fselector 0.6.0 → 0.7.0

data/ChangeLog

@@ -1,3 +1,12 @@
+2012-04-20	Tiejun Cheng	<need47@gmail.com>
+
+  * update to version 0.7.0
+
+2012-04-19	Tiejun Cheng	<need47@gmail.com>
+
+  * add new algorithm BetweenWithinClassesSumOfSquare (BSS_WSS) for continuous feature
+  * add new algorithm WilcoxonRankSum (WRS) for continuous feature
+
 2012-04-18	Tiejun Cheng	<need47@gmail.com>
 
   * require the RinRuby gem (http://rinruby.ddahl.org) to access the 

data/README.md

@@ -3,13 +3,13 @@ FSelector: a Ruby gem for feature selection and ranking
 
 **Home** [https://rubygems.org/gems/fselector](https://rubygems.org/gems/fselector)  
 **Source Code**: [https://github.com/need47/fselector](https://github.com/need47/fselector)  
-**Documentation** [http://rubydoc.info/github/need47/fselector/master/frames](http://rubydoc.info/github/need47/fselector/master/frames)  
+**Documentation** [http://rubydoc.info/gems/fselector/frames](http://rubydoc.info/gems/fselector/frames)  
 **Author**: Tiejun Cheng  
 **Email**: [need47@gmail.com](mailto:need47@gmail.com)  
 **Copyright**: 2012  
 **License**: MIT License  
-**Latest Version**: 0.6.0  
-**Release Date**: April 19 2012
+**Latest Version**: 0.7.0  
+**Release Date**: April 20 2012
 
 Synopsis
 --------
@@ -41,8 +41,8 @@ Feature List
 
 **2. available feature selection/ranking algorithms**
     
-    algorithm                         alias       feature_type
-    ----------------------------------------------------------
+    algorithm                         alias       feature_type  applicability
+    --------------------------------------------------------------------------------------
     Accuracy                          Acc         discrete
     AccuracyBalanced                  Acc2        discrete
     BiNormalSeparation                BNS         discrete
@@ -67,16 +67,18 @@ Feature List
     ProbabilityRatio                  PR          discrete
     Random                            Random      discrete
     Recall                            Recall      discrete
-    Relief_d                          Relief_d    discrete
+    Relief_d                          Relief_d    discrete      two-class, no missing data
     ReliefF_d                         ReliefF_d   discrete
     Sensitivity                       SN, Recall  discrete
     Specificity                       SP          discrete
     SymmetricalUncertainty            SU          discrete
+    BetweenWithinClassesSumOfSquare   BSS_WSS     continuous
     CFS_c                             CFS_c       continuous
-    PMetric                           PM          continuous
-    Relief_c                          Relief_c    continuous
+    PMetric                           PM          continuous    two-class
+    Relief_c                          Relief_c    continuous    two-class, no missing data
     ReliefF_c                         ReliefF_c   continuous
-    TScore                            TS          continuous
+    TScore                            TS          continuous    two-class
+    WilcoxonRankSum                   WRS         continuous    two-class
     
   **note for feature selection interace:**   
     - for the algorithms of CFS\_d, FCBF and CFS\_c, use select\_feature!  
@@ -120,7 +122,7 @@ To install FSelector, use the following command:
   as a seemless bridge to access the statistical routines in the R package (http://www.r-project.org), 
   which will greatly expand the inclusion of algorithms to FSelector, especially for those relying 
   on statistical test. To this end, please pre-install the R package. RinRuby should have been 
-  auto-installed with FSelector.
+  auto-installed with FSelector by the above command.
   
 Usage
 -----

data/lib/fselector.rb

@@ -6,9 +6,10 @@ require 'rinruby'
 #
 module FSelector
   # module version
-  VERSION = '0.6.0'
+  VERSION = '0.7.0'
 end
 
+# the root dir of FSelector
 ROOT = File.expand_path(File.dirname(__FILE__))
 
 #

data/lib/fselector/algo_continuous/BSS_WSS.rb

@@ -0,0 +1,48 @@
+#
+# FSelector: a Ruby gem for feature selection and ranking
+#
+module FSelector
+#
+# between-within classes sum of squares (BSS/WSS) for continous feature
+# 
+#                   sigma_i sigma_k I(yi=k)(xbar_kj - xbar_xj)2
+#     BSS_WSS(f) = ----------------------------------------------
+#                     sigma_i sigma_k I(yi=k)(x_ij - xbar_kj)2
+#
+# ref: [Comparison of Discrimination Methods for the Classification of Tumors Using Gene Expression Data](http://amstat.tandfonline.com/doi/abs/10.1198/016214502753479248)
+#
+  class BetweenWithinClassesSumOfSquare < BaseContinuous
+        
+    private    
+    
+    # calculate contribution of each feature (f) across all classes
+    def calc_contribution(f)
+      xbar_xj = get_feature_values(f).mean
+      
+      a, b, s = 0.0, 0.0, 0.0
+      
+      each_sample do |k, sam|
+        # get the feature values for class k, without missing values
+        xbar_kj = get_feature_values(f, nil, k).mean
+        a += (xbar_kj - xbar_xj)**2
+        
+        if sam.has_key? f
+          x_ij = sam[f]
+          b += (x_ij - xbar_kj)**2
+        end
+      end
+      
+      s = a/b if not b.zero?
+      
+      set_feature_score(f, :BEST, s)
+    end # calc_contribution
+    
+    
+  end # class
+  
+  
+  # shortcut so that you can use FSelector::BSS_WSS instead of FSelector::BetweenWithinClassesSumOfSquare
+  BSS_WSS = BetweenWithinClassesSumOfSquare
+  
+  
+end # module

data/lib/fselector/algo_continuous/PMetric.rb

@@ -24,14 +24,10 @@ module FSelector
               "suitable only for two-class problem with continuous feature"
       end
       
