source: trunk/yat/classifier/IGP.h @ 1189

Last change on this file since 1189 was 1158, checked in by Markus Ringnér, 13 years ago

Fixed #322

  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date ID
File size: 3.4 KB
Line 
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, Peter Johansson
8
9  This file is part of the yat library, http://trac.thep.lu.se/yat
10
11  The yat library is free software; you can redistribute it and/or
12  modify it under the terms of the GNU General Public License as
13  published by the Free Software Foundation; either version 2 of the
14  License, or (at your option) any later version.
15
16  The yat library is distributed in the hope that it will be useful,
17  but WITHOUT ANY WARRANTY; without even the implied warranty of
18  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19  General Public License for more details.
20
21  You should have received a copy of the GNU General Public License
22  along with this program; if not, write to the Free Software
23  Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
24  02111-1307, USA.
25*/
26
27#include "DataLookup1D.h"
28#include "MatrixLookup.h"
29#include "Target.h"
30#include "yat/utility/Vector.h"
31#include "yat/utility/yat_assert.h"
32
33#include <cmath>
34#include <limits>
35#include <stdexcept>
36
37namespace theplu {
38namespace yat {
39namespace classifier { 
40
41  class Target;
42  class MatrixLookup;
43
44  ///
45  /// @brief Class for In Group Proportions (IGP)
46  /// See Kapp and Tibshirani, Biostatistics (2006).
47  ///
48  template <typename Distance>
49  class IGP
50  {
51 
52  public:
53    ///
54    /// Constructor taking the training data and the target vector and
55    /// as input.
56    ///
57    IGP(const MatrixLookup&, const Target&);
58
59
60    ///
61    /// Constructor taking the training data, the target vector and
62    /// the distance measure as input.
63    ///
64    IGP(const MatrixLookup&, const Target&, const Distance&);
65
66    ///
67    /// Destrucutor
68    ///
69    virtual ~IGP();
70
71    ///
72    /// @return the IGP score for each class as elements in a vector.
73    ///
74    const utility::Vector& score(void) const;
75
76
77  private:
78    void calculate();
79
80    utility::Vector igp_;
81    Distance distance_;
82
83    const MatrixLookup& matrix_;
84    const Target& target_;
85  }; 
86
87 
88  // templates
89
90  template <typename Distance>
91  IGP<Distance>::IGP(const MatrixLookup& data, const Target& target) 
92    : matrix_(data), target_(target)
93  {   
94    calculate();
95  }
96
97  template <typename Distance>
98  IGP<Distance>::IGP(const MatrixLookup& data, const Target& target, const Distance& dist) 
99    : matrix_(data), target_(target), distance_(dist)
100  {   
101    calculate();
102  }
103
104 
105  template <typename Distance>
106  IGP<Distance>::~IGP()   
107  {
108  }
109
110  template <typename Distance>
111  void IGP<Distance>::calculate() 
112  {
113    utility::yat_assert<std::runtime_error>(target_.size()==matrix_.columns());
114   
115    // Calculate IGP for each class
116    igp_ = utility::Vector(target_.nof_classes());
117   
118    for(u_int i=0; i<target_.size(); i++) {
119      u_int neighbor=i;
120      double mindist=std::numeric_limits<double>::max();
121      const DataLookup1D a(matrix_,i,false);
122      for(u_int j=0; j<target_.size(); j++) {           
123        DataLookup1D b(matrix_,j,false);
124        double dist=distance_(a.begin, a.end(), b.begin());
125        if(j!=i && dist<mindist) {
126          mindist=dist;
127          neighbor=j;
128        }
129      }
130      if(target_(i)==target_(neighbor))
131        igp_(target_(i))++;
132     
133    }
134    for(u_int i=0; i<target_.nof_classes(); i++) {
135      igp_(i)/=static_cast<double>(target_.size(i));
136    }
137  }
138
139 
140  template <typename Distance>
141  const utility::Vector& IGP<Distance>::score(void) const 
142  {
143    return igp_;
144  }
145 
146}}} // of namespace classifier, yat, and theplu
147
148#endif
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