1 | /* |
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2 | * This program is free software; you can redistribute it and/or modify |
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3 | * it under the terms of the GNU General Public License as published by |
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4 | * the Free Software Foundation; either version 2 of the License, or |
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5 | * (at your option) any later version. |
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6 | * |
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7 | * This program is distributed in the hope that it will be useful, |
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8 | * but WITHOUT ANY WARRANTY; without even the implied warranty of |
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9 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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10 | * GNU General Public License for more details. |
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11 | * |
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12 | * You should have received a copy of the GNU General Public License |
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13 | * along with this program; if not, write to the Free Software |
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14 | * Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA. |
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15 | */ |
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16 | |
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17 | /* |
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18 | * LibSVM.java |
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19 | * Copyright (C) 2005 Yasser EL-Manzalawy (original code) |
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20 | * Copyright (C) 2005 University of Waikato, Hamilton, NZ (adapted code) |
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21 | * |
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22 | */ |
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23 | |
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24 | package weka.classifiers.functions; |
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25 | |
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26 | import weka.classifiers.Classifier; |
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27 | import weka.classifiers.AbstractClassifier; |
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28 | import weka.core.Capabilities; |
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29 | import weka.core.Instance; |
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30 | import weka.core.Instances; |
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31 | import weka.core.Option; |
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32 | import weka.core.RevisionUtils; |
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33 | import weka.core.SelectedTag; |
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34 | import weka.core.Tag; |
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35 | import weka.core.TechnicalInformation; |
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36 | import weka.core.TechnicalInformationHandler; |
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37 | import weka.core.Utils; |
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38 | import weka.core.Capabilities.Capability; |
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39 | import weka.core.TechnicalInformation.Type; |
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40 | import weka.filters.Filter; |
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41 | import weka.filters.unsupervised.attribute.Normalize; |
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42 | import weka.filters.unsupervised.attribute.ReplaceMissingValues; |
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43 | |
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44 | import java.io.File; |
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45 | import java.lang.reflect.Array; |
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46 | import java.lang.reflect.Field; |
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47 | import java.lang.reflect.Method; |
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48 | import java.util.Enumeration; |
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49 | import java.util.StringTokenizer; |
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50 | import java.util.Vector; |
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51 | |
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52 | /* |
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53 | * Modifications by FracPete: |
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54 | * - complete overhaul to make it useable in Weka |
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55 | * - accesses libsvm classes only via Reflection to make Weka compile without |
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56 | * the libsvm classes |
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57 | * - uses more efficient code to transfer the data into the libsvm sparse format |
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58 | */ |
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59 | |
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60 | /** |
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61 | <!-- globalinfo-start --> |
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62 | * A wrapper class for the libsvm tools (the libsvm classes, typically the jar file, need to be in the classpath to use this classifier).<br/> |
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63 | * LibSVM runs faster than SMO since it uses LibSVM to build the SVM classifier.<br/> |
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64 | * LibSVM allows users to experiment with One-class SVM, Regressing SVM, and nu-SVM supported by LibSVM tool. LibSVM reports many useful statistics about LibSVM classifier (e.g., confusion matrix,precision, recall, ROC score, etc.).<br/> |
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65 | * <br/> |
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66 | * Yasser EL-Manzalawy (2005). WLSVM. URL http://www.cs.iastate.edu/~yasser/wlsvm/.<br/> |
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67 | * <br/> |
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68 | * Chih-Chung Chang, Chih-Jen Lin (2001). LIBSVM - A Library for Support Vector Machines. URL http://www.csie.ntu.edu.tw/~cjlin/libsvm/. |
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69 | * <p/> |
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70 | <!-- globalinfo-end --> |
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71 | * |
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72 | <!-- technical-bibtex-start --> |
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73 | * BibTeX: |
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74 | * <pre> |
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75 | * @misc{EL-Manzalawy2005, |
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76 | * author = {Yasser EL-Manzalawy}, |
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77 | * note = {You don't need to include the WLSVM package in the CLASSPATH}, |
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78 | * title = {WLSVM}, |
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79 | * year = {2005}, |
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80 | * URL = {http://www.cs.iastate.edu/\~yasser/wlsvm/} |
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81 | * } |
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82 | * |
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83 | * @misc{Chang2001, |
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84 | * author = {Chih-Chung Chang and Chih-Jen Lin}, |
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85 | * note = {The Weka classifier works with version 2.82 of LIBSVM}, |
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86 | * title = {LIBSVM - A Library for Support Vector Machines}, |
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87 | * year = {2001}, |
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88 | * URL = {http://www.csie.ntu.edu.tw/\~cjlin/libsvm/} |
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89 | * } |
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90 | * </pre> |
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91 | * <p/> |
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92 | <!-- technical-bibtex-end --> |
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93 | * |
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94 | <!-- options-start --> |
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95 | * Valid options are: <p/> |
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96 | * |
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97 | * <pre> -S <int> |
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98 | * Set type of SVM (default: 0) |
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99 | * 0 = C-SVC |
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100 | * 1 = nu-SVC |
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101 | * 2 = one-class SVM |
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102 | * 3 = epsilon-SVR |
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103 | * 4 = nu-SVR</pre> |
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104 | * |
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105 | * <pre> -K <int> |
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106 | * Set type of kernel function (default: 2) |
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107 | * 0 = linear: u'*v |
