<?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.BackPropagation.Layer</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> :: <a href="Bio.NeuralNetwork.BackPropagation-module.html">Package BackPropagation</a> :: Module Layer </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.BackPropagation.Layer-pysrc.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <h1 class="epydoc">Source Code for <a href="Bio.NeuralNetwork.BackPropagation.Layer-module.html">Module Bio.NeuralNetwork.BackPropagation.Layer</a></h1> <pre class="py-src"> <a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-docstring">"""Model a single layer in a nueral 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">These classes deal with a layers in the neural network (ie. the input layer,</tt> </tt> <a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring">hidden layers and the output layer).</tt> </tt> <a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt> <a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"># standard library</tt> </tt> <a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">math</tt> </tt> <a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">random</tt> </tt> <a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"> </tt> <a name="logistic_function"></a><div id="logistic_function-def"><a name="L10"></a><tt class="py-lineno"> 10</tt> <a class="py-toggle" href="#" id="logistic_function-toggle" onclick="return toggle('logistic_function');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.NeuralNetwork.BackPropagation.Layer-module.html#logistic_function">logistic_function</a><tt class="py-op">(</tt><tt class="py-param">value</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="logistic_function-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="logistic_function-expanded"><a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"> <tt class="py-docstring">"""Transform the value with the logistic function.</tt> </tt> <a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring"> XXX This is in the wrong place -- I need to find a place to put it</tt> </tt> <a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring"> that makes sense.</tt> </tt> <a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">1.0</tt> <tt class="py-op">/</tt> <tt class="py-op">(</tt><tt class="py-number">1.0</tt> <tt class="py-op">+</tt> <tt class="py-name">math</tt><tt class="py-op">.</tt><tt id="link-0" class="py-name" targets="Variable Bio.Affy.CelFile.exp=Bio.Affy.CelFile-module.html#exp"><a title="Bio.Affy.CelFile.exp" class="py-name" href="#" onclick="return doclink('link-0', 'exp', 'link-0');">exp</a></tt><tt class="py-op">(</tt><tt class="py-op">-</tt><tt id="link-1" class="py-name" targets="Method Bio.Phylo.PhyloXMLIO.Writer.value()=Bio.Phylo.PhyloXMLIO.Writer-class.html#value"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-1', 'value', 'link-1');">value</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt> </div><a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"> </tt> <a name="AbstractLayer"></a><div id="AbstractLayer-def"><a name="L18"></a><tt class="py-lineno"> 18</tt> <a class="py-toggle" href="#" id="AbstractLayer-toggle" onclick="return toggle('AbstractLayer');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer-class.html">AbstractLayer</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="AbstractLayer-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="AbstractLayer-expanded"><a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"> <tt class="py-docstring">"""Abstract base class for all layers.</tt> </tt> <a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="AbstractLayer.__init__"></a><div id="AbstractLayer.__init__-def"><a name="L21"></a><tt class="py-lineno"> 21</tt> <a class="py-toggle" href="#" id="AbstractLayer.__init__-toggle" onclick="return toggle('AbstractLayer.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer-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">num_nodes</tt><tt class="py-op">,</tt> <tt class="py-param">has_bias_node</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="AbstractLayer.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AbstractLayer.__init__-expanded"><a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"> <tt class="py-docstring">"""Initialize the layer.</tt> </tt> <a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt> <a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring"> o num_nodes -- The number of nodes that are contained in this layer.</tt> </tt> <a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring"> o has_bias_node -- Specify whether or not this node has a bias</tt> </tt> <a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring"> node. This node is not included in the number of nodes in the network,</tt> </tt> <a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring"> but is used in constructing and dealing with the network.</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-comment"># specify all of the nodes in the network</tt> </tt> <a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">has_bias_node</tt><tt class="py-op">:</tt> </tt> <a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> <tt class="py-name">lower_range</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt> <a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt> <a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-name">lower_range</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt> <a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> </tt> <a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Method Bio.Pathway.Rep.Graph.Graph.nodes()=Bio.Pathway.Rep.Graph.Graph-class.html#nodes,Method Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes()=Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#nodes"><a title="Bio.Pathway.Rep.Graph.Graph.nodes Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-2', 'nodes', 'link-2');">nodes</a></tt> <tt class="py-op">=</tt> <tt id="link-3" class="py-name" targets="Method Bio.Graphics.GenomeDiagram._Diagram.Diagram.range()=Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#range,Method Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range()=Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet-class.html#range,Method Bio.Graphics.GenomeDiagram._Graph.GraphData.range()=Bio.Graphics.GenomeDiagram._Graph.GraphData-class.html#range,Method Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range()=Bio.Graphics.GenomeDiagram._GraphSet.GraphSet-class.html#range,Method Bio.Graphics.GenomeDiagram._Track.Track.range()=Bio.Graphics.GenomeDiagram._Track.Track-class.html#range"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.range Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range Bio.Graphics.GenomeDiagram._Graph.GraphData.range Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range Bio.Graphics.GenomeDiagram._Track.Track.range" class="py-name" href="#" onclick="return doclink('link-3', 'range', 'link-3');">range</a></tt><tt class="py-op">(</tt><tt class="py-name">lower_range</tt><tt class="py-op">,</tt> <tt class="py-name">num_nodes</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt> <a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> </tt> <a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">weights</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt> </div><a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> </tt> <a name="AbstractLayer.__str__"></a><div id="AbstractLayer.__str__-def"><a name="L42"></a><tt class="py-lineno"> 42</tt> <a class="py-toggle" href="#" id="AbstractLayer.__str__-toggle" onclick="return toggle('AbstractLayer.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer-class.html#__str__">__str__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="AbstractLayer.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AbstractLayer.__str__-expanded"><a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-docstring">"""Debugging output.</tt> </tt> <a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"weights: %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">weights</tt> </tt> </div><a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> </tt> <a name="AbstractLayer.set_weight"></a><div id="AbstractLayer.set_weight-def"><a name="L47"></a><tt class="py-lineno"> 47</tt> <a class="py-toggle" href="#" id="AbstractLayer.set_weight-toggle" onclick="return toggle('AbstractLayer.set_weight');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer-class.html#set_weight">set_weight</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">this_node</tt><tt class="py-op">,</tt> <tt class="py-param">next_node</tt><tt class="py-op">,</tt> <tt class="py-param">value</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="AbstractLayer.set_weight-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AbstractLayer.set_weight-expanded"><a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-docstring">"""Set a weight value from one node to the next.</tt> </tt> <a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-docstring"> If weights are not explicitly set, they will be initialized to</tt> </tt> <a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-docstring"> random values to start with.</tt> </tt> <a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">this_node</tt><tt class="py-op">,</tt> <tt class="py-name">next_node</tt><tt class="py-op">)</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">weights</tt><tt class="py-op">:</tt> </tt> <a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Invalid node values passed."</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-name">self</tt><tt class="py-op">.</tt><tt class="py-name">weights</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">this_node</tt><tt class="py-op">,</tt> <tt class="py-name">next_node</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-4" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-4', 'value', 'link-1');">value</a></tt> </tt> </div></div><a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> </tt> <a name="InputLayer"></a><div id="InputLayer-def"><a name="L58"></a><tt class="py-lineno"> 58</tt> <a class="py-toggle" href="#" id="InputLayer-toggle" onclick="return toggle('InputLayer');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.NeuralNetwork.BackPropagation.Layer.InputLayer-class.html">InputLayer</a><tt class="py-op">(</tt><tt class="py-base-class">AbstractLayer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="InputLayer-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="InputLayer-expanded"><a name="InputLayer.__init__"></a><div id="InputLayer.__init__-def"><a name="L59"></a><tt class="py-lineno"> 59</tt> <a class="py-toggle" href="#" id="InputLayer.__init__-toggle" onclick="return toggle('InputLayer.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.NeuralNetwork.BackPropagation.Layer.InputLayer-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">num_nodes</tt><tt class="py-op">,</tt> <tt class="py-param">next_layer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="InputLayer.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="InputLayer.__init__-expanded"><a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-docstring">"""Initialize the input layer.</tt> </tt> <a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt> <a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-docstring"> o num_nodes -- The number of nodes in the input layer.</tt> </tt> <a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"><tt class="py-docstring"> o next_layer -- The next layer in the neural network this is</tt> </tt> <a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"><tt class="py-docstring"> connected to.</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 id="link-5" class="py-name" targets="Class Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer=Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer-class.html"><a title="Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer" class="py-name" href="#" onclick="return doclink('link-5', 'AbstractLayer', 'link-5');">AbstractLayer</a></tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Method Bio.Affy.CelFile.CelConsumer.__init__()=Bio.Affy.CelFile.CelConsumer-class.html#__init__,Method Bio.Affy.CelFile.CelParser.__init__()=Bio.Affy.CelFile.CelParser-class.html#__init__,Method Bio.Affy.CelFile.CelRecord.__init__()=Bio.Affy.CelFile.CelRecord-class.html#__init__,Method 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Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__ Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.__init__ Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__ Bio.Restriction._Update.Update.ConnectionError.__init__ Bio.Restriction._Update.Update.FtpNameError.__init__ Bio.Restriction._Update.Update.FtpPasswordError.__init__ Bio.Restriction._Update.Update.RebaseUpdate.__init__ Bio.SCOP.Astral.__init__ Bio.SCOP.Cla.Index.__init__ Bio.SCOP.Cla.Record.__init__ Bio.SCOP.Des.Record.__init__ Bio.SCOP.Dom.Record.__init__ Bio.SCOP.Domain.__init__ Bio.SCOP.Hie.Record.__init__ Bio.SCOP.Node.__init__ Bio.SCOP.Raf.Res.__init__ Bio.SCOP.Raf.SeqMap.__init__ Bio.SCOP.Raf.SeqMapIndex.__init__ Bio.SCOP.Residues'.Residues.__init__ Bio.SCOP.Scop.__init__ Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__ Bio.Search.Algorithm.__init__ Bio.Search.Database.__init__ Bio.Search.HSP.__init__ Bio.Search.HSPSeq.__init__ Bio.Search.Hit.__init__ Bio.Search.HomologySeq.__init__ Bio.Search.Query.__init__ Bio.Search.Search.__init__ Bio.Search.TableInfo.__init__ Bio.Search._SeqLength.__init__ Bio.Seq.MutableSeq.__init__ Bio.Seq.Seq.__init__ Bio.Seq.UnknownSeq.__init__ Bio.SeqFeature.AbstractPosition.__init__ Bio.SeqFeature.AfterPosition.__init__ Bio.SeqFeature.BeforePosition.__init__ Bio.SeqFeature.BetweenPosition.__init__ Bio.SeqFeature.ExactPosition.__init__ Bio.SeqFeature.FeatureLocation.__init__ Bio.SeqFeature.OneOfPosition.__init__ Bio.SeqFeature.PositionGap.__init__ Bio.SeqFeature.Reference.__init__ Bio.SeqFeature.SeqFeature.__init__ Bio.SeqFeature.UnknownPosition.__init__ Bio.SeqFeature.WithinPosition.__init__ Bio.SeqIO.FastaIO.FastaWriter.__init__ Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__ Bio.SeqIO.Interfaces.SequenceIterator.