<?xml version="1.0" encoding="ascii"?> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> <head> <title>Bio.NeuralNetwork.Training</title> <link rel="stylesheet" href="epydoc.css" type="text/css" /> <script type="text/javascript" src="epydoc.js"></script> </head> <body bgcolor="white" text="black" link="blue" vlink="#204080" alink="#204080"> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> <tr valign="middle"> <!-- Tree link --> <th> <a href="module-tree.html">Trees</a> </th> <!-- Index link --> <th> <a href="identifier-index.html">Indices</a> </th> <!-- Help link --> <th> <a href="help.html">Help</a> </th> <th class="navbar" width="100%"></th> </tr> </table> <table width="100%" cellpadding="0" cellspacing="0"> <tr valign="top"> <td width="100%"> <span class="breadcrumbs"> <a href="Bio-module.html">Package Bio</a> :: <a href="Bio.NeuralNetwork-module.html">Package NeuralNetwork</a> :: Module Training </span> </td> <td> <table cellpadding="0" cellspacing="0"> <!-- hide/show private --> <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink" onclick="toggle_private();">hide private</a>]</span></td></tr> <tr><td align="right"><span class="options" >[<a href="frames.html" target="_top">frames</a >] | <a href="Bio.NeuralNetwork.Training-pysrc.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <h1 class="epydoc">Source Code for <a href="Bio.NeuralNetwork.Training-module.html">Module Bio.NeuralNetwork.Training</a></h1> <pre class="py-src"> <a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-docstring">"""Provide classes for dealing with Training Neural Networks.</tt> </tt> <a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt> <a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"># standard modules</tt> </tt> <a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">random</tt> </tt> <a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"> </tt> <a name="TrainingExample"></a><div id="TrainingExample-def"><a name="L6"></a><tt class="py-lineno"> 6</tt> <a class="py-toggle" href="#" id="TrainingExample-toggle" onclick="return toggle('TrainingExample');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.NeuralNetwork.Training.TrainingExample-class.html">TrainingExample</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="TrainingExample-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="TrainingExample-expanded"><a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"> <tt class="py-docstring">"""Hold inputs and outputs of a training example.</tt> </tt> <a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring"> XXX Do I really need this? </tt> </tt> <a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="TrainingExample.__init__"></a><div id="TrainingExample.__init__-def"><a name="L11"></a><tt class="py-lineno">11</tt> <a class="py-toggle" href="#" id="TrainingExample.__init__-toggle" onclick="return toggle('TrainingExample.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.NeuralNetwork.Training.TrainingExample-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">inputs</tt><tt class="py-op">,</tt> <tt class="py-param">outputs</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="TrainingExample.__init__-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="TrainingExample.__init__-expanded"><a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-0" class="py-name" targets="Method Bio.Phylo.PhyloXMLIO.Writer.name()=Bio.Phylo.PhyloXMLIO.Writer-class.html#name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-0', 'name', 'link-0');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-1" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-1', 'name', 'link-0');">name</a></tt> </tt> <a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">inputs</tt> <tt class="py-op">=</tt> <tt class="py-name">inputs</tt> </tt> <a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">outputs</tt> <tt class="py-op">=</tt> <tt class="py-name">outputs</tt> </tt> </div></div><a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"> </tt> <a name="ExampleManager"></a><div id="ExampleManager-def"><a name="L16"></a><tt class="py-lineno">16</tt> <a class="py-toggle" href="#" id="ExampleManager-toggle" onclick="return toggle('ExampleManager');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.NeuralNetwork.Training.ExampleManager-class.html">ExampleManager</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="ExampleManager-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="ExampleManager-expanded"><a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"> <tt class="py-docstring">"""Manage a grouping of Training Examples.</tt> </tt> <a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"><tt class="py-docstring"> This is meant to make it easy to split a bunch of training examples</tt> </tt> <a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"><tt class="py-docstring"> into three types of data:</tt> </tt> <a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"><tt class="py-docstring"> o Training Data -- These are the data used to do the actual training</tt> </tt> <a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"><tt class="py-docstring"> of the network.</tt> </tt> <a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"><tt class="py-docstring"> o Validation Data -- These data are used to validate the network</tt> </tt> <a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"><tt class="py-docstring"> while training. They provide an independent method to evaluate how</tt> </tt> <a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"><tt class="py-docstring"> the network is doing, and make sure the network gets trained independent</tt> </tt> <a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"><tt class="py-docstring"> of noise in the training data set.