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108 | * 1 = polynomial: (gamma*u'*v + coef0)^degree |
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109 | * 2 = radial basis function: exp(-gamma*|u-v|^2) |
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110 | * 3 = sigmoid: tanh(gamma*u'*v + coef0)</pre> |
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111 | * |
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112 | * <pre> -D <int> |
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113 | * Set degree in kernel function (default: 3)</pre> |
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114 | * |
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115 | * <pre> -G <double> |
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116 | * Set gamma in kernel function (default: 1/k)</pre> |
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117 | * |
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118 | * <pre> -R <double> |
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119 | * Set coef0 in kernel function (default: 0)</pre> |
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120 | * |
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121 | * <pre> -C <double> |
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122 | * Set the parameter C of C-SVC, epsilon-SVR, and nu-SVR |
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123 | * (default: 1)</pre> |
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124 | * |
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125 | * <pre> -N <double> |
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126 | * Set the parameter nu of nu-SVC, one-class SVM, and nu-SVR |
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127 | * (default: 0.5)</pre> |
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128 | * |
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129 | * <pre> -Z |
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130 | * Turns on normalization of input data (default: off)</pre> |
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131 | * |
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132 | * <pre> -J |
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133 | * Turn off nominal to binary conversion. |
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134 | * WARNING: use only if your data is all numeric!</pre> |
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135 | * |
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136 | * <pre> -V |
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137 | * Turn off missing value replacement. |
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138 | * WARNING: use only if your data has no missing values.</pre> |
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139 | * |
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140 | * <pre> -P <double> |
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141 | * Set the epsilon in loss function of epsilon-SVR (default: 0.1)</pre> |
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142 | * |
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143 | * <pre> -M <double> |
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144 | * Set cache memory size in MB (default: 40)</pre> |
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145 | * |
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146 | * <pre> -E <double> |
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147 | * Set tolerance of termination criterion (default: 0.001)</pre> |
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148 | * |
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149 | * <pre> -H |
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150 | * Turns the shrinking heuristics off (default: on)</pre> |
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151 | * |
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152 | * <pre> -W <double> |
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153 | * Set the parameters C of class i to weight[i]*C, for C-SVC. |
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154 | * E.g., for a 3-class problem, you could use "1 1 1" for equally |
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155 | * weighted classes. |
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156 | * (default: 1 for all classes)</pre> |
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157 | * |
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158 | * <pre> -B |
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159 | * Trains a SVC model instead of a SVR one (default: SVR)</pre> |
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160 | * |
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161 | * <pre> -model <file> |
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162 | * Specifies the filename to save the libsvm-internal model to. |
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163 | * Gets ignored if a directory is provided.</pre> |
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164 | * |
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165 | * <pre> -D |
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166 | * If set, classifier is run in debug mode and |
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167 | * may output additional info to the console</pre> |
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168 | * |
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169 | <!-- options-end --> |
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170 | * |
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171 | * @author Yasser EL-Manzalawy |
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172 | * @author FracPete (fracpete at waikato dot ac dot nz) |
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173 | * @version $Revision: 5928 $ |
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174 | * @see weka.core.converters.LibSVMLoader |
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175 | * @see weka.core.converters.LibSVMSaver |
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176 | */ |
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177 | public class LibSVM |
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178 | extends AbstractClassifier |
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179 | implements TechnicalInformationHandler { |
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180 | |
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181 | /** the svm classname. */ |
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182 | protected final static String CLASS_SVM = "libsvm.svm"; |
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183 | |
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184 | /** the svm_model classname. */ |
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185 | protected final static String CLASS_SVMMODEL = "libsvm.svm_model"; |
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186 | |
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187 | /** the svm_problem classname. */ |
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188 | protected final static String CLASS_SVMPROBLEM = "libsvm.svm_problem"; |
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189 | |
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190 | /** the svm_parameter classname. */ |
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191 | protected final static String CLASS_SVMPARAMETER = "libsvm.svm_parameter"; |
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192 | |
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193 | /** the svm_node classname. */ |
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194 | protected final static String CLASS_SVMNODE = "libsvm.svm_node"; |
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195 | |
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196 | /** serial UID. */ |
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197 | protected static final long serialVersionUID = 14172; |
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198 | |
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199 | /** LibSVM Model. */ |
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200 | protected Object m_Model; |
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201 | |
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202 | /** for normalizing the data. */ |
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203 | protected Filter m_Filter = null; |
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204 | |
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205 | /** The filter used to get rid of missing values. */ |
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206 | protected ReplaceMissingValues m_ReplaceMissingValues; |
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207 | |
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208 | /** normalize input data. */ |
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209 | protected boolean m_Normalize = false; |
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210 | |
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211 | /** If true, the replace missing values filter is not applied. */ |
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212 | private boolean m_noReplaceMissingValues; |
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213 | |
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214 | /** SVM type C-SVC (classification). */ |
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215 | public static final int SVMTYPE_C_SVC = 0; |
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216 | /** SVM type nu-SVC (classification). */ |
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217 | public static final int SVMTYPE_NU_SVC = 1; |
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218 | /** SVM type one-class SVM (classification). */ |