__init__ Bio.SeqIO.Interfaces.SequenceWriter.__init__ Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__ Bio.SeqIO.PhdIO.PhdWriter.__init__ Bio.SeqIO.QualityIO.QualPhredWriter.__init__ Bio.SeqIO.SeqXmlIO.SeqXmlIterator.__init__ Bio.SeqIO.SeqXmlIO.SeqXmlWriter.__init__ Bio.SeqIO.SeqXmlIO.XMLRecordIterator.__init__ Bio.SeqIO.SffIO.SffWriter.__init__ Bio.SeqIO.SffIO._AddTellHandle.__init__ Bio.SeqIO.UniprotIO.Parser.__init__ Bio.SeqIO._index.IntelliGeneticsRandomAccess.__init__ Bio.SeqIO._index.SeqFileRandomAccess.__init__ Bio.SeqIO._index.SequentialSeqFileRandomAccess.__init__ Bio.SeqIO._index.SffRandomAccess.__init__ Bio.SeqIO._index._IndexedSeqFileDict.__init__ Bio.SeqIO._index._SQLiteManySeqFilesDict.__init__ Bio.SeqRecord.SeqRecord.__init__ Bio.SeqRecord._RestrictedDict.__init__ Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__ Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__ Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__ Bio.Sequencing.Ace.ACEFileRecord.__init__ Bio.Sequencing.Ace.Contig.__init__ Bio.Sequencing.Ace.Reads.__init__ Bio.Sequencing.Ace.af.__init__ Bio.Sequencing.Ace.bs.__init__ Bio.Sequencing.Ace.ct.__init__ Bio.Sequencing.Ace.ds.__init__ Bio.Sequencing.Ace.qa.__init__ Bio.Sequencing.Ace.rd.__init__ Bio.Sequencing.Ace.rt.__init__ Bio.Sequencing.Ace.wa.__init__ Bio.Sequencing.Ace.wr.__init__ Bio.Sequencing.Applications._Novoalign.NovoalignCommandline.__init__ Bio.Sequencing.Phd.Record.__init__ Bio.SubsMat.FreqTable.FreqTable.__init__ Bio.SubsMat.SeqMat.__init__ Bio.SwissProt.KeyWList.Record.__init__ Bio.SwissProt.Record.__init__ Bio.SwissProt.Reference.__init__ Bio.UniGene.Iterator.__init__ Bio.UniGene.ProtsimLine.__init__ Bio.UniGene.Record.__init__ Bio.UniGene.RecordParser.__init__ Bio.UniGene.STSLine.__init__ Bio.UniGene.SequenceLine.__init__ Bio.UniGene.UnigeneProtsimRecord.__init__ Bio.UniGene.UnigeneRecord.__init__ Bio.UniGene.UnigeneSTSRecord.__init__ Bio.UniGene.UnigeneSequenceRecord.__init__ Bio.UniGene._RecordConsumer.__init__ Bio.UniGene._Scanner.__init__ Bio.Wise.dnal.Statistics.__init__ Bio.Wise.psw.AlignmentColumn.__init__ Bio.Wise.psw.ColumnUnit.__init__ Bio.kNN.kNN.__init__ Bio.pairwise2.affine_penalty.__init__ Bio.pairwise2.dictionary_match.__init__ Bio.pairwise2.identity_match.__init__ BioSQL.BioSeq.DBSeq.__init__ BioSQL.BioSeq.DBSeqRecord.__init__ BioSQL.BioSeqDatabase.Adaptor.__init__ BioSQL.BioSeqDatabase.BioSeqDatabase.__init__ BioSQL.BioSeqDatabase.DBServer.__init__ BioSQL.DBUtils.Generic_dbutils.__init__ BioSQL.Loader.DatabaseLoader.__init__ BioSQL.Loader.DatabaseRemover.__init__" class="py-name" href="#" onclick="return doclink('link-6', '__init__', 'link-6');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">num_nodes</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt> <a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> </tt> <a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_next_layer</tt> <tt class="py-op">=</tt> <tt class="py-name">next_layer</tt> </tt> <a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> </tt> <a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-comment"># set up the weights</tt> </tt> <a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">weights</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt> <a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">own_node</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-7', 'nodes', 'link-2');">nodes</a></tt><tt class="py-op">:</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">other_node</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_next_layer</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-8', 'nodes', 'link-2');">nodes</a></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">self</tt><tt class="py-op">.</tt><tt class="py-name">weights</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">own_node</tt><tt class="py-op">,</tt> <tt class="py-name">other_node</tt><tt class="py-op">)</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-name">random</tt><tt class="py-op">.</tt><tt class="py-name">randrange</tt><tt class="py-op">(</tt><tt class="py-op">-</tt><tt class="py-number">2.0</tt><tt class="py-op">,</tt> <tt class="py-number">2.0</tt><tt class="py-op">)</tt> </tt> <a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> </tt> <a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-comment"># set up the weight changes</tt> </tt> <a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">weight_changes</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt> <a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">own_node</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-9', 'nodes', 'link-2');">nodes</a></tt><tt class="py-op">:</tt> </tt> <a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">other_node</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_next_layer</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-10', 'nodes', 'link-2');">nodes</a></tt><tt class="py-op">:</tt> </tt> <a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">weight_changes</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">own_node</tt><tt class="py-op">,</tt> <tt class="py-name">other_node</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">0.0</tt> </tt> <a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> </tt> <a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-comment"># set up the calculated values for each node -- these will</tt> </tt> <a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-comment"># actually just be set from inputs into the network.</tt> </tt> <a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Method Bio.Crystal.Crystal.values()=Bio.Crystal.Crystal-class.html#values,Method Bio.Phylo.PhyloXML.Events.values()=Bio.Phylo.PhyloXML.Events-class.html#values,Method Bio.SeqIO._index._IndexedSeqFileDict.values()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#values,Method BioSQL.BioSeqDatabase.BioSeqDatabase.values()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#values,Method BioSQL.BioSeqDatabase.DBServer.values()=BioSQL.BioSeqDatabase.DBServer-class.html#values"><a title="Bio.Crystal.Crystal.values Bio.Phylo.PhyloXML.Events.values Bio.SeqIO._index._IndexedSeqFileDict.values BioSQL.BioSeqDatabase.BioSeqDatabase.values BioSQL.BioSeqDatabase.DBServer.values" class="py-name" href="#" onclick="return doclink('link-11', 'values', 'link-11');">values</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt> <a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-12" class="py-name" targets="Method Bio.Nexus.Trees.Tree.node()=Bio.Nexus.Trees.Tree-class.html#node"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-12', 'node', 'link-12');">node</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-13" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-13', 'nodes', 'link-2');">nodes</a></tt><tt class="py-op">:</tt> </tt> <a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-comment"># set the bias node -- always has a value of 1</tt> </tt> <a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-14" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-14', 'node', 'link-12');">node</a></tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt> <a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name"><a title="Bio.Crystal.Crystal.values Bio.Phylo.PhyloXML.Events.values Bio.SeqIO._index._IndexedSeqFileDict.values BioSQL.BioSeqDatabase.BioSeqDatabase.values BioSQL.BioSeqDatabase.DBServer.values" class="py-name" href="#" onclick="return doclink('link-15', 'values', 'link-11');">values</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt> <a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt> <a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-16" class="py-name"><a title="Bio.Crystal.Crystal.values Bio.Phylo.PhyloXML.Events.values Bio.SeqIO._index._IndexedSeqFileDict.values BioSQL.BioSeqDatabase.BioSeqDatabase.values BioSQL.BioSeqDatabase.DBServer.values" class="py-name" href="#" onclick="return doclink('link-16', 'values', 'link-11');">values</a></tt><tt class="py-op">[</tt><tt id="link-17" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-17', 'node', 'link-12');">node</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt> </div><a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> </tt> <a name="InputLayer.update"></a><div id="InputLayer.update-def"><a name="L96"></a><tt class="py-lineno"> 96</tt> <a class="py-toggle" href="#" id="InputLayer.update-toggle" onclick="return toggle('InputLayer.update');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.NeuralNetwork.BackPropagation.Layer.InputLayer-class.html#update">update</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-op">:</tt> </tt> </div><div id="InputLayer.update-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="InputLayer.update-expanded"><a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-docstring">"""Update the values of the nodes using given inputs.</tt> </tt> <a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt> <a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"><tt class="py-docstring"> o inputs -- A list of inputs into the network -- this must be</tt> </tt> <a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"><tt class="py-docstring"> equal to the number of nodes in the layer.</tt> </tt> <a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">inputs</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name"><a title="Bio.Crystal.Crystal.values Bio.Phylo.PhyloXML.Events.values Bio.SeqIO._index._IndexedSeqFileDict.values BioSQL.BioSeqDatabase.BioSeqDatabase.values BioSQL.BioSeqDatabase.DBServer.values" class="py-name" href="#" onclick="return doclink('link-18', 'values', 'link-11');">values</a></tt><tt class="py-op">.</tt><tt id="link-19" class="py-name" targets="Method Bio.Crystal.Crystal.keys()=Bio.Crystal.Crystal-class.html#keys,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#keys,Method Bio.Phylo.PhyloXML.Events.keys()=Bio.Phylo.PhyloXML.Events-class.html#keys,Method Bio.SeqIO._index._IndexedSeqFileDict.keys()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#keys,Method Bio.SeqIO._index._SQLiteManySeqFilesDict.keys()=Bio.SeqIO._index._SQLiteManySeqFilesDict-class.html#keys,Method BioSQL.BioSeqDatabase.BioSeqDatabase.keys()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#keys,Method BioSQL.BioSeqDatabase.DBServer.keys()=BioSQL.BioSeqDatabase.DBServer-class.html#keys"><a title="Bio.Crystal.Crystal.keys Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys Bio.Phylo.PhyloXML.Events.keys Bio.SeqIO._index._IndexedSeqFileDict.keys Bio.SeqIO._index._SQLiteManySeqFilesDict.keys BioSQL.BioSeqDatabase.BioSeqDatabase.keys BioSQL.BioSeqDatabase.DBServer.keys" class="py-name" href="#" onclick="return doclink('link-19', 'keys', 'link-19');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt> <a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Inputs do not match input layer nodes."</tt><tt class="py-op">)</tt> </tt> <a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> </tt> <a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-comment"># set the node values from the inputs</tt> </tt> <a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">input_num</tt> <tt class="py-keyword">in</tt> <tt id="link-20" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.range Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range Bio.Graphics.GenomeDiagram._Graph.GraphData.range Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range Bio.Graphics.GenomeDiagram._Track.Track.range" class="py-name" href="#" onclick="return doclink('link-20', 'range', 'link-3');">range</a></tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">inputs</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name"><a title="Bio.Crystal.Crystal.values Bio.Phylo.PhyloXML.Events.values Bio.SeqIO._index._IndexedSeqFileDict.values BioSQL.BioSeqDatabase.BioSeqDatabase.values BioSQL.BioSeqDatabase.DBServer.values" class="py-name" href="#" onclick="return doclink('link-21', 'values', 'link-11');">values</a></tt><tt class="py-op">[</tt><tt class="py-name">input_num</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">inputs</tt><tt class="py-op">[</tt><tt class="py-name">input_num</tt><tt class="py-op">]</tt> </tt> <a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> </tt> <a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-comment"># propogate the update to the next layer</tt> </tt> <a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_next_layer</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name" targets="Method Bio.Index._InMemoryIndex.update()=Bio.Index._InMemoryIndex-class.html#update,Method Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update()=Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer-class.html#update,Method Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update()=Bio.NeuralNetwork.BackPropagation.Layer.InputLayer-class.html#update,Method Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update()=Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer-class.html#update,Method Bio.Restriction._Update.Update.RebaseUpdate.update()=Bio.Restriction._Update.Update.RebaseUpdate-class.html#update,Method Bio.SeqIO._index._IndexedSeqFileDict.update()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#update,Method Bio.SeqRecord._RestrictedDict.update()=Bio.SeqRecord._RestrictedDict-class.html#update"><a title="Bio.Index._InMemoryIndex.update Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update Bio.Restriction._Update.Update.RebaseUpdate.update Bio.SeqIO._index._IndexedSeqFileDict.update Bio.SeqRecord._RestrictedDict.update" class="py-name" href="#" onclick="return doclink('link-22', 'update', 'link-22');">update</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt> </div><a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> </tt> <a name="InputLayer.backpropagate"></a><div id="InputLayer.backpropagate-def"><a name="L114"></a><tt class="py-lineno">114</tt> <a class="py-toggle" href="#" id="InputLayer.backpropagate-toggle" onclick="return toggle('InputLayer.backpropagate');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.NeuralNetwork.BackPropagation.Layer.InputLayer-class.html#backpropagate">backpropagate</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">outputs</tt><tt class="py-op">,</tt> <tt class="py-param">learning_rate</tt><tt class="py-op">,</tt> <tt class="py-param">momentum</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="InputLayer.backpropagate-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="InputLayer.backpropagate-expanded"><a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-docstring">"""Recalculate all weights based on the last round of prediction.