bn4r 0.1.0 → 0.1.2
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- data/CHANGELOG +12 -0
- data/README +71 -5
- data/doc/classes/BNTPGFromPositiveNegativeRelations.html +172 -0
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<pre><span class="ruby-comment cmt"># File lib/bn4r/bn_export.rb, line 26</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_xbn</span>(<span class="ruby-identifier">bn</span> = <span class="ruby-keyword kw">self</span>)
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<span class="ruby-identifier">xbn_str</span> <span class="ruby-operator">+=</span> <span class="ruby-value str">"<ANALYSISNOTEBOOK NAME=\"Notebook.bndefault\" ROOT=\"bndefault\">\n"</span>
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<span class="ruby-identifier">xbn_str</span> <span class="ruby-operator">+=</span> <span class="ruby-value str">"<BNMODEL NAME=\"bndefault\"><STATICPROPERTIES><FORMAT>MSR DTAS XML</FORMAT>\n"</span>
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<span class="ruby-identifier">xbn_str</span> <span class="ruby-operator">+=</span> <span class="ruby-value str">" <VERSION>1.0</VERSION>\n"</span>
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<span class="ruby-identifier">xbn_str</span> <span class="ruby-operator">+=</span> <span class="ruby-value str">" <CREATOR>Microsoft Research DTAS</CREATOR>\n"</span>
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<span class="ruby-identifier">xbn_str</span> <span class="ruby-operator">+=</span> <span class="ruby-value str">" </STATICPROPERTIES>\n"</span>
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<span class="ruby-identifier">xbn_str</span> <span class="ruby-operator">+=</span> <span class="ruby-value str">" <DYNAMICPROPERTIES><PROPERTYTYPE NAME=\"DTASDG_Notes\" TYPE=\"stringarray\"><COMMENT>Notes on the diagram</COMMENT>\n"</span>
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<span class="ruby-identifier">xbn_str</span> <span class="ruby-operator">+=</span> <span class="ruby-value str">" </PROPERTYTYPE>\n"</span>
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<span class="ruby-identifier">xbn_str</span> <span class="ruby-operator">+=</span> <span class="ruby-value str">" <PROPERTYTYPE NAME=\"MS_Addins\" TYPE=\"stringarray\"/>\n"</span>
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<span class="ruby-identifier">xbn_str</span> <span class="ruby-operator">+=</span> <span class="ruby-value str">" </DYNAMICPROPERTIES>\n"</span>
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<span class="ruby-identifier">xbn_str</span> <span class="ruby-operator">+=</span> <span class="ruby-identifier">xbn_variables</span>(<span class="ruby-identifier">bn</span>)
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<span class="ruby-identifier">xbn_str</span> <span class="ruby-operator">+=</span> <span class="ruby-identifier">xbn_structure</span>(<span class="ruby-identifier">bn</span>)
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<span class="ruby-identifier">xbn_str</span> <span class="ruby-operator">+=</span> <span class="ruby-identifier">xbn_distributions</span>(<span class="ruby-identifier">bn</span>)
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<span class="ruby-identifier">xbn_str</span> <span class="ruby-operator">+=</span> <span class="ruby-value str">" </BNMODEL>\n"</span>
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<pre><span class="ruby-comment cmt"># File lib/bn4r/bn_import.rb, line 26</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">create_from_xmlbif</span>(<span class="ruby-identifier">file</span>, <span class="ruby-identifier">bn</span>=<span class="ruby-keyword kw">self</span>)
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<span class="ruby-identifier">doc</span> = <span class="ruby-constant">Document</span>.<span class="ruby-identifier">new</span> <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">file</span>, <span class="ruby-value str">"r"</span>)
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<span class="ruby-identifier">doc</span>.<span class="ruby-identifier">elements</span>.<span class="ruby-identifier">each</span>(<span class="ruby-value str">"BIF/NETWORK/VARIABLE"</span>) { <span class="ruby-operator">|</span><span class="ruby-identifier">variable</span><span class="ruby-operator">|</span>
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<span class="ruby-identifier">name</span> = <span class="ruby-identifier">variable</span>.<span class="ruby-identifier">elements</span>[<span class="ruby-value str">"NAME"</span>]
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<span class="ruby-identifier">outcomes</span> = []
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<span class="ruby-identifier">variable</span>.<span class="ruby-identifier">elements</span>.<span class="ruby-identifier">each</span>(<span class="ruby-value str">"OUTCOME"</span>) { <span class="ruby-operator">|</span><span class="ruby-identifier">outcome</span><span class="ruby-operator">|</span>
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<span class="ruby-identifier">outcomes</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">outcome</span>.<span class="ruby-identifier">text</span>
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}