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219 | public static final int SVMTYPE_ONE_CLASS_SVM = 2; |
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220 | /** SVM type epsilon-SVR (regression). */ |
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221 | public static final int SVMTYPE_EPSILON_SVR = 3; |
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222 | /** SVM type nu-SVR (regression). */ |
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223 | public static final int SVMTYPE_NU_SVR = 4; |
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224 | /** SVM types. */ |
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225 | public static final Tag[] TAGS_SVMTYPE = { |
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226 | new Tag(SVMTYPE_C_SVC, "C-SVC (classification)"), |
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227 | new Tag(SVMTYPE_NU_SVC, "nu-SVC (classification)"), |
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228 | new Tag(SVMTYPE_ONE_CLASS_SVM, "one-class SVM (classification)"), |
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229 | new Tag(SVMTYPE_EPSILON_SVR, "epsilon-SVR (regression)"), |
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230 | new Tag(SVMTYPE_NU_SVR, "nu-SVR (regression)") |
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231 | }; |
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232 | |
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233 | /** the SVM type. */ |
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234 | protected int m_SVMType = SVMTYPE_C_SVC; |
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235 | |
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236 | /** kernel type linear: u'*v. */ |
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237 | public static final int KERNELTYPE_LINEAR = 0; |
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238 | /** kernel type polynomial: (gamma*u'*v + coef0)^degree. */ |
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239 | public static final int KERNELTYPE_POLYNOMIAL = 1; |
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240 | /** kernel type radial basis function: exp(-gamma*|u-v|^2). */ |
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241 | public static final int KERNELTYPE_RBF = 2; |
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242 | /** kernel type sigmoid: tanh(gamma*u'*v + coef0). */ |
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243 | public static final int KERNELTYPE_SIGMOID = 3; |
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244 | /** the different kernel types. */ |
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245 | public static final Tag[] TAGS_KERNELTYPE = { |
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246 | new Tag(KERNELTYPE_LINEAR, "linear: u'*v"), |
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247 | new Tag(KERNELTYPE_POLYNOMIAL, "polynomial: (gamma*u'*v + coef0)^degree"), |
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248 | new Tag(KERNELTYPE_RBF, "radial basis function: exp(-gamma*|u-v|^2)"), |
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249 | new Tag(KERNELTYPE_SIGMOID, "sigmoid: tanh(gamma*u'*v + coef0)") |
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250 | }; |
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251 | |
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252 | /** the kernel type. */ |
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253 | protected int m_KernelType = KERNELTYPE_RBF; |
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254 | |
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255 | /** for poly - in older versions of libsvm declared as a double. |
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256 | * At least since 2.82 it is an int. */ |
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257 | protected int m_Degree = 3; |
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258 | |
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259 | /** for poly/rbf/sigmoid. */ |
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260 | protected double m_Gamma = 0; |
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261 | |
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262 | /** for poly/rbf/sigmoid (the actual gamma). */ |
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263 | protected double m_GammaActual = 0; |
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264 | |
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265 | /** for poly/sigmoid. */ |
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266 | protected double m_Coef0 = 0; |
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267 | |
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268 | /** in MB. */ |
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269 | protected double m_CacheSize = 40; |
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270 | |
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271 | /** stopping criteria. */ |
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272 | protected double m_eps = 1e-3; |
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273 | |
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274 | /** cost, for C_SVC, EPSILON_SVR and NU_SVR. */ |
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275 | protected double m_Cost = 1; |
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276 | |
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277 | /** for C_SVC. */ |
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278 | protected int[] m_WeightLabel = new int[0]; |
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279 | |
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280 | /** for C_SVC. */ |
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281 | protected double[] m_Weight = new double[0]; |
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282 | |
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283 | /** for NU_SVC, ONE_CLASS, and NU_SVR. */ |
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284 | protected double m_nu = 0.5; |
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285 | |
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286 | /** loss, for EPSILON_SVR. */ |
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287 | protected double m_Loss = 0.1; |
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288 | |
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289 | /** use the shrinking heuristics. */ |
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290 | protected boolean m_Shrinking = true; |
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291 | |
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292 | /** whether to generate probability estimates instead of +1/-1 in case of |
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293 | * classification problems. */ |
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294 | protected boolean m_ProbabilityEstimates = false; |
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295 | |
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296 | /** the file to save the libsvm-internal model to. */ |
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297 | protected File m_ModelFile = new File(System.getProperty("user.dir")); |
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298 | |
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299 | /** whether the libsvm classes are in the Classpath. */ |
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300 | protected static boolean m_Present = false; |
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301 | static { |
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302 | try { |
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303 | Class.forName(CLASS_SVM); |
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304 | m_Present = true; |
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305 | } |
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306 | catch (Exception e) { |
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307 | m_Present = false; |
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308 | } |
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309 | } |
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310 | |
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311 | /** |
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312 | * Returns a string describing classifier. |
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313 | * |
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314 | * @return a description suitable for displaying in the |
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315 | * explorer/experimenter gui |
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316 | */ |
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317 | public String globalInfo() { |
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318 | return |
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319 | "A wrapper class for the libsvm tools (the libsvm classes, typically " |
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320 | + "the jar file, need to be in the classpath to use this classifier).\n" |
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321 | + "LibSVM runs faster than SMO since it uses LibSVM to build the SVM " |
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322 | + "classifier.\n" |
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323 | + "LibSVM allows users to experiment with One-class SVM, Regressing SVM, " |
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324 | + "and nu-SVM supported by LibSVM tool. LibSVM reports many useful " |
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325 | + "statistics about LibSVM classifier (e.g., confusion matrix," |