</tt> </tt> <a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt> <a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt> <a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"><tt class="py-docstring"> o learning_rate -- The learning rate of the network</tt> </tt> <a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"><tt class="py-docstring"> o momentum - The amount of weight to place on the previous weight</tt> </tt> <a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"><tt class="py-docstring"> change.</tt> </tt> <a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"><tt class="py-docstring"> o outputs - The output info we are using to calculate error.</tt> </tt> <a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-comment"># first backpropogate to the next layers</tt> </tt> <a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-name">next_errors</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_next_layer</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name" targets="Method Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.backpropagate()=Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer-class.html#backpropagate,Method Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.backpropagate()=Bio.NeuralNetwork.BackPropagation.Layer.InputLayer-class.html#backpropagate,Method Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.backpropagate()=Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer-class.html#backpropagate"><a title="Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.backpropagate Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.backpropagate Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.backpropagate" class="py-name" href="#" onclick="return doclink('link-23', 'backpropagate', 'link-23');">backpropagate</a></tt><tt class="py-op">(</tt><tt class="py-name">outputs</tt><tt class="py-op">,</tt> <tt class="py-name">learning_rate</tt><tt class="py-op">,</tt> </tt> <a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-name">momentum</tt><tt class="py-op">)</tt> </tt> <a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> </tt> <a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">this_node</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-24" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-24', 'nodes', 'link-2');">nodes</a></tt><tt class="py-op">:</tt> </tt> <a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">next_node</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_next_layer</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-25', 'nodes', 'link-2');">nodes</a></tt><tt class="py-op">:</tt> </tt> <a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-name">error_deriv</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">next_errors</tt><tt class="py-op">[</tt><tt class="py-name">next_node</tt><tt class="py-op">]</tt> <tt class="py-op">*</tt> </tt> <a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name"><a title="Bio.Crystal.Crystal.values Bio.Phylo.PhyloXML.Events.values Bio.SeqIO._index._IndexedSeqFileDict.values BioSQL.BioSeqDatabase.BioSeqDatabase.values BioSQL.BioSeqDatabase.DBServer.values" class="py-name" href="#" onclick="return doclink('link-26', 'values', 'link-11');">values</a></tt><tt class="py-op">[</tt><tt class="py-name">this_node</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt> <a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> </tt> <a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-name">delta</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">learning_rate</tt> <tt class="py-op">*</tt> <tt class="py-name">error_deriv</tt> <tt class="py-op">+</tt> </tt> <a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-name">momentum</tt> <tt class="py-op">*</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">weight_changes</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">this_node</tt><tt class="py-op">,</tt> <tt class="py-name">next_node</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt> <a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> </tt> <a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-comment"># apply the change to the weight</tt> </tt> <a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">weights</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">this_node</tt><tt class="py-op">,</tt> <tt class="py-name">next_node</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">+=</tt> <tt class="py-name">delta</tt> </tt> <a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> </tt> <a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-comment"># remember the weight change for next time</tt> </tt> <a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">weight_changes</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">this_node</tt><tt class="py-op">,</tt> <tt class="py-name">next_node</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">delta</tt> </tt> </div></div><a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> </tt> <a name="HiddenLayer"></a><div id="HiddenLayer-def"><a name="L144"></a><tt class="py-lineno">144</tt> <a class="py-toggle" href="#" id="HiddenLayer-toggle" onclick="return toggle('HiddenLayer');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer-class.html">HiddenLayer</a><tt class="py-op">(</tt><tt class="py-base-class">AbstractLayer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="HiddenLayer-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="HiddenLayer-expanded"><a name="HiddenLayer.__init__"></a><div id="HiddenLayer.__init__-def"><a name="L145"></a><tt class="py-lineno">145</tt> <a class="py-toggle" href="#" id="HiddenLayer.__init__-toggle" onclick="return toggle('HiddenLayer.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer-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">num_nodes</tt><tt class="py-op">,</tt> <tt class="py-param">next_layer</tt><tt class="py-op">,</tt> <tt class="py-param">activation</tt> <tt class="py-op">=</tt> <tt id="link-27" class="py-name" targets="Function Bio.NeuralNetwork.BackPropagation.Layer.logistic_function()=Bio.NeuralNetwork.BackPropagation.Layer-module.html#logistic_function"><a title="Bio.NeuralNetwork.BackPropagation.Layer.logistic_function" class="py-name" href="#" onclick="return doclink('link-27', 'logistic_function', 'link-27');">logistic_function</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="HiddenLayer.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="HiddenLayer.__init__-expanded"><a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-docstring">"""Initialize a hidden layer.</tt> </tt> <a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt> <a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"><tt class="py-docstring"> o num_nodes -- The number of nodes in this hidden layer.</tt> </tt> <a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"><tt class="py-docstring"> o next_layer -- The next layer in the neural network that this</tt> </tt> <a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"><tt class="py-docstring"> is connected to.</tt> </tt> <a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"><tt class="py-docstring"> o activation -- The transformation function used to transform</tt> </tt> <a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"><tt class="py-docstring"> predicted values.</tt> </tt> <a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt id="link-28" class="py-name"><a title="Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer" class="py-name" href="#" onclick="return doclink('link-28', 'AbstractLayer', 'link-5');">AbstractLayer</a></tt><tt class="py-op">.</tt><tt id="link-29" class="py-name"><a title="Bio.Affy.CelFile.CelConsumer.__init__ Bio.Affy.CelFile.CelParser.__init__ Bio.Affy.CelFile.CelRecord.__init__ Bio.Affy.CelFile.CelScanner.__init__ Bio.Affy.CelFile.Record.__init__ Bio.Align.AlignInfo.PSSM.__init__ Bio.Align.AlignInfo.SummaryInfo.__init__ Bio.Align.Applications._Clustalw.ClustalwCommandline.__init__ Bio.Align.Applications._Dialign.DialignCommandline.__init__ Bio.Align.Applications._Mafft.MafftCommandline.__init__ Bio.Align.Applications._Muscle.MuscleCommandline.__init__ Bio.Align.Applications._Prank.PrankCommandline.__init__ Bio.Align.Applications._Probcons.ProbconsCommandline.__init__ Bio.Align.Applications._TCoffee.TCoffeeCommandline.__init__ Bio.Align.Generic.Alignment.__init__ Bio.Align.MultipleSeqAlignment.__init__ Bio.AlignIO.Interfaces.AlignmentIterator.__init__ Bio.AlignIO.Interfaces.AlignmentWriter.__init__ Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__ Bio.Alphabet.AlphabetEncoder.__init__ Bio.Alphabet.Gapped.__init__ Bio.Alphabet.HasStopCodon.__init__ Bio.Application.AbstractCommandline.__init__ Bio.Application.ApplicationError.__init__ Bio.Application._AbstractParameter.__init__ Bio.Application._Argument.__init__ Bio.Application._Option.__init__ Bio.Application._Switch.__init__ Bio.Blast.Applications.BlastallCommandline.__init__ Bio.Blast.Applications.BlastpgpCommandline.__init__ Bio.Blast.Applications.FastacmdCommandline.__init__ Bio.Blast.Applications.NcbiblastformatterCommandline.__init__ Bio.Blast.Applications.NcbiblastnCommandline.__init__ Bio.Blast.Applications.NcbiblastpCommandline.__init__ Bio.Blast.Applications.NcbiblastxCommandline.__init__ Bio.Blast.Applications.NcbipsiblastCommandline.__init__ Bio.Blast.Applications.NcbirpsblastCommandline.__init__ Bio.Blast.Applications.NcbirpstblastnCommandline.__init__ Bio.Blast.Applications.NcbitblastnCommandline.__init__ Bio.Blast.Applications.NcbitblastxCommandline.__init__ Bio.Blast.Applications.RpsBlastCommandline.__init__ Bio.Blast.Applications._BlastAllOrPgpCommandLine.__init__ Bio.Blast.Applications._BlastCommandLine.__init__ Bio.Blast.Applications._NcbibaseblastCommandline.__init__ Bio.Blast.Applications._Ncbiblast2SeqCommandline.__init__ Bio.Blast.Applications._NcbiblastCommandline.__init__ Bio.Blast.Applications._NcbiblastMain2SeqCommandline.__init__ Bio.Blast.NCBIStandalone.BlastErrorParser.__init__ Bio.Blast.NCBIStandalone.BlastParser.__init__ Bio.Blast.NCBIStandalone.Iterator.__init__ Bio.Blast.NCBIStandalone.PSIBlastParser.__init__ Bio.Blast.NCBIStandalone._BlastConsumer.__init__ Bio.Blast.NCBIStandalone._BlastErrorConsumer.__init__ Bio.Blast.NCBIStandalone._PSIBlastConsumer.__init__ Bio.Blast.NCBIXML.BlastParser.__init__ Bio.Blast.NCBIXML._XMLparser.__init__ Bio.Blast.ParseBlastTable.BlastTableEntry.__init__ Bio.Blast.ParseBlastTable.BlastTableReader.__init__ Bio.Blast.ParseBlastTable.BlastTableRec.__init__ Bio.Blast.Record.Alignment.__init__ Bio.Blast.Record.Blast.__init__ Bio.Blast.Record.DatabaseReport.__init__ Bio.Blast.Record.Description.__init__ Bio.Blast.Record.HSP.__init__ Bio.Blast.Record.Header.__init__ Bio.Blast.Record.MultipleAlignment.__init__ Bio.Blast.Record.PSIBlast.__init__ Bio.Blast.Record.Parameters.__init__ Bio.Blast.Record.Round.__init__ Bio.CAPS.CAPSMap.__init__ Bio.CAPS.DifferentialCutsite.__init__ Bio.Cluster.Record.__init__ Bio.Compass.Iterator.__init__ Bio.Compass.Record.__init__ Bio.Compass.RecordParser.__init__ Bio.Compass._Consumer.__init__ Bio.Compass._Scanner.__init__ Bio.Crystal.Chain.__init__ Bio.Crystal.Crystal.__init__ Bio.Crystal.Hetero.__init__ Bio.Data.CodonTable.AmbiguousCodonTable.__init__ Bio.Data.CodonTable.AmbiguousForwardTable.__init__ Bio.Data.CodonTable.CodonTable.__init__ Bio.Data.CodonTable.NCBICodonTable.__init__ Bio.DocSQL.Create.__init__ Bio.DocSQL.Insert.__init__ Bio.DocSQL.IterationCursor.__init__ Bio.DocSQL.Query.__init__ Bio.DocSQL.QueryAll.__init__ Bio.DocSQL.QueryGeneric.__init__ Bio.DocSQL.QueryRow.__init__ Bio.DocSQL.QuerySingle.__init__ Bio.Emboss.Applications.DiffseqCommandline.__init__ Bio.Emboss.Applications.EInvertedCommandline.__init__ Bio.Emboss.Applications.ETandemCommandline.__init__ Bio.Emboss.Applications.Est2GenomeCommandline.__init__ Bio.Emboss.Applications.FConsenseCommandline.__init__ Bio.Emboss.Applications.FDNADistCommandline.__init__ Bio.Emboss.Applications.FDNAParsCommandline.__init__ Bio.Emboss.Applications.FNeighborCommandline.__init__ Bio.Emboss.Applications.FProtDistCommandline.__init__ Bio.Emboss.Applications.FProtParsCommandline.__init__ Bio.Emboss.Applications.FSeqBootCommandline.__init__ Bio.Emboss.Applications.FTreeDistCommandline.__init__ Bio.Emboss.Applications.FuzznucCommandline.__init__ Bio.Emboss.Applications.IepCommandline.__init__ Bio.Emboss.Applications.NeedleCommandline.__init__ Bio.Emboss.Applications.PalindromeCommandline.__init__ Bio.Emboss.Applications.Primer3Commandline.__init__ Bio.Emboss.Applications.PrimerSearchCommandline.__init__ Bio.Emboss.Applications.SeqmatchallCommandline.__init__ Bio.Emboss.Applications.SeqretCommandline.__init__ Bio.Emboss.Applications.TranalignCommandline.__init__ Bio.Emboss.Applications.WaterCommandline.__init__ Bio.Emboss.Applications._EmbossCommandLine.__init__ Bio.Emboss.Applications._EmbossMinimalCommandLine.__init__ Bio.Emboss.Primer3.Primers.__init__ Bio.Emboss.Primer3.Record.__init__ Bio.Emboss.PrimerSearch.Amplifier.__init__ Bio.Emboss.PrimerSearch.InputRecord.__init__ Bio.Emboss.PrimerSearch.OutputRecord.__init__ Bio.Entrez.Parser.CorruptedXMLError.__init__ Bio.Entrez.Parser.DataHandler.__init__ Bio.Entrez.Parser.NotXMLError.__init__ Bio.Entrez.Parser.StructureElement.__init__ Bio.Entrez.Parser.ValidationError.__init__ Bio.ExPASy.Enzyme.Record.__init__ Bio.ExPASy.Prodoc.Record.__init__ Bio.ExPASy.Prodoc.Reference.__init__ Bio.ExPASy.Prosite.Record.__init__ Bio.ExPASy.ScanProsite.ContentHandler.__init__ Bio.ExPASy.ScanProsite.Parser.__init__ Bio.ExPASy.ScanProsite.Record.__init__ Bio.FSSP.FSSPAlignDict.__init__ Bio.FSSP.FSSPAlignRec.__init__ Bio.FSSP.FSSPHeader.__init__ Bio.FSSP.FSSPSumRec.__init__ Bio.FSSP.FSSPTools.FSSPMultAlign.__init__ Bio.FSSP.PosAlign.__init__ Bio.FSSP.fssp_rec.fff_rec.