sbn 0.9.0

data/test/test_variable.rb

@@ -0,0 +1,373 @@
+require 'test/unit'
+require File.dirname(__FILE__) + '/../lib/sbn'
+
+class TestVariable < Test::Unit::TestCase # :nodoc:
+  def setup
+    @net = Sbn::Net.new
+    @var1 = Sbn::Variable.new(@net, "var1")
+    @var2 = Sbn::Variable.new(@net, "var2")
+  end
+
+  def test_add_child
+    assert !@var1.children.include?(@var2)
+    @var1.add_child(@var2)
+    assert @var1.children.include?(@var2)
+  end
+
+  def test_add_child_no_recurse
+    # variable shouldn't be able to add itself as a child
+    children_before = @var1.children.dup
+    @var1.add_child_no_recurse(@var1)
+    children_after = @var1.children.dup
+    assert_equal children_before, children_after
+    
+    # add child normally
+    children_before = @var1.children.dup
+    @var1.add_child_no_recurse(@var2)
+    children_after = @var1.children.dup
+    assert_not_equal children_before, children_after
+    assert children_after.include?(@var2)
+
+    # variable shouldn't be able to add same child twice
+    children_before = @var1.children.dup
+    @var1.add_child_no_recurse(@var2)
+    children_after = @var1.children.dup
+    assert_equal children_before, children_after
+  end
+
+  def test_add_parent
+    assert !@var1.parents.include?(@var2)
+    @var1.add_parent(@var2)
+    assert @var1.parents.include?(@var2)
+  end
+
+  def test_add_parent_no_recurse
+    # variable shouldn't be able to add itself as a parent
+    parents_before = @var1.parents.dup
+    @var1.add_parent_no_recurse(@var1)
+    parents_after = @var1.parents.dup
+    assert_equal parents_before, parents_after
+    
+    # add parent normally
+    parents_before = @var1.parents.dup
+    @var1.add_parent_no_recurse(@var2)
+    parents_after = @var1.parents.dup
+    assert_not_equal parents_before, parents_after
+    assert parents_after.include?(@var2)
+
+    # variable shouldn't be able to add same parent twice
+    parents_before = @var1.parents.dup
+    @var1.add_parent_no_recurse(@var2)
+    parents_after = @var1.parents.dup
+    assert_equal parents_before, parents_after
+  end
+  
+  def test_to_s
+    assert_equal "#{@var1.name}", "#{@var1}"
+  end
+  
+  def test_equality
+    assert_equal(@var1, @var1.dup)
+  end
+  
+  def test_can_be_evaluated_eh
+    @var1.add_child(@var2)
+    assert @var1.can_be_evaluated?({})
+    assert !@var2.can_be_evaluated?({})
+  end
+
+  def test_children
+    assert @var1.children.class == Array and @var1.children.empty?
+  end
+
+  def test_evaluate_marginal
+    assert_equal @var1.evaluate_marginal(:true, {}), 0.5
+    assert_equal @var1.evaluate_marginal(:false, {}), 0.5
+    
+    @var1.add_child(@var2)
+    @var2.set_probabilities([0.25, 0.75, 0.2, 0.8])
+    assert_equal @var2.evaluate_marginal(:true, {:var1 => :true}), 0.25
+    assert_equal @var2.evaluate_marginal(:false, {:var1 => :true}), 0.75
+    assert_equal @var2.evaluate_marginal(:true, {:var1 => :false}), 0.2
+    assert_equal @var2.evaluate_marginal(:false, {:var1 => :false}), 0.8
+  end
+
+  def test_evidence_name
+    assert_equal @var1.evidence_name, @var1.name
+  end
+
+  def test_generate_probability_table
+    test_probability_table
+  end
+
+  def test_get_observed_state
+    evidence = {:var1 => :true}
+    assert_equal evidence[@var1.name], @var1.get_observed_state(evidence)
+  end
+
+  def test_get_random_state
+    states = [:good, :bad, :ugly]
+    n = Sbn::Variable.new(@net, :george, [0.25, 0.25, 0.5], states)
+    evidence = {}
+    assert states.include?(n.get_random_state(evidence))
+    assert states.include?(n.get_random_state_with_markov_blanket(evidence))
+  end
+
+  def test_parents
+    assert @var1.parents.class == Array and @var1.parents.empty?
