sbn 0.9.0 → 0.9.1

data/.gitignore

@@ -0,0 +1,2 @@
+pkg
+doc

data/Gemfile

@@ -0,0 +1,4 @@
+source "http://rubygems.org"
+
+# Specify your gem's dependencies in sbn.gemspec
+gemspec

data/Gemfile.lock

@@ -0,0 +1,26 @@
+PATH
+  remote: .
+  specs:
+    sbn (0.9.1)
+      activesupport (~> 3.1.0)
+      builder (~> 3.0.0)
+      i18n (~> 0.6.0)
+      xml-simple (~> 1.1.0)
+
+GEM
+  remote: http://rubygems.org/
+  specs:
+    activesupport (3.1.0)
+      multi_json (~> 1.0)
+    builder (3.0.0)
+    i18n (0.6.0)
+    multi_json (1.0.3)
+    rake (0.9.2)
+    xml-simple (1.1.0)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  rake (~> 0.9.2)
+  sbn!

data/{README → README.rdoc}

@@ -1,6 +1,6 @@
 = SBN - Simple Bayesian Networks
 == Software License Agreement
-Copyright (c) 2005-2007 Carl Youngblood mailto:carl@youngbloods.org
+Copyright (c) 2005-2011 Carl Youngblood mailto:carl@youngbloods.org
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -38,7 +38,7 @@ Installation of SBN is simple:
  # gem install sbn
 
 == A Basic Example
-http://youngbloods.org/sbn/images/grass_wetness.png
+http://dl.dropbox.com/u/654274/sbn/images/grass_wetness.png
 
 We'll begin with a network whose probabilities have been pre-determined. This
 example comes from the excellent <em>Artificial Intelligence: A Modern
@@ -284,7 +284,7 @@ The following example shows a network that uses these advanced variable types:
 
 Before parameter learning occurs on this network, it looks like this:
 
-http://youngbloods.org/sbn/images/stringvar1.png
+http://dl.dropbox.com/u/654274/sbn/images/stringvar1.png
 
 The <em>Category</em> variable represents a budget category for a financial
 transaction. The <em>Amount</em> variable is for the amount of the transaction
@@ -296,7 +296,7 @@ this network:
 
 After adding that sample point, the network would look something like this:
 
-http://youngbloods.org/sbn/images/stringvar2.png
+http://dl.dropbox.com/u/654274/sbn/images/stringvar2.png
 
 The variables with dashed edges are the string covariables that were created
 by the managing string variable when it saw a new string in the sample points.
@@ -312,9 +312,9 @@ are some of the possible improvements that may be added in future releases:
 * Saving the sample points along with the network when saving to XMLBIF
 * Speedier inference using native C++ with vectorization provided by macstl[http://www.pixelglow.com/macstl/]
 * Speedier inference through parallelization
-* Support for learning network structure
+* Support for inference of variable relationships from sample points
 * Support for customizing the number of iterations in the MCMC algorithm (currently hard-coded)
 * Support for customizing the size of ngrams used in string variables
 * Support for intelligently determining the best number of iterations for MCMC at runtime based on the desired level of precision
 
-Please share your own ideas with us and help to improve this library.
+Please share your own ideas with us and help to improve this library.

data/Rakefile

@@ -0,0 +1,11 @@
+require "bundler/gem_tasks"
+
+task :default => :test
+
+task :test do
+  exec "testrb test"
+end
+
+task :doc do
+  exec "rdoc --quiet --main README --exclude test* README lib/*"
+end

data/data/grass_wetness.dot

@@ -0,0 +1,9 @@
+digraph untitled
+	{
+		cloudy[label=""];
+		sprinkler[label=""]
+		rain[label=""]
+		
+		cloudy -> sprinkler;
+		cloudy -> rain[style="dashed"];
+	}