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326 | + "precision, recall, ROC score, etc.).\n" |
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327 | + "\n" |
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328 | + getTechnicalInformation().toString(); |
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329 | } |
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330 | |
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331 | /** |
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332 | * Returns an instance of a TechnicalInformation object, containing |
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333 | * detailed information about the technical background of this class, |
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334 | * e.g., paper reference or book this class is based on. |
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335 | * |
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336 | * @return the technical information about this class |
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337 | */ |
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338 | public TechnicalInformation getTechnicalInformation() { |
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339 | TechnicalInformation result; |
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340 | TechnicalInformation additional; |
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341 | |
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342 | result = new TechnicalInformation(Type.MISC); |
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343 | result.setValue(TechnicalInformation.Field.AUTHOR, "Yasser EL-Manzalawy"); |
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344 | result.setValue(TechnicalInformation.Field.YEAR, "2005"); |
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345 | result.setValue(TechnicalInformation.Field.TITLE, "WLSVM"); |
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346 | result.setValue(TechnicalInformation.Field.NOTE, "LibSVM was originally developed as 'WLSVM'"); |
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347 | result.setValue(TechnicalInformation.Field.URL, "http://www.cs.iastate.edu/~yasser/wlsvm/"); |
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348 | result.setValue(TechnicalInformation.Field.NOTE, "You don't need to include the WLSVM package in the CLASSPATH"); |
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349 | |
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350 | additional = result.add(Type.MISC); |
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351 | additional.setValue(TechnicalInformation.Field.AUTHOR, "Chih-Chung Chang and Chih-Jen Lin"); |
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352 | additional.setValue(TechnicalInformation.Field.TITLE, "LIBSVM - A Library for Support Vector Machines"); |
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353 | additional.setValue(TechnicalInformation.Field.YEAR, "2001"); |
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354 | additional.setValue(TechnicalInformation.Field.URL, "http://www.csie.ntu.edu.tw/~cjlin/libsvm/"); |
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355 | additional.setValue(TechnicalInformation.Field.NOTE, "The Weka classifier works with version 2.82 of LIBSVM"); |
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356 | |
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357 | return result; |
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358 | } |
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359 | |
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360 | /** |
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361 | * Returns an enumeration describing the available options. |
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362 | * |
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363 | * @return an enumeration of all the available options. |
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364 | */ |
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365 | public Enumeration listOptions() { |
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366 | Vector result; |
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367 | |
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368 | result = new Vector(); |
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369 | |
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370 | result.addElement( |
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371 | new Option( |
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372 | "\tSet type of SVM (default: 0)\n" |
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373 | + "\t\t 0 = C-SVC\n" |
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374 | + "\t\t 1 = nu-SVC\n" |
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375 | + "\t\t 2 = one-class SVM\n" |
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376 | + "\t\t 3 = epsilon-SVR\n" |
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377 | + "\t\t 4 = nu-SVR", |
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378 | "S", 1, "-S <int>")); |
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379 | |
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380 | result.addElement( |
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381 | new Option( |
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382 | "\tSet type of kernel function (default: 2)\n" |
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383 | + "\t\t 0 = linear: u'*v\n" |
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384 | + "\t\t 1 = polynomial: (gamma*u'*v + coef0)^degree\n" |
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385 | + "\t\t 2 = radial basis function: exp(-gamma*|u-v|^2)\n" |
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386 | + "\t\t 3 = sigmoid: tanh(gamma*u'*v + coef0)", |
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387 | "K", 1, "-K <int>")); |
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388 | |
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389 | result.addElement( |
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390 | new Option( |
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391 | "\tSet degree in kernel function (default: 3)", |
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392 | "D", 1, "-D <int>")); |
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393 | |
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394 | result.addElement( |
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395 | new Option( |
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396 | "\tSet gamma in kernel function (default: 1/k)", |
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397 | "G", 1, "-G <double>")); |
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398 | |
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399 | result.addElement( |
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400 | new Option( |
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401 | "\tSet coef0 in kernel function (default: 0)", |
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402 | "R", 1, "-R <double>")); |
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403 | |
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404 | result.addElement( |
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405 | new Option( |
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406 | "\tSet the parameter C of C-SVC, epsilon-SVR, and nu-SVR\n" |
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407 | + "\t (default: 1)", |
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408 | "C", 1, "-C <double>")); |
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409 | |
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410 | result.addElement( |
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411 | new Option( |
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412 | "\tSet the parameter nu of nu-SVC, one-class SVM, and nu-SVR\n" |
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413 | + "\t (default: 0.5)", |
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414 | "N", 1, "-N <double>")); |
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415 | |
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416 | result.addElement( |
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417 | new Option( |
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418 | "\tTurns on normalization of input data (default: off)", |
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419 | "Z", 0, "-Z")); |
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420 | |
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421 | result.addElement( |
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422 | new Option("\tTurn off nominal to binary conversion." |
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423 | + "\n\tWARNING: use only if your data is all numeric!", |
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424 | "J", 0, "-J")); |
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425 | |
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426 | result.addElement( |
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427 | new Option("\tTurn off missing value replacement." |
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428 | + "\n\tWARNING: use only if your data has no missing " |
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429 | + "values.", "V", 0, "-V")); |
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430 | |
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431 | result.addElement( |
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432 | new Option( |
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433 | "\tSet the epsilon in loss function of epsilon-SVR (default: 0.1)", |
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434 | "P", 1, "-P <double>")); |
