Changeset 862 for trunk

Timestamp:

Sep 10, 2007, 3:18:40 PM (16 years ago)

Author:

Markus Ringnér

Message:

Fixed bug in InputRanker? that sometimes gave rise to a bus error crash. Also added more testing in some tests

Location:

trunk

Files:

• test/feature_selection_test.cc (modified) (3 diffs)
• test/score_test.cc (modified) (2 diffs)
• yat/classifier/FeatureSelectorIR.cc (modified) (2 diffs)
• yat/classifier/InputRanker.cc (modified) (1 diff)

trunk/test/feature_selection_test.cc

@@ -25 +25 @@
 #include "yat/classifier/FeatureSelectorIR.h"
 #include "yat/classifier/FeatureSelectorRandom.h"
+#include "yat/classifier/MatrixLookupWeighted.h"
+#include "yat/classifier/Target.h"
 #include "yat/statistics/AUC.h"
 
+#include "yat/utility/matrix.h"
+
+#include <algorithm>
+#include <cmath>
 #include <fstream>
+#include <iterator>
 #include <iostream>
 #include <string>
@@ -43 +50 @@
       std::cout << "feature_selection -v : for printing extra information\n";
   }
-  *error << "testing ferature_selection" << std::endl;
+  *error << "testing feature_selection" << std::endl;
   bool ok = true;
 
@@ -50 +57 @@
   classifier::FeatureSelectorRandom f2(12);
 
+  *error << "Reading in Sorlie data to identify top gene ..." << std::endl;
+  std::ifstream is("data/sorlie_centroid_data.txt");
+  utility::matrix data(is,'\t');
+  is.close();
+
+  is.open("data/sorlie_centroid_classes.txt");
+  classifier::Target targets(is);
+  is.close();
+
+  *error << "... done" << std::endl;
+
+  // Generate weight matrix with 0 for missing values and 1 for others.
+  utility::matrix weights(data.rows(),data.columns(),0.0);
+  for(size_t i=0;i<data.rows();++i)
+    for(size_t j=0;j<data.columns();++j)
+      if(!std::isnan(data(i,j)))
+        weights(i,j)=1.0;
+  
+  classifier::MatrixLookupWeighted dataviewweighted(data,weights);
+  
+  f2.update(dataviewweighted,targets);
+  *error << "\nRandomly ordered features (top 12):\n";
+  std::vector<size_t> features=f2.features();
+  std::copy(features.begin(),features.end(),
+            std::ostream_iterator<size_t>(*error," ")); 
+  *error << std::endl;
+
+  f.update(dataviewweighted,targets);
+  *error << "\nAUC ordered ordered features (top 12):\n";
+  features=f.features();
+  std::copy(features.begin(),features.end(),
+            std::ostream_iterator<size_t>(*error," ")); 
+  *error << std::endl;
+
+
   if (ok)
     return 0;

trunk/test/score_test.cc

@@ -27 +27 @@
 #include "yat/statistics/AUC.h"
 #include "yat/statistics/SAMScore.h"
+#include "yat/statistics/SNRScore.h"
 #include "yat/statistics/tScore.h"
 #include "yat/statistics/WilcoxonFoldChange.h"
@@ -131 +132 @@
   statistics::SAMScore sam(1.0,true);
 
+  *error << "testing SNRScore" << std::endl;
+  statistics::SNRScore snr(true);
+
 
   if (ok)

trunk/yat/classifier/FeatureSelectorIR.cc

@@ -26 +26 @@
 #include "FeatureSelector.h"
 #include "MatrixLookup.h"
+#include "MatrixLookupWeighted.h"
 #include "InputRanker.h"
 #include "Target.h"
@@ -72 +73 @@
                                  const Target& target)
   {
+    assert(data.columns()==target.size());
     InputRanker ir = InputRanker(data, target, score_);
     features_.resize(N_);

trunk/yat/classifier/InputRanker.cc

@@ -92 +92 @@
     id_.resize(nof_genes);
     rank_.resize(nof_genes);
+    score_.resize(nof_genes);
     for (size_t i=0; i<nof_genes; i++){
       id_[i]=score[i].second;