Changeset 820

Timestamp:

Mar 17, 2007, 10:54:52 PM (17 years ago)

Author:

Peter

Message:

Changed name again. ROCScore is now called AUC. Also fixed several bugs and added test for these.

Location:

trunk

Files:

• test/consensus_inputranker_test.cc (modified) (2 diffs)
• test/data_lookup_1d_test.cc (modified) (3 diffs)
• test/distance_test.cc (modified) (2 diffs)
• test/feature_selection_test.cc (modified) (2 diffs)
• test/inputranker_test.cc (modified) (2 diffs)
• test/score_test.cc (modified) (6 diffs)
• test/subset_generator_test.cc (modified) (3 diffs)
• yat/classifier/DataLookup1D.cc (modified) (1 diff)
• yat/random/random.h (modified) (2 diffs)
• yat/statistics/AUC.cc (moved) (moved from trunk/yat/statistics/ROCScore.cc) (5 diffs)
• yat/statistics/AUC.h (moved) (moved from trunk/yat/statistics/ROCScore.h) (3 diffs)
• yat/statistics/Makefile.am (modified) (2 diffs)

trunk/test/consensus_inputranker_test.cc

@@ -23 +23 @@
 
 #include "yat/classifier/ConsensusInputRanker.h"
-#include "yat/statistics/ROCScore.h"
+#include "yat/statistics/AUC.h"
 #include "yat/utility/matrix.h"
 #include "yat/classifier/MatrixLookup.h"
@@ -59 +59 @@
 
   
-  theplu::yat::statistics::ROCScore roc;
+  theplu::yat::statistics::AUC roc;
   theplu::yat::classifier::CrossValidationSampler sampler(target,30,3);
   *error << "Building Consensus_Inputranker" << std::endl;

trunk/test/data_lookup_1d_test.cc

@@ -25 +25 @@
 #include "yat/classifier/DataLookup1D.h"
 #include "yat/classifier/MatrixLookup.h"
+#include "yat/classifier/utility.h"
 
 
@@ -54 +55 @@
   *error << "Testing Lookup Classes" << std::endl;
   bool ok = true;
+
+  
 
   if(!std::numeric_limits<double>::has_quiet_NaN) {
@@ -166 +169 @@
   }
   std::remove("data/tmp_test_datalookup1D.txt");
-   
+  *error << "\n";
+
+  DataLookup1D dl(v5);
+  utility::vector v8;
+  classifier::convert(dl, v8);
+  if (!v5.equal(v8,0.0)) {
+    ok = false;
+    *error << "Error: Creating a DataLookup1D(utility::vector)\n"
+           << "and classifier::convert(DataLookup, utility::vector)\n"
+           << "does not give back original vector\n"
+           << "orginal:      " << v5 << "\n"
+           << "DataLookup1D: " << dl << "\n"
+           << "final result: " << v8 << "\n"
+           << std::endl;
+  }
+
   return end_test(error,ok);
 }

trunk/test/distance_test.cc

@@ -58 +58 @@
   b(2) = 1;
 
+  *error << "testing PearsonDistance" << std::endl;
   statistics::Distance* distance = new statistics::PearsonDistance;
   ok = ok && test(a, b, distance, 1.5, error);
   delete distance;
   
+  *error << "testing Euclidean" << std::endl;
   distance = new statistics::Euclidean;
   ok = ok && test(a, b, distance, 5, error);
@@ -79 +81 @@
           std::ostream* error)
 {
+  // distance between a and a is always zero
   if (a!=b && !test(a, a, distance, 0, error))
     return false;
+  else 
+    *error << "Testing that distance between x and x is zero" 
+           << std::endl;
   if ((*distance)(a,b) != facit) {
     *error << "Error: calculating distance with utility::vector\n"

trunk/test/feature_selection_test.cc

@@ -24 +24 @@
 #include "yat/classifier/FeatureSelectorIR.h"
 #include "yat/classifier/FeatureSelectorRandom.h"
-#include "yat/statistics/ROCScore.h"
+#include "yat/statistics/AUC.h"
 
 #include <fstream>
@@ -45 +45 @@
   bool ok = true;
 