__init__ Bio.File.SGMLStripper.MyParser.__init__ Bio.File.SGMLStripper.__init__ Bio.File.UndoHandle.__init__ Bio.GA.Crossover.General.SafeFitnessCrossover.__init__ Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover.__init__ Bio.GA.Crossover.GeneralPoint.InterleaveCrossover.__init__ Bio.GA.Crossover.Point.SinglePointCrossover.__init__ Bio.GA.Crossover.TwoPoint.TwoPointCrossover.__init__ Bio.GA.Crossover.Uniform.UniformCrossover.__init__ Bio.GA.Evolver.GenerationEvolver.__init__ Bio.GA.Evolver.SteadyStateEvolver.__init__ Bio.GA.Mutation.General.SafeFitnessMutation.__init__ Bio.GA.Mutation.Simple.ConversionMutation.__init__ Bio.GA.Mutation.Simple.SinglePositionMutation.__init__ Bio.GA.Organism.Organism.__init__ Bio.GA.Repair.Stabilizing.AmbiguousRepair.__init__ Bio.GA.Selection.Abstract.AbstractSelection.__init__ Bio.GA.Selection.Diversity.DiversitySelection.__init__ Bio.GA.Selection.RouletteWheel.RouletteWheelSelection.__init__ Bio.GA.Selection.Tournament.TournamentSelection.__init__ Bio.GenBank.FeatureParser.__init__ Bio.GenBank.Iterator.__init__ Bio.GenBank.LocationParser.AbsoluteLocation.__init__ Bio.GenBank.LocationParser.Between.__init__ Bio.GenBank.LocationParser.FeatureName.__init__ Bio.GenBank.LocationParser.Function.__init__ Bio.GenBank.LocationParser.HighBound.__init__ Bio.GenBank.LocationParser.Integer.__init__ Bio.GenBank.LocationParser.LocationParser.__init__ Bio.GenBank.LocationParser.LocationScanner.__init__ Bio.GenBank.LocationParser.LowBound.__init__ Bio.GenBank.LocationParser.Path.__init__ Bio.GenBank.LocationParser.Range.__init__ Bio.GenBank.LocationParser.Symbol.__init__ Bio.GenBank.LocationParser.Token.__init__ Bio.GenBank.LocationParser.TwoBound.__init__ Bio.GenBank.Record.Feature.__init__ Bio.GenBank.Record.Qualifier.__init__ Bio.GenBank.Record.Record.__init__ Bio.GenBank.Record.Reference.__init__ Bio.GenBank.RecordParser.__init__ Bio.GenBank.Scanner.InsdcScanner.__init__ Bio.GenBank._BaseGenBankConsumer.__init__ Bio.GenBank._FeatureConsumer.__init__ Bio.GenBank._RecordConsumer.__init__ Bio.GenBank.utils.FeatureValueCleaner.__init__ Bio.Geo.Record.Record.__init__ Bio.Graphics.BasicChromosome.Chromosome.__init__ Bio.Graphics.BasicChromosome.ChromosomeSegment.__init__ Bio.Graphics.BasicChromosome.Organism.__init__ Bio.Graphics.BasicChromosome.TelomereSegment.__init__ Bio.Graphics.BasicChromosome._ChromosomeComponent.__init__ Bio.Graphics.Comparative.ComparativeScatterPlot.__init__ Bio.Graphics.DisplayRepresentation.ChromosomeCounts.__init__ Bio.Graphics.Distribution.BarChartDistribution.__init__ Bio.Graphics.Distribution.DistributionPage.__init__ Bio.Graphics.Distribution.LineDistribution.__init__ Bio.Graphics.GenomeDiagram._AbstractDrawer.AbstractDrawer.__init__ Bio.Graphics.GenomeDiagram._CircularDrawer.CircularDrawer.__init__ Bio.Graphics.GenomeDiagram._Colors.ColorTranslator.__init__ Bio.Graphics.GenomeDiagram._Diagram.Diagram.__init__ Bio.Graphics.GenomeDiagram._Feature.Feature.__init__ Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.__init__ Bio.Graphics.GenomeDiagram._Graph.GraphData.__init__ Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.__init__ Bio.Graphics.GenomeDiagram._LinearDrawer.LinearDrawer.__init__ Bio.Graphics.GenomeDiagram._Track.Track.__init__ Bio.HMM.DynamicProgramming.AbstractDPAlgorithms.__init__ Bio.HMM.DynamicProgramming.LogDPAlgorithms.__init__ Bio.HMM.DynamicProgramming.ScaledDPAlgorithms.__init__ Bio.HMM.MarkovModel.HiddenMarkovModel.__init__ Bio.HMM.MarkovModel.MarkovModelBuilder.__init__ Bio.HMM.Trainer.AbstractTrainer.__init__ Bio.HMM.Trainer.BaumWelchTrainer.__init__ Bio.HMM.Trainer.KnownStateTrainer.__init__ Bio.HMM.Trainer.TrainingSequence.__init__ Bio.HotRand.HotCache.__init__ Bio.HotRand.HotRandom.__init__ Bio.Index._InMemoryIndex.__init__ Bio.Index._ShelveIndex.__init__ Bio.KDTree.KDTree.KDTree.__init__ Bio.KEGG.Compound.Record.__init__ Bio.KEGG.Enzyme.Record.__init__ Bio.LogisticRegression.LogisticRegression.__init__ Bio.MarkovModel.MarkovModel.__init__ Bio.MaxEntropy.MaxEntropy.__init__ Bio.Motif.Applications._AlignAce.AlignAceCommandline.__init__ Bio.Motif.Applications._AlignAce.CompareAceCommandline.__init__ Bio.Motif.Parsers.AlignAce.Record.__init__ Bio.Motif.Parsers.MAST.Record.__init__ Bio.Motif.Parsers.MEME.MEMEInstance.__init__ Bio.Motif.Parsers.MEME.MEMEMotif.__init__ Bio.Motif.Parsers.MEME.MEMERecord.__init__ Bio.Motif.Thresholds.ScoreDistribution.__init__ Bio.Motif._Motif.Motif.__init__ Bio.NMR.xpktools.Peaklist.__init__ Bio.NMR.xpktools.XpkEntry.__init__ Bio.NaiveBayes.NaiveBayes.__init__ Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer.__init__ Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.__init__ Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.__init__ Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.__init__ Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork.__init__ Bio.NeuralNetwork.Gene.Motif.MotifCoder.__init__ Bio.NeuralNetwork.Gene.Motif.MotifFinder.__init__ Bio.NeuralNetwork.Gene.Pattern.PatternIO.__init__ Bio.NeuralNetwork.Gene.Pattern.PatternRepository.__init__ Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness.__init__ Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder.__init__ Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness.__init__ Bio.NeuralNetwork.Gene.Schema.RandomMotifGenerator.__init__ Bio.NeuralNetwork.Gene.Schema.Schema.__init__ Bio.NeuralNetwork.Gene.Schema.SchemaCoder.__init__ Bio.NeuralNetwork.Gene.Schema.SchemaFactory.__init__ Bio.NeuralNetwork.Gene.Schema.SchemaFinder.__init__ Bio.NeuralNetwork.Gene.Schema.SimpleFinisher.__init__ Bio.NeuralNetwork.Gene.Signature.SignatureCoder.__init__ Bio.NeuralNetwork.Gene.Signature.SignatureFinder.__init__ Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop.__init__ Bio.NeuralNetwork.Training.ExampleManager.__init__ Bio.NeuralNetwork.Training.TrainingExample.__init__ Bio.Nexus.Nexus.Block.__init__ Bio.Nexus.Nexus.CharBuffer.__init__ Bio.Nexus.Nexus.Commandline.__init__ Bio.Nexus.Nexus.Nexus.__init__ Bio.Nexus.Nexus.StepMatrix.__init__ Bio.Nexus.Nodes.Chain.__init__ Bio.Nexus.Nodes.Node.__init__ Bio.Nexus.Trees.NodeData.__init__ Bio.Nexus.Trees.Tree.__init__ Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap.__init__ Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__init__ Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap.__init__ Bio.PDB.Atom.Atom.__init__ Bio.PDB.Atom.DisorderedAtom.__init__ Bio.PDB.Chain.Chain.__init__ Bio.PDB.DSSP'.DSSP.__init__ Bio.PDB.Dice.ChainSelector.__init__ Bio.PDB.Entity.DisorderedEntityWrapper.__init__ Bio.PDB.Entity.Entity.__init__ Bio.PDB.FragmentMapper'.Fragment.__init__ Bio.PDB.FragmentMapper'.FragmentMapper.__init__ Bio.PDB.HSExposure.ExposureCN.__init__ Bio.PDB.HSExposure.HSExposureCA.__init__ Bio.PDB.HSExposure.HSExposureCB.__init__ Bio.PDB.HSExposure._AbstractHSExposure.__init__ Bio.PDB.MMCIF2Dict.MMCIF2Dict.__init__ Bio.PDB.Model.Model.__init__ Bio.PDB.NACCESS.NACCESS.__init__ Bio.PDB.NACCESS.NACCESS_atomic.__init__ Bio.PDB.NeighborSearch.NeighborSearch.__init__ Bio.PDB.PDBIO'.PDBIO.__init__ Bio.PDB.PDBList'.PDBList.__init__ Bio.PDB.PDBParser'.PDBParser.__init__ Bio.PDB.PSEA.PSEA.__init__ Bio.PDB.Polypeptide.CaPPBuilder.__init__ Bio.PDB.Polypeptide.PPBuilder.__init__ Bio.PDB.Polypeptide._PPBuilder.__init__ Bio.PDB.Residue.DisorderedResidue.__init__ Bio.PDB.Residue.Residue.__init__ Bio.PDB.ResidueDepth'.ResidueDepth.__init__ Bio.PDB.Structure.Structure.__init__ Bio.PDB.StructureAlignment'.StructureAlignment.__init__ Bio.PDB.StructureBuilder.StructureBuilder.__init__ Bio.PDB.Superimposer'.Superimposer.__init__ Bio.PDB.Vector'.Vector.__init__ Bio.ParserSupport.EventGenerator.__init__ Bio.ParserSupport.SGMLStrippingConsumer.__init__ Bio.ParserSupport.TaggingConsumer.__init__ Bio.Parsers.spark.GenericASTBuilder.__init__ Bio.Parsers.spark.GenericASTMatcher.__init__ Bio.Parsers.spark.GenericASTTraversal.__init__ Bio.Parsers.spark.GenericParser.__init__ Bio.Parsers.spark.GenericScanner.__init__ Bio.Pathway.Network.__init__ Bio.Pathway.Reaction.__init__ Bio.Pathway.Rep.Graph.Graph.__init__ Bio.Pathway.Rep.HashSet.HashSet.__init__ Bio.Pathway.Rep.MultiGraph.MultiGraph.__init__ Bio.Pathway.System.__init__ Bio.Phylo.Applications._Phyml.PhymlCommandline.__init__ Bio.Phylo.BaseTree.Clade.__init__ Bio.Phylo.BaseTree.Tree.__init__ Bio.Phylo.Newick.Clade.__init__ Bio.Phylo.Newick.Tree.__init__ Bio.Phylo.NewickIO.Parser.__init__ Bio.Phylo.NewickIO.Writer.__init__ Bio.Phylo.PAML._paml.Paml.__init__ Bio.Phylo.PAML.baseml.Baseml.__init__ Bio.Phylo.PAML.codeml.Codeml.__init__ Bio.Phylo.PAML.yn00.Yn00.__init__ Bio.Phylo.PhyloXML.Accession.__init__ Bio.Phylo.PhyloXML.Annotation.__init__ Bio.Phylo.PhyloXML.BinaryCharacters.__init__ Bio.Phylo.PhyloXML.BranchColor.__init__ Bio.Phylo.PhyloXML.Clade.__init__ Bio.Phylo.PhyloXML.CladeRelation.__init__ Bio.Phylo.PhyloXML.Confidence.__init__ Bio.Phylo.PhyloXML.Date.__init__ Bio.Phylo.PhyloXML.Distribution.__init__ Bio.Phylo.PhyloXML.DomainArchitecture.__init__ Bio.Phylo.PhyloXML.Events.__init__ Bio.Phylo.PhyloXML.Id.__init__ Bio.Phylo.PhyloXML.MolSeq.__init__ Bio.Phylo.PhyloXML.Other.__init__ Bio.Phylo.PhyloXML.Phylogeny.__init__ Bio.Phylo.PhyloXML.Phyloxml.__init__ Bio.Phylo.PhyloXML.Point.__init__ Bio.Phylo.PhyloXML.Polygon.__init__ Bio.Phylo.PhyloXML.Property.__init__ Bio.Phylo.PhyloXML.ProteinDomain.__init__ Bio.Phylo.PhyloXML.Reference.__init__ Bio.Phylo.PhyloXML.Sequence.__init__ Bio.Phylo.PhyloXML.SequenceRelation.__init__ Bio.Phylo.PhyloXML.Taxonomy.__init__ Bio.Phylo.PhyloXML.Uri.__init__ Bio.Phylo.PhyloXMLIO.Parser.__init__ Bio.Phylo.PhyloXMLIO.Writer.__init__ Bio.PopGen.Async.Async.__init__ Bio.PopGen.Async.DirectoryRetriever.__init__ Bio.PopGen.Async.FileRetriever.__init__ Bio.PopGen.Async.Local.Local.__init__ Bio.PopGen.FDist.Async.FDistAsync.__init__ Bio.PopGen.FDist.Async.SplitFDist.__init__ Bio.PopGen.FDist.Controller.FDistController.__init__ Bio.PopGen.FDist.Record.__init__ Bio.PopGen.GenePop.Controller.GenePopController.__init__ Bio.PopGen.GenePop.Controller._FileIterator.__init__ Bio.PopGen.GenePop.Controller._GenePopCommandline.__init__ Bio.PopGen.GenePop.EasyController.EasyController.__init__ Bio.PopGen.GenePop.FileParser.FileRecord.__init__ Bio.PopGen.GenePop.LargeFileParser.Record.__init__ Bio.PopGen.GenePop.Record.__init__ Bio.PopGen.SimCoal.Async.SimCoalCache.__init__ Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__ Bio.PopGen.SimCoal.Controller.SimCoalController.__init__ Bio.Restriction.PrintFormat.PrintFormat.__init__ Bio.Restriction.Restriction.Analysis.__init__ Bio.Restriction.Restriction.FormattedSeq.__init__ Bio.Restriction.Restriction.RestrictionBatch.__init__ Bio.Restriction.Restriction.RestrictionType.__init__ Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__ Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.__init__ Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__ Bio.Restriction._Update.Update.ConnectionError.__init__ Bio.Restriction._Update.Update.FtpNameError.__init__ Bio.Restriction._Update.Update.FtpPasswordError.__init__ Bio.Restriction._Update.Update.RebaseUpdate.__init__ Bio.SCOP.Astral.__init__ Bio.SCOP.Cla.Index.__init__ Bio.SCOP.Cla.Record.__init__ Bio.SCOP.Des.Record.__init__ Bio.SCOP.Dom.Record.__init__ Bio.SCOP.Domain.__init__ Bio.SCOP.Hie.Record.__init__ Bio.SCOP.Node.__init__ Bio.SCOP.Raf.Res.__init__ Bio.SCOP.Raf.SeqMap.__init__ Bio.SCOP.Raf.SeqMapIndex.__init__ Bio.SCOP.Residues'.Residues.__init__ Bio.SCOP.Scop.__init__ Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__ Bio.Search.Algorithm.__init__ Bio.Search.Database.__init__ Bio.Search.HSP.__init__ Bio.Search.HSPSeq.__init__ Bio.Search.Hit.__init__ Bio.Search.HomologySeq.__init__ Bio.Search.Query.__init__ Bio.Search.Search.__init__ Bio.Search.TableInfo.__init__ Bio.Search._SeqLength.__init__ Bio.Seq.MutableSeq.__init__ Bio.Seq.Seq.__init__ Bio.Seq.UnknownSeq.__init__ Bio.SeqFeature.AbstractPosition.__init__ Bio.SeqFeature.AfterPosition.__init__ Bio.SeqFeature.BeforePosition.__init__ Bio.SeqFeature.BetweenPosition.__init__ Bio.SeqFeature.ExactPosition.__init__ Bio.SeqFeature.FeatureLocation.__init__ Bio.SeqFeature.OneOfPosition.__init__ Bio.SeqFeature.PositionGap.__init__ Bio.SeqFeature.Reference.__init__ Bio.SeqFeature.SeqFeature.__init__ Bio.SeqFeature.UnknownPosition.__init__ Bio.SeqFeature.WithinPosition.__init__ Bio.SeqIO.FastaIO.FastaWriter.__init__ Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__ Bio.SeqIO.Interfaces.SequenceIterator.__init__ Bio.SeqIO.Interfaces.SequenceWriter.__init__ Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__ Bio.SeqIO.PhdIO.PhdWriter.__init__ Bio.SeqIO.QualityIO.QualPhredWriter.__init__ Bio.SeqIO.SeqXmlIO.SeqXmlIterator.__init__ Bio.SeqIO.SeqXmlIO.SeqXmlWriter.__init__ Bio.SeqIO.SeqXmlIO.XMLRecordIterator.__init__ Bio.SeqIO.SffIO.SffWriter.__init__ Bio.SeqIO.SffIO._AddTellHandle.__init__ Bio.SeqIO.UniprotIO.Parser.__init__ Bio.SeqIO._index.IntelliGeneticsRandomAccess.__init__ Bio.SeqIO._index.SeqFileRandomAccess.__init__ Bio.SeqIO._index.SequentialSeqFileRandomAccess.__init__ Bio.SeqIO._index.SffRandomAccess.__init__ Bio.SeqIO._index._IndexedSeqFileDict.__init__ Bio.SeqIO._index._SQLiteManySeqFilesDict.__init__ Bio.SeqRecord.SeqRecord.__init__ Bio.SeqRecord._RestrictedDict.__init__ Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__ Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__ Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__ Bio.Sequencing.Ace.ACEFileRecord.__init__ Bio.Sequencing.Ace.Contig.__init__ Bio.Sequencing.Ace.Reads.__init__ Bio.Sequencing.Ace.af.__init__ Bio.Sequencing.Ace.bs.__init__ Bio.Sequencing.Ace.ct.__init__ Bio.Sequencing.Ace.ds.__init__ Bio.Sequencing.Ace.qa.__init__ Bio.Sequencing.Ace.rd.__init__ Bio.Sequencing.Ace.rt.__init__ Bio.Sequencing.Ace.wa.__init__ Bio.Sequencing.Ace.wr.__init__ Bio.Sequencing.Applications._Novoalign.NovoalignCommandline.__init__ Bio.Sequencing.Phd.Record.__init__ Bio.SubsMat.FreqTable.FreqTable.__init__ Bio.SubsMat.SeqMat.__init__ Bio.SwissProt.KeyWList.Record.__init__ Bio.SwissProt.Record.__init__ Bio.SwissProt.Reference.__init__ Bio.UniGene.Iterator.__init__ Bio.UniGene.ProtsimLine.__init__ Bio.UniGene.Record.__init__ Bio.UniGene.RecordParser.__init__ Bio.UniGene.STSLine.__init__ Bio.UniGene.SequenceLine.