hmm 0.1.0 → 0.2.0

data/Rakefile

@@ -12,6 +12,7 @@ begin
     gem.authors = ["David Tresner-Kirsch"]
     gem.add_development_dependency "thoughtbot-shoulda", ">= 0"
     gem.add_development_dependency "narray", ">= 0"
+    gem.add_dependency "narray", ">= 0"
     # gem is a Gem::Specification... see http://www.rubygems.org/read/chapter/20 for additional settings
   end
   Jeweler::GemcutterTasks.new

data/VERSION

@@ -1 +1 @@
-0.1.0
+0.2.0

data/hmm.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{hmm}
-  s.version = "0.1.0"
+  s.version = "0.2.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["David Tresner-Kirsch"]
-  s.date = %q{2009-12-02}
+  s.date = %q{2010-03-08}
   s.description = %q{This project is a Ruby gem ('hmm') for machine learning that natively implements a (somewhat) generalized Hidden Markov Model classifier.}
   s.email = %q{dwkirsch@gmail.com}
   s.extra_rdoc_files = [
@@ -45,13 +45,16 @@ Gem::Specification.new do |s|
     if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
       s.add_development_dependency(%q<thoughtbot-shoulda>, [">= 0"])
       s.add_development_dependency(%q<narray>, [">= 0"])
+      s.add_runtime_dependency(%q<narray>, [">= 0"])
     else
       s.add_dependency(%q<thoughtbot-shoulda>, [">= 0"])
       s.add_dependency(%q<narray>, [">= 0"])
+      s.add_dependency(%q<narray>, [">= 0"])
     end
   else
     s.add_dependency(%q<thoughtbot-shoulda>, [">= 0"])
     s.add_dependency(%q<narray>, [">= 0"])
+    s.add_dependency(%q<narray>, [">= 0"])
   end
 end
 

data/lib/hmm.rb

@@ -309,6 +309,15 @@ class HMM
 			alpha
 		end
 		
+		def log_likelihood(sequence)
+			alpha = forward_probability(sequence)
+			log_add(alpha[-1, true])
+		end
+		
+		def likelihood(sequence)
+			exp(log_likelihood(sequence))
+		end
+		
 		def log_add(values)
 			x = values.max
 			if x > -Infinity
@@ -407,9 +416,13 @@ class HMM
 			end
 		end
 		
-		def exp(array)
-			# e to the power of each element
-			array.collect{|n| Math::E ** n}
+		def exp(subject)
+			if subject.is_a?(Array) or subject.is_a?(NArray)
+				# e to the power of each element
+				subject.collect{|n| Math::E ** n}
+			else
+				return Math::E ** subject
+			end
 		end
 		
 		def argmax(narray)

data/test/test_hmm.rb

@@ -46,6 +46,14 @@ class TestHmm < Test::Unit::TestCase
 		assert close_enough(expected_beta, \
 			@simple_model.backward_probability(["A","B","A"]).collect{|x| Math::E**x})
 	end
+	
+	should "compute sequence likelihoods" do
+		assert @simple_model.likelihood(["A", "A"]) \
+			+@simple_model.likelihood(["A", "B"]) \
+			+@simple_model.likelihood(["B", "B"]) \
+			+@simple_model.likelihood(["B", "A"]) \
+			== 1
+	end
 		
 	should "compute xi" do
 		@simple_model.gamma(@simple_model.xi(["A","B","A"]))

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: hmm
 version: !ruby/object:Gem::Version 
-  version: 0.1.0
+  version: 0.2.0
 platform: ruby
 authors: 
 - David Tresner-Kirsch
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2009-12-02 00:00:00 -05:00
+date: 2010-03-08 00:00:00 -05:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -32,6 +32,16 @@ dependencies:
       - !ruby/object:Gem::Version 
         version: "0"
     version: 
+- !ruby/object:Gem::Dependency 
+  name: narray
+  type: :runtime
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+    version: 
 description: This project is a Ruby gem ('hmm') for machine learning that natively implements a (somewhat) generalized Hidden Markov Model classifier.
 email: dwkirsch@gmail.com
 executables: []