source: trunk/yat/classifier/IGP.h @ 1615

Last change on this file since 1615 was 1487, checked in by Jari Häkkinen, 13 years ago

Addresses #436. GPL license copy reference should also be updated.

  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date ID
File size: 3.3 KB
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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, 2007 Jari Häkkinen, Peter Johansson, Markus Ringnér
8  Copyright (C) 2008 Peter Johansson, Markus Ringnér
9
10  This file is part of the yat library, http://dev.thep.lu.se/yat
11
12  The yat library is free software; you can redistribute it and/or
13  modify it under the terms of the GNU General Public License as
14  published by the Free Software Foundation; either version 3 of the
15  License, or (at your option) any later version.
16
17  The yat library is distributed in the hope that it will be useful,
18  but WITHOUT ANY WARRANTY; without even the implied warranty of
19  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
20  General Public License for more details.
21
22  You should have received a copy of the GNU General Public License
23  along with yat. If not, see <http://www.gnu.org/licenses/>.
24*/
25
26#include "DataLookup1D.h"
27#include "MatrixLookup.h"
28#include "Target.h"
29#include "yat/utility/Vector.h"
30#include "yat/utility/yat_assert.h"
31
32#include <cmath>
33#include <limits>
34#include <stdexcept>
35
36namespace theplu {
37namespace yat {
38namespace classifier { 
39
40  class Target;
41  class MatrixLookup;
42
43  ///
44  /// @brief Class for In Group Proportions (IGP)
45  /// See Kapp and Tibshirani, Biostatistics (2006).
46  ///
47  template <typename Distance>
48  class IGP
49  {
50 
51  public:
52    ///
53    /// Constructor taking the training data and the target vector and
54    /// as input.
55    ///
56    IGP(const MatrixLookup&, const Target&);
57
58
59    ///
60    /// Constructor taking the training data, the target vector and
61    /// the distance measure as input.
62    ///
63    IGP(const MatrixLookup&, const Target&, const Distance&);
64
65    ///
66    /// Destrucutor
67    ///
68    virtual ~IGP();
69
70    ///
71    /// @return the IGP score for each class as elements in a vector.
72    ///
73    const utility::Vector& score(void) const;
74
75
76  private:
77    void calculate();
78
79    utility::Vector igp_;
80    Distance distance_;
81
82    const MatrixLookup& matrix_;
83    const Target& target_;
84  }; 
85
86 
87  // templates
88
89  template <typename Distance>
90  IGP<Distance>::IGP(const MatrixLookup& data, const Target& target) 
91    : matrix_(data), target_(target)
92  {   
93    calculate();
94  }
95
96  template <typename Distance>
97  IGP<Distance>::IGP(const MatrixLookup& data, const Target& target, const Distance& dist) 
98    : matrix_(data), target_(target), distance_(dist)
99  {   
100    calculate();
101  }
102
103 
104  template <typename Distance>
105  IGP<Distance>::~IGP()   
106  {
107  }
108
109  template <typename Distance>
110  void IGP<Distance>::calculate() 
111  {
112    utility::yat_assert<std::runtime_error>(target_.size()==matrix_.columns());
113   
114    // Calculate IGP for each class
115    igp_ = utility::Vector(target_.nof_classes());
116   
117    for(size_t i=0; i<target_.size(); i++) {
118      size_t neighbor=i;
119      double mindist=std::numeric_limits<double>::max();
120      const DataLookup1D a(matrix_,i,false);
121      for(size_t j=0; j<target_.size(); j++) {           
122        DataLookup1D b(matrix_,j,false);
123        double dist=distance_(a.begin, a.end(), b.begin());
124        if(j!=i && dist<mindist) {
125          mindist=dist;
126          neighbor=j;
127        }
128      }
129      if(target_(i)==target_(neighbor))
130        igp_(target_(i))++;
131     
132    }
133    for(size_t i=0; i<target_.nof_classes(); i++) {
134      igp_(i)/=static_cast<double>(target_.size(i));
135    }
136  }
137
138 
139  template <typename Distance>
140  const utility::Vector& IGP<Distance>::score(void) const 
141  {
142    return igp_;
143  }
144 
145}}} // of namespace classifier, yat, and theplu
146
147#endif
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