+  end
+
+  def test_probability_table
+    @var1.add_child(@var2)
+    
+    # number of probabilities no longer matches number of states because
+    # var2 now has a parent.
+    assert_nil @var2.probability_table
+    
+    @var2.set_probabilities([0.25, 0.75, 0.2, 0.8])
+    assert_not_nil @var2.probability_table
+    
+    expected_table = [[[:true, :true], 0.25],
+                      [[:true, :false], 0.75],
+                      [[:false, :true], 0.2],
+                      [[:false, :false], 0.8]]
+    assert_equal @var2.probability_table, expected_table
+  end
+
+  def test_set_in_evidence_eh
+    evidence = {:var1 => :true, :var2 => :false}
+    assert @var1.set_in_evidence?(evidence)
+    assert @var2.set_in_evidence?(evidence)
+  end
+
+  def test_set_probabilities
+    @var1.add_child(@var2)
+    probs = @var2.instance_variable_get('@probabilities')
+    new_probs = [0.25, 0.75, 0.2, 0.8]
+    assert_not_equal probs, new_probs
+  
+    @var2.set_probabilities(new_probs)
+    probs = @var2.instance_variable_get('@probabilities')
+    assert_not_nil probs, new_probs
+  end
+
+  def test_set_probability
+    @var1.add_child(@var2)
+    @var2.set_probability(0.75, {:var1 => :false, :var2 => :false})
+    probs = @var2.instance_variable_get('@probabilities')
+    assert_equal probs[3], 0.75
+  end
+
+  def test_set_states
+    var = Sbn::Variable.new(@net, :var3, [], [])
+    assert var.states.empty?
+    var.set_states([:true, :false])
+    assert !var.states.empty?
+    assert_equal var.states, [:true, :false]
+  end
+
+  def test_states
+    var = Sbn::Variable.new(@net, :var3, [], [])
+    assert_not_nil var.states
+    assert_equal var.states, []
+  end
+
+  def test_to_xmlbif_definition
+    xml = Builder::XmlMarkup.new(:indent => 2)
+    expected_output = <<-EOS
+    <definition>
+      <for>var1</for>
+      <table>0.5 0.5</table>
+    </definition>    
+    EOS
+    assert_equal @var1.to_xmlbif_definition(xml).gsub(/\s+/, ''), expected_output.gsub(/\s+/, '')
+  end
+
+  def test_to_xmlbif_variable
+    xml = Builder::XmlMarkup.new(:indent => 2)
+    expected_output = <<-EOS
+    <variable type="nature">
+      <name>var1</name>
+      <outcome>true</outcome>
+      <outcome>false</outcome>
+      <property>SbnVariableType = Sbn::Variable</property>
+    </variable>
+    EOS
+    assert_equal @var1.to_xmlbif_variable(xml).gsub(/\s+/, ''), expected_output.gsub(/\s+/, '')
+  end
+end
+
+class TestNumericVariable < Test::Unit::TestCase # :nodoc:
+  def setup
+    @net = Sbn::Net.new
+    @var1 = Sbn::NumericVariable.new(@net, "var1", [0.25, 0.25, 0.25, 0.25], [5.0, 10.0, 15.0])
+  end
+
+  def test_get_observed_state
+    evidence = {:var1 => 7.68}
+    states = @var1.states
+    assert_equal @var1.get_observed_state(evidence), states[1]
+  end
+
+  def test_set_probabilities_from_sample_points
+    data = [0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10.0]
+    temp_data = data.dup
+    @var1.add_sample_point({:var1 => temp_data.shift})
+    @var1.add_sample_point({:var1 => temp_data.shift})
+    @var1.add_sample_point({:var1 => temp_data.shift})
+    @var1.add_sample_point({:var1 => temp_data.shift})
+    @var1.add_sample_point({:var1 => temp_data.shift})
+    @var1.add_sample_point({:var1 => temp_data.shift})
+    @var1.add_sample_point({:var1 => temp_data.shift})
+    @var1.add_sample_point({:var1 => temp_data.shift})
+    @var1.add_sample_point({:var1 => temp_data.shift})
+    @var1.add_sample_point({:var1 => temp_data.shift})
+    @var1.add_sample_point({:var1 => temp_data.shift})
+    @var1.set_probabilities_from_sample_points!