__init__ Bio.UniGene.UnigeneProtsimRecord.__init__ Bio.UniGene.UnigeneRecord.__init__ Bio.UniGene.UnigeneSTSRecord.__init__ Bio.UniGene.UnigeneSequenceRecord.__init__ Bio.UniGene._RecordConsumer.__init__ Bio.UniGene._Scanner.__init__ Bio.Wise.dnal.Statistics.__init__ Bio.Wise.psw.AlignmentColumn.__init__ Bio.Wise.psw.ColumnUnit.__init__ Bio.kNN.kNN.__init__ Bio.pairwise2.affine_penalty.__init__ Bio.pairwise2.dictionary_match.__init__ Bio.pairwise2.identity_match.__init__ BioSQL.BioSeq.DBSeq.__init__ BioSQL.BioSeq.DBSeqRecord.__init__ BioSQL.BioSeqDatabase.Adaptor.__init__ BioSQL.BioSeqDatabase.BioSeqDatabase.__init__ BioSQL.BioSeqDatabase.DBServer.__init__ BioSQL.DBUtils.Generic_dbutils.__init__ BioSQL.Loader.DatabaseLoader.__init__ BioSQL.Loader.DatabaseRemover.__init__" class="py-name" href="#" onclick="return doclink('link-29', '__init__', 'link-6');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">num_nodes</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt> <a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> </tt> <a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_next_layer</tt> <tt class="py-op">=</tt> <tt class="py-name">next_layer</tt> </tt> <a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_activation</tt> <tt class="py-op">=</tt> <tt class="py-name">activation</tt> </tt> <a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> </tt> <a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-comment"># set up the weights</tt> </tt> <a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">weights</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt> <a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">own_node</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-30', 'nodes', 'link-2');">nodes</a></tt><tt class="py-op">:</tt> </tt> <a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">other_node</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_next_layer</tt><tt class="py-op">.</tt><tt id="link-31" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-31', 'nodes', 'link-2');">nodes</a></tt><tt class="py-op">:</tt> </tt> <a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">weights</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">own_node</tt><tt class="py-op">,</tt> <tt class="py-name">other_node</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> \ </tt> <a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-name">random</tt><tt class="py-op">.</tt><tt class="py-name">randrange</tt><tt class="py-op">(</tt><tt class="py-op">-</tt><tt class="py-number">2.0</tt><tt class="py-op">,</tt> <tt class="py-number">2.0</tt><tt class="py-op">)</tt> </tt> <a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> </tt> <a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-comment"># set up the weight changes</tt> </tt> <a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">weight_changes</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt> <a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">own_node</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-32', 'nodes', 'link-2');">nodes</a></tt><tt class="py-op">:</tt> </tt> <a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">other_node</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_next_layer</tt><tt class="py-op">.</tt><tt id="link-33" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-33', 'nodes', 'link-2');">nodes</a></tt><tt class="py-op">:</tt> </tt> <a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">weight_changes</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">own_node</tt><tt class="py-op">,</tt> <tt class="py-name">other_node</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">0.0</tt> </tt> <a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> </tt> <a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-comment"># set up the calculated values for each node</tt> </tt> <a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-34" class="py-name"><a title="Bio.Crystal.Crystal.values Bio.Phylo.PhyloXML.Events.values Bio.SeqIO._index._IndexedSeqFileDict.values BioSQL.BioSeqDatabase.BioSeqDatabase.values BioSQL.BioSeqDatabase.DBServer.values" class="py-name" href="#" onclick="return doclink('link-34', 'values', 'link-11');">values</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt> <a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-35" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-35', 'node', 'link-12');">node</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-36" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-36', 'nodes', 'link-2');">nodes</a></tt><tt class="py-op">:</tt> </tt> <a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-comment"># bias node</tt> </tt> <a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-37" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-37', 'node', 'link-12');">node</a></tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt> <a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-38" class="py-name"><a title="Bio.Crystal.Crystal.values Bio.Phylo.PhyloXML.Events.values Bio.SeqIO._index._IndexedSeqFileDict.values BioSQL.BioSeqDatabase.BioSeqDatabase.values BioSQL.BioSeqDatabase.DBServer.values" class="py-name" href="#" onclick="return doclink('link-38', 'values', 'link-11');">values</a></tt><tt class="py-op">[</tt><tt id="link-39" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-39', 'node', 'link-12');">node</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt> <a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt> <a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name"><a title="Bio.Crystal.Crystal.values Bio.Phylo.PhyloXML.Events.values Bio.SeqIO._index._IndexedSeqFileDict.values BioSQL.BioSeqDatabase.BioSeqDatabase.values BioSQL.BioSeqDatabase.DBServer.values" class="py-name" href="#" onclick="return doclink('link-40', 'values', 'link-11');">values</a></tt><tt class="py-op">[</tt><tt id="link-41" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-41', 'node', 'link-12');">node</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt> </div><a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> </tt> <a name="HiddenLayer.update"></a><div id="HiddenLayer.update-def"><a name="L185"></a><tt class="py-lineno">185</tt> <a class="py-toggle" href="#" id="HiddenLayer.update-toggle" onclick="return toggle('HiddenLayer.update');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer-class.html#update">update</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">previous_layer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="HiddenLayer.update-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="HiddenLayer.update-expanded"><a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-docstring">"""Update the values of nodes from the previous layer info.</tt> </tt> <a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt> <a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"><tt class="py-docstring"> o previous_layer -- The previous layer in the network.</tt> </tt> <a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-comment"># update each node in this network</tt> </tt> <a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">update_node</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-42" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-42', 'nodes', 'link-2');">nodes</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt> <a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-comment"># sum up the weighted inputs from the previous network</tt> </tt> <a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt id="link-43" class="py-name" targets="Method Bio.Nexus.Nexus.StepMatrix.sum()=Bio.Nexus.Nexus.StepMatrix-class.html#sum,Method Bio.SubsMat.SeqMat.sum()=Bio.SubsMat.SeqMat-class.html#sum"><a title="Bio.Nexus.Nexus.StepMatrix.sum Bio.SubsMat.SeqMat.sum" class="py-name" href="#" onclick="return doclink('link-43', 'sum', 'link-43');">sum</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0.0</tt> </tt> <a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-44" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-44', 'node', 'link-12');">node</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">previous_layer</tt><tt class="py-op">.</tt><tt id="link-45" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-45', 'nodes', 'link-2');">nodes</a></tt><tt class="py-op">:</tt> </tt> <a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt id="link-46" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.sum Bio.SubsMat.SeqMat.sum" class="py-name" href="#" onclick="return doclink('link-46', 'sum', 'link-43');">sum</a></tt> <tt class="py-op">+=</tt> <tt class="py-op">(</tt><tt class="py-name">previous_layer</tt><tt class="py-op">.</tt><tt id="link-47" class="py-name"><a title="Bio.Crystal.Crystal.values Bio.Phylo.PhyloXML.Events.values Bio.SeqIO._index._IndexedSeqFileDict.values BioSQL.BioSeqDatabase.BioSeqDatabase.values BioSQL.BioSeqDatabase.DBServer.values" class="py-name" href="#" onclick="return doclink('link-47', 'values', 'link-11');">values</a></tt><tt class="py-op">[</tt><tt id="link-48" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-48', 'node', 'link-12');">node</a></tt><tt class="py-op">]</tt> <tt class="py-op">*</tt> </tt> <a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-name">previous_layer</tt><tt class="py-op">.</tt><tt class="py-name">weights</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt id="link-49" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-49', 'node', 'link-12');">node</a></tt><tt class="py-op">,</tt> <tt class="py-name">update_node</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt> <a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> </tt> <a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-50" class="py-name"><a title="Bio.Crystal.Crystal.values Bio.Phylo.PhyloXML.Events.values Bio.SeqIO._index._IndexedSeqFileDict.values BioSQL.BioSeqDatabase.BioSeqDatabase.values BioSQL.BioSeqDatabase.DBServer.values" class="py-name" href="#" onclick="return doclink('link-50', 'values', 'link-11');">values</a></tt><tt class="py-op">[</tt><tt class="py-name">update_node</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">_activation</tt><tt class="py-op">(</tt><tt id="link-51" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.sum Bio.SubsMat.SeqMat.sum" class="py-name" href="#" onclick="return doclink('link-51', 'sum', 'link-43');">sum</a></tt><tt class="py-op">)</tt> </tt> <a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> </tt> <a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-comment"># propogate the update to the next layer</tt> </tt> <a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_next_layer</tt><tt class="py-op">.</tt><tt id="link-52" class="py-name"><a title="Bio.Index._InMemoryIndex.update Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update Bio.Restriction._Update.Update.RebaseUpdate.update Bio.SeqIO._index._IndexedSeqFileDict.update Bio.SeqRecord._RestrictedDict.update" class="py-name" href="#" onclick="return doclink('link-52', 'update', 'link-22');">update</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt> </div><a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> </tt> <a name="HiddenLayer.backpropagate"></a><div id="HiddenLayer.backpropagate-def"><a name="L205"></a><tt class="py-lineno">205</tt> <a class="py-toggle" href="#" id="HiddenLayer.backpropagate-toggle" onclick="return toggle('HiddenLayer.backpropagate');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer-class.html#backpropagate">backpropagate</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">outputs</tt><tt class="py-op">,</tt> <tt class="py-param">learning_rate</tt><tt class="py-op">,</tt> <tt class="py-param">momentum</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="HiddenLayer.backpropagate-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="HiddenLayer.backpropagate-expanded"><a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt class="py-docstring">"""Recalculate all weights based on the last round of prediction.</tt> </tt> <a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt> <a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"><tt class="py-docstring"> o learning_rate -- The learning rate of the network</tt> </tt> <a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"><tt class="py-docstring"> o momentum - The amount of weight to place on the previous weight</tt> </tt> <a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"><tt class="py-docstring"> change.</tt> </tt> <a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"><tt class="py-docstring"> o outputs - The output values we are using to see how good our</tt> </tt> <a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"><tt class="py-docstring"> network is at predicting things.</tt> </tt> <a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt class="py-comment"># first backpropogate to the next layers</tt> </tt> <a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-name">next_errors</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_next_layer</tt><tt class="py-op">.