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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.NeuralNetwork-module.html">Package NeuralNetwork</a> ::
Module StopTraining
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<h1 class="epydoc">Source Code for <a href="Bio.NeuralNetwork.StopTraining-module.html">Module Bio.NeuralNetwork.StopTraining</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-docstring">"""Classes to help deal with stopping training a neural network.</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-docstring">One of the key issues with training a neural network is knowning when to</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring">stop the training of the network. This is tricky since you want to keep</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring">training until the neural network has 'learned' the data, but want to</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">stop before starting to learn the noise in the data.</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">This module contains classes and functions which are different ways to</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">know when to stop training. Remember that the neural network classifier</tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"><tt class="py-docstring">takes a function to call to know when to stop training, so the classes</tt> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"><tt class="py-docstring">in this module should be instaniated, and then the stop_training function</tt> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"><tt class="py-docstring">of the classes passed to the network.</tt> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"> </tt>
<a name="ValidationIncreaseStop"></a><div id="ValidationIncreaseStop-def"><a name="L15"></a><tt class="py-lineno">15</tt> <a class="py-toggle" href="#" id="ValidationIncreaseStop-toggle" onclick="return toggle('ValidationIncreaseStop');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop-class.html">ValidationIncreaseStop</a><tt class="py-op">:</tt> </tt>
</div><div id="ValidationIncreaseStop-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="ValidationIncreaseStop-expanded"><a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> <tt class="py-docstring">"""Class to stop training on a network when the validation error increases.</tt> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"><tt class="py-docstring"> Normally, during training of a network, the error will always decrease</tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"><tt class="py-docstring"> on the set of data used in the training. However, if an independent</tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"><tt class="py-docstring"> set of data is used for validation, the error will decrease to a point,</tt> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"><tt class="py-docstring"> and then start to increase. This increase normally occurs due to the</tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"><tt class="py-docstring"> fact that the network is starting to learn noise in the training data</tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"><tt class="py-docstring"> set. This stopping criterion function will stop when the validation</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"><tt class="py-docstring"> error increases.</tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="ValidationIncreaseStop.__init__"></a><div id="ValidationIncreaseStop.__init__-def"><a name="L26"></a><tt class="py-lineno">26</tt> <a class="py-toggle" href="#" id="ValidationIncreaseStop.__init__-toggle" onclick="return toggle('ValidationIncreaseStop.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop-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">max_iterations</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">min_iterations</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"> <tt class="py-param">verbose</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ValidationIncreaseStop.__init__-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="ValidationIncreaseStop.__init__-expanded"><a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"> <tt class="py-docstring">"""Initialize the stopping criterion class.</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"> Arguments:</tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"><tt class="py-docstring"> o max_iterations - The maximum number of iterations that</tt> </tt>
<a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"><tt class="py-docstring"> should be performed, regardless of error.</tt> </tt>
<a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"><tt class="py-docstring"> o min_iterations - The minimum number of iterations to perform,</tt> </tt>
<a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"><tt class="py-docstring"> to prevent premature stoppage of training.</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"> o verbose - Whether or not the error should be printed during</tt> </tt>
<a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"><tt class="py-docstring"> training.</tt> </tt>
<a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">verbose</tt> <tt class="py-op">=</tt> <tt class="py-name">verbose</tt> </tt>
<a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">max_iterations</tt> <tt class="py-op">=</tt> <tt class="py-name">max_iterations</tt> </tt>
<a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">min_iterations</tt> <tt class="py-op">=</tt> <tt class="py-name">min_iterations</tt> </tt>
<a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"> </tt>
<a name="L45"></a><tt class="py-lineno">45</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">last_error</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
</div><a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"> </tt>
<a name="ValidationIncreaseStop.stopping_criteria"></a><div id="ValidationIncreaseStop.stopping_criteria-def"><a name="L47"></a><tt class="py-lineno">47</tt> <a class="py-toggle" href="#" id="ValidationIncreaseStop.stopping_criteria-toggle" onclick="return toggle('ValidationIncreaseStop.stopping_criteria');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop-class.html#stopping_criteria">stopping_criteria</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">num_iterations</tt><tt class="py-op">,</tt> <tt class="py-param">training_error</tt><tt class="py-op">,</tt> </tt>
<a name="L48"></a><tt class="py-lineno">48</tt> <tt class="py-line"> <tt class="py-param">validation_error</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ValidationIncreaseStop.stopping_criteria-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="ValidationIncreaseStop.stopping_criteria-expanded"><a name="L49"></a><tt class="py-lineno">49</tt> <tt class="py-line"> <tt class="py-docstring">"""Define when to stop iterating.</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-keyword">if</tt> <tt class="py-name">num_iterations</tt> <tt class="py-op">%</tt> <tt class="py-number">10</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L52"></a><tt class="py-lineno">52</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">verbose</tt><tt class="py-op">:</tt> </tt>
<a name="L53"></a><tt class="py-lineno">53</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"%s; Training Error:%s; Validation Error:%s"</tt>\ </tt>
<a name="L54"></a><tt class="py-lineno">54</tt> <tt class="py-line"> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">num_iterations</tt><tt class="py-op">,</tt> <tt class="py-name">training_error</tt><tt class="py-op">,</tt> <tt class="py-name">validation_error</tt><tt class="py-op">)</tt> </tt>
<a name="L55"></a><tt class="py-lineno">55</tt> <tt class="py-line"> </tt>
<a name="L56"></a><tt class="py-lineno">56</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">num_iterations</tt> <tt class="py-op">></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">min_iterations</tt><tt class="py-op">:</tt> </tt>
<a name="L57"></a><tt class="py-lineno">57</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">last_error</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L58"></a><tt class="py-lineno">58</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">validation_error</tt> <tt class="py-op">></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">last_error</tt><tt class="py-op">:</tt> </tt>
<a name="L59"></a><tt class="py-lineno">59</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">verbose</tt><tt class="py-op">:</tt> </tt>
<a name="L60"></a><tt class="py-lineno">60</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Validation Error increasing -- Stop"</tt> </tt>
<a name="L61"></a><tt class="py-lineno">61</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">1</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-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">max_iterations</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L64"></a><tt class="py-lineno">64</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">num_iterations</tt> <tt class="py-op">></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">max_iterations</tt><tt class="py-op">:</tt> </tt>
<a name="L65"></a><tt class="py-lineno">65</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">verbose</tt><tt class="py-op">:</tt> </tt>
<a name="L66"></a><tt class="py-lineno">66</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Reached maximum number of iterations -- Stop"</tt> </tt>
<a name="L67"></a><tt class="py-lineno">67</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
<a name="L68"></a><tt class="py-lineno">68</tt> <tt class="py-line"> </tt>
<a name="L69"></a><tt class="py-lineno">69</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">last_error</tt> <tt class="py-op">=</tt> <tt class="py-name">validation_error</tt> </tt>
<a name="L70"></a><tt class="py-lineno">70</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
</div></div><a name="L71"></a><tt class="py-lineno">71</tt> <tt class="py-line"> </tt><script type="text/javascript">
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