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435 | |
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436 | result.addElement( |
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437 | new Option( |
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438 | "\tSet cache memory size in MB (default: 40)", |
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439 | "M", 1, "-M <double>")); |
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440 | |
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441 | result.addElement( |
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442 | new Option( |
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443 | "\tSet tolerance of termination criterion (default: 0.001)", |
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444 | "E", 1, "-E <double>")); |
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445 | |
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446 | result.addElement( |
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447 | new Option( |
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448 | "\tTurns the shrinking heuristics off (default: on)", |
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449 | "H", 0, "-H")); |
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450 | |
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451 | result.addElement( |
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452 | new Option( |
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453 | "\tSet the parameters C of class i to weight[i]*C, for C-SVC.\n" |
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454 | + "\tE.g., for a 3-class problem, you could use \"1 1 1\" for equally\n" |
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455 | + "\tweighted classes.\n" |
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456 | + "\t(default: 1 for all classes)", |
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457 | "W", 1, "-W <double>")); |
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458 | |
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459 | result.addElement( |
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460 | new Option( |
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461 | "\tTrains a SVC model instead of a SVR one (default: SVR)", |
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462 | "B", 0, "-B")); |
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463 | |
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464 | result.addElement( |
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465 | new Option( |
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466 | "\tSpecifies the filename to save the libsvm-internal model to.\n" |
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467 | + "\tGets ignored if a directory is provided.", |
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468 | "model", 1, "-model <file>")); |
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469 | |
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470 | Enumeration en = super.listOptions(); |
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471 | while (en.hasMoreElements()) |
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472 | result.addElement(en.nextElement()); |
---|
473 | |
---|
474 | return result.elements(); |
---|
475 | } |
---|
476 | |
---|
477 | /** |
---|
478 | * Sets the classifier options <p/> |
---|
479 | * |
---|
480 | <!-- options-start --> |
---|
481 | * Valid options are: <p/> |
---|
482 | * |
---|
483 | * <pre> -S <int> |
---|
484 | * Set type of SVM (default: 0) |
---|
485 | * 0 = C-SVC |
---|
486 | * 1 = nu-SVC |
---|
487 | * 2 = one-class SVM |
---|
488 | * 3 = epsilon-SVR |
---|
489 | * 4 = nu-SVR</pre> |
---|
490 | * |
---|
491 | * <pre> -K <int> |
---|
492 | * Set type of kernel function (default: 2) |
---|
493 | * 0 = linear: u'*v |
---|
494 | * 1 = polynomial: (gamma*u'*v + coef0)^degree |
---|
495 | * 2 = radial basis function: exp(-gamma*|u-v|^2) |
---|
496 | * 3 = sigmoid: tanh(gamma*u'*v + coef0)</pre> |
---|
497 | * |
---|
498 | * <pre> -D <int> |
---|
499 | * Set degree in kernel function (default: 3)</pre> |
---|
500 | * |
---|
501 | * <pre> -G <double> |
---|
502 | * Set gamma in kernel function (default: 1/k)</pre> |
---|
503 | * |
---|
504 | * <pre> -R <double> |
---|
505 | * Set coef0 in kernel function (default: 0)</pre> |
---|
506 | * |
---|
507 | * <pre> -C <double> |
---|
508 | * Set the parameter C of C-SVC, epsilon-SVR, and nu-SVR |
---|
509 | * (default: 1)</pre> |
---|
510 | * |
---|
511 | * <pre> -N <double> |
---|
512 | * Set the parameter nu of nu-SVC, one-class SVM, and nu-SVR |
---|
513 | * (default: 0.5)</pre> |
---|
514 | * |
---|
515 | * <pre> -Z |
---|
516 | * Turns on normalization of input data (default: off)</pre> |
---|
517 | * |
---|
518 | * <pre> -J |
---|
519 | * Turn off nominal to binary conversion. |
---|
520 | * WARNING: use only if your data is all numeric!</pre> |
---|
521 | * |
---|
522 | * <pre> -V |
---|
523 | * Turn off missing value replacement. |
---|
524 | * WARNING: use only if your data has no missing values.</pre> |
---|
525 | * |
---|
526 | * <pre> -P <double> |
---|
527 | * Set the epsilon in loss function of epsilon-SVR (default: 0.1)</pre> |
---|
528 | * |
---|
529 | * <pre> -M <double> |
---|
530 | * Set cache memory size in MB (default: 40)</pre> |
---|
531 | * |
---|
532 | * <pre> -E <double> |
---|
533 | * Set tolerance of termination criterion (default: 0.001)</pre> |
---|
534 | * |
---|
535 | * <pre> -H |
---|
536 | * Turns the shrinking heuristics off (default: on)</pre> |
---|
537 | * |
---|
538 | * <pre> -W <double> |
---|
539 | * Set the parameters C of class i to weight[i]*C, for C-SVC. |
---|
540 | * E.g., for a 3-class problem, you could use "1 1 1" for equally |
---|
541 | * weighted classes. |
---|
542 | * (default: 1 for all classes)</pre> |
---|
543 | * |
---|
544 | * <pre> -B |
---|
545 | * Trains a SVC model instead of a SVR one (default: SVR)</pre> |
---|
546 | * |
---|
547 | * <pre> -model <file> |
---|
548 | * Specifies the filename to save the libsvm-internal model to. |
---|
549 | * Gets ignored if a directory is provided.</pre> |
---|
550 | * |
---|
551 | * <pre> -D |
---|
552 | * If set, classifier is run in debug mode and |
---|
553 | * may output additional info to the console</pre> |
---|
554 | * |
---|
555 | <!-- options-end --> |
---|
556 | * |
---|
557 | * @param options the options to parse |
---|
558 | * @throws Exception if parsing fails |
---|
559 | */ |
---|
560 | public void setOptions(String[] options) throws Exception { |
---|
561 | String tmpStr; |
---|
562 | |
---|
563 | tmpStr = Utils.getOption('S', options); |
---|
564 | if (tmpStr.length() != 0) |
---|
565 | setSVMType( |
---|
566 | new SelectedTag(Integer.parseInt(tmpStr), TAGS_SVMTYPE)); |
---|
567 | else |
---|
568 | setSVMType( |
---|
569 | new SelectedTag(SVMTYPE_C_SVC, TAGS_SVMTYPE)); |
---|
570 | |
---|
571 | tmpStr = Utils.getOption('K', options); |
---|
572 | if (tmpStr.length() != 0) |
---|
573 | setKernelType( |
---|
574 | new SelectedTag(Integer.parseInt(tmpStr), TAGS_KERNELTYPE)); |
---|
575 | else |
---|
576 | setKernelType( |
---|
577 | new SelectedTag(KERNELTYPE_RBF, TAGS_KERNELTYPE)); |
---|
578 | |
---|
579 | tmpStr = Utils.getOption('D', options); |
---|
580 | if (tmpStr.length() != 0) |
---|
581 | setDegree(Integer.parseInt(tmpStr)); |
---|
582 | else |
---|
583 | setDegree(3); |
---|
584 | |
---|
585 | tmpStr = Utils.getOption('G', options); |
---|
586 | if (tmpStr.length() != 0) |
---|
587 | setGamma(Double.parseDouble(tmpStr)); |
---|
588 | else |
---|
589 | setGamma(0); |
---|
590 | |
---|
591 | tmpStr = Utils.getOption('R', options); |
---|
592 | if (tmpStr.length() != 0) |
---|
593 | setCoef0(Double.parseDouble(tmpStr)); |
---|
594 | else |
---|
595 | setCoef0(0); |
---|
596 | |
---|
597 | tmpStr = Utils.getOption('N', options); |
---|
598 | if (tmpStr.length() != 0) |
---|
599 | setNu(Double.parseDouble(tmpStr)); |
---|
600 | else |
---|
601 | setNu(0.5); |
---|
602 | |
---|
603 | tmpStr = Utils.getOption('M', options); |
---|
604 | if (tmpStr.length() != 0) |
---|
605 | setCacheSize(Double.parseDouble(tmpStr)); |
---|
606 | else |
---|
607 | setCacheSize(40); |
---|
608 | |
---|
609 | tmpStr = Utils.getOption('C', options); |
---|
610 | if (tmpStr.length() != 0) |
---|
611 | setCost(Double.parseDouble(tmpStr)); |
---|
612 | else |
---|
613 | setCost(1); |
---|
614 | |
---|
615 | tmpStr = Utils.getOption('E', options); |
---|
616 | if (tmpStr.length() != 0) |
---|
617 | setEps(Double.parseDouble(tmpStr)); |
---|
618 | else |
---|
619 | setEps(1e-3); |
---|
620 | |
---|
621 | setNormalize(Utils.getFlag('Z', options)); |
---|
622 | |
---|
623 | setDoNotReplaceMissingValues(Utils.getFlag("V", options)); |
---|
624 | |
---|
625 | tmpStr = Utils.getOption('P', options); |
---|
626 | if (tmpStr.length() != 0) |
---|
627 | setLoss(Double.parseDouble(tmpStr)); |
---|
628 | else |
---|
629 | setLoss(0.1); |
---|
630 | |
---|
631 | setShrinking(!Utils.getFlag('H', options)); |
---|
632 | |
---|
633 | setWeights(Utils.getOption('W', options)); |
---|
634 | |
---|
635 | setProbabilityEstimates(Utils.getFlag('B', options)); |
---|
636 | |
---|
637 | tmpStr = Utils.getOption("model", options); |
---|
638 | if (tmpStr.length() == 0) |
---|
639 | m_ModelFile = new File(System.getProperty("user.dir")); |
---|
640 | else |
---|
641 | m_ModelFile = new File(tmpStr); |
---|
642 | } |
---|
643 | |
---|
644 | /** |
---|
645 | * Returns the current options. |
---|
646 | * |
---|
647 | * @return the current setup |
---|
648 | */ |
---|
649 | public String[] getOptions() { |
---|
650 | Vector result; |
---|
651 | |
---|
652 | result = new Vector(); |
---|
653 | |
---|
654 | result.add("-S"); |
---|
655 | result.add("" + m_SVMType); |
---|
656 | |
---|
657 | result.add("-K"); |
---|
658 | result.add("" + m_KernelType); |
---|
659 | |