</tt><tt id="link-53" class="py-name"><a title="Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.backpropagate Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.backpropagate Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.backpropagate" class="py-name" href="#" onclick="return doclink('link-53', 'backpropagate', 'link-23');">backpropagate</a></tt><tt class="py-op">(</tt><tt class="py-name">outputs</tt><tt class="py-op">,</tt> <tt class="py-name">learning_rate</tt><tt class="py-op">,</tt> </tt> <a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-name">momentum</tt><tt class="py-op">)</tt> </tt> <a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> </tt> <a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-comment"># --- update the weights</tt> </tt> <a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">this_node</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-54" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-54', 'nodes', 'link-2');">nodes</a></tt><tt class="py-op">:</tt> </tt> <a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">next_node</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_next_layer</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-55', 'nodes', 'link-2');">nodes</a></tt><tt class="py-op">:</tt> </tt> <a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> <tt class="py-name">error_deriv</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">next_errors</tt><tt class="py-op">[</tt><tt class="py-name">next_node</tt><tt class="py-op">]</tt> <tt class="py-op">*</tt> </tt> <a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-56" class="py-name"><a title="Bio.Crystal.Crystal.values Bio.Phylo.PhyloXML.Events.values Bio.SeqIO._index._IndexedSeqFileDict.values BioSQL.BioSeqDatabase.BioSeqDatabase.values BioSQL.BioSeqDatabase.DBServer.values" class="py-name" href="#" onclick="return doclink('link-56', 'values', 'link-11');">values</a></tt><tt class="py-op">[</tt><tt class="py-name">this_node</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt> <a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> </tt> <a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-name">delta</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">learning_rate</tt> <tt class="py-op">*</tt> <tt class="py-name">error_deriv</tt> <tt class="py-op">+</tt> </tt> <a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> <tt class="py-name">momentum</tt> <tt class="py-op">*</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">weight_changes</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">this_node</tt><tt class="py-op">,</tt> <tt class="py-name">next_node</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt> <a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> </tt> <a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-comment"># apply the change to the weight</tt> </tt> <a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">weights</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">this_node</tt><tt class="py-op">,</tt> <tt class="py-name">next_node</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">+=</tt> <tt class="py-name">delta</tt> </tt> <a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> </tt> <a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> <tt class="py-comment"># remember the weight change for next time</tt> </tt> <a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">weight_changes</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">this_node</tt><tt class="py-op">,</tt> <tt class="py-name">next_node</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">delta</tt> </tt> <a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> </tt> <a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> <tt class="py-comment"># --- calculate error terms</tt> </tt> <a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> <tt class="py-name">errors</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt> <a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">error_node</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-57" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-57', 'nodes', 'link-2');">nodes</a></tt><tt class="py-op">:</tt> </tt> <a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-comment"># get the error info propogated from the next layer</tt> </tt> <a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-name">previous_error</tt> <tt class="py-op">=</tt> <tt class="py-number">0.0</tt> </tt> <a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">next_node</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_next_layer</tt><tt class="py-op">.</tt><tt id="link-58" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-58', 'nodes', 'link-2');">nodes</a></tt><tt class="py-op">:</tt> </tt> <a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-name">previous_error</tt> <tt class="py-op">+=</tt> <tt class="py-op">(</tt><tt class="py-name">next_errors</tt><tt class="py-op">[</tt><tt class="py-name">next_node</tt><tt class="py-op">]</tt> <tt class="py-op">*</tt> </tt> <a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">weights</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">error_node</tt><tt class="py-op">,</tt> <tt class="py-name">next_node</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt> <a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> </tt> <a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> <tt class="py-comment"># get the correction factor</tt> </tt> <a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> <tt class="py-name">corr_factor</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-59" class="py-name"><a title="Bio.Crystal.Crystal.values Bio.Phylo.PhyloXML.Events.values Bio.SeqIO._index._IndexedSeqFileDict.values BioSQL.BioSeqDatabase.BioSeqDatabase.values BioSQL.BioSeqDatabase.DBServer.values" class="py-name" href="#" onclick="return doclink('link-59', 'values', 'link-11');">values</a></tt><tt class="py-op">[</tt><tt class="py-name">error_node</tt><tt class="py-op">]</tt> <tt class="py-op">*</tt> </tt> <a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-number">1</tt> <tt class="py-op">-</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-60" class="py-name"><a title="Bio.Crystal.Crystal.values Bio.Phylo.PhyloXML.Events.values Bio.SeqIO._index._IndexedSeqFileDict.values BioSQL.BioSeqDatabase.BioSeqDatabase.values BioSQL.BioSeqDatabase.DBServer.values" class="py-name" href="#" onclick="return doclink('link-60', 'values', 'link-11');">values</a></tt><tt class="py-op">[</tt><tt class="py-name">error_node</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt> <a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> </tt> <a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-comment"># calculate the error</tt> </tt> <a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> <tt class="py-name">errors</tt><tt class="py-op">[</tt><tt class="py-name">error_node</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">previous_error</tt> <tt class="py-op">*</tt> <tt class="py-name">corr_factor</tt> </tt> <a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> </tt> <a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">errors</tt> </tt> </div></div><a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> </tt> <a name="OutputLayer"></a><div id="OutputLayer-def"><a name="L255"></a><tt class="py-lineno">255</tt> <a class="py-toggle" href="#" id="OutputLayer-toggle" onclick="return toggle('OutputLayer');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer-class.html">OutputLayer</a><tt class="py-op">(</tt><tt class="py-base-class">AbstractLayer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="OutputLayer-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="OutputLayer-expanded"><a name="OutputLayer.__init__"></a><div id="OutputLayer.__init__-def"><a name="L256"></a><tt class="py-lineno">256</tt> <a class="py-toggle" href="#" id="OutputLayer.__init__-toggle" onclick="return toggle('OutputLayer.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer-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">num_nodes</tt><tt class="py-op">,</tt> <tt class="py-param">activation</tt> <tt class="py-op">=</tt> <tt id="link-61" class="py-name"><a title="Bio.NeuralNetwork.BackPropagation.Layer.logistic_function" class="py-name" href="#" onclick="return doclink('link-61', 'logistic_function', 'link-27');">logistic_function</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="OutputLayer.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="OutputLayer.__init__-expanded"><a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> <tt class="py-docstring">"""Initialize the Output Layer.</tt> </tt> <a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt> <a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"><tt class="py-docstring"> o num_nodes -- The number of nodes in this layer. This corresponds</tt> </tt> <a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"><tt class="py-docstring"> to the number of outputs in the neural network.</tt> </tt> <a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"><tt class="py-docstring"> o activation -- The transformation function used to transform</tt> </tt> <a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"><tt class="py-docstring"> predicted values.</tt> </tt> <a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> <tt id="link-62" class="py-name"><a title="Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer" class="py-name" href="#" onclick="return doclink('link-62', 'AbstractLayer', 'link-5');">AbstractLayer</a></tt><tt class="py-op">.</tt><tt id="link-63" class="py-name"><a title="Bio.Affy.CelFile.CelConsumer.__init__ Bio.Affy.CelFile.CelParser.__init__ Bio.Affy.CelFile.CelRecord.__init__ Bio.Affy.CelFile.CelScanner.__init__ Bio.Affy.CelFile.Record.__init__ Bio.Align.AlignInfo.PSSM.__init__ Bio.Align.AlignInfo.SummaryInfo.__init__ Bio.Align.Applications._Clustalw.ClustalwCommandline.__init__ Bio.Align.Applications._Dialign.DialignCommandline.__init__ Bio.Align.Applications._Mafft.MafftCommandline.__init__ Bio.Align.Applications._Muscle.MuscleCommandline.__init__ Bio.Align.Applications._Prank.PrankCommandline.__init__ Bio.Align.Applications._Probcons.ProbconsCommandline.__init__ Bio.Align.Applications._TCoffee.TCoffeeCommandline.__init__ Bio.Align.Generic.Alignment.__init__ Bio.Align.MultipleSeqAlignment.__init__ Bio.AlignIO.Interfaces.AlignmentIterator.__init__ Bio.AlignIO.Interfaces.AlignmentWriter.__init__ Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__ Bio.Alphabet.AlphabetEncoder.__init__ Bio.Alphabet.Gapped.__init__ Bio.Alphabet.HasStopCodon.__init__ Bio.Application.AbstractCommandline.__init__ Bio.Application.ApplicationError.__init__ Bio.Application._AbstractParameter.__init__ Bio.Application._Argument.__init__ Bio.Application._Option.__init__ Bio.Application._Switch.__init__ Bio.Blast.Applications.BlastallCommandline.__init__ Bio.Blast.Applications.BlastpgpCommandline.__init__ Bio.Blast.Applications.FastacmdCommandline.__init__ Bio.Blast.Applications.NcbiblastformatterCommandline.__init__ Bio.Blast.Applications.NcbiblastnCommandline.__init__ Bio.Blast.Applications.NcbiblastpCommandline.__init__ Bio.Blast.Applications.NcbiblastxCommandline.__init__ Bio.Blast.Applications.NcbipsiblastCommandline.__init__ Bio.Blast.Applications.NcbirpsblastCommandline.__init__ Bio.Blast.Applications.NcbirpstblastnCommandline.__init__ Bio.Blast.Applications.NcbitblastnCommandline.__init__ Bio.Blast.Applications.NcbitblastxCommandline.__init__ Bio.Blast.Applications.RpsBlastCommandline.__init__ Bio.Blast.Applications._BlastAllOrPgpCommandLine.__init__ Bio.Blast.Applications._BlastCommandLine.__init__ Bio.Blast.Applications._NcbibaseblastCommandline.__init__ Bio.Blast.Applications._Ncbiblast2SeqCommandline.__init__ Bio.Blast.Applications._NcbiblastCommandline.__init__ Bio.Blast.Applications._NcbiblastMain2SeqCommandline.__init__ Bio.Blast.NCBIStandalone.BlastErrorParser.__init__ Bio.Blast.NCBIStandalone.BlastParser.__init__ Bio.Blast.NCBIStandalone.Iterator.__init__ Bio.Blast.NCBIStandalone.PSIBlastParser.__init__ Bio.Blast.NCBIStandalone._BlastConsumer.__init__ Bio.Blast.NCBIStandalone._BlastErrorConsumer.__init__ Bio.Blast.NCBIStandalone._PSIBlastConsumer.__init__ Bio.Blast.NCBIXML.BlastParser.__init__ Bio.Blast.NCBIXML._XMLparser.__init__ Bio.Blast.ParseBlastTable.BlastTableEntry.__init__ Bio.Blast.ParseBlastTable.BlastTableReader.__init__ Bio.Blast.ParseBlastTable.BlastTableRec.__init__ Bio.Blast.Record.Alignment.__init__ Bio.Blast.Record.Blast.__init__ Bio.Blast.Record.DatabaseReport.__init__ Bio.Blast.Record.Description.__init__ Bio.Blast.Record.HSP.__init__ Bio.Blast.Record.Header.__init__ Bio.Blast.Record.MultipleAlignment.__init__ Bio.Blast.Record.PSIBlast.__init__ Bio.Blast.Record.Parameters.__init__ Bio.Blast.Record.Round.__init__ Bio.CAPS.CAPSMap.__init__ Bio.CAPS.DifferentialCutsite.__init__ Bio.Cluster.Record.__init__ Bio.Compass.Iterator.__init__ Bio.Compass.Record.__init__ Bio.Compass.RecordParser.__init__ Bio.Compass._Consumer.__init__ Bio.Compass._Scanner.__init__ Bio.Crystal.Chain.__init__ Bio.Crystal.Crystal.__init__ Bio.Crystal.Hetero.__init__ Bio.Data.CodonTable.AmbiguousCodonTable.__init__ Bio.Data.CodonTable.AmbiguousForwardTable.__init__ Bio.Data.CodonTable.CodonTable.__init__ Bio.Data.CodonTable.NCBICodonTable.__init__ Bio.DocSQL.Create.__init__ Bio.DocSQL.Insert.__init__ Bio.DocSQL.IterationCursor.__init__ Bio.DocSQL.Query.__init__ Bio.DocSQL.QueryAll.__init__ Bio.DocSQL.QueryGeneric.__init__ Bio.DocSQL.QueryRow.__init__ Bio.DocSQL.QuerySingle.__init__ Bio.Emboss.Applications.DiffseqCommandline.__init__ Bio.Emboss.Applications.EInvertedCommandline.__init__ Bio.Emboss.Applications.ETandemCommandline.__init__ Bio.Emboss.Applications.Est2GenomeCommandline.__init__ Bio.Emboss.Applications.FConsenseCommandline.__init__ Bio.Emboss.Applications.FDNADistCommandline.__init__ Bio.Emboss.Applications.FDNAParsCommandline.__init__ Bio.Emboss.Applications.FNeighborCommandline.__init__ Bio.Emboss.Applications.FProtDistCommandline.__init__ Bio.Emboss.Applications.FProtParsCommandline.__init__ Bio.Emboss.Applications.FSeqBootCommandline.__init__ Bio.Emboss.Applications.FTreeDistCommandline.__init__ Bio.Emboss.Applications.FuzznucCommandline.__init__ Bio.Emboss.Applications.IepCommandline.__init__ Bio.Emboss.Applications.NeedleCommandline.__init__ Bio.Emboss.Applications.PalindromeCommandline.__init__ Bio.Emboss.Applications.Primer3Commandline.__init__ Bio.Emboss.Applications.PrimerSearchCommandline.__init__ Bio.Emboss.Applications.SeqmatchallCommandline.__init__ Bio.Emboss.Applications.SeqretCommandline.__init__ Bio.Emboss.Applications.TranalignCommandline.__init__ Bio.Emboss.Applications.WaterCommandline.__init__ Bio.Emboss.Applications._EmbossCommandLine.__init__ Bio.Emboss.Applications._EmbossMinimalCommandLine.__init__ Bio.Emboss.Primer3.Primers.__init__ Bio.Emboss.Primer3.Record.__init__ Bio.Emboss.PrimerSearch.Amplifier.__init__ Bio.Emboss.PrimerSearch.InputRecord.__init__ Bio.Emboss.PrimerSearch.OutputRecord.__init__ Bio.Entrez.Parser.CorruptedXMLError.__init__ Bio.Entrez.Parser.DataHandler.__init__ Bio.Entrez.Parser.NotXMLError.__init__ Bio.Entrez.Parser.StructureElement.__init__ Bio.Entrez.Parser.ValidationError.__init__ Bio.ExPASy.Enzyme.Record.__init__ Bio.ExPASy.Prodoc.Record.__init__ Bio.ExPASy.Prodoc.Reference.