source: branches/0.4-stable/yat/classifier/IGP.h @ 1743

Last change on this file since 1743 was 1743, checked in by Peter, 12 years ago

updating copyright statements

  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date ID
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1#ifndef _theplu_yat_classifier_igp_
2#define _theplu_yat_classifier_igp_
3
4// $Id$
5
6/*
7  Copyright (C) 2006 Jari Häkkinen, Markus Ringnér
8  Copyright (C) 2007 Jari Häkkinen, Peter Johansson, Markus Ringnér
9  Copyright (C) 2008 Peter Johansson, Markus Ringnér
10
11  This file is part of the yat library, http://dev.thep.lu.se/yat
12
13  The yat library is free software; you can redistribute it and/or
14  modify it under the terms of the GNU General Public License as
15  published by the Free Software Foundation; either version 2 of the
16  License, or (at your option) any later version.
17
18  The yat library is distributed in the hope that it will be useful,
19  but WITHOUT ANY WARRANTY; without even the implied warranty of
20  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
21  General Public License for more details.
22
23  You should have received a copy of the GNU General Public License
24  along with this program; if not, write to the Free Software
25  Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
26  02111-1307, USA.
27*/
28
29#include "DataLookup1D.h"
30#include "MatrixLookup.h"
31#include "Target.h"
32#include "yat/utility/Vector.h"
33#include "yat/utility/yat_assert.h"
34
35#include <cmath>
36#include <limits>
37#include <stdexcept>
38
39namespace theplu {
40namespace yat {
41namespace classifier { 
42
43  class Target;
44  class MatrixLookup;
45
46  ///
47  /// @brief Class for In Group Proportions (IGP)
48  /// See Kapp and Tibshirani, Biostatistics (2006).
49  ///
50  template <typename Distance>
51  class IGP
52  {
53 
54  public:
55    ///
56    /// Constructor taking the training data and the target vector and
57    /// as input.
58    ///
59    IGP(const MatrixLookup&, const Target&);
60
61
62    ///
63    /// Constructor taking the training data, the target vector and
64    /// the distance measure as input.
65    ///
66    IGP(const MatrixLookup&, const Target&, const Distance&);
67
68    ///
69    /// Destrucutor
70    ///
71    virtual ~IGP();
72
73    ///
74    /// @return the IGP score for each class as elements in a vector.
75    ///
76    const utility::Vector& score(void) const;
77
78
79  private:
80    void calculate();
81
82    utility::Vector igp_;
83    Distance distance_;
84
85    const MatrixLookup& matrix_;
86    const Target& target_;
87  }; 
88
89 
90  // templates
91
92  template <typename Distance>
93  IGP<Distance>::IGP(const MatrixLookup& data, const Target& target) 
94    : matrix_(data), target_(target)
95  {   
96    calculate();
97  }
98
99  template <typename Distance>
100  IGP<Distance>::IGP(const MatrixLookup& data, const Target& target, const Distance& dist) 
101    : matrix_(data), target_(target), distance_(dist)
102  {   
103    calculate();
104  }
105
106 
107  template <typename Distance>
108  IGP<Distance>::~IGP()   
109  {
110  }
111
112  template <typename Distance>
113  void IGP<Distance>::calculate() 
114  {
115    utility::yat_assert<std::runtime_error>(target_.size()==matrix_.columns());
116   
117    // Calculate IGP for each class
118    igp_ = utility::Vector(target_.nof_classes());
119   
120    for(size_t i=0; i<target_.size(); i++) {
121      size_t neighbor=i;
122      double mindist=std::numeric_limits<double>::max();
123      const DataLookup1D a(matrix_,i,false);
124      for(size_t j=0; j<target_.size(); j++) {           
125        DataLookup1D b(matrix_,j,false);
126        double dist=distance_(a.begin, a.end(), b.begin());
127        if(j!=i && dist<mindist) {
128          mindist=dist;
129          neighbor=j;
130        }
131      }
132      if(target_(i)==target_(neighbor))
133        igp_(target_(i))++;
134     
135    }
136    for(size_t i=0; i<target_.nof_classes(); i++) {
137      igp_(i)/=static_cast<double>(target_.size(i));
138    }
139  }
140
141 
142  template <typename Distance>
143  const utility::Vector& IGP<Distance>::score(void) const 
144  {
145    return igp_;
146  }
147 
148}}} // of namespace classifier, yat, and theplu
149
150#endif
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