---|
660 | result.add("-D"); |
---|
661 | result.add("" + getDegree()); |
---|
662 | |
---|
663 | result.add("-G"); |
---|
664 | result.add("" + getGamma()); |
---|
665 | |
---|
666 | result.add("-R"); |
---|
667 | result.add("" + getCoef0()); |
---|
668 | |
---|
669 | result.add("-N"); |
---|
670 | result.add("" + getNu()); |
---|
671 | |
---|
672 | result.add("-M"); |
---|
673 | result.add("" + getCacheSize()); |
---|
674 | |
---|
675 | result.add("-C"); |
---|
676 | result.add("" + getCost()); |
---|
677 | |
---|
678 | result.add("-E"); |
---|
679 | result.add("" + getEps()); |
---|
680 | |
---|
681 | result.add("-P"); |
---|
682 | result.add("" + getLoss()); |
---|
683 | |
---|
684 | if (!getShrinking()) |
---|
685 | result.add("-H"); |
---|
686 | |
---|
687 | if (getNormalize()) |
---|
688 | result.add("-Z"); |
---|
689 | |
---|
690 | if (getDoNotReplaceMissingValues()) |
---|
691 | result.add("-V"); |
---|
692 | |
---|
693 | if (getWeights().length() != 0) { |
---|
694 | result.add("-W"); |
---|
695 | result.add("" + getWeights()); |
---|
696 | } |
---|
697 | |
---|
698 | if (getProbabilityEstimates()) |
---|
699 | result.add("-B"); |
---|
700 | |
---|
701 | result.add("-model"); |
---|
702 | result.add(m_ModelFile.getAbsolutePath()); |
---|
703 | |
---|
704 | return (String[]) result.toArray(new String[result.size()]); |
---|
705 | } |
---|
706 | |
---|
707 | /** |
---|
708 | * returns whether the libsvm classes are present or not, i.e. whether the |
---|
709 | * classes are in the classpath or not |
---|
710 | * |
---|
711 | * @return whether the libsvm classes are available |
---|
712 | */ |
---|
713 | public static boolean isPresent() { |
---|
714 | return m_Present; |
---|
715 | } |
---|
716 | |
---|
717 | /** |
---|
718 | * Sets type of SVM (default SVMTYPE_C_SVC). |
---|
719 | * |
---|
720 | * @param value the type of the SVM |
---|
721 | */ |
---|
722 | public void setSVMType(SelectedTag value) { |
---|
723 | if (value.getTags() == TAGS_SVMTYPE) |
---|
724 | m_SVMType = value.getSelectedTag().getID(); |
---|
725 | } |
---|
726 | |
---|
727 | /** |
---|
728 | * Gets type of SVM. |
---|
729 | * |
---|
730 | * @return the type of the SVM |
---|
731 | */ |
---|
732 | public SelectedTag getSVMType() { |
---|
733 | return new SelectedTag(m_SVMType, TAGS_SVMTYPE); |
---|
734 | } |
---|
735 | |
---|
736 | /** |
---|
737 | * Returns the tip text for this property. |
---|
738 | * |
---|
739 | * @return tip text for this property suitable for |
---|
740 | * displaying in the explorer/experimenter gui |
---|
741 | */ |
---|
742 | public String SVMTypeTipText() { |
---|
743 | return "The type of SVM to use."; |
---|
744 | } |
---|
745 | |
---|
746 | /** |
---|
747 | * Sets type of kernel function (default KERNELTYPE_RBF). |
---|
748 | * |
---|
749 | * @param value the kernel type |
---|
750 | */ |
---|
751 | public void setKernelType(SelectedTag value) { |
---|
752 | if (value.getTags() == TAGS_KERNELTYPE) |
---|
753 | m_KernelType = value.getSelectedTag().getID(); |
---|
754 | } |
---|
755 | |
---|
756 | /** |
---|
757 | * Gets type of kernel function. |
---|
758 | * |
---|
759 | * @return the kernel type |
---|
760 | */ |
---|
761 | public SelectedTag getKernelType() { |
---|
762 | return new SelectedTag(m_KernelType, TAGS_KERNELTYPE); |
---|
763 | } |
---|
764 | |
---|
765 | /** |
---|
766 | * Returns the tip text for this property. |
---|
767 | * |
---|
768 | * @return tip text for this property suitable for |
---|
769 | * displaying in the explorer/experimenter gui |
---|
770 | */ |
---|
771 | public String kernelTypeTipText() { |
---|
772 | return "The type of kernel to use"; |
---|
773 | } |
---|
774 | |
---|
775 | /** |
---|
776 | * Sets the degree of the kernel. |
---|
777 | * |
---|
778 | * @param value the degree of the kernel |
---|
779 | */ |
---|
780 | public void setDegree(int value) { |
---|
781 | m_Degree = value; |
---|
782 | } |
---|
783 | |
---|
784 | /** |
---|
785 | * Gets the degree of the kernel. |
---|
786 | * |
---|
787 | * @return the degree of the kernel |
---|
788 | */ |
---|
789 | public int getDegree() { |
---|
790 | return m_Degree; |
---|
791 | } |
---|
792 | |
---|
793 | /** |
---|
794 | * Returns the tip text for this property. |
---|
795 | * |
---|
796 | * @return tip text for this property suitable for |
---|
797 | * displaying in the explorer/experimenter gui |
---|
798 | */ |
---|
799 | public String degreeTipText() { |
---|
800 | return "The degree of the kernel."; |
---|
801 | } |
---|
802 | |
---|
803 | /** |
---|
804 | * Sets gamma (default = 1/no of attributes). |
---|
805 | * |
---|
806 | * @param value the gamma value |
---|
807 | */ |
---|
808 | public void setGamma(double value) { |
---|
809 | m_Gamma = value; |
---|
810 | } |
---|
811 | |
---|
812 | /** |
---|
813 | * Gets gamma. |
---|
814 | * |
---|
815 | * @return the current gamma |
---|
816 | */ |
---|
817 | public double getGamma() { |
---|
818 | return m_Gamma; |
---|
819 | } |
---|
820 | |
---|
821 | /** |
---|
822 | * Returns the tip text for this property. |
---|
823 | * |
---|
824 | * @return tip text for this property suitable for |
---|
825 | * displaying in the explorer/experimenter gui |
---|
826 | */ |
---|
827 | public String gammaTipText() { |
---|
828 | return "The gamma to use, if 0 then 1/max_index is used."; |
---|
829 | } |
---|
830 | |
---|
831 | /** |
---|
832 | * Sets coef (default 0). |
---|
833 | * |
---|
834 | * @param value the coef |
---|
835 | */ |
---|
836 | public void setCoef0(double value) { |
---|
837 | m_Coef0 = value; |
---|
838 | } |
---|
839 | |
---|
840 | /** |
---|
841 | * Gets coef. |
---|
842 | * |
---|
843 | * @return the coef |
---|
844 | */ |
---|
845 | public double getCoef0() { |
---|
846 | return m_Coef0; |
---|
847 | } |
---|
848 | |
---|
849 | /** |
---|
850 | * Returns the tip text for this property. |
---|
851 | * |
---|
852 | * @return tip text for this property suitable for |
---|
853 | * displaying in the explorer/experimenter gui |
---|
854 | */ |
---|
855 | public String coef0TipText() { |
---|
856 | return "The coefficient to use."; |
---|
857 | } |
---|
858 | |
---|
859 | /** |
---|
860 | * Sets nu of nu-SVC, one-class SVM, and nu-SVR (default 0.5). |
---|
861 | * |
---|
862 | * @param value the new nu value |
---|
863 | */ |
---|
864 | public void setNu(double value) { |
---|
865 | m_nu = value; |
---|
866 | } |
---|
867 | |
---|
868 | /** |
---|
869 | * Gets nu of nu-SVC, one-class SVM, and nu-SVR (default 0.5). |
---|
870 | * |
---|
871 | * @return the current nu value |
---|
872 | */ |
---|
873 | public double getNu() { |
---|
874 | return m_nu; |
---|
875 | } |
---|
876 | |
---|
877 | /** |
---|
878 | * Returns the tip text for this property. |
---|
879 | * |
---|
880 | * @return tip text for this property suitable for |
---|
881 | * displaying in the explorer/experimenter gui |
---|
882 | */ |
---|
883 | public String nuTipText() { |
---|
884 | return "The value of nu for nu-SVC, one-class SVM and nu-SVR."; |
---|
885 | } |
---|
886 | |
---|
887 | /** |
---|
888 | * Sets cache memory size in MB (default 40). |
---|
889 | * |
---|
890 | * @param value the memory size in MB |
---|
891 | */ |
---|
892 | public void setCacheSize(double value) { |
---|
893 | m_CacheSize = value; |
---|
894 | } |
---|
895 | |
---|
896 | /** |
---|
897 | * Gets cache memory size in MB. |
---|
898 | * |
---|
899 | * @return the memory size in MB |
---|
900 | */ |
---|
901 | public double getCacheSize() { |
---|
902 | return m_CacheSize; |
---|
903 | } |
---|
904 | |
---|
905 | /** |
---|
906 | * Returns the tip text for this property. |
---|
907 | * |
---|
908 | * @return tip text for this property suitable for |
---|
909 | * displaying in the explorer/experimenter gui |
---|
910 | */ |
---|
911 | public String cacheSizeTipText() { |
---|
912 | return "The cache size in MB."; |
---|
913 | } |
---|
914 | |
---|
915 | /** |
---|
916 | * Sets the parameter C of C-SVC, epsilon-SVR, and nu-SVR (default 1). |
---|
917 | * |
---|
918 | * @param value the cost value |
---|
919 | */ |
---|
920 | public void setCost(double value) { |
---|
921 | m_Cost = value; |
---|
922 | } |
---|
923 | |
---|
924 | /** |
---|
925 | * Sets the parameter C of C-SVC, epsilon-SVR, and nu-SVR. |
---|
926 | * |
---|
927 | * @return the cost value |
---|
928 | */ |
---|
929 | public double getCost() { |
---|
930 | return m_Cost; |
---|
931 | } |
---|
932 | |
---|
933 | /** |
---|
934 | * Returns the tip text for this property. |
---|
935 | * |
---|
936 | * @return tip text for this property suitable for |
---|
937 | * displaying in the explorer/experimenter gui |
---|
938 | */ |
---|
939 | public String costTipText() { |
---|
940 | return "The cost parameter C for C-SVC, epsilon-SVR and nu-SVR."; |
---|
941 | } |
---|
942 | |
---|
943 | /** |
---|
944 | * Sets tolerance of termination criterion (default 0.001). |
---|
945 | * |
---|
946 | * @param value the tolerance |
---|
947 | */ |
---|
948 | public void setEps(double value) { |
---|
949 | m_eps = value; |
---|
950 | } |
---|
951 | |
---|
952 | /** |
---|
953 | * Gets tolerance of termination criterion. |
---|
954 | * |
---|
955 | * @return the current tolerance |
---|
956 | */ |
---|
957 | public double getEps() { |
---|
958 | return m_eps; |
---|
959 | } |
---|
960 | |
---|
961 | /** |
---|
962 | * Returns the tip text for this property. |
---|
963 | * |
---|
964 | * @return tip text for this property suitable for |
---|
965 | * displaying in the explorer/experimenter gui |
---|
966 | */ |
---|
967 | public String epsTipText() { |
---|
968 | return "The tolerance of the termination criterion."; |
---|
969 | } |
---|
970 | |
---|
971 | /** |
---|
972 | * Sets the epsilon in loss function of epsilon-SVR (default 0.1). |
---|
973 | * |
---|
974 | * @param value the loss epsilon |
---|
975 | */ |
---|
976 | public void setLoss(double value) { |
---|
977 | m_Loss = value; |
---|
978 | } |
---|
979 | |