data/data/grass_wetness.xml

@@ -0,0 +1,71 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--       
+        Bayesian network in XMLBIF v0.3 (BayesNet Interchange Format)
+        Produced by SBN4R (Simple Bayesian Network library for Ruby)
+        Output created Sat Jan 27 17:00:04 -0700 2007
+ -->
+
+<!-- DTD for the XMLBIF 0.3 format -->
+<!DOCTYPE bif [
+  <!ELEMENT bif (network)*>
+  <!ATTLIST bif version CDATA #REQUIRED>
+  <!ELEMENT network (name, (property | variable | definition)*)>
+  <!ELEMENT name (#PCDATA)>
+  <!ELEMENT variable (name, (outcome | property)*)>
+  <!ATTLIST variable type (nature | decision | utility) "nature">
+  <!ELEMENT outcome (#PCDATA)>
+  <!ELEMENT definition (for | given | table | property)*>
+  <!ELEMENT for (#PCDATA)>
+  <!ELEMENT given (#PCDATA)>
+  <!ELEMENT table (#PCDATA)>
+  <!ELEMENT property (#PCDATA)>
+]>
+<bif version="0.3">
+  <network>
+    <name>Grass_Wetness_Belief_Net</name>
+
+    <!-- Variables -->
+    <variable type="nature">
+      <name>Cloudy</name>
+      <outcome>true</outcome>
+      <outcome>false</outcome>
+    </variable>
+    <variable type="nature">
+      <name>Grass_Wet</name>
+      <outcome>true</outcome>
+      <outcome>false</outcome>
+    </variable>
+    <variable type="nature">
+      <name>Sprinkler</name>
+      <outcome>true</outcome>
+      <outcome>false</outcome>
+    </variable>
+    <variable type="nature">
+      <name>Rain</name>
+      <outcome>true</outcome>
+      <outcome>false</outcome>
+    </variable>
+
+    <!-- Probability distributions -->
+    <definition>
+      <for>Cloudy</for>
+      <table>0.5 0.5</table>
+    </definition>
+    <definition>
+      <for>Grass_Wet</for>
+      <given>Sprinkler</given>
+      <given>Rain</given>
+      <table>0.99 0.01 0.9 0.1 0.9 0.1 0.0 1.0</table>
+    </definition>
+    <definition>
+      <for>Sprinkler</for>
+      <given>Cloudy</given>
+      <table>0.1 0.9 0.5 0.5</table>
+    </definition>
+    <definition>
+      <for>Rain</for>
+      <given>Cloudy</given>
+      <table>0.8 0.2 0.2 0.8</table>
+    </definition>
+  </network>
+</bif>

data/data/stringvar1.dot

@@ -0,0 +1,9 @@
+digraph untitled
+	{
+	  category[label="Category"]
+		amount[label="Amount\n(NumericVariable)"];
+		merchant[label="Merchant\n(StringVariable)"]
+		
+		category -> amount;
+		category -> merchant;
+	}

data/data/stringvar2.dot

@@ -0,0 +1,25 @@
+digraph untitled
+	{
+	  category[label="Category"];
+		amount[label="Amount\n(NumericVariable)"];
+		merchant[label="Merchant\n(StringVariable)"];
+		covar1[label="merchant_covar_che",style="dashed"]
+		covar2[label="merchant_covar_hev",style="dashed"]
+		covar3[label="merchant_covar_evr",style="dashed"]
+		covar4[label="merchant_covar_vro",style="dashed"]
+		covar5[label="merchant_covar_ron",style="dashed"]
+		covar6[label="merchant_covar_chevro",style="dashed"]
+		covar7[label="merchant_covar_hevron",style="dashed"]
+		covar8[label="merchant_covar_chevron",style="dashed"]
+		
+		category -> amount;
+		category -> merchant;
+		category -> covar1[style="dashed"];
+		category -> covar2[style="dashed"];
+		category -> covar3[style="dashed"];
+		category -> covar4[style="dashed"];
+		category -> covar5[style="dashed"];
+		category -> covar6[style="dashed"];
+		category -> covar7[style="dashed"];
+		category -> covar8[style="dashed"];
+	}

data/lib/sbn.rb

@@ -1,6 +1,12 @@
-require 'rubygems'
-require 'active_support'
-gem 'builder', '>=2.0'
-require 'builder'
+require 'active_support/inflector'
 