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<span class="ruby-comment cmt"># transform from text to boolean</span>
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<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">outcomes</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">==</span> <span class="ruby-value">2</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">outcomes</span>.<span class="ruby-identifier">include?</span>(<span class="ruby-value str">"true"</span>) <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">outcomes</span>.<span class="ruby-identifier">include?</span>(<span class="ruby-value str">"false"</span>)
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<span class="ruby-identifier">outcomes</span> = <span class="ruby-identifier">outcomes</span>.<span class="ruby-identifier">collect</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">o</span><span class="ruby-operator">|</span> <span class="ruby-identifier">o</span> <span class="ruby-operator">==</span> <span class="ruby-value str">"true"</span>}
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<span class="ruby-identifier">node</span> = <span class="ruby-constant">BayesNetNode</span>.<span class="ruby-identifier">new</span>( <span class="ruby-identifier">name</span>.<span class="ruby-identifier">text</span>, <span class="ruby-identifier">outcomes</span> )
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<span class="ruby-identifier">bn</span>.<span class="ruby-identifier">add_vertex</span>(<span class="ruby-identifier">node</span>)
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}
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<span class="ruby-comment cmt"># for each variable we list, we will look up </span>
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<span class="ruby-identifier">doc</span>.<span class="ruby-identifier">elements</span>.<span class="ruby-identifier">each</span>(<span class="ruby-value str">"BIF/NETWORK/DEFINITION/"</span>) { <span class="ruby-operator">|</span><span class="ruby-identifier">definition</span><span class="ruby-operator">|</span>
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<span class="ruby-identifier">node</span> = <span class="ruby-identifier">get_variable</span>( <span class="ruby-identifier">definition</span>.<span class="ruby-identifier">elements</span>[<span class="ruby-value str">"FOR"</span>].<span class="ruby-identifier">text</span> )
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<span class="ruby-identifier">givens_array</span> = []
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<span class="ruby-identifier">definition</span>.<span class="ruby-identifier">elements</span>.<span class="ruby-identifier">each</span>(<span class="ruby-value str">"GIVEN"</span>) { <span class="ruby-operator">|</span><span class="ruby-identifier">given</span><span class="ruby-operator">|</span>
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<span class="ruby-identifier">givens_array</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">get_variable</span>( <span class="ruby-identifier">given</span>.<span class="ruby-identifier">text</span> )
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}
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<span class="ruby-identifier">table</span> = <span class="ruby-identifier">definition</span>.<span class="ruby-identifier">elements</span>[<span class="ruby-value str">"TABLE"</span>].<span class="ruby-identifier">text</span>.<span class="ruby-identifier">split</span>
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<span class="ruby-identifier">givens_array</span>.<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-identifier">bn</span>.<span class="ruby-identifier">add_edge</span>(<span class="ruby-identifier">g</span>, <span class="ruby-identifier">node</span>) }
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<span class="ruby-identifier">node</span>.<span class="ruby-identifier">set_probability_table</span>(<span class="ruby-identifier">givens_array</span>, <span class="ruby-identifier">table</span>)
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}
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<span class="ruby-keyword kw">end</span></pre>
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<pre><span class="ruby-comment cmt"># File lib/bn4r/bn.rb, line 41</span>
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<span class="ruby-identifier">vertices</span>.<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">v</span><span class="ruby-operator">|</span> <span class="ruby-identifier">v</span>.<span class="ruby-identifier">clear_value</span> }
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<span class="ruby-identifier">vertices</span>.<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">v</span><span class="ruby-operator">|</span> <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">v</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">v</span>.<span class="ruby-identifier">name</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">text</span> }
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<pre><span class="ruby-comment cmt"># File lib/bn4r/bn.rb, line 51</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">roots</span>