---|
980 | /** |
---|
981 | * Gets the epsilon in loss function of epsilon-SVR. |
---|
982 | * |
---|
983 | * @return the loss epsilon |
---|
984 | */ |
---|
985 | public double getLoss() { |
---|
986 | return m_Loss; |
---|
987 | } |
---|
988 | |
---|
989 | /** |
---|
990 | * Returns the tip text for this property. |
---|
991 | * |
---|
992 | * @return tip text for this property suitable for |
---|
993 | * displaying in the explorer/experimenter gui |
---|
994 | */ |
---|
995 | public String lossTipText() { |
---|
996 | return "The epsilon for the loss function in epsilon-SVR."; |
---|
997 | } |
---|
998 | |
---|
999 | /** |
---|
1000 | * whether to use the shrinking heuristics. |
---|
1001 | * |
---|
1002 | * @param value true uses shrinking |
---|
1003 | */ |
---|
1004 | public void setShrinking(boolean value) { |
---|
1005 | m_Shrinking = value; |
---|
1006 | } |
---|
1007 | |
---|
1008 | /** |
---|
1009 | * whether to use the shrinking heuristics. |
---|
1010 | * |
---|
1011 | * @return true, if shrinking is used |
---|
1012 | */ |
---|
1013 | public boolean getShrinking() { |
---|
1014 | return m_Shrinking; |
---|
1015 | } |
---|
1016 | |
---|
1017 | /** |
---|
1018 | * Returns the tip text for this property. |
---|
1019 | * |
---|
1020 | * @return tip text for this property suitable for |
---|
1021 | * displaying in the explorer/experimenter gui |
---|
1022 | */ |
---|
1023 | public String shrinkingTipText() { |
---|
1024 | return "Whether to use the shrinking heuristic."; |
---|
1025 | } |
---|
1026 | |
---|
1027 | /** |
---|
1028 | * whether to normalize input data. |
---|
1029 | * |
---|
1030 | * @param value whether to normalize the data |
---|
1031 | */ |
---|
1032 | public void setNormalize(boolean value) { |
---|
1033 | m_Normalize = value; |
---|
1034 | } |
---|
1035 | |
---|
1036 | /** |
---|
1037 | * whether to normalize input data. |
---|
1038 | * |
---|
1039 | * @return true, if the data is normalized |
---|
1040 | */ |
---|
1041 | public boolean getNormalize() { |
---|
1042 | return m_Normalize; |
---|
1043 | } |
---|
1044 | |
---|
1045 | /** |
---|
1046 | * Returns the tip text for this property. |
---|
1047 | * |
---|
1048 | * @return tip text for this property suitable for |
---|
1049 | * displaying in the explorer/experimenter gui |
---|
1050 | */ |
---|
1051 | public String normalizeTipText() { |
---|
1052 | return "Whether to normalize the data."; |
---|
1053 | } |
---|
1054 | |
---|
1055 | /** |
---|
1056 | * Returns the tip text for this property. |
---|
1057 | * |
---|
1058 | * @return tip text for this property suitable for |
---|
1059 | * displaying in the explorer/experimenter gui |
---|
1060 | */ |
---|
1061 | public String doNotReplaceMissingValuesTipText() { |
---|
1062 | return "Whether to turn off automatic replacement of missing " |
---|
1063 | + "values. WARNING: set to true only if the data does not " |
---|
1064 | + "contain missing values."; |
---|
1065 | } |
---|
1066 | |
---|
1067 | /** |
---|
1068 | * Whether to turn off automatic replacement of missing values. |
---|
1069 | * Set to true only if the data does not contain missing values. |
---|
1070 | * |
---|
1071 | * @param b true if automatic missing values replacement is |
---|
1072 | * to be disabled. |
---|
1073 | */ |
---|
1074 | public void setDoNotReplaceMissingValues(boolean b) { |
---|
1075 | m_noReplaceMissingValues = b; |
---|
1076 | } |
---|
1077 | |
---|
1078 | /** |
---|
1079 | * Gets whether automatic replacement of missing values is |
---|
1080 | * disabled. |
---|
1081 | * |
---|
1082 | * @return true if automatic replacement of missing values |
---|
1083 | * is disabled. |
---|
1084 | */ |
---|
1085 | public boolean getDoNotReplaceMissingValues() { |
---|
1086 | return m_noReplaceMissingValues; |
---|
1087 | } |
---|
1088 | |
---|
1089 | /** |
---|
1090 | * Sets the parameters C of class i to weight[i]*C, for C-SVC (default 1). |
---|
1091 | * Blank separated list of doubles. |
---|
1092 | * |
---|
1093 | * @param weightsStr the weights (doubles, separated by blanks) |
---|
1094 | */ |
---|
1095 | public void setWeights(String weightsStr) { |
---|
1096 | StringTokenizer tok; |
---|
1097 | int i; |
---|
1098 | |
---|
1099 | tok = new StringTokenizer(weightsStr, " "); |
---|
1100 | m_Weight = new double[tok.countTokens()]; |
---|
1101 | m_WeightLabel = new int[tok.countTokens()]; |
---|
1102 | |
---|
1103 | if (m_Weight.length == 0) |
---|
1104 | System.out.println( |
---|
1105 | "Zero Weights processed. Default weights will be used"); |
---|
1106 | |
---|
1107 | for (i = 0; i < m_Weight.length; i++) { |
---|
1108 | m_Weight[i] = Double.parseDouble(tok.nextToken()); |
---|
1109 | m_WeightLabel[i] = i; |
---|
1110 | } |
---|
1111 | } |
---|
1112 | |
---|
1113 | /** |
---|
1114 | * Gets the parameters C of class i to weight[i]*C, for C-SVC (default 1). |
---|
1115 | * Blank separated doubles. |
---|
1116 | * |
---|
1117 | * @return the weights (doubles separated by blanks) |
---|
1118 | */ |
---|
1119 | public String getWeights() { |
---|
1120 | String result; |
---|
1121 | int i; |
---|
1122 | |
---|
1123 | result = ""; |
---|
1124 | for (i = 0; i < m_Weight.length; i++) { |
---|
1125 | if (i > 0) |
---|
1126 | result += " "; |
---|
1127 | result += Double.toString(m_Weight[i]); |
---|
1128 | } |
---|
1129 | |
---|
1130 | return result; |
---|
1131 | } |
---|
1132 | |
---|
1133 | /** |
---|
1134 | * Returns the tip text for this property. |
---|
1135 | * |
---|
1136 | * @return tip text for this property suitable for |
---|
1137 | * displaying in the explorer/experimenter gui |
---|
1138 | */ |
---|
1139 | public String weightsTipText() { |
---|
1140 | return "The weights to use for the classes (blank-separated list, eg, \"1 1 1\" for a 3-class problem), if empty 1 is used by default."; |
---|
1141 | } |
---|
1142 | |
---|
1143 | /** |
---|
1144 | * Sets whether probability estimates are generated instead of -1/+1 for |
---|
1145 | * classification problems. |
---|
1146 | * |
---|
1147 | * @param value whether to predict probabilities |
---|
1148 | */ |
---|
1149 | public void setProbabilityEstimates(boolean value) { |
---|
1150 | m_ProbabilityEstimates = value; |
---|
1151 | } |
---|
1152 | |
---|
1153 | /** |
---|
1154 | * Returns whether to generate probability estimates instead of -1/+1 for |
---|
1155 | * classification problems. |
---|
1156 | * |
---|
1157 | * @return true, if probability estimates should be returned |
---|
1158 | */ |
---|
1159 | public boolean getProbabilityEstimates() { |
---|
1160 | return m_ProbabilityEstimates; |
---|
1161 | } |
---|
1162 | |
---|
1163 | /** |
---|
1164 | * Returns the tip text for this property. |
---|
1165 | * |
---|
1166 | * @return tip text for this property suitable for |
---|
1167 | * displaying in the explorer/experimenter gui |
---|
1168 | */ |
---|
1169 | public String probabilityEstimatesTipText() { |
---|
1170 | return "Whether to generate probability estimates instead of -1/+1 for classification problems."; |
---|
1171 | } |
---|
1172 | |
---|
1173 | /** |
---|
1174 | * Sets the file to save the libsvm-internal model to. No model is saved if |
---|
1175 | * pointing to a directory. |
---|
1176 | * |
---|
1177 | * @param value the filename/directory |
---|
1178 | */ |
---|
1179 | public void setModelFile(File value) { |
---|
1180 | if (value == null) |
---|
1181 | m_ModelFile = new File(System.getProperty("user.dir")); |
---|
1182 | else |
---|
1183 | m_ModelFile = value; |
---|
1184 | } |
---|
1185 | |
---|
1186 | /** |
---|
1187 | * Returns the file to save the libsvm-internal model to. No model is saved |
---|
1188 | * if pointing to a directory. |
---|
1189 | * |
---|
1190 | * @return the file object |
---|
1191 | */ |
---|
1192 | public File getModelFile() { |
---|
1193 | return m_ModelFile; |
---|
1194 | } |
---|
1195 | |
---|
1196 | /** |
---|
1197 | * Returns the tip text for this property. |
---|
1198 | * |
---|
1199 | * @return tip text for this property suitable for |
---|
1200 | * displaying in the explorer/experimenter gui |
---|
1201 | */ |
---|
1202 | public String modelFileTipText() { |
---|
1203 | return "The file to save the libsvm-internal model to; no model is saved if pointing to a directory."; |
---|
1204 | } |
---|
1205 | |
---|
1206 | /** |
---|
1207 | * sets the specified field. |
---|
1208 | * |
---|
1209 | * @param o the object to set the field for |
---|
1210 | * @param name the name of the field |
---|
1211 | * @param value the new value of the field |
---|
1212 | */ |
---|
1213 | protected void setField(Object o, String name, Object value) { |
---|
1214 | Field f; |
---|
1215 | |
---|
1216 | try { |
---|
1217 | f = o.getClass().getField(name); |
---|
1218 | f.set(o, value); |
---|
1219 | } |
---|
1220 | catch (Exception e) { |
---|
1221 | e.printStackTrace(); |
---|
1222 | } |
---|
1223 | } |
---|
1224 | |
---|
1225 | /** |
---|
1226 | * sets the specified field in an array. |
---|
1227 | * |
---|
1228 | * @param o the object to set the field for |
---|
1229 | * @param name the name of the field |
---|
1230 | * @param index the index in the array |
---|
1231 | * @param value the new value of the field |
---|
1232 | */ |
---|
1233 | protected void setField(Object o, String name, int index, Object value) { |
---|
1234 | Field f; |
---|
1235 | |
---|
1236 | try { |
---|
1237 | f = o.getClass().getField(name); |
---|
1238 | Array.set(f.get(o), index, value); |
---|
1239 | } |
---|
1240 | catch (Exception e) { |
---|
1241 | e.printStackTrace(); |
---|
1242 | } |
---|
1243 | } |
---|
1244 | |
---|
1245 | /** |
---|
1246 | * returns the current value of the specified field. |
---|
1247 | * |
---|
1248 | * @param o the object the field is member of |
---|
1249 | * @param name the name of the field |
---|
1250 | * @return the value |
---|
1251 | */ |
---|
1252 | protected Object getField(Object o, String name) { |
---|
1253 | Field f; |
---|
1254 | Object result; |