-Dir[File.join(File.dirname(__FILE__), '*.rb')].sort.each { |lib| require lib unless lib == 'sbn.rb' }
+require 'sbn/version'
+require 'sbn/helpers'
+require 'sbn/variable'
+require 'sbn/numeric_variable'
+require 'sbn/string_variable'
+require 'sbn/combination'
+require 'sbn/formats'
+require 'sbn/inference'
+require 'sbn/learning'
+require 'sbn/net'

data/lib/sbn/combination.rb

@@ -0,0 +1,80 @@
+# = combination.rb: Class for handling variable state combinations
+# Copyright (C) 2005-2007  Carl Youngblood mailto:carl@youngbloods.org
+#
+# Takes an array of arrays and iterates over all combinations of sub-elements.
+# For example:
+# 
+#  c = Sbn::Combination.new([[1, 2], [6, 7, 8]])
+#  c.each {|comb| p comb }
+#
+# Will produce:
+#
+#  [1, 6]
+#  [1, 7]
+#  [1, 8]
+#  [2, 6]
+#  [2, 7]
+#  [2, 8]
+
+module Sbn
+  class Combination # :nodoc:
+    include Enumerable
+  
+    def initialize(arr)
+      @arr = arr
+      @current = Array.new(arr.size, 0)
+    end
+  
+    def each
+      iterations = @arr.inject(1) {|product, element| product * element.size } - 1
+      yield current
+      iterations.times { yield self.next_combination }
+    end
+  
+    def <=>(other)
+      @current <=> other.current
+    end
+
+    def first
+      @current.fill 0
+    end
+  
+    def last
+      @current.size.times {|i| @current[i] = @arr[i].size - 1 }
+    end
+  
+    def current
+      returnval = []
+      @current.size.times {|i| returnval[i] = @arr[i][@current[i]] }
+      returnval
+    end 
+  
+    def next_combination
+      i = @current.size - 1
+      @current.reverse.each do |e|
+        if e == @arr[i].size - 1
+          @current[i] = 0
+        else
+          @current[i] += 1
+          break
+        end
+        i -= 1
+      end
+      current
+    end
+  
+    def prev_combination
+      i = @current.size - 1
+      @current.reverse.each do |e|
+        if e == 0
+          @current[i] = @arr[i].size - 1
+        else
+          @current[i] -= 1
+          break
+        end
+        i -= 1
+      end
+      current
+    end
+  end
+end

data/lib/{formats.rb → sbn/formats.rb}

@@ -1,4 +1,7 @@
-class Sbn
+require 'builder'
+require 'xmlsimple'
+
+module Sbn
   class Net
     # Returns a string containing a representation of the network in XMLBIF format.
     # http://www.cs.cmu.edu/afs/cs/user/fgcozman/www/Research/InterchangeFormat

data/lib/{inference.rb → sbn/inference.rb}

@@ -1,4 +1,4 @@
-class Sbn
+module Sbn
   class Net
     MCMC_DEFAULT_SAMPLE_COUNT = 2000
 

data/lib/{learning.rb → sbn/learning.rb}

@@ -1,4 +1,4 @@
-class Sbn
+module Sbn
   class Variable
     NEGLIGIBLE_PROBABILITY = 0.0001
     

data/lib/{net.rb → sbn/net.rb}

@@ -1,4 +1,4 @@
-class Sbn
+module Sbn
   class Net
     attr_reader :name, :variables
     

data/lib/{numeric_variable.rb → sbn/numeric_variable.rb}

@@ -1,6 +1,4 @@
-require File.dirname(__FILE__) + '/variable'
-
-class Sbn
+module Sbn
   class NumericVariable < Variable
     DEFAULT_FIRST_STDEV_STATE_COUNT = 14
     DEFAULT_SECOND_STDEV_STATE_COUNT = 6

data/lib/{string_variable.rb → sbn/string_variable.rb}

@@ -1,6 +1,4 @@
-require File.dirname(__FILE__) + '/variable'
-
-class Sbn
+module Sbn
   class StringCovariable < Variable # :nodoc:
     attr_reader :text_to_match
     