-      # collect data for class 1 and 2, respectively
-      s1, s2 = [], []      
+      # collect data for class 1 and 2, respectively   
       k1, k2 = get_classes
-      
-      each_sample do |k, ss|
-        s1 << ss[f] if k == k1 and ss.has_key? f 
-        s2 << ss[f] if k == k2 and ss.has_key? f
-      end
+      s1 = get_feature_values(f, nil, k1)
+      s2 = get_feature_values(f, nil, k2)
       
       # calc
       s = 0.0

data/lib/fselector/algo_continuous/TScore.rb

@@ -24,14 +24,10 @@ module FSelector
               "suitable only for two-class problem with continuous feature"
       end
       
-      # collect data for class 1 and 2, respectively
-      s1, s2 = [], []      
+      # collect data for class 1 and 2, respectively   
       k1, k2 = get_classes
-           
-      each_sample do |k, ss|
-        s1 << ss[f] if k == k1 and ss.has_key? f
-        s2 << ss[f] if k == k2 and ss.has_key? f
-      end
+      s1 = get_feature_values(f, nil, k1)
+      s2 = get_feature_values(f, nil, k2)
       
       # calc
       n1, n2 = s1.size, s2.size

data/lib/fselector/algo_continuous/WilcoxonRankSum.rb

@@ -0,0 +1,49 @@
+#
+# FSelector: a Ruby gem for feature selection and ranking
+#
+module FSelector
+#
+# Wilcoxon Rank Sum (WRS) for continous feature
+#
+# @note WRS applicable only to two-class problems
+#
+# for WRS (p-value), the smaller, the better, but we intentionally negate it
+# so that the larger is always the better (consistent with other algorithms).
+# R equivalent: wilcox.test
+#
+# ref: [An Efficient and Robust Statistical Modeling Approach to Discover Differentially Expressed Genes Using Genomic Expression Profiles](http://genome.cshlp.org/content/11/7/1227)
+#
+  class WilcoxonRankSum < BaseContinuous
+        
+    private    
+    
+    # calculate contribution of each feature (f) across all classes
+    def calc_contribution(f)
+      if not get_classes.size == 2
+        abort "[#{__FILE__}@#{__LINE__}]: "+
+              "suitable only for two-class problem with continuous feature"
+      end
+      
+      # collect data for class 1 and 2, respectively     
+      k1, k2 = get_classes
+      R.s1 = get_feature_values(f, nil, k1) # class 1
+      R.s2 = get_feature_values(f, nil, k2) # class 2
+      
+      # Wilcoxon rank sum test
+      R.eval "rv <- wilcox.test(s1, s2)$p.value"
+      
+      # intensionally negate it
+      s = -1.0 * R.rv # pull the p-value from R
+      
+      set_feature_score(f, :BEST, s)
+    end # calc_contribution
+    
+    
+  end # class
+  
+  
+  # shortcut so that you can use FSelector::WRS instead of FSelector::WilcoxonRankSum
+  WRS = WilcoxonRankSum
+  
+  
+end # module

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: fselector
 version: !ruby/object:Gem::Version
-  version: 0.6.0
+  version: 0.7.0
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-04-19 00:00:00.000000000 Z
+date: 2012-04-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rinruby
-  requirement: &22515480 !ruby/object:Gem::Requirement
+  requirement: &26347848 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,7 +21,7 @@ dependencies:
         version: 2.0.2
   type: :runtime
   prerelease: false
-  version_requirements: *22515480
+  version_requirements: *26347848
 description: FSelector is a Ruby gem that aims to integrate various feature selection/ranking
   algorithms and related functions into one single package. Welcome to contact me
   (need47@gmail.com) if you'd like to contribute your own algorithms or report a bug.
@@ -49,11 +49,13 @@ files:
 - lib/fselector/algo_base/base_discrete.rb
 - lib/fselector/algo_base/base_Relief.rb
 - lib/fselector/algo_base/base_ReliefF.rb
+- lib/fselector/algo_continuous/BSS_WSS.rb
 - lib/fselector/algo_continuous/CFS_c.rb
 - lib/fselector/algo_continuous/PMetric.rb
 - lib/fselector/algo_continuous/ReliefF_c.rb
 - lib/fselector/algo_continuous/Relief_c.rb
 - lib/fselector/algo_continuous/TScore.rb
+- lib/fselector/algo_continuous/WilcoxonRankSum.rb
 - lib/fselector/algo_discrete/Accuracy.rb
 - lib/fselector/algo_discrete/AccuracyBalanced.rb
 - lib/fselector/algo_discrete/BiNormalSeparation.rb