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<span class="ruby-identifier">vertices</span>.<span class="ruby-identifier">select</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">v</span><span class="ruby-operator">|</span> <span class="ruby-identifier">root?</span>(<span class="ruby-identifier">v</span>) }
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">root?</span>(<span class="ruby-identifier">v</span>)
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<span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">true</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">num_parents</span>(<span class="ruby-identifier">v</span>) <span class="ruby-operator">==</span> <span class="ruby-value">0</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">num_parents</span>(<span class="ruby-identifier">v</span>)
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<span class="ruby-keyword kw">return</span> <span class="ruby-identifier">v</span>.<span class="ruby-identifier">parents</span>.<span class="ruby-identifier">size</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">inference_by_enumeration</span>
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<span class="ruby-identifier">prob</span> = <span class="ruby-value">1.0</span>;
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<span class="ruby-identifier">vertices</span>.<span class="ruby-identifier">each</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">v</span><span class="ruby-operator">|</span> <span class="ruby-identifier">prob</span> = <span class="ruby-identifier">prob</span> <span class="ruby-operator">*</span> <span class="ruby-identifier">p_v_cond_parents</span>(<span class="ruby-identifier">v</span>)}
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<pre><span class="ruby-comment cmt"># File lib/bn4r/bn.rb, line 77</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">p_v_cond_parents</span>(<span class="ruby-identifier">v</span>)
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<span class="ruby-identifier">givens_assignments</span> = <span class="ruby-identifier">v</span>.<span class="ruby-identifier">parents</span>.<span class="ruby-identifier">collect</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">parents</span><span class="ruby-operator">|</span> <span class="ruby-identifier">parents</span>.<span class="ruby-identifier">value</span>}
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<span class="ruby-identifier">v</span>.<span class="ruby-identifier">get_probability</span>(<span class="ruby-identifier">v</span>.<span class="ruby-identifier">value</span>, <span class="ruby-identifier">givens_assignments</span>).<span class="ruby-identifier">to_f</span>
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<pre><span class="ruby-comment cmt"># File lib/bn4r/bn.rb, line 83</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">all_nodes_with_values?</span>
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<span class="ruby-identifier">vertices</span>.<span class="ruby-identifier">select</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">v</span><span class="ruby-operator">|</span> <span class="ruby-operator">!</span><span class="ruby-identifier">v</span>.<span class="ruby-identifier">value</span>.<span class="ruby-identifier">nil?</span> }.<span class="ruby-identifier">size</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">vertices</span>.<span class="ruby-identifier">size</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">nodes_ordered_by_dependencies</span>(<span class="ruby-identifier">nodes</span> = <span class="ruby-identifier">vertices</span>, <span class="ruby-identifier">bn_ordered</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>)
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<span class="ruby-identifier">nodes</span>.<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">v</span><span class="ruby-operator">|</span>
|
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<span class="ruby-keyword kw">next</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">bn_ordered</span>.<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">v</span>)
|
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<span class="ruby-identifier">nodes_ordered_by_dependencies</span>(<span class="ruby-identifier">v</span>.<span class="ruby-identifier">parents</span>, <span class="ruby-identifier">bn_ordered</span>) <span class="ruby-keyword kw">if</span> <span class="ruby-operator">!</span><span class="ruby-identifier">v</span>.<span class="ruby-identifier">root?</span>
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<span class="ruby-identifier">bn_ordered</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">v</span>
|
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}
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<span class="ruby-keyword kw">return</span> <span class="ruby-identifier">bn_ordered</span>.<span class="ruby-identifier">flatten</span>
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<pre><span class="ruby-comment cmt"># File lib/bn4r/bn.rb, line 26</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add_edge</span>(<span class="ruby-identifier">parent</span>, <span class="ruby-identifier">child</span>, <span class="ruby-identifier">tag</span>=<span class="ruby-keyword kw">nil</span>)