data/lib/{variable.rb → sbn/variable.rb}

@@ -1,4 +1,4 @@
-class Sbn
+module Sbn
   class Variable
     attr_reader :name, :states, :parents, :children, :probability_table
     

data/lib/sbn/version.rb

@@ -0,0 +1,3 @@
+module Sbn
+  VERSION = "0.9.1"
+end

data/sbn.gemspec

@@ -0,0 +1,26 @@
+# -*- encoding: utf-8 -*-
+$:.push File.expand_path("../lib", __FILE__)
+require "sbn/version"
+
+Gem::Specification.new do |s|
+  s.name        = "sbn"
+  s.version     = Sbn::VERSION
+  s.authors     = ["Carl Youngblood"]
+  s.email       = ["carl@youngbloods.org"]
+  s.homepage    = "http://github.com/cayblood/sbn"
+  s.summary     = "Simple Bayesian Network Library"
+  s.description = "SBN makes it easy to use Bayesian Networks in your ruby application."
+
+  s.rubyforge_project = "sbn"
+
+  s.files         = `git ls-files`.split("\n")
+  s.test_files    = `git ls-files -- {test,spec,features}/*`.split("\n")
+  s.executables   = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) }
+  s.require_paths = ["lib"]
+
+  s.add_development_dependency "rake",          "~> 0.9.2"
+  s.add_runtime_dependency     "builder",       "~> 3.0.0"
+  s.add_runtime_dependency     "xml-simple",    "~> 1.1.0"
+  s.add_runtime_dependency     "i18n",          "~> 0.6.0"
+  s.add_runtime_dependency     "activesupport", "~> 3.1.0"
+end

data/test/test_combination.rb

@@ -1,9 +1,9 @@
 require 'test/unit'
-require File.dirname(__FILE__) + '/../lib/sbn'
+require 'sbn/combination'
 
 class TestCombination < Test::Unit::TestCase # :nodoc:
   def setup
-    @c = Combination.new([[1, 2], [3, 4, 5]])
+    @c = Sbn::Combination.new([[1, 2], [3, 4, 5]])
   end
 
   def test_current

data/test/test_helpers.rb

@@ -1,5 +1,5 @@
 require 'test/unit'
-require File.dirname(__FILE__) + '/../lib/sbn'
+require 'sbn/helpers'
 
 class EnumsTester
   enums %w(FOO BAR BAZ)

data/test/test_learning.rb

@@ -1,5 +1,5 @@
 require 'test/unit'
-require File.dirname(__FILE__) + '/../lib/sbn'
+require 'sbn'
 
 class TestLearning < Test::Unit::TestCase # :nodoc:
   def setup

data/test/test_net.rb

@@ -1,5 +1,5 @@
 require 'test/unit'
-require File.dirname(__FILE__) + '/../lib/sbn'
+require 'sbn'
 
 class TestNet < Test::Unit::TestCase # :nodoc:
   def setup

data/test/test_variable.rb

@@ -1,5 +1,5 @@
 require 'test/unit'
-require File.dirname(__FILE__) + '/../lib/sbn'
+require 'sbn'
 