+    assert_equal @var1.state_thresholds.shift, data.average - (data.standard_deviation * 2.0)
+  end
+
+  def test_state_thresholds
+    assert_equal @var1.state_thresholds, [5.0, 10.0, 15.0]
+  end
+
+  def test_to_xmlbif_variable
+    xml = Builder::XmlMarkup.new(:indent => 2)
+    expected_output = <<-EOS
+    <variable type="nature">
+      <name>var1</name>
+      <outcome>lt5.0</outcome>
+      <outcome>gte5.0lt10.0</outcome>
+      <outcome>gte10.0lt15.0</outcome>
+      <outcome>gte15.0</outcome>
+      <property>SbnVariableType = Sbn::NumericVariable</property>
+      <property>StateThresholds = 5.0,10.0,15.0</property>
+    </variable>
+    EOS
+    assert_equal @var1.to_xmlbif_variable(xml).gsub(/\s+/, ''), expected_output.gsub(/\s+/, '')
+  end
+end
+
+class TestStringVariable < Test::Unit::TestCase # :nodoc:
+  def setup
+    @net = Sbn::Net.new("Categorization")
+    @category = Sbn::Variable.new(@net, :category, [0.33, 0.33, 0.33], [:food, :groceries, :gas])
+    @text = Sbn::StringVariable.new(@net, :text)
+    @category.add_child(@text)
+    @net.learn([
+      {:category => :food, :text => 'foo'},
+      {:category => :food, :text => 'gro'},
+      {:category => :food, :text => 'foo'},
+      {:category => :food, :text => 'foo'},
+      {:category => :groceries, :text => 'gro'},
+      {:category => :groceries, :text => 'gro'},
+      {:category => :groceries, :text => 'foo'},
+      {:category => :groceries, :text => 'gro'},
+      {:category => :gas, :text => 'gas'},
+      {:category => :gas, :text => 'gas'},
+      {:category => :gas, :text => 'gas'},
+      {:category => :gas, :text => 'gas'}
+    ])
+    @covars = @text.covariables
+  end
+  
+  def test_covar_evidence_name
+    @covars.each do |covar|
+      manager_name = covar.instance_variable_get('@manager_name')
+      assert_equal @text.name, manager_name
+    end
+  end
+
+  def test_covar_get_observed_state
+    evidence = {:text => "groceries"}
+    @covars.each do |covar|
+      manager_name = covar.instance_variable_get('@manager_name')
+      text_to_match = covar.instance_variable_get('@text_to_match')
+      assert_equal covar.get_observed_state(evidence), (evidence[manager_name].include?(text_to_match) ? :true : :false)
+    end
+  end
+
+  def test_covar_to_xmlbif_variable
+    xml = Builder::XmlMarkup.new(:indent => 2)
+    expected_output = <<-EOS
+    <variable type="nature">
+      <name>text_covar_foo</name>
+      <outcome>true</outcome>
+      <outcome>false</outcome>
+      <property>SbnVariableType = Sbn::StringCovariable</property>
+      <property>ManagerVariableName = text</property>
+      <property>TextToMatch = "foo"</property>
+    </variable>
+    EOS
+    assert @covars.first.to_xmlbif_variable(xml).gsub(/\s+/, ''), expected_output.gsub(/\s+/, '') 
+  end
+
+  def test_add_child_no_recurse
+    covariable_children = @text.instance_variable_get('@covariable_children')
+    newvar = Sbn::Variable.new(@net, :newvar)
+    assert !covariable_children.include?(newvar)
+    @text.add_child(newvar)
+    covariable_children = @text.instance_variable_get('@covariable_children')
+    assert covariable_children.include?(newvar)
+  end
+
+  def test_add_covariable
+    covar = Sbn::StringCovariable.new(@net, :text, 'something', [0.5, 0.5])