-  statistics::ROCScore roc;
+  statistics::AUC roc;
   classifier::FeatureSelectorIR f(roc, 12);
   classifier::FeatureSelectorRandom f2(12);

trunk/test/inputranker_test.cc

@@ -23 +23 @@
 
 #include "yat/classifier/InputRanker.h"
-#include "yat/statistics/ROCScore.h"
+#include "yat/statistics/AUC.h"
 #include "yat/utility/matrix.h"
 #include "yat/classifier/MatrixLookup.h"
@@ -57 +57 @@
   is.close();
 
-  statistics::ROCScore roc;
+  statistics::AUC roc;
   classifier::InputRanker ir(data,target,roc);
   if (ir.id()[0]!=2 || ir.id()[1]!=0 || ir.id()[2]!=1){

trunk/test/score_test.cc

@@ -25 +25 @@
 #include "yat/statistics/FoldChange.h"
 #include "yat/statistics/Pearson.h"
-#include "yat/statistics/ROCScore.h"
+#include "yat/statistics/AUC.h"
 #include "yat/statistics/SAMScore.h"
 #include "yat/statistics/tScore.h"
@@ -52 +52 @@
   bool ok = true;
 
-  *error << "testing ROCScore" << std::endl;
+  *error << "testing AUC" << std::endl;
   utility::vector value(31);
   std::vector<std::string> label(31,"negative");
@@ -60 +60 @@
   for (size_t i=0; i<value.size(); i++) 
     value(i)=i;
-  statistics::ROCScore roc;
-  double area = roc.score(target, value);
+  statistics::AUC auc;
+  double area = auc.score(target, value);
   if (area!=1.0){
-    *error << "test_roc: area is " << area << " should be 1.0" 
+    *error << "test_auc: area is " << area << " should be 1.0" 
            << std::endl;
     ok = false;
@@ -69 +69 @@
   target.set_binary(0,false);
   target.set_binary(1,true);
-  area = roc.score(target, value);
+  area = auc.score(target, value);
   if (area!=1.0){
-    *error << "test_roc: area is " << area << " should be 1.0" 
+    *error << "test_auc: area is " << area << " should be 1.0" 
            << std::endl;
     ok = false;
@@ -97 +97 @@
       ok=false;
     }
-    area = roc.score(target2,vec);
+    area = auc.score(target2,vec);
     if (area<correct_area(i)-tol || area>correct_area(i)+tol){
       *error << "test_roc: area is " << area << " should be " 
@@ -108 +108 @@
   for (size_t i=0; i<data.rows(); i++){
     utility::vector vec(data,i);
-    area = roc.score(target2, vec, weight);
+    area = auc.score(target2, vec, weight);
     if (area<correct_area(i)-tol || area>correct_area(i)+tol){
       *error << "test_roc: weighted area is " << area << " should be " 

trunk/test/subset_generator_test.cc

@@ -32 +32 @@
 #include "yat/classifier/SVM.h"
 #include "yat/classifier/NCC.h"
-#include "yat/statistics/ROCScore.h"
+#include "yat/statistics/AUC.h"
 #include "yat/statistics/PearsonDistance.h"
 #include "yat/utility/matrix.h"
@@ -79 +79 @@
   classifier::CrossValidationSampler sampler(target, 30, 3);
 
-  statistics::ROCScore score;
+  statistics::AUC score;
   classifier::FeatureSelectorIR fs(score, 96, 0);
   *error << "building SubsetGenerator" << std::endl;
@@ -97 +97 @@
   for (size_t i = 0; i<out.size(); ++i)
     out(i)=ensemble_svm.validate()[0][i].mean(); 
-  statistics::ROCScore roc;
+  statistics::AUC roc;
   *error << roc.score(target,out) << std::endl;
 

trunk/yat/classifier/DataLookup1D.cc

@@ -74 +74 @@
 
   DataLookup1D::DataLookup1D(const utility::vector& v)
-    : column_vector_(true), index_(0), owner_(true)
+    : column_vector_(false), index_(0), owner_(true)
   {
     utility::matrix* m = new utility::matrix(1,v.size());

