bayesnet 0.0.3 → 0.1.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/CHANGELOG.md

@@ -1,5 +1,15 @@
 ## [Unreleased]
 
+## [0.5.0] - 2022-02-26
+
+- Constructing networks out of the `.BIF` ([Interchange Format for Bayesian Networks](https://www.cs.washington.edu/dm/vfml/appendixes/bif.htm)) files.
+- Fixing inference bug
+- Network children nodes could be specified ***before** their parents
+
+## [0.0.3] - 2021-12-29
+
+- Fixing terminoloty used in Factor class
+
 ## [0.0.2] - 2021-12-28
 
 - README, CI/CD for Ruby 2.6, 2.7, 3.1 added

data/Gemfile

@@ -6,10 +6,10 @@ source "https://rubygems.org"
 gemspec
 
 gem "rake", "~> 13.0"
+gem "treetop", "~> 1.6"
 
 group :development, :test do
   gem "m", "~> 1.5.0"
   gem "minitest", "~> 5.0"
   gem "pry-byebug", "~> 3.9.0"
-  gem "standard", "~> 1.3"
 end

data/Gemfile.lock

@@ -1,12 +1,11 @@
 PATH
   remote: .
   specs:
-    bayesnet (0.0.3)
+    bayesnet (0.1.0)
 
 GEM
   remote: https://rubygems.org/
   specs:
-    ast (2.4.2)
     byebug (11.1.3)
     coderay (1.1.3)
     m (1.5.1)
@@ -14,38 +13,16 @@ GEM
       rake (>= 0.9.2.2)
     method_source (1.0.0)
     minitest (5.15.0)
-    parallel (1.21.0)
-    parser (3.0.3.2)
-      ast (~> 2.4.1)
+    polyglot (0.3.5)
     pry (0.13.1)
       coderay (~> 1.1)
       method_source (~> 1.0)
     pry-byebug (3.9.0)
       byebug (~> 11.0)
       pry (~> 0.13.0)
-    rainbow (3.0.0)
     rake (13.0.6)
-    regexp_parser (2.2.0)
-    rexml (3.2.5)
-    rubocop (1.23.0)
-      parallel (~> 1.10)
-      parser (>= 3.0.0.0)
-      rainbow (>= 2.2.2, < 4.0)
-      regexp_parser (>= 1.8, < 3.0)
-      rexml
-      rubocop-ast (>= 1.12.0, < 2.0)
-      ruby-progressbar (~> 1.7)
-      unicode-display_width (>= 1.4.0, < 3.0)
-    rubocop-ast (1.15.0)
-      parser (>= 3.0.1.1)
-    rubocop-performance (1.12.0)
-      rubocop (>= 1.7.0, < 2.0)
-      rubocop-ast (>= 0.4.0)
-    ruby-progressbar (1.11.0)
-    standard (1.5.0)
-      rubocop (= 1.23.0)
-      rubocop-performance (= 1.12.0)
-    unicode-display_width (2.1.0)
+    treetop (1.6.11)
+      polyglot (~> 0.3)
 
 PLATFORMS
   x86_64-darwin-19
@@ -57,7 +34,7 @@ DEPENDENCIES
   minitest (~> 5.0)
   pry-byebug (~> 3.9.0)
   rake (~> 13.0)
-  standard (~> 1.3)
+  treetop (~> 1.6)
 
 BUNDLED WITH
-   2.2.32
+   2.3.3

data/README.md

@@ -1,6 +1,7 @@
 # Bayesnet
 
-This gem provides an API for building a Bayesian network and executing some queries against it.
+This gem provides an DSL for constructing Bayesian networks and let to execute basic inference queries. It is also capable of parsing .BIF format ([The Interchange Format for Bayesian Networks](https://www.cs.washington.edu/dm/vfml/appendixes/bif.htm)).
+
 
 ### Example:
 
@@ -66,12 +67,14 @@ The inference is based on summing over joint distribution, i.e. it is the simple
 most expensive way to calculate it. No optimization is implemented in this version; the code
 is more a proof of API.
 
+### [Another example](https://afurmanov.com/reducing-anxiety-with-bayesian-network) of using this gem
+
 ## Installation
 
 Add this line to your application's Gemfile:
 
 ```ruby
-gem 'bayesnet'
+em 'bayesnet'
 ```
 
 And then execute:

data/Rakefile

@@ -9,6 +9,9 @@ Rake::TestTask.new(:test) do |t|
   t.test_files = FileList["test/**/*_test.rb"]
 end
 
-require "standard/rake"
+Rake::TestTask.new("regen-bif") do |t|
+  `rm ./lib/bayesnet/parsers/bif.rb`
+  `tt ./lib/bayesnet/parsers/bif.treetop`
+end
 
-task default: %i[test standard]
+task default: %i[test]

data/bayesnet.gemspec

@@ -34,7 +34,6 @@ Gem::Specification.new do |spec|
   spec.add_development_dependency "m", "~> 1.5.0"
   spec.add_development_dependency "minitest", "~> 5.0"
   spec.add_development_dependency "pry-byebug", "~> 3.9.0"
-  spec.add_development_dependency "standard", "~> 1.3"
 
   # For more information and examples about making a new gem, checkout our
   # guide at: https://bundler.io/guides/creating_gem.html

data/lib/bayesnet/dsl.rb

@@ -1,10 +1,14 @@
+# frozen_string_literal: true
+
 require "bayesnet/graph"
 
 module Bayesnet
+  # Bayesnet::DSL.define ...
   module DSL
     def define(&block)
       graph = Graph.new
       graph.instance_eval(&block) if block
+      graph.resolve_factors
       graph
     end
   end

data/lib/bayesnet/error.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 module Bayesnet
   class Error < StandardError
   end

data/lib/bayesnet/factor.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 module Bayesnet
   # Factor if a function of sevaral variables (A, B, ...) each defined on values from finite set
   class Factor
@@ -14,9 +16,7 @@ module Bayesnet
 