</tt> </tt> <a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"><tt class="py-docstring"> o Testing Data -- The data which are used to verify how well a network</tt> </tt> <a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"><tt class="py-docstring"> works. They should not be used at all in the training process, so they</tt> </tt> <a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"><tt class="py-docstring"> provide a completely independent method of testing how well a network</tt> </tt> <a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"><tt class="py-docstring"> performs.</tt> </tt> <a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="ExampleManager.__init__"></a><div id="ExampleManager.__init__-def"><a name="L35"></a><tt class="py-lineno">35</tt> <a class="py-toggle" href="#" id="ExampleManager.__init__-toggle" onclick="return toggle('ExampleManager.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.NeuralNetwork.Training.ExampleManager-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">training_percent</tt> <tt class="py-op">=</tt> <tt class="py-number">.4</tt><tt class="py-op">,</tt> <tt class="py-param">validation_percent</tt> <tt class="py-op">=</tt> <tt class="py-number">.4</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="ExampleManager.__init__-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="ExampleManager.__init__-expanded"><a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"> <tt class="py-docstring">"""Initialize the manager with the training examples.</tt> </tt> <a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt> <a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"><tt class="py-docstring"> o training_percent - The percentage of the training examples that</tt> </tt> <a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"><tt class="py-docstring"> should be used for training the network.</tt> </tt> <a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"><tt class="py-docstring"> o validation_percent - Percent of training examples for validating</tt> </tt> <a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"><tt class="py-docstring"> a network during training.</tt> </tt> <a name="L45"></a><tt class="py-lineno">45</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"><tt class="py-docstring"> Attributes:</tt> </tt> <a name="L47"></a><tt class="py-lineno">47</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L48"></a><tt class="py-lineno">48</tt> <tt class="py-line"><tt class="py-docstring"> o train_examples - A randomly chosen set of examples for training</tt> </tt> <a name="L49"></a><tt class="py-lineno">49</tt> <tt class="py-line"><tt class="py-docstring"> purposes.</tt> </tt> <a name="L50"></a><tt class="py-lineno">50</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L51"></a><tt class="py-lineno">51</tt> <tt class="py-line"><tt class="py-docstring"> o valdiation_examples - Randomly chosesn set of examples for</tt> </tt> <a name="L52"></a><tt class="py-lineno">52</tt> <tt class="py-line"><tt class="py-docstring"> use in validation of a network during training.</tt> </tt> <a name="L53"></a><tt class="py-lineno">53</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L54"></a><tt class="py-lineno">54</tt> <tt class="py-line"><tt class="py-docstring"> o test_examples - Examples for training purposes.</tt> </tt> <a name="L55"></a><tt class="py-lineno">55</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="L56"></a><tt class="py-lineno">56</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">training_percent</tt> <tt class="py-op">+</tt> <tt class="py-name">validation_percent</tt> <tt class="py-op"><=</tt> <tt class="py-number">1.0</tt><tt class="py-op">,</tt> \ </tt> <a name="L57"></a><tt class="py-lineno">57</tt> <tt class="py-line"> <tt class="py-string">"Training and validation percentages more than 100 percent"</tt> </tt> <a name="L58"></a><tt class="py-lineno">58</tt> <tt class="py-line"> </tt> <a name="L59"></a><tt class="py-lineno">59</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">train_examples</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt> <a name="L60"></a><tt class="py-lineno">60</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">validation_examples</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt> <a name="L61"></a><tt class="py-lineno">61</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">test_examples</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt> <a name="L62"></a><tt class="py-lineno">62</tt> <tt class="py-line"> </tt> <a name="L63"></a><tt class="py-lineno">63</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">training_percent</tt> <tt class="py-op">=</tt> <tt class="py-name">training_percent</tt> </tt> <a name="L64"></a><tt class="py-lineno">64</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">validation_percent</tt> <tt class="py-op">=</tt> <tt class="py-name">validation_percent</tt> </tt> </div><a name="L65"></a><tt class="py-lineno">65</tt> <tt class="py-line"> </tt> <a name="ExampleManager.add_examples"></a><div id="ExampleManager.add_examples-def"><a name="L66"></a><tt class="py-lineno">66</tt> <a class="py-toggle" href="#" id="ExampleManager.add_examples-toggle" onclick="return toggle('ExampleManager.add_examples');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.NeuralNetwork.Training.ExampleManager-class.html#add_examples">add_examples</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">training_examples</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="ExampleManager.add_examples-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="ExampleManager.add_examples-expanded"><a name="L67"></a><tt class="py-lineno">67</tt> <tt class="py-line"> <tt class="py-docstring">"""Add a set of training examples to the manager.