 class TestVariable < Test::Unit::TestCase # :nodoc:
   def setup

metadata

@@ -1,63 +1,140 @@
---- !ruby/object:Gem::Specification 
-rubygems_version: 0.9.2
-specification_version: 1
+--- !ruby/object:Gem::Specification
 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: 
+version: !ruby/object:Gem::Version
+  version: 0.9.1
+  prerelease: 
 platform: ruby
-signing_key: 
-cert_chain: 
-post_install_message: 
-authors: 
+authors:
 - Carl Youngblood
-files: 
-- test/sbn.rb
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2011-09-18 00:00:00.000000000Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: &70106710764580 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.9.2
+  type: :development
+  prerelease: false
+  version_requirements: *70106710764580
+- !ruby/object:Gem::Dependency
+  name: builder
+  requirement: &70106710763900 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 3.0.0
+  type: :runtime
+  prerelease: false
+  version_requirements: *70106710763900
+- !ruby/object:Gem::Dependency
+  name: xml-simple
+  requirement: &70106710763320 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.1.0
+  type: :runtime
+  prerelease: false
+  version_requirements: *70106710763320
+- !ruby/object:Gem::Dependency
+  name: i18n
+  requirement: &70106710762480 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.6.0
+  type: :runtime
+  prerelease: false
+  version_requirements: *70106710762480
+- !ruby/object:Gem::Dependency
+  name: activesupport
+  requirement: &70106710761320 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 3.1.0
+  type: :runtime
+  prerelease: false
+  version_requirements: *70106710761320
+description: SBN makes it easy to use Bayesian Networks in your ruby application.
+email:
+- carl@youngbloods.org
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- .gitignore
+- Gemfile
+- Gemfile.lock
+- README.rdoc
+- Rakefile
+- data/grass_wetness.dot
+- data/grass_wetness.xml
+- data/images/grass_wetness.png
+- data/images/stringvar1.png
+- data/images/stringvar2.png
+- data/stringvar1.dot
+- data/stringvar2.dot
+- lib/sbn.rb
+- lib/sbn/combination.rb
+- lib/sbn/formats.rb
+- lib/sbn/helpers.rb
+- lib/sbn/inference.rb
+- lib/sbn/learning.rb
+- lib/sbn/net.rb
+- lib/sbn/numeric_variable.rb
+- lib/sbn/string_variable.rb
+- lib/sbn/variable.rb
+- lib/sbn/version.rb
+- sbn.gemspec
 - 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: []
-
+homepage: http://github.com/cayblood/sbn
+licenses: []
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
+      - 0
+      hash: -2564604872438714073
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
+      - 0
+      hash: -2564604872438714073
 requirements: []
-
-dependencies: []
-
+rubyforge_project: sbn
+rubygems_version: 1.8.6
+signing_key: 
+specification_version: 3
+summary: Simple Bayesian Network Library
+test_files:
+- test/test_combination.rb
+- test/test_helpers.rb
+- test/test_learning.rb
+- test/test_net.rb
+- test/test_variable.rb

data/lib/combination.rb

@@ -1,78 +0,0 @@
-# = combination.rb: Class for handling variable state combinations
-# Copyright (C) 2005-2007  Carl Youngblood mailto:carl@youngbloods.org
-#
-# Takes an array of arrays and iterates over all combinations of sub-elements.
-# For example:
-# 
-#  c = Combination.new([[1, 2], [6, 7, 8]])
-#  c.each {|comb| p comb }
-#
-# Will produce:
-#
-#  [1, 6]
-#  [1, 7]
-#  [1, 8]
-#  [2, 6]
-#  [2, 7]
-#  [2, 8]
-
-class Combination # :nodoc:
-  include Enumerable
-  
-  def initialize(arr)
-    @arr = arr
-    @current = Array.new(arr.size, 0)
-  end
-  
-  def each
-    iterations = @arr.inject(1) {|product, element| product * element.size } - 1
-    yield current
-    iterations.times { yield self.next_combination }
-  end
-  
-  def <=>(other)
-    @current <=> other.current
-  end
-
-  def first
-    @current.fill 0
-  end
-  
-  def last
-    @current.size.times {|i| @current[i] = @arr[i].size - 1 }
-  end
-  
-  def current
-    returnval = []
-    @current.size.times {|i| returnval[i] = @arr[i][@current[i]] }
-    returnval
-  end 
-  
-  def next_combination
-    i = @current.size - 1
-    @current.reverse.each do |e|
-      if e == @arr[i].size - 1
-        @current[i] = 0
-      else
-        @current[i] += 1
-        break
-      end
-      i -= 1
-    end
-    current
-  end
-  
-  def prev_combination
-    i = @current.size - 1
-    @current.reverse.each do |e|
-      if e == 0
-        @current[i] = @arr[i].size - 1
-      else
-        @current[i] -= 1
-        break
-      end
-      i -= 1
-    end
-    current
-  end
-end

data/test/sbn.rb

@@ -1,5 +0,0 @@
-require 'test/unit'
-files = Dir[File.dirname(__FILE__) + '/*.rb']
-files.each do |f|
-  require f unless f =~ /sbn/
-end