source: trunk/yat/utility/kNNI.cc @ 1615

Last change on this file since 1615 was 1554, checked in by Jari Häkkinen, 13 years ago

Fixes #192. Using std::numeric_limits, since impute algorithms are slightly changed template results also changes.

  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 2.7 KB
Line 
1// $Id: kNNI.cc 1554 2008-10-09 18:31:34Z jari $
2
3/*
4  Copyright (C) 2004 Jari Häkkinen
5  Copyright (C) 2005 Peter Johansson
6  Copyright (C) 2006 Jari Häkkinen
7  Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson
8
9  This file is part of the yat library, http://dev.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 3 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 yat. If not, see <http://www.gnu.org/licenses/>.
23*/
24
25#include "kNNI.h"
26#include "stl_utility.h"
27
28#include <algorithm>
29#include <cmath>
30#include <fstream>
31#include <vector>
32#include <limits>
33
34namespace theplu {
35namespace yat {
36namespace utility {
37
38  kNNI::kNNI(const utility::Matrix& matrix,const utility::Matrix& flag,
39             const unsigned int neighbours)
40    : NNI(matrix,flag,neighbours)
41  {
42    for (unsigned int i=0; i<weight_.rows(); i++)
43      for (unsigned int j=0; j<weight_.columns(); j++)
44        if (!weight_(i,j)) {
45          mv_rows_.push_back(i);
46          break;
47        }
48    //estimate();
49  }
50
51
52
53  // \hat{x_{ij}}=\frac{ \sum_{k=1,N} \frac{x_{kj}}{d_{ki}} }
54  //                   { \sum_{k=1,N} \frac{1     }{d_{ki}} },
55  // where N is defined in the paper cited in the NNI class definition
56  // documentation.
57  unsigned int kNNI::estimate(void)
58  {
59    double small_number=std::numeric_limits<double>::epsilon();
60    for (size_t i=0; i<mv_rows_.size(); i++) {
61      std::vector<std::pair<size_t,double> >
62        distance(calculate_distances(mv_rows_[i]));
63      std::sort(distance.begin(),distance.end(),
64                pair_value_compare<size_t,double>());
65      for (size_t j=0; j<data_.columns(); j++)
66        if (!weight_(mv_rows_[i],j)) {
67          std::vector<size_t> knn=nearest_neighbours(j,distance);
68          double new_value=0.0;
69          double norm=0.0;
70          for (std::vector<size_t>::const_iterator k=knn.begin(); k!=knn.end();
71               ++k) {
72            // Avoid division with zero (perfect match vectors)
73            double d=(distance[*k].second ? distance[*k].second : small_number);
74            new_value+=data_(distance[*k].first,j)/d;
75            norm+=1.0/d;
76          }
77          // No impute if no contributions from neighbours.
78          if (norm)
79            imputed_data_(mv_rows_[i],j)=new_value/norm;
80          else {
81            not_imputed_.push_back(i);
82            // if norm is zero for one column it is zero for all columns
83            // having zero weight
84            break;
85          }
86        }
87    }
88    return not_imputed_.size();
89  }
90
91
92}}} // of namespace utility, yat, and theplu
Note: See TracBrowser for help on using the repository browser.