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        <a href="Bio.NeuralNetwork-module.html">Package&nbsp;NeuralNetwork</a> ::
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<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">&lt;=</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">&lt;=</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">&lt;=</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">
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