|
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<span class="ruby-identifier">raise</span> <span class="ruby-value str">"Nodes must be of the class BayesNetNodes"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">parent</span>.<span class="ruby-identifier">class</span> <span class="ruby-operator">!=</span> <span class="ruby-constant">BayesNetNode</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">child</span>.<span class="ruby-identifier">class</span> <span class="ruby-operator">!=</span> <span class="ruby-constant">BayesNetNode</span>
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<span class="ruby-identifier">raise</span> <span class="ruby-value str">"Self relations not allowed in BayesNet"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">parent</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">child</span>
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<span class="ruby-identifier">raise</span> <span class="ruby-value str">"Diferent BayesNetNodes with equal name: "</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">parent</span>.<span class="ruby-identifier">name</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">parent</span>.<span class="ruby-identifier">name</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">child</span>.<span class="ruby-identifier">name</span>
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<span class="ruby-identifier">child</span>.<span class="ruby-identifier">parents</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">parent</span>
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<span class="ruby-identifier">child</span>.<span class="ruby-identifier">relations</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">tag</span> <span class="ruby-keyword kw">if</span> <span class="ruby-operator">!</span><span class="ruby-identifier">tag</span>.<span class="ruby-identifier">nil?</span>
|
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<pre><span class="ruby-comment cmt"># File lib/bn4r/bn.rb, line 41</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">clear_values!</span>
|
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<span class="ruby-identifier">vertices</span>.<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">v</span><span class="ruby-operator">|</span> <span class="ruby-identifier">v</span>.<span class="ruby-identifier">clear_value</span> }
|
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<pre><span class="ruby-comment cmt"># File lib/bn4r/bn.rb, line 46</span>
|
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">get_variable</span>( <span class="ruby-identifier">text</span> )
|
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<span class="ruby-identifier">vertices</span>.<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">v</span><span class="ruby-operator">|</span> <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">v</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">v</span>.<span class="ruby-identifier">name</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">text</span> }
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">roots</span>
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<span class="ruby-identifier">vertices</span>.<span class="ruby-identifier">select</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">v</span><span class="ruby-operator">|</span> <span class="ruby-identifier">root?</span>(<span class="ruby-identifier">v</span>) }
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">root?</span>(<span class="ruby-identifier">v</span>)
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<span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">true</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">num_parents</span>(<span class="ruby-identifier">v</span>) <span class="ruby-operator">==</span> <span class="ruby-value">0</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">num_parents</span>(<span class="ruby-identifier">v</span>)
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<span class="ruby-keyword kw">return</span> <span class="ruby-identifier">v</span>.<span class="ruby-identifier">parents</span>.<span class="ruby-identifier">size</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">inference_by_enumeration</span>
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<span class="ruby-identifier">prob</span> = <span class="ruby-value">1.0</span>;
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<span class="ruby-identifier">vertices</span>.<span class="ruby-identifier">each</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">v</span><span class="ruby-operator">|</span> <span class="ruby-identifier">prob</span> = <span class="ruby-identifier">prob</span> <span class="ruby-operator">*</span> <span class="ruby-identifier">p_v_cond_parents</span>(<span class="ruby-identifier">v</span>)}
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<pre><span class="ruby-comment cmt"># File lib/bn4r/bn.rb, line 77</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">p_v_cond_parents</span>(<span class="ruby-identifier">v</span>)