</tt> </tt> <a name="L68"></a><tt class="py-lineno">68</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L69"></a><tt class="py-lineno">69</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt> <a name="L70"></a><tt class="py-lineno">70</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L71"></a><tt class="py-lineno">71</tt> <tt class="py-line"><tt class="py-docstring"> o training_examples - A list of TrainingExamples to manage.</tt> </tt> <a name="L72"></a><tt class="py-lineno">72</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="L73"></a><tt class="py-lineno">73</tt> <tt class="py-line"> <tt class="py-name">placement_rand</tt> <tt class="py-op">=</tt> <tt class="py-name">random</tt><tt class="py-op">.</tt><tt class="py-name">Random</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L74"></a><tt class="py-lineno">74</tt> <tt class="py-line"> </tt> <a name="L75"></a><tt class="py-lineno">75</tt> <tt class="py-line"> <tt class="py-comment"># assign exact example randomly to the example types</tt> </tt> <a name="L76"></a><tt class="py-lineno">76</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">example</tt> <tt class="py-keyword">in</tt> <tt class="py-name">training_examples</tt><tt class="py-op">:</tt> </tt> <a name="L77"></a><tt class="py-lineno">77</tt> <tt class="py-line"> <tt class="py-name">chance_num</tt> <tt class="py-op">=</tt> <tt class="py-name">placement_rand</tt><tt class="py-op">.</tt><tt class="py-name">random</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L78"></a><tt class="py-lineno">78</tt> <tt class="py-line"> <tt class="py-comment"># assign with the specified percentage</tt> </tt> <a name="L79"></a><tt class="py-lineno">79</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">chance_num</tt> <tt class="py-op"><=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">training_percent</tt><tt class="py-op">:</tt> </tt> <a name="L80"></a><tt class="py-lineno">80</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">train_examples</tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Method Bio.Align.MultipleSeqAlignment.append()=Bio.Align.MultipleSeqAlignment-class.html#append,Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.SCOP.Raf.SeqMap.append()=Bio.SCOP.Raf.SeqMap-class.html#append,Method Bio.Seq.MutableSeq.append()=Bio.Seq.MutableSeq-class.html#append,Method Bio.Wise.psw.Alignment.append()=Bio.Wise.psw.Alignment-class.html#append,Method Bio.Wise.psw.AlignmentColumn.append()=Bio.Wise.psw.AlignmentColumn-class.html#append"><a title="Bio.Align.MultipleSeqAlignment.append Bio.Crystal.Chain.append Bio.SCOP.Raf.SeqMap.append Bio.Seq.MutableSeq.append Bio.Wise.psw.Alignment.append Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-2', 'append', 'link-2');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">example</tt><tt class="py-op">)</tt> </tt> <a name="L81"></a><tt class="py-lineno">81</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">chance_num</tt> <tt class="py-op"><=</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">training_percent</tt> <tt class="py-op">+</tt> </tt> <a name="L82"></a><tt class="py-lineno">82</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">validation_percent</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L83"></a><tt class="py-lineno">83</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">validation_examples</tt><tt class="py-op">.</tt><tt id="link-3" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append Bio.Crystal.Chain.append Bio.SCOP.Raf.SeqMap.append Bio.Seq.MutableSeq.append Bio.Wise.psw.Alignment.append Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-3', 'append', 'link-2');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">example</tt><tt class="py-op">)</tt> </tt> <a name="L84"></a><tt class="py-lineno">84</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt> <a name="L85"></a><tt class="py-lineno">85</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">test_examples</tt><tt class="py-op">.</tt><tt id="link-4" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append Bio.Crystal.Chain.append Bio.SCOP.Raf.SeqMap.append Bio.Seq.MutableSeq.append Bio.Wise.psw.Alignment.append Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-4', 'append', 'link-2');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">example</tt><tt class="py-op">)</tt> </tt> </div></div><a name="L86"></a><tt class="py-lineno">86</tt> <tt class="py-line"> </tt><script type="text/javascript"> <!-- expandto(location.href); // --> </script> </pre> <br /> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> <tr valign="middle"> <!-- Tree link --> <th> <a href="module-tree.html">Trees</a> </th> <!-- Index link --> <th> <a href="identifier-index.html">Indices</a> </th> <!-- Help link --> <th> <a href="help.html">Help</a> </th> <th class="navbar" width="100%"></th> </tr> </table> <table border="0" cellpadding="0" cellspacing="0" width="100%%"> <tr> <td align="left" class="footer"> Generated by Epydoc 3.0.1 on Thu Aug 18 18:22:47 2011 </td> <td align="right" class="footer"> <a target="mainFrame" href="http://epydoc.sourceforge.net" >http://epydoc.sourceforge.net</a> </td> </tr> </table> <script type="text/javascript"> <!-- // Private objects are initially displayed (because if // javascript is turned off then we want them to be // visible); but by default, we want to hide 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