<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
<title>Transformer — 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="Message Passing Neural Network (MPNN)" href="mpnn.html" />
<link rel="prev" title="Drug/Target Encoder" href="encoder.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="transformer">
<h1>Transformer<a class="headerlink" href="#transformer" title="Permalink to this headline">¶</a></h1>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">DeepPurpose</span><span class="o">.</span><span class="n">models</span><span class="o">.</span><span class="n">transformer</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://arxiv.org/pdf/1908.06760.pdf">Transformer</a> can be used to encode both drug and protein on <a class="reference external" href="https://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system">SMILES</a>.</p>
<p>name of function: <strong>constructor</strong> create Transformer.</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">encoding</span><span class="p">,</span> <span class="o">**</span><span class="n">config</span><span class="p">)</span>
</pre></div>
</div>
<ul class="simple">
<li><p><strong>encoding</strong> (string, “drug” or “protein”) - specify input type of the model, “drug” or “protein”.</p></li>
<li><dl class="simple">
<dt><strong>config</strong> (kwargs, keyword arguments) - specify the parameter of transformer. The keys include</dt><dd><ul>
<li><p>transformer_dropout_rate (float) - dropout rate of transformer.</p></li>
<li><p>input_dim_drug (int) - input dimension when encoding drug.</p></li>
<li><p>transformer_emb_size_drug (int) - dimension of embedding in input layer when encoding drug.</p></li>
<li><p>transformer_n_layer_drug (int) - number of layers in transformer when encoding drug.</p></li>
<li><p><strong>todo</strong></p></li>
</ul>
</dd>
</dl>
</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">v</span><span class="p">)</span>
</pre></div>
</div>
<ul class="simple">
<li><p><strong>v</strong> (tuple of length 2) - input feature of transformer. v[0] (np.array) is index of atoms. v[1] (np.array) is the corresponding mask.</p></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="encoder.html" title="previous chapter">Drug/Target Encoder</a></li>
<li>Next: <a href="mpnn.html" title="next chapter">Message Passing Neural Network (MPNN)</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/transformer.rst.txt"
rel="nofollow">Page source</a>
</div>
</body>
</html>
Datasets
Models