     # Specifies value for a scope context. Value is the last element in `context_and_val`
     def val(*context_and_val)
-      if context_and_val.size == 1 && context_and_val[0].is_a?(Array)
-        context_and_val = context_and_val[0]
-      end
+      context_and_val = context_and_val[0] if context_and_val.size == 1 && context_and_val[0].is_a?(Array)
       @vals[context_and_val[0..-2]] = context_and_val[-1]
     end
 
@@ -26,10 +26,10 @@ module Bayesnet
 
     def [](*context)
       key = if context.size == 1 && context[0].is_a?(Hash)
-        context[0].slice(*var_names).values
-      else
-        context
-      end
+              context[0].slice(*var_names).values
+            else
+              context
+            end
       @vals[key]
     end
 
@@ -39,6 +39,7 @@ module Bayesnet
 
     def contextes(*var_names)
       return [] if var_names.empty?
+
       @scope[var_names[0]].product(*var_names[1..].map { |var_name| @scope[var_name] })
     end
 
@@ -49,29 +50,35 @@ module Bayesnet
     def normalize
       vals = @vals.clone
       norm_factor = vals.map(&:last).sum * 1.0
-      vals.each { |k, v| vals[k] /= norm_factor }
+      vals.each { |k, _v| vals[k] /= norm_factor }
       self.class.new(@scope.clone, vals)
     end
 
     def reduce_to(context)
-      # todo: use Hash#except when Ruby 2.6 support no longer needed
+      # TODO: use Hash#except when Ruby 2.6 support no longer needed
       context_keys_set = context.keys.to_set
       scope = @scope.reject { |k, _| context_keys_set.include?(k) }
 
       context_vals = context.values
       indices = context.keys.map { |k| index_by_var_name[k] }
-      vals = @vals.select { |k, v| indices.map { |i| k[i] } == context_vals }
-      vals.transform_keys! { |k| k - context_vals }
+      vals = @vals.select { |k, _v| indices.map { |i| k[i] } == context_vals }
+      vals.transform_keys! { |k| delete_by_indices(k, indices) }
 
       self.class.new(scope, vals)
     end
 
+    def delete_by_indices(array, indices)
+      result = array.dup
+      indices.map { |i| result[i] = nil }
+      result.compact
+    end
+
     # groups by `var_names` having same context and sum out values.
     def marginalize(var_names)
       scope = @scope.slice(*var_names)
 
       indices = scope.keys.map { |k| index_by_var_name[k] }
-      vals = @vals.group_by { |context, val| indices.map { |i| context[i] } }
+      vals = @vals.group_by { |context, _val| indices.map { |i| context[i] } }
       vals.transform_values! { |v| v.map(&:last).sum }
 
       self.class.new(scope, vals)
@@ -86,8 +93,9 @@ module Bayesnet
 
     def index_by_var_name
       return @index_by_var_name if @index_by_var_name
+
       @index_by_var_name = {}
-      @scope.each_with_index { |(k, v), i| @index_by_var_name[k] = i }
+      @scope.each_with_index { |(k, _v), i| @index_by_var_name[k] = i }
       @index_by_var_name
     end
   end

data/lib/bayesnet/graph.rb

@@ -1,6 +1,9 @@
+# frozen_string_literal: true
+
 require "bayesnet/node"
 
 module Bayesnet
+  # Acyclic graph
   class Graph
     attr_reader :nodes
 
@@ -14,11 +17,18 @@ module Bayesnet
 
     def node(name, parents: [], &block)
       raise Error, "DSL error, #node requires a &block" unless block
-      node = Node.new(name, @nodes.slice(*parents))
+
+      node = Node.new(name, parents)
       node.instance_eval(&block)
       @nodes[name] = node
     end
 
+    def resolve_factors
+      @nodes.values.each do |node|
+        node.resolve_factor(@nodes.slice(*node.parent_nodes))
+      end
+    end
+
     def distribution(over: [], evidence: {})
       joint_distribution
         .reduce_to(evidence)
@@ -61,5 +71,9 @@ module Bayesnet
       end
       @joint_distribution = factor.normalize
     end
+
+    def parameters
+      nodes.values.map(&:parameters).sum
+    end
   end
 end

data/lib/bayesnet/node.rb

@@ -24,6 +24,14 @@ module Bayesnet
       when Array
         raise Error, "DSL error, #values requires a &block when first argument is an Array" unless block
         @values = hash_or_array
+        @factor = block
+      end
+    end
+
+    def resolve_factor(parent_nodes)
+      @parent_nodes = parent_nodes
+      if @factor.is_a?(Proc)
+        proc = @factor
         node = self
         @factor = Factor.build do
           scope node.name => node.values
@@ -31,7 +39,7 @@ module Bayesnet
             scope parent_node_name => parent_node.values
           end
         end
-        instance_eval(&block)
+        instance_eval(&proc)
       end
     end
 
@@ -39,6 +47,10 @@ module Bayesnet
       instance_eval(&block)
     end
 
+    def parameters
+      (values.size - 1) * parent_nodes.values.reduce(1) { |mul, n| mul * n.values.size }
+    end
+
     def as(distribution, given:)
       @values.zip(distribution).each do |value, probability|
         @factor.val [value] + given + [probability]