---|
1255 | |
---|
1256 | try { |
---|
1257 | f = o.getClass().getField(name); |
---|
1258 | result = f.get(o); |
---|
1259 | } |
---|
1260 | catch (Exception e) { |
---|
1261 | e.printStackTrace(); |
---|
1262 | result = null; |
---|
1263 | } |
---|
1264 | |
---|
1265 | return result; |
---|
1266 | } |
---|
1267 | |
---|
1268 | /** |
---|
1269 | * sets a new array for the field. |
---|
1270 | * |
---|
1271 | * @param o the object to set the array for |
---|
1272 | * @param name the name of the field |
---|
1273 | * @param type the type of the array |
---|
1274 | * @param length the length of the one-dimensional array |
---|
1275 | */ |
---|
1276 | protected void newArray(Object o, String name, Class type, int length) { |
---|
1277 | newArray(o, name, type, new int[]{length}); |
---|
1278 | } |
---|
1279 | |
---|
1280 | /** |
---|
1281 | * sets a new array for the field. |
---|
1282 | * |
---|
1283 | * @param o the object to set the array for |
---|
1284 | * @param name the name of the field |
---|
1285 | * @param type the type of the array |
---|
1286 | * @param dimensions the dimensions of the array |
---|
1287 | */ |
---|
1288 | protected void newArray(Object o, String name, Class type, int[] dimensions) { |
---|
1289 | Field f; |
---|
1290 | |
---|
1291 | try { |
---|
1292 | f = o.getClass().getField(name); |
---|
1293 | f.set(o, Array.newInstance(type, dimensions)); |
---|
1294 | } |
---|
1295 | catch (Exception e) { |
---|
1296 | e.printStackTrace(); |
---|
1297 | } |
---|
1298 | } |
---|
1299 | |
---|
1300 | /** |
---|
1301 | * executes the specified method and returns the result, if any. |
---|
1302 | * |
---|
1303 | * @param o the object the method should be called from |
---|
1304 | * @param name the name of the method |
---|
1305 | * @param paramClasses the classes of the parameters |
---|
1306 | * @param paramValues the values of the parameters |
---|
1307 | * @return the return value of the method, if any (in that case null) |
---|
1308 | */ |
---|
1309 | protected Object invokeMethod(Object o, String name, Class[] paramClasses, Object[] paramValues) { |
---|
1310 | Method m; |
---|
1311 | Object result; |
---|
1312 | |
---|
1313 | result = null; |
---|
1314 | |
---|
1315 | try { |
---|
1316 | m = o.getClass().getMethod(name, paramClasses); |
---|
1317 | result = m.invoke(o, paramValues); |
---|
1318 | } |
---|
1319 | catch (Exception e) { |
---|
1320 | e.printStackTrace(); |
---|
1321 | result = null; |
---|
1322 | } |
---|
1323 | |
---|
1324 | return result; |
---|
1325 | } |
---|
1326 | |
---|
1327 | /** |
---|
1328 | * transfers the local variables into a svm_parameter object. |
---|
1329 | * |
---|
1330 | * @return the configured svm_parameter object |
---|
1331 | */ |
---|
1332 | protected Object getParameters() { |
---|
1333 | Object result; |
---|
1334 | int i; |
---|
1335 | |
---|
1336 | try { |
---|
1337 | result = Class.forName(CLASS_SVMPARAMETER).newInstance(); |
---|
1338 | |
---|
1339 | setField(result, "svm_type", new Integer(m_SVMType)); |
---|
1340 | setField(result, "kernel_type", new Integer(m_KernelType)); |
---|
1341 | setField(result, "degree", new Integer(m_Degree)); |
---|
1342 | setField(result, "gamma", new Double(m_GammaActual)); |
---|
1343 | setField(result, "coef0", new Double(m_Coef0)); |
---|
1344 | setField(result, "nu", new Double(m_nu)); |
---|
1345 | setField(result, "cache_size", new Double(m_CacheSize)); |
---|
1346 | setField(result, "C", new Double(m_Cost)); |
---|
1347 | setField(result, "eps", new Double(m_eps)); |
---|
1348 | setField(result, "p", new Double(m_Loss)); |
---|
1349 | setField(result, "shrinking", new Integer(m_Shrinking ? 1 : 0)); |
---|
1350 | setField(result, "nr_weight", new Integer(m_Weight.length)); |
---|
1351 | setField(result, "probability", new Integer(m_ProbabilityEstimates ? 1 : 0)); |
---|
1352 | |
---|
1353 | newArray(result, "weight", Double.TYPE, m_Weight.length); |
---|
1354 | newArray(result, "weight_label", Integer.TYPE, m_Weight.length); |
---|
1355 | for (i = 0; i < m_Weight.length; i++) { |
---|
1356 | setField(result, "weight", i, new Double(m_Weight[i])); |
---|
1357 | setField(result, "weight_label", i, new Integer(m_WeightLabel[i])); |
---|
1358 | } |
---|
1359 | } |
---|
1360 | catch (Exception e) { |
---|
1361 | e.printStackTrace(); |
---|
1362 | result = null; |
---|
1363 | } |
---|
1364 | |
---|
1365 | return result; |
---|
1366 | } |
---|
1367 | |
---|
1368 | /** |
---|
1369 | * returns the svm_problem. |
---|
1370 | * |
---|
1371 | * @param vx the x values |
---|
1372 | * @param vy the y values |
---|
1373 | * @return the svm_problem object |
---|
1374 | */ |
---|
1375 | protected Object getProblem(Vector vx, Vector vy) { |
---|
1376 | Object result; |
---|
1377 | |
---|
1378 | try { |
---|
1379 | result = Class.forName(CLASS_SVMPROBLEM).newInstance(); |
---|
1380 | |
---|
1381 | setField(result, "l", new Integer(vy.size())); |
---|
1382 | |
---|
1383 | newArray(result, "x", Class.forName(CLASS_SVMNODE), new int[]{vy.size(), 0}); |
---|
1384 | for (int i = 0; i < vy.size(); i++) |
---|
1385 | setField(result, "x", i, vx.elementAt(i)); |
---|
1386 | |
---|
1387 | newArray(result, "y", Double.TYPE, vy.size()); |
---|
1388 | for (int i = 0; i < vy.size(); i++) |
---|
1389 | setField(result, "y", i, vy.elementAt(i)); |
---|
1390 | } |
---|
1391 | catch (Exception e) { |
---|
1392 | e.printStackTrace(); |
---|
1393 | result = null; |
---|
1394 | } |
---|
1395 | |
---|
1396 | return result; |
---|
1397 | } |
---|
1398 | |
---|
1399 | /** |
---|
1400 | * returns an instance into a sparse libsvm array. |
---|
1401 | * |
---|
1402 | * @param instance the instance to work on |
---|
1403 | * @return the libsvm array |
---|
1404 | * @throws Exception if setup of array fails |
---|
1405 | */ |
---|
1406 | protected Object instanceToArray(Instance instance) throws Exception { |
---|
1407 | int index; |
---|
1408 | int count; |
---|
1409 | int i; |
---|
1410 | Object result; |
---|
1411 | |
---|
1412 | // determine number of non-zero attributes |
---|
1413 | /*for (i = 0; i < instance.numAttributes(); i++) { |
---|
1414 | if (i == instance.classIndex()) |
---|
1415 | continue; |
---|
1416 | if (instance.value(i) != 0) |
---|
1417 | count++; |
---|
1418 | } */ |
---|
1419 | count = 0; |
---|
1420 | for (i = 0; i < instance.numValues(); i++) { |
---|
1421 | if (instance.index(i) == instance.classIndex()) |
---|
1422 | continue; |
---|
1423 | if (instance.valueSparse(i) != 0) |
---|
1424 | count++; |
---|
1425 | } |
---|
1426 | |
---|
1427 | // fill array |
---|
1428 | /* result = Array.newInstance(Class.forName(CLASS_SVMNODE), count); |
---|
1429 | index = 0; |
---|
1430 | for (i = 0; i < instance.numAttributes(); i++) { |
---|
1431 | if (i == instance.classIndex()) |
---|
1432 | continue; |
---|
1433 | if (instance.value(i) == 0) |
---|
1434 | continue; |
---|
1435 | |
---|
1436 | Array.set(result, index, Class.forName(CLASS_SVMNODE).newInstance()); |
---|
1437 | setField(Array.get(result, index), "index", new Integer(i + 1)); |
---|
1438 | setField(Array.get(result, index), "value", new Double(instance.value(i))); |
---|
1439 | index++; |
---|
1440 | } */ |
---|
1441 | |
---|
1442 | result = Array.newInstance(Class.forName(CLASS_SVMNODE), count); |
---|
1443 | index = 0; |
---|
1444 | for (i = 0; i < instance.numValues(); i++) { |
---|
1445 | |
---|
1446 | int idx = instance.index(i); |
---|
1447 | if (idx == instance.classIndex()) |
---|
1448 | continue; |
---|
1449 | if (instance.valueSparse(i) == 0) |
---|
1450 | continue; |
---|
1451 | |
---|
1452 | Array.set(result, index, Class.forName(CLASS_SVMNODE).newInstance()); |
---|
1453 | setField(Array.get(result, index), "index", new Integer(idx + 1)); |
---|
1454 | setField(Array.get(result, index), "value", new Double(instance.valueSparse(i))); |
---|
1455 | index++; |
---|
1456 | } |
---|
1457 | |
---|
1458 | return result; |
---|
1459 | } |
---|
1460 | |
---|
1461 | /** |
---|
1462 | * Computes the distribution for a given instance. |
---|
1463 | * In case of 1-class classification, 1 is returned at index 0 if libsvm |
---|
1464 | * returns 1 and NaN (= missing) if libsvm returns -1. |
---|
1465 | * |
---|
1466 | * @param instance the instance for which distribution is computed |
---|
1467 | * @return the distribution |
---|
1468 | * @throws Exception if the distribution can't be computed successfully |
---|
1469 | */ |
---|
1470 | public double[] distributionForInstance (Instance instance) throws Exception { |
---|
1471 | int[] labels = new int[instance.numClasses()]; |
---|
1472 | double[] prob_estimates = null; |
---|
1473 | |
---|
1474 | if (m_ProbabilityEstimates) { |
---|
1475 | invokeMethod( |
---|
1476 | Class.forName(CLASS_SVM).newInstance(), |
---|
1477 | "svm_get_labels", |
---|
1478 | new Class[]{ |
---|
1479 | Class.forName(CLASS_SVMMODEL), |
---|
1480 | Array.newInstance(Integer.TYPE, instance.numClasses()).getClass()}, |
---|
1481 | new Object[]{ |
---|
1482 | m_Model, |
---|
1483 | labels}); |
---|
1484 | |
---|
1485 | prob_estimates = new double[instance.numClasses()]; |
---|
1486 | } |
---|
1487 | |
---|
1488 | if (!getDoNotReplaceMissingValues()) { |
---|
1489 | m_ReplaceMissingValues.input(instance); |
---|
1490 | m_ReplaceMissingValues.batchFinished(); |
---|
1491 | instance = m_ReplaceMissingValues.output(); |
---|
1492 | } |
---|
1493 | |
---|
1494 | if (m_Filter != null) { |
---|
1495 | m_Filter.input(instance); |
---|
1496 | m_Filter.batchFinished(); |
---|
1497 | instance = m_Filter.output(); |
---|
1498 | } |
---|
1499 | |
---|
1500 | Object x = instanceToArray(instance); |
---|
1501 | double v; |
---|
1502 | double[] result = new double[instance.numClasses()]; |
---|
1503 | if ( m_ProbabilityEstimates |
---|
1504 | && ((m_SVMType == SVMTYPE_C_SVC) || (m_SVMType == SVMTYPE_NU_SVC)) ) { |
---|
1505 | v = ((Double) invokeMethod( |
---|
1506 | Class.forName(CLASS_SVM).newInstance(), |
---|
1507 | "