__init__ Bio.ExPASy.Prosite.Record.__init__ Bio.ExPASy.ScanProsite.ContentHandler.__init__ Bio.ExPASy.ScanProsite.Parser.__init__ Bio.ExPASy.ScanProsite.Record.__init__ Bio.FSSP.FSSPAlignDict.__init__ Bio.FSSP.FSSPAlignRec.__init__ Bio.FSSP.FSSPHeader.__init__ Bio.FSSP.FSSPSumRec.__init__ Bio.FSSP.FSSPTools.FSSPMultAlign.__init__ Bio.FSSP.PosAlign.__init__ Bio.FSSP.fssp_rec.fff_rec.__init__ Bio.File.SGMLStripper.MyParser.__init__ Bio.File.SGMLStripper.__init__ Bio.File.UndoHandle.__init__ Bio.GA.Crossover.General.SafeFitnessCrossover.__init__ Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover.__init__ Bio.GA.Crossover.GeneralPoint.InterleaveCrossover.__init__ Bio.GA.Crossover.Point.SinglePointCrossover.__init__ Bio.GA.Crossover.TwoPoint.TwoPointCrossover.__init__ Bio.GA.Crossover.Uniform.UniformCrossover.__init__ Bio.GA.Evolver.GenerationEvolver.__init__ Bio.GA.Evolver.SteadyStateEvolver.__init__ Bio.GA.Mutation.General.SafeFitnessMutation.__init__ Bio.GA.Mutation.Simple.ConversionMutation.__init__ Bio.GA.Mutation.Simple.SinglePositionMutation.__init__ Bio.GA.Organism.Organism.__init__ Bio.GA.Repair.Stabilizing.AmbiguousRepair.__init__ Bio.GA.Selection.Abstract.AbstractSelection.__init__ Bio.GA.Selection.Diversity.DiversitySelection.__init__ Bio.GA.Selection.RouletteWheel.RouletteWheelSelection.__init__ Bio.GA.Selection.Tournament.TournamentSelection.__init__ Bio.GenBank.FeatureParser.__init__ Bio.GenBank.Iterator.__init__ Bio.GenBank.LocationParser.AbsoluteLocation.__init__ Bio.GenBank.LocationParser.Between.__init__ Bio.GenBank.LocationParser.FeatureName.__init__ Bio.GenBank.LocationParser.Function.__init__ Bio.GenBank.LocationParser.HighBound.__init__ Bio.GenBank.LocationParser.Integer.__init__ Bio.GenBank.LocationParser.LocationParser.__init__ Bio.GenBank.LocationParser.LocationScanner.__init__ Bio.GenBank.LocationParser.LowBound.__init__ Bio.GenBank.LocationParser.Path.__init__ Bio.GenBank.LocationParser.Range.__init__ Bio.GenBank.LocationParser.Symbol.__init__ Bio.GenBank.LocationParser.Token.__init__ Bio.GenBank.LocationParser.TwoBound.__init__ Bio.GenBank.Record.Feature.__init__ Bio.GenBank.Record.Qualifier.__init__ Bio.GenBank.Record.Record.__init__ Bio.GenBank.Record.Reference.__init__ Bio.GenBank.RecordParser.__init__ Bio.GenBank.Scanner.InsdcScanner.__init__ Bio.GenBank._BaseGenBankConsumer.__init__ Bio.GenBank._FeatureConsumer.__init__ Bio.GenBank._RecordConsumer.__init__ Bio.GenBank.utils.FeatureValueCleaner.__init__ Bio.Geo.Record.Record.__init__ Bio.Graphics.BasicChromosome.Chromosome.__init__ Bio.Graphics.BasicChromosome.ChromosomeSegment.__init__ Bio.Graphics.BasicChromosome.Organism.__init__ Bio.Graphics.BasicChromosome.TelomereSegment.__init__ Bio.Graphics.BasicChromosome._ChromosomeComponent.__init__ Bio.Graphics.Comparative.ComparativeScatterPlot.__init__ Bio.Graphics.DisplayRepresentation.ChromosomeCounts.__init__ Bio.Graphics.Distribution.BarChartDistribution.__init__ Bio.Graphics.Distribution.DistributionPage.__init__ Bio.Graphics.Distribution.LineDistribution.__init__ Bio.Graphics.GenomeDiagram._AbstractDrawer.AbstractDrawer.__init__ Bio.Graphics.GenomeDiagram._CircularDrawer.CircularDrawer.__init__ Bio.Graphics.GenomeDiagram._Colors.ColorTranslator.__init__ Bio.Graphics.GenomeDiagram._Diagram.Diagram.__init__ Bio.Graphics.GenomeDiagram._Feature.Feature.__init__ Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.__init__ Bio.Graphics.GenomeDiagram._Graph.GraphData.__init__ Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.__init__ Bio.Graphics.GenomeDiagram._LinearDrawer.LinearDrawer.__init__ Bio.Graphics.GenomeDiagram._Track.Track.__init__ Bio.HMM.DynamicProgramming.AbstractDPAlgorithms.__init__ Bio.HMM.DynamicProgramming.LogDPAlgorithms.__init__ Bio.HMM.DynamicProgramming.ScaledDPAlgorithms.__init__ Bio.HMM.MarkovModel.HiddenMarkovModel.__init__ Bio.HMM.MarkovModel.MarkovModelBuilder.__init__ Bio.HMM.Trainer.AbstractTrainer.__init__ Bio.HMM.Trainer.BaumWelchTrainer.__init__ Bio.HMM.Trainer.KnownStateTrainer.__init__ Bio.HMM.Trainer.TrainingSequence.__init__ Bio.HotRand.HotCache.__init__ Bio.HotRand.HotRandom.__init__ Bio.Index._InMemoryIndex.__init__ Bio.Index._ShelveIndex.__init__ Bio.KDTree.KDTree.KDTree.__init__ Bio.KEGG.Compound.Record.__init__ Bio.KEGG.Enzyme.Record.__init__ Bio.LogisticRegression.LogisticRegression.__init__ Bio.MarkovModel.MarkovModel.__init__ Bio.MaxEntropy.MaxEntropy.__init__ Bio.Motif.Applications._AlignAce.AlignAceCommandline.__init__ Bio.Motif.Applications._AlignAce.CompareAceCommandline.__init__ Bio.Motif.Parsers.AlignAce.Record.__init__ Bio.Motif.Parsers.MAST.Record.__init__ Bio.Motif.Parsers.MEME.MEMEInstance.__init__ Bio.Motif.Parsers.MEME.MEMEMotif.__init__ Bio.Motif.Parsers.MEME.MEMERecord.__init__ Bio.Motif.Thresholds.ScoreDistribution.__init__ Bio.Motif._Motif.Motif.__init__ Bio.NMR.xpktools.Peaklist.__init__ Bio.NMR.xpktools.XpkEntry.__init__ Bio.NaiveBayes.NaiveBayes.__init__ Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer.__init__ Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.__init__ Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.__init__ Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.__init__ Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork.__init__ Bio.NeuralNetwork.Gene.Motif.MotifCoder.__init__ Bio.NeuralNetwork.Gene.Motif.MotifFinder.__init__ Bio.NeuralNetwork.Gene.Pattern.PatternIO.__init__ Bio.NeuralNetwork.Gene.Pattern.PatternRepository.__init__ Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness.__init__ Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder.__init__ Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness.__init__ Bio.NeuralNetwork.Gene.Schema.RandomMotifGenerator.__init__ Bio.NeuralNetwork.Gene.Schema.Schema.__init__ Bio.NeuralNetwork.Gene.Schema.SchemaCoder.__init__ Bio.NeuralNetwork.Gene.Schema.SchemaFactory.__init__ Bio.NeuralNetwork.Gene.Schema.SchemaFinder.__init__ Bio.NeuralNetwork.Gene.Schema.SimpleFinisher.__init__ Bio.NeuralNetwork.Gene.Signature.SignatureCoder.__init__ Bio.NeuralNetwork.Gene.Signature.SignatureFinder.__init__ Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop.__init__ Bio.NeuralNetwork.Training.ExampleManager.__init__ Bio.NeuralNetwork.Training.TrainingExample.__init__ Bio.Nexus.Nexus.Block.__init__ Bio.Nexus.Nexus.CharBuffer.__init__ Bio.Nexus.Nexus.Commandline.__init__ Bio.Nexus.Nexus.Nexus.__init__ Bio.Nexus.Nexus.StepMatrix.__init__ Bio.Nexus.Nodes.Chain.__init__ Bio.Nexus.Nodes.Node.__init__ Bio.Nexus.Trees.NodeData.__init__ Bio.Nexus.Trees.Tree.__init__ Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap.__init__ Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__init__ Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap.__init__ Bio.PDB.Atom.Atom.__init__ Bio.PDB.Atom.DisorderedAtom.__init__ Bio.PDB.Chain.Chain.__init__ Bio.PDB.DSSP'.DSSP.__init__ Bio.PDB.Dice.ChainSelector.__init__ Bio.PDB.Entity.DisorderedEntityWrapper.__init__ Bio.PDB.Entity.Entity.__init__ Bio.PDB.FragmentMapper'.Fragment.__init__ Bio.PDB.FragmentMapper'.FragmentMapper.__init__ Bio.PDB.HSExposure.ExposureCN.__init__ Bio.PDB.HSExposure.HSExposureCA.__init__ Bio.PDB.HSExposure.HSExposureCB.__init__ Bio.PDB.HSExposure._AbstractHSExposure.__init__ Bio.PDB.MMCIF2Dict.MMCIF2Dict.__init__ Bio.PDB.Model.Model.__init__ Bio.PDB.NACCESS.NACCESS.__init__ Bio.PDB.NACCESS.NACCESS_atomic.__init__ Bio.PDB.NeighborSearch.NeighborSearch.__init__ Bio.PDB.PDBIO'.PDBIO.__init__ Bio.PDB.PDBList'.PDBList.__init__ Bio.PDB.PDBParser'.PDBParser.__init__ Bio.PDB.PSEA.PSEA.__init__ Bio.PDB.Polypeptide.CaPPBuilder.__init__ Bio.PDB.Polypeptide.PPBuilder.__init__ Bio.PDB.Polypeptide._PPBuilder.__init__ Bio.PDB.Residue.DisorderedResidue.__init__ Bio.PDB.Residue.Residue.__init__ Bio.PDB.ResidueDepth'.ResidueDepth.__init__ Bio.PDB.Structure.Structure.__init__ Bio.PDB.StructureAlignment'.StructureAlignment.__init__ Bio.PDB.StructureBuilder.StructureBuilder.__init__ Bio.PDB.Superimposer'.Superimposer.__init__ Bio.PDB.Vector'.Vector.__init__ Bio.ParserSupport.EventGenerator.__init__ Bio.ParserSupport.SGMLStrippingConsumer.__init__ Bio.ParserSupport.TaggingConsumer.__init__ Bio.Parsers.spark.GenericASTBuilder.__init__ Bio.Parsers.spark.GenericASTMatcher.__init__ Bio.Parsers.spark.GenericASTTraversal.__init__ Bio.Parsers.spark.GenericParser.__init__ Bio.Parsers.spark.GenericScanner.__init__ Bio.Pathway.Network.__init__ Bio.Pathway.Reaction.__init__ Bio.Pathway.Rep.Graph.Graph.__init__ Bio.Pathway.Rep.HashSet.HashSet.__init__ Bio.Pathway.Rep.MultiGraph.MultiGraph.__init__ Bio.Pathway.System.__init__ Bio.Phylo.Applications._Phyml.PhymlCommandline.__init__ Bio.Phylo.BaseTree.Clade.__init__ Bio.Phylo.BaseTree.Tree.__init__ Bio.Phylo.Newick.Clade.__init__ Bio.Phylo.Newick.Tree.__init__ Bio.Phylo.NewickIO.Parser.__init__ Bio.Phylo.NewickIO.Writer.__init__ Bio.Phylo.PAML._paml.Paml.__init__ Bio.Phylo.PAML.baseml.Baseml.__init__ Bio.Phylo.PAML.codeml.Codeml.__init__ Bio.Phylo.PAML.yn00.Yn00.__init__ Bio.Phylo.PhyloXML.Accession.__init__ Bio.Phylo.PhyloXML.Annotation.__init__ Bio.Phylo.PhyloXML.BinaryCharacters.__init__ Bio.Phylo.PhyloXML.BranchColor.__init__ Bio.Phylo.PhyloXML.Clade.__init__ Bio.Phylo.PhyloXML.CladeRelation.__init__ Bio.Phylo.PhyloXML.Confidence.__init__ Bio.Phylo.PhyloXML.Date.__init__ Bio.Phylo.PhyloXML.Distribution.__init__ Bio.Phylo.PhyloXML.DomainArchitecture.__init__ Bio.Phylo.PhyloXML.Events.__init__ Bio.Phylo.PhyloXML.Id.__init__ Bio.Phylo.PhyloXML.MolSeq.__init__ Bio.Phylo.PhyloXML.Other.__init__ Bio.Phylo.PhyloXML.Phylogeny.__init__ Bio.Phylo.PhyloXML.Phyloxml.__init__ Bio.Phylo.PhyloXML.Point.__init__ Bio.Phylo.PhyloXML.Polygon.__init__ Bio.Phylo.PhyloXML.Property.__init__ Bio.Phylo.PhyloXML.ProteinDomain.__init__ Bio.Phylo.PhyloXML.Reference.__init__ Bio.Phylo.PhyloXML.Sequence.__init__ Bio.Phylo.PhyloXML.SequenceRelation.__init__ Bio.Phylo.PhyloXML.Taxonomy.__init__ Bio.Phylo.PhyloXML.Uri.__init__ Bio.Phylo.PhyloXMLIO.Parser.__init__ Bio.Phylo.PhyloXMLIO.Writer.__init__ Bio.PopGen.Async.Async.__init__ Bio.PopGen.Async.DirectoryRetriever.__init__ Bio.PopGen.Async.FileRetriever.__init__ Bio.PopGen.Async.Local.Local.__init__ Bio.PopGen.FDist.Async.FDistAsync.__init__ Bio.PopGen.FDist.Async.SplitFDist.__init__ Bio.PopGen.FDist.Controller.FDistController.__init__ Bio.PopGen.FDist.Record.__init__ Bio.PopGen.GenePop.Controller.GenePopController.__init__ Bio.PopGen.GenePop.Controller._FileIterator.__init__ Bio.PopGen.GenePop.Controller._GenePopCommandline.__init__ Bio.PopGen.GenePop.EasyController.EasyController.__init__ Bio.PopGen.GenePop.FileParser.FileRecord.__init__ Bio.PopGen.GenePop.LargeFileParser.Record.__init__ Bio.PopGen.GenePop.Record.__init__ Bio.PopGen.SimCoal.Async.SimCoalCache.__init__ Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__ Bio.PopGen.SimCoal.Controller.SimCoalController.__init__ Bio.Restriction.PrintFormat.PrintFormat.__init__ Bio.Restriction.Restriction.Analysis.__init__ Bio.Restriction.Restriction.FormattedSeq.__init__ Bio.Restriction.Restriction.RestrictionBatch.__init__ Bio.Restriction.Restriction.RestrictionType.__init__ Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__ Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.__init__ Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__ Bio.Restriction._Update.Update.ConnectionError.__init__ Bio.Restriction._Update.Update.FtpNameError.__init__ Bio.Restriction._Update.Update.FtpPasswordError.__init__ Bio.Restriction._Update.Update.RebaseUpdate.__init__ Bio.SCOP.Astral.__init__ Bio.SCOP.Cla.Index.__init__ Bio.SCOP.Cla.Record.__init__ Bio.SCOP.Des.Record.__init__ Bio.SCOP.Dom.Record.__init__ Bio.SCOP.Domain.__init__ Bio.SCOP.Hie.Record.__init__ Bio.SCOP.Node.__init__ Bio.SCOP.Raf.Res.__init__ Bio.SCOP.Raf.SeqMap.__init__ Bio.SCOP.Raf.SeqMapIndex.__init__ Bio.SCOP.Residues'.Residues.__init__ Bio.SCOP.Scop.__init__ Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__ Bio.Search.Algorithm.__init__ Bio.Search.Database.__init__ Bio.Search.HSP.__init__ Bio.Search.HSPSeq.__init__ Bio.Search.Hit.__init__ Bio.Search.HomologySeq.__init__ Bio.Search.Query.__init__ Bio.Search.Search.__init__ Bio.Search.TableInfo.__init__ Bio.Search._SeqLength.__init__ Bio.Seq.MutableSeq.__init__ Bio.Seq.Seq.__init__ Bio.Seq.UnknownSeq.__init__ Bio.SeqFeature.AbstractPosition.__init__ Bio.SeqFeature.AfterPosition.__init__ Bio.SeqFeature.BeforePosition.__init__ Bio.SeqFeature.BetweenPosition.__init__ Bio.SeqFeature.ExactPosition.__init__ Bio.SeqFeature.FeatureLocation.__init__ Bio.SeqFeature.OneOfPosition.__init__ Bio.SeqFeature.PositionGap.__init__ Bio.SeqFeature.Reference.__init__ Bio.SeqFeature.SeqFeature.__init__ Bio.SeqFeature.UnknownPosition.__init__ Bio.SeqFeature.WithinPosition.__init__ Bio.SeqIO.FastaIO.FastaWriter.__init__ Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__ Bio.SeqIO.Interfaces.SequenceIterator.__init__ Bio.SeqIO.Interfaces.SequenceWriter.__init__ Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__ Bio.SeqIO.PhdIO.PhdWriter.__init__ Bio.SeqIO.QualityIO.QualPhredWriter.__init__ Bio.SeqIO.SeqXmlIO.SeqXmlIterator.__init__ Bio.SeqIO.SeqXmlIO.SeqXmlWriter.__init__ Bio.SeqIO.SeqXmlIO.XMLRecordIterator.__init__ Bio.SeqIO.SffIO.SffWriter.__init__ Bio.SeqIO.SffIO._AddTellHandle.__init__ Bio.SeqIO.UniprotIO.Parser.__init__ Bio.SeqIO._index.IntelliGeneticsRandomAccess.__init__ Bio.SeqIO._index.SeqFileRandomAccess.__init__ Bio.SeqIO._index.SequentialSeqFileRandomAccess.__init__ Bio.SeqIO._index.SffRandomAccess.__init__ Bio.SeqIO._index._IndexedSeqFileDict.__init__ Bio.SeqIO._index._SQLiteManySeqFilesDict.__init__ Bio.SeqRecord.SeqRecord.__init__ Bio.SeqRecord._RestrictedDict.__init__ Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__ Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__ Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__ Bio.Sequencing.Ace.ACEFileRecord.__init__ Bio.Sequencing.Ace.Contig.__init__ Bio.Sequencing.Ace.Reads.__init__ Bio.Sequencing.Ace.af.__init__ Bio.Sequencing.Ace.bs.__init__ Bio.Sequencing.Ace.ct.__init__ Bio.Sequencing.Ace.ds.__init__ Bio.Sequencing.Ace.qa.__init__ Bio.Sequencing.Ace.rd.__init__ Bio.Sequencing.Ace.rt.__init__ Bio.Sequencing.Ace.wa.__init__ Bio.Sequencing.Ace.wr.__init__ Bio.Sequencing.Applications._Novoalign.NovoalignCommandline.