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<span class="ruby-identifier">givens_assignments</span> = <span class="ruby-identifier">v</span>.<span class="ruby-identifier">parents</span>.<span class="ruby-identifier">collect</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">parents</span><span class="ruby-operator">|</span> <span class="ruby-identifier">parents</span>.<span class="ruby-identifier">value</span>}
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<span class="ruby-identifier">v</span>.<span class="ruby-identifier">get_probability</span>(<span class="ruby-identifier">v</span>.<span class="ruby-identifier">value</span>, <span class="ruby-identifier">givens_assignments</span>).<span class="ruby-identifier">to_f</span>
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<pre><span class="ruby-comment cmt"># File lib/bn4r/bn.rb, line 83</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">all_nodes_with_values?</span>
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<span class="ruby-identifier">vertices</span>.<span class="ruby-identifier">select</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">v</span><span class="ruby-operator">|</span> <span class="ruby-operator">!</span><span class="ruby-identifier">v</span>.<span class="ruby-identifier">value</span>.<span class="ruby-identifier">nil?</span> }.<span class="ruby-identifier">size</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">vertices</span>.<span class="ruby-identifier">size</span>
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<pre><span class="ruby-comment cmt"># File lib/bn4r/bn.rb, line 89</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">nodes_ordered_by_dependencies</span>(<span class="ruby-identifier">nodes</span> = <span class="ruby-identifier">vertices</span>, <span class="ruby-identifier">bn_ordered</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>)
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<span class="ruby-identifier">nodes</span>.<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">v</span><span class="ruby-operator">|</span>
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<span class="ruby-keyword kw">next</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">bn_ordered</span>.<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">v</span>)
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<span class="ruby-identifier">nodes_ordered_by_dependencies</span>(<span class="ruby-identifier">v</span>.<span class="ruby-identifier">parents</span>, <span class="ruby-identifier">bn_ordered</span>) <span class="ruby-keyword kw">if</span> <span class="ruby-operator">!</span><span class="ruby-identifier">v</span>.<span class="ruby-identifier">root?</span>
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}
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<pre><span class="ruby-comment cmt"># File lib/bn4r/bn_algorithms.rb, line 29</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">enumeration_ask</span>(<span class="ruby-identifier">x</span>,<span class="ruby-identifier">e</span>, <span class="ruby-identifier">bn_vertices</span> = <span class="ruby-identifier">vertices</span>)
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<span class="ruby-identifier">e</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">x</span>
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<span class="ruby-identifier">q</span> = []
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<span class="ruby-comment cmt">#p bn_vertices.collect { |v| v.name }</span>
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<span class="ruby-identifier">x</span>.<span class="ruby-identifier">outcomes</span>.<span class="ruby-identifier">each</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">outcome</span><span class="ruby-operator">|</span>
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<span class="ruby-identifier">x</span>.<span class="ruby-identifier">set_value</span>(<span class="ruby-identifier">outcome</span>)
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<span class="ruby-identifier">q</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">enumerate_all</span>(<span class="ruby-identifier">bn_vertices</span>, <span class="ruby-identifier">e</span>)
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}
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<pre><span class="ruby-comment cmt"># File lib/bn4r/bn_algorithms.rb, line 46</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">prior_sample</span>(<span class="ruby-identifier">nodes_ordered</span> = <span class="ruby-identifier">nodes_ordered_by_dependencies</span>)
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<span class="ruby-identifier">value</span> = <span class="ruby-identifier">rand</span> <span class="ruby-operator"><</span> <span class="ruby-identifier">v</span>.<span class="ruby-identifier">get_probability</span>(<span class="ruby-keyword kw">true</span>)
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<span class="ruby-comment cmt"># leave the bn clear of values.</span>
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<span class="ruby-identifier">nodes_ordered</span>.<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">v</span><span class="ruby-operator">|</span> <span class="ruby-identifier">v</span>.<span class="ruby-identifier">clear_value</span> }
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