trunk/yat/random/random.h

@@ -25 +25 @@
 */
 
+#include "yat/statistics/Histogram.h"
+
 #include <gsl/gsl_rng.h>
 #include <gsl/gsl_randist.h>
@@ -32 +34 @@
 namespace theplu {
 namespace yat {
-namespace statistics {
-  class Histogram;
-}
 namespace random {
 

trunk/yat/statistics/AUC.cc

@@ -22 +22 @@
 */
 
-#include "ROCScore.h"
+#include "AUC.h"
 #include "yat/classifier/DataLookupWeighted1D.h"
 #include "yat/classifier/Target.h"
@@ -37 +37 @@
 namespace statistics {  
 
-  ROCScore::ROCScore(bool absolute)
+  AUC::AUC(bool absolute)
     : Score(absolute)
   {
   }
 
-  double ROCScore::score(const classifier::Target& target, 
-                         const utility::vector& value) const
+  double AUC::score(const classifier::Target& target, 
+                    const utility::vector& value) const
   {
     assert(target.size()==value.size());
@@ -57 +57 @@
 
 
-  double ROCScore::score(const classifier::Target& target, 
-                         const classifier::DataLookupWeighted1D& value) const
+  double AUC::score(const classifier::Target& target, 
+                    const classifier::DataLookupWeighted1D& value) const
   {
     assert(target.size()==value.size());
@@ -73 +73 @@
 
 
-  double ROCScore::score(const classifier::Target& target, 
-                         const utility::vector& value, 
-                         const utility::vector& weight) const
+  double AUC::score(const classifier::Target& target, 
+                    const utility::vector& value, 
+                    const utility::vector& weight) const
   {
     assert(target.size()==value.size());
@@ -90 +90 @@
 
 
-  double 
-  ROCScore::score(const MultiMap& m) const
+  double AUC::score(const MultiMap& m) const
   {
     double area=0;

trunk/yat/statistics/AUC.h

@@ -1 @@
-#ifndef _theplu_yat_statistics_roc_score_ 
-#define _theplu_yat_statistics_roc_score_ 
+#ifndef _theplu_yat_statistics_auc_ 
+#define _theplu_yat_statistics_auc_ 
 
 // $Id$
@@ -42 +42 @@
 
   ///
-  /// @brief Class for Reciever Operating Characteristic. 
+  /// @brief Class calculating Area Under ROC Curve
   ///   
-  class ROCScore : public Score
+  class AUC : public Score
   {
   
@@ -51 +51 @@
     ///
     ///
-    ROCScore(bool absolute=true);
+    AUC(bool absolute=true);
 
     /// Function taking \a value, \a target (+1 or -1) and vector

trunk/yat/statistics/Makefile.am

@@ -24 +24 @@
 
 noinst_LTLIBRARIES = libstatistics.la
-libstatistics_la_SOURCES = Averager.cc AveragerPair.cc      \
+libstatistics_la_SOURCES = AUC.cc Averager.cc AveragerPair.cc     \
   AveragerWeighted.cc AveragerPairWeighted.cc Distance.cc   \
   Euclidean.cc Fisher.cc FoldChange.cc Histogram.cc Pearson.cc      \
-  PearsonCorrelation.cc PearsonDistance.cc ROC.cc ROCScore.cc \
+  PearsonCorrelation.cc PearsonDistance.cc ROC.cc \
   SAMScore.cc Score.cc SNR.cc tScore.cc tTest.cc \
   utility.cc WilcoxonFoldChange.cc
@@ -33 +33 @@
 include_statisticsdir = $(includedir)/yat/statistics
 
-include_statistics_HEADERS = Averager.h AveragerPair.h      \
+include_statistics_HEADERS = AUC.h Averager.h AveragerPair.h      \
   AveragerWeighted.h AveragerPairWeighted.h Distance.h Euclidean.h \
   Fisher.h  \
   FoldChange.h Histogram.h Pearson.h PearsonCorrelation.h \
-  PearsonDistance.h ROC.h ROCScore.h \
+  PearsonDistance.h ROC.h \
   SAMScore.h Score.h SNR.h tScore.h tTest.h \
   utility.h WilcoxonFoldChange.h