class="o">.</span><span class="n">MPNN</span><span class="p">(</span><span class="n">nn</span><span class="o">.</span><span class="n">Sequential</span><span class="p">)</span> +</pre></div> +</div> +<p><a class="reference external" href="https://www.biorxiv.org/content/10.1101/684662v3">Message Passing Neural Network (MPNN)</a> encode drug in its graph representation.</p> +<p><strong>constructor</strong> create MPNN class.</p> +<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">mpnn_hidden_size</span><span class="p">,</span> <span class="n">mpnn_depth</span><span class="p">)</span> +</pre></div> +</div> +<ul class="simple"> +<li><p><strong>mpnn_hidden_size</strong> (int) - specify dimension of hidden layer in MPNN, e.g, mpnn_hidden_size = 256.</p></li> +<li><p><strong>mpnn_depth</strong> (int) - specify depth of MPNN, e.g., mpnn_depth = 3.</p></li> +</ul> +<p><strong>Calling functions</strong> implement the feedforward procedure of MPNN.</p> +<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">forward</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">feature</span><span class="p">)</span> +</pre></div> +</div> +<ul class="simple"> +<li><dl class="simple"> +<dt><strong>feature</strong> (tuple of length 5)</dt><dd><ul> +<li><p><strong>todo</strong></p></li> +<li></li> +</ul> +</dd> +</dl> +</li> +</ul> +</div> + + + </div> + + </div> + </div> + <div class="sphinxsidebar" role="navigation" aria-label="main navigation"> + <div class="sphinxsidebarwrapper"> +<h1 class="logo"><a href="../index.html">DeepPurpose</a></h1> + + + + + + + + +<h3>Navigation</h3> +<p class="caption"><span class="caption-text">Background</span></p> +<ul> +<li class="toctree-l1"><a class="reference internal" href="introduction.html">Feature of DeepPurpose</a></li> +<li class="toctree-l1"><a class="reference internal" href="DTI.html">What is Drug Target Interaction?</a></li> +</ul> +<p class="caption"><span class="caption-text">How to run</span></p> +<ul> +<li class="toctree-l1"><a class="reference internal" href="download.html">Download</a></li> +<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li> +<li class="toctree-l1"><a class="reference internal" href="casestudy.html">Case Study</a></li> +</ul> +<p class="caption"><span class="caption-text">Package Reference</span></p> +<ul class="current"> +<li class="toctree-l1"><a class="reference internal" href="model.html">Model</a></li> +<li class="toctree-l1 current"><a class="reference internal" href="encoder.html">Drug/Target Encoder</a></li> +<li class="toctree-l1"><a class="reference internal" href="process_data.html">Processing Data</a></li> +<li class="toctree-l1"><a class="reference internal" href="configuration.html">Configuration</a></li> +<li class="toctree-l1"><a class="reference internal" href="utility_function.html">Utility Function</a></li> +</ul> + +<div class="relations"> +<h3>Related Topics</h3> +<ul> + <li><a href="../index.html">Documentation overview</a><ul> + <li><a href="encoder.html">Drug/Target Encoder</a><ul> + <li>Previous: <a href="transformer.html" title="previous chapter">Transformer</a></li> + <li>Next: <a href="cnnrnn.html" title="next chapter">CNN+RNN</a></li> + </ul></li> + </ul></li> +</ul> +</div> +<div id="searchbox" style="display: none" role="search"> + <h3 id="searchlabel">Quick search</h3> + <div class="searchformwrapper"> + <form class="search" action="../search.html" method="get"> + <input type="text" name="q" aria-labelledby="searchlabel" /> + <input type="submit" value="Go" /> + </form> + </div> +</div> +<script>$('#searchbox').show(0);</script> + + + + + + + + + </div> + </div> + <div class="clearer"></div> + </div> + <div class="footer"> + ©2020, Kexin Huang, Tianfan Fu. + + | + Powered by <a href="http://sphinx-doc.org/">Sphinx 3.0.0</a> + & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a> + + | + <a href="../_sources/notes/mpnn.rst.txt" + rel="nofollow">Page source</a> + </div> + + + + + </body> +</html> \ No newline at end of file