+    assert !@text.covariables.include?(covar)
+    @text.add_covariable(covar)
+    assert @text.covariables.include?(covar)
+  end
+
+  def test_add_parent_no_recurse
+    covariable_parents = @text.instance_variable_get('@covariable_parents')
+    newvar = Sbn::Variable.new(@net, :newvar)
+    assert !covariable_parents.include?(newvar)
+    @text.add_parent(newvar)
+    covariable_parents = @text.instance_variable_get('@covariable_parents')
+    assert covariable_parents.include?(newvar)
+  end
+
+  def test_add_sample_point
+    # make sure covariables are created with each sample point
+    newtext = "newtext"
+    assert_equal 3, @text.covariables.size
+    @text.add_sample_point({:text => newtext, :category => :gas})
+    ngrams = []
+    Sbn::StringVariable::DEFAULT_NGRAM_SIZES.each {|len| ngrams.concat(newtext.ngrams(len)) }
+    assert_equal 3 + ngrams.size, @text.covariables.size
+  end
+
+  def test_covariables
+    assert_not_nil @text.covariables
+  end
+
+  def test_set_in_evidence_eh
+    # assert_raise(RuntimeError) { @text.set_in_evidence?({:text => "newtext", :category => :gas}) } 
+    assert @text.set_in_evidence?({:text => "newtext", :category => :gas})
+  end
+
+  def test_to_xmlbif_definition
+    xml = Builder::XmlMarkup.new(:indent => 2)
+    assert_nil @text.to_xmlbif_definition(xml)
+  end
+
+  def test_to_xmlbif_variable
+    xml = Builder::XmlMarkup.new(:indent => 2)
+    expected_output = <<-EOS
+    <variable type="nature">
+      <name>text</name>
+      <property>SbnVariableType = Sbn::StringVariable</property>
+      <property>Covariables = foo,gas,gro</property>
+      <property>Parents = category</property>
+    </variable>
+    EOS
+    assert_equal expected_output.gsub(/\s+/, ''), @text.to_xmlbif_variable(xml).gsub(/\s+/, '')
+  end
+  
+  def test_is_complete_evidence_eh
+    evidence = {}
+    assert !@text.is_complete_evidence?(evidence)    
+    evidence = {:category => :food, :text => "foo"}
+    assert @text.is_complete_evidence?(evidence)
+  end
+end

metadata

@@ -0,0 +1,63 @@
+--- !ruby/object:Gem::Specification 
+rubygems_version: 0.9.2
+specification_version: 1
+name: sbn
+version: !ruby/object:Gem::Version 
+  version: 0.9.0
+date: 2007-03-15 00:00:00 -06:00
+summary: Simple Bayesian Network Library
+require_paths: 
+- lib
+email: carl@youngbloods.org
+homepage: http://youngbloods.org/
+rubyforge_project: 
+description: 
+autorequire: sbn
+default_executable: 
+bindir: bin
+has_rdoc: true
+required_ruby_version: !ruby/object:Gem::Version::Requirement 
+  requirements: 
+  - - ">"
+    - !ruby/object:Gem::Version 
+      version: 0.0.0
+  version: 
+platform: ruby
+signing_key: 
+cert_chain: 
+post_install_message: 
+authors: 
+- Carl Youngblood
+files: 
+- test/sbn.rb
+- test/test_combination.rb
+- test/test_helpers.rb
+- test/test_learning.rb
+- test/test_net.rb
+- test/test_variable.rb
+- lib/combination.rb
+- lib/formats.rb
+- lib/helpers.rb
+- lib/inference.rb
+- lib/learning.rb
+- lib/net.rb
+- lib/numeric_variable.rb
+- lib/sbn.rb
+- lib/string_variable.rb
+- lib/variable.rb
+- README
+test_files: 
+- test/sbn.rb
+rdoc_options: 
+- --main
+- README
+extra_rdoc_files: 
+- README
+executables: []
+
+extensions: []
+
+requirements: []
+
+dependencies: []
+