__init__ Bio.Sequencing.Phd.Record.__init__ Bio.SubsMat.FreqTable.FreqTable.__init__ Bio.SubsMat.SeqMat.__init__ Bio.SwissProt.KeyWList.Record.__init__ Bio.SwissProt.Record.__init__ Bio.SwissProt.Reference.__init__ Bio.UniGene.Iterator.__init__ Bio.UniGene.ProtsimLine.__init__ Bio.UniGene.Record.__init__ Bio.UniGene.RecordParser.__init__ Bio.UniGene.STSLine.__init__ Bio.UniGene.SequenceLine.__init__ Bio.UniGene.UnigeneProtsimRecord.__init__ Bio.UniGene.UnigeneRecord.__init__ Bio.UniGene.UnigeneSTSRecord.__init__ Bio.UniGene.UnigeneSequenceRecord.__init__ Bio.UniGene._RecordConsumer.__init__ Bio.UniGene._Scanner.__init__ Bio.Wise.dnal.Statistics.__init__ Bio.Wise.psw.AlignmentColumn.__init__ Bio.Wise.psw.ColumnUnit.__init__ Bio.kNN.kNN.__init__ Bio.pairwise2.affine_penalty.__init__ Bio.pairwise2.dictionary_match.__init__ Bio.pairwise2.identity_match.__init__ BioSQL.BioSeq.DBSeq.__init__ BioSQL.BioSeq.DBSeqRecord.__init__ BioSQL.BioSeqDatabase.Adaptor.__init__ BioSQL.BioSeqDatabase.BioSeqDatabase.__init__ BioSQL.BioSeqDatabase.DBServer.__init__ BioSQL.DBUtils.Generic_dbutils.__init__ BioSQL.Loader.DatabaseLoader.__init__ BioSQL.Loader.DatabaseRemover.__init__" class="py-name" href="#" onclick="return doclink('link-63', '__init__', 'link-6');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">num_nodes</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt> <a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> </tt> <a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_activation</tt> <tt class="py-op">=</tt> <tt class="py-name">activation</tt> </tt> <a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> </tt> <a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-64" class="py-name"><a title="Bio.Crystal.Crystal.values Bio.Phylo.PhyloXML.Events.values Bio.SeqIO._index._IndexedSeqFileDict.values BioSQL.BioSeqDatabase.BioSeqDatabase.values BioSQL.BioSeqDatabase.DBServer.values" class="py-name" href="#" onclick="return doclink('link-64', 'values', 'link-11');">values</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt> <a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-65" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-65', 'node', 'link-12');">node</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-66" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-66', 'nodes', 'link-2');">nodes</a></tt><tt class="py-op">:</tt> </tt> <a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-67" class="py-name"><a title="Bio.Crystal.Crystal.values Bio.Phylo.PhyloXML.Events.values Bio.SeqIO._index._IndexedSeqFileDict.values BioSQL.BioSeqDatabase.BioSeqDatabase.values BioSQL.BioSeqDatabase.DBServer.values" class="py-name" href="#" onclick="return doclink('link-67', 'values', 'link-11');">values</a></tt><tt class="py-op">[</tt><tt id="link-68" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-68', 'node', 'link-12');">node</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt> </div><a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> </tt> <a name="OutputLayer.update"></a><div id="OutputLayer.update-def"><a name="L275"></a><tt class="py-lineno">275</tt> <a class="py-toggle" href="#" id="OutputLayer.update-toggle" onclick="return toggle('OutputLayer.update');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer-class.html#update">update</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">previous_layer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="OutputLayer.update-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="OutputLayer.update-expanded"><a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> <tt class="py-docstring">"""Update the value of output nodes from the previous layers.</tt> </tt> <a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt> <a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"><tt class="py-docstring"> o previous_layer -- The hidden layer preceeding this.</tt> </tt> <a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> <tt class="py-comment"># update all of the nodes in this layer</tt> </tt> <a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">update_node</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-69" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-69', 'nodes', 'link-2');">nodes</a></tt><tt class="py-op">:</tt> </tt> <a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> <tt class="py-comment"># sum up the contribution from all of the previous inputs</tt> </tt> <a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> <tt id="link-70" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.sum Bio.SubsMat.SeqMat.sum" class="py-name" href="#" onclick="return doclink('link-70', 'sum', 'link-43');">sum</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0.0</tt> </tt> <a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-71" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-71', 'node', 'link-12');">node</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">previous_layer</tt><tt class="py-op">.</tt><tt id="link-72" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-72', 'nodes', 'link-2');">nodes</a></tt><tt class="py-op">:</tt> </tt> <a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> <tt id="link-73" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.sum Bio.SubsMat.SeqMat.sum" class="py-name" href="#" onclick="return doclink('link-73', 'sum', 'link-43');">sum</a></tt> <tt class="py-op">+=</tt> <tt class="py-op">(</tt><tt class="py-name">previous_layer</tt><tt class="py-op">.</tt><tt id="link-74" class="py-name"><a title="Bio.Crystal.Crystal.values Bio.Phylo.PhyloXML.Events.values Bio.SeqIO._index._IndexedSeqFileDict.values BioSQL.BioSeqDatabase.BioSeqDatabase.values BioSQL.BioSeqDatabase.DBServer.values" class="py-name" href="#" onclick="return doclink('link-74', 'values', 'link-11');">values</a></tt><tt class="py-op">[</tt><tt id="link-75" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-75', 'node', 'link-12');">node</a></tt><tt class="py-op">]</tt> <tt class="py-op">*</tt> </tt> <a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> <tt class="py-name">previous_layer</tt><tt class="py-op">.</tt><tt class="py-name">weights</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt id="link-76" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-76', 'node', 'link-12');">node</a></tt><tt class="py-op">,</tt> <tt class="py-name">update_node</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt> <a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> </tt> <a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-77" class="py-name"><a title="Bio.Crystal.Crystal.values Bio.Phylo.PhyloXML.Events.values Bio.SeqIO._index._IndexedSeqFileDict.values BioSQL.BioSeqDatabase.BioSeqDatabase.values BioSQL.BioSeqDatabase.DBServer.values" class="py-name" href="#" onclick="return doclink('link-77', 'values', 'link-11');">values</a></tt><tt class="py-op">[</tt><tt class="py-name">update_node</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">_activation</tt><tt class="py-op">(</tt><tt id="link-78" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.sum Bio.SubsMat.SeqMat.sum" class="py-name" href="#" onclick="return doclink('link-78', 'sum', 'link-43');">sum</a></tt><tt class="py-op">)</tt> </tt> </div><a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> </tt> <a name="OutputLayer.backpropagate"></a><div id="OutputLayer.backpropagate-def"><a name="L292"></a><tt class="py-lineno">292</tt> <a class="py-toggle" href="#" id="OutputLayer.backpropagate-toggle" onclick="return toggle('OutputLayer.backpropagate');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer-class.html#backpropagate">backpropagate</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">outputs</tt><tt class="py-op">,</tt> <tt class="py-param">learning_rate</tt><tt class="py-op">,</tt> <tt class="py-param">momentum</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="OutputLayer.backpropagate-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="OutputLayer.backpropagate-expanded"><a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"> <tt class="py-docstring">"""Calculate the backpropagation error at a given node.</tt> </tt> <a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"><tt class="py-docstring"> This calculates the error term using the formula:</tt> </tt> <a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"><tt class="py-docstring"> p = (z - t) z (1 - z)</tt> </tt> <a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"><tt class="py-docstring"> where z is the calculated value for the node, and t is the</tt> </tt> <a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"><tt class="py-docstring"> real value.</tt> </tt> <a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt> <a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"><tt class="py-docstring"> o outputs - The list of output values we use to calculate the</tt> </tt> <a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"><tt class="py-docstring"> errors in our predictions.</tt> </tt> <a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"> <tt class="py-name">errors</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt> <a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-79" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-79', 'node', 'link-12');">node</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-80" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-80', 'nodes', 'link-2');">nodes</a></tt><tt class="py-op">:</tt> </tt> <a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"> <tt class="py-name">calculated_value</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-81" class="py-name"><a title="Bio.Crystal.Crystal.values Bio.Phylo.PhyloXML.Events.values Bio.SeqIO._index._IndexedSeqFileDict.values BioSQL.BioSeqDatabase.BioSeqDatabase.values BioSQL.BioSeqDatabase.DBServer.values" class="py-name" href="#" onclick="return doclink('link-81', 'values', 'link-11');">values</a></tt><tt class="py-op">[</tt><tt id="link-82" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-82', 'node', 'link-12');">node</a></tt><tt class="py-op">]</tt> </tt> <a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> <tt class="py-name">real_value</tt> <tt class="py-op">=</tt> <tt class="py-name">outputs</tt><tt class="py-op">[</tt><tt id="link-83" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-83', 'node', 'link-12');">node</a></tt> <tt class="py-op">-</tt> <tt class="py-number">1</tt><tt class="py-op">]</tt> </tt> <a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"> </tt> <a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"> <tt class="py-name">errors</tt><tt class="py-op">[</tt><tt id="link-84" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-84', 'node', 'link-12');">node</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">real_value</tt> <tt class="py-op">-</tt> <tt class="py-name">calculated_value</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> </tt> <a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"> <tt class="py-name">calculated_value</tt> <tt class="py-op">*</tt> </tt> <a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-number">1</tt> <tt class="py-op">-</tt> <tt class="py-name">calculated_value</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt> <a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"> </tt> <a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">errors</tt> </tt> </div><a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"> </tt> <a name="OutputLayer.get_error"></a><div id="OutputLayer.get_error-def"><a name="L318"></a><tt class="py-lineno">318</tt> <a class="py-toggle" href="#" id="OutputLayer.get_error-toggle" onclick="return toggle('OutputLayer.get_error');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer-class.html#get_error">get_error</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">real_value</tt><tt class="py-op">,</tt> <tt class="py-param">node_number</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="OutputLayer.get_error-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="OutputLayer.get_error-expanded"><a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> <tt class="py-docstring">"""Return the error value at a particular node.</tt> </tt> <a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"> <tt class="py-name">predicted_value</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-85" class="py-name"><a title="Bio.Crystal.Crystal.values Bio.Phylo.PhyloXML.Events.values Bio.SeqIO._index._IndexedSeqFileDict.values BioSQL.BioSeqDatabase.BioSeqDatabase.values BioSQL.BioSeqDatabase.DBServer.values" class="py-name" href="#" onclick="return doclink('link-85', 'values', 'link-11');">values</a></tt><tt class="py-op">[</tt><tt class="py-name">node_number</tt><tt class="py-op">]</tt> </tt> <a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">0.5</tt> <tt class="py-op">*</tt> <tt class="py-name">math</tt><tt class="py-op">.</tt><tt class="py-name">pow</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">real_value</tt> <tt class="py-op">-</tt> <tt class="py-name">predicted_value</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-number">2</tt><tt class="py-op">)</tt> </tt> </div><a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"> </tt> <a name="OutputLayer.set_weight"></a><div id="OutputLayer.set_weight-def"><a name="L324"></a><tt class="py-lineno">324</tt> <a class="py-toggle" href="#" id="OutputLayer.set_weight-toggle" onclick="return toggle('OutputLayer.set_weight');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer-class.html#set_weight">set_weight</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">this_node</tt><tt class="py-op">,</tt> <tt class="py-param">next_node</tt><tt class="py-op">,</tt> <tt class="py-param">value</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="OutputLayer.set_weight-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="OutputLayer.set_weight-expanded"><a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt><tt class="py-op">(</tt><tt class="py-string">"Can't set weights for the output layer"</tt><tt class="py-op">)</tt> </tt> </div></div><a name="L326"></a><tt class="py-lineno">326</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> <!-- 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