source: trunk/test/subset_generator_test.cc @ 722

Last change on this file since 722 was 722, checked in by Markus Ringnér, 15 years ago

Closes #129

  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 3.4 KB
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1// $Id: subset_generator_test.cc 722 2006-12-27 20:49:11Z markus $
2
3/*
4  Copyright (C) The authors contributing to this file.
5
6  This file is part of the yat library, http://lev.thep.lu.se/trac/yat
7
8  The yat library is free software; you can redistribute it and/or
9  modify it under the terms of the GNU General Public License as
10  published by the Free Software Foundation; either version 2 of the
11  License, or (at your option) any later version.
12
13  The yat library is distributed in the hope that it will be useful,
14  but WITHOUT ANY WARRANTY; without even the implied warranty of
15  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
16  General Public License for more details.
17
18  You should have received a copy of the GNU General Public License
19  along with this program; if not, write to the Free Software
20  Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
21  02111-1307, USA.
22*/
23
24#include "yat/classifier/CrossValidationSampler.h"
25#include "yat/classifier/EnsembleBuilder.h"
26#include "yat/classifier/FeatureSelectorIR.h"
27#include "yat/classifier/Kernel_SEV.h"
28#include "yat/classifier/KernelLookup.h"
29#include "yat/classifier/MatrixLookup.h"
30#include "yat/classifier/PolynomialKernelFunction.h"
31#include "yat/classifier/SubsetGenerator.h"
32#include "yat/classifier/SVM.h"
33#include "yat/classifier/NCC.h"
34#include "yat/statistics/ROC.h"
35#include "yat/statistics/PearsonDistance.h"
36#include "yat/utility/matrix.h"
37
38#include <fstream>
39#include <iostream>
40#include <string>
41
42using namespace theplu::yat;
43
44int main(const int argc,const char* argv[])
45{ 
46  std::ostream* error;
47  if (argc>1 && argv[1]==std::string("-v"))
48    error = &std::cerr;
49  else {
50    error = new std::ofstream("/dev/null");
51    if (argc>1)
52      std::cout << "feature_selection -v : for printing extra information\n";
53  }
54  *error << "testing ferature_selection" << std::endl;
55  bool ok = true;
56
57
58  std::ifstream is("data/nm_target_bin.txt");
59  *error << "loading target " << std::endl;
60  classifier::Target target(is);
61  is.close();
62  *error << "number of targets: " << target.size() << std::endl;
63  *error << "number of classes: " << target.nof_classes() << std::endl;
64  is.open("data/nm_data_centralized.txt");
65  *error << "loading data " << std::endl;
66  utility::matrix m(is);
67  is.close();
68  classifier::MatrixLookup data(m);
69  *error << "number of samples: " << data.columns() << std::endl;
70  *error << "number of features: " << data.rows() << std::endl;
71  assert(data.columns()==target.size());
72
73  *error << "building kernel" << std::endl;
74  classifier::PolynomialKernelFunction kf(1);
75  classifier::Kernel_SEV kernel_core(data,kf);
76  classifier::KernelLookup kernel(kernel_core);
77  *error << "building Sampler" << std::endl;
78  classifier::CrossValidationSampler sampler(target, 30, 3);
79
80  statistics::ROC score;
81  classifier::FeatureSelectorIR fs(score, 96, 0);
82  *error << "building SubsetGenerator" << std::endl;
83  classifier::SubsetGenerator subset_data(sampler, data, fs);
84  classifier::SubsetGenerator subset_kernel(sampler, kernel, fs);
85
86  classifier::SVM svm(kernel,target);
87  statistics::PearsonDistance distance;
88  classifier::NCC ncc(data,target,distance);
89  *error << "building Ensemble" << std::endl;
90  //  classifier::EnsembleBuilder ensemble_ncc(ncc,subset_data);
91  //ensemble_ncc.build();
92  classifier::EnsembleBuilder ensemble_svm(svm,sampler);
93  ensemble_svm.build();
94 
95  utility::vector out(target.size(),0);
96  for (size_t i = 0; i<out.size(); ++i)
97    out(i)=ensemble_svm.validate()[0][i].mean();
98  statistics::ROC roc;
99  *error << roc.score(target,out) << std::endl;
100
101  if (ok)
102    return 0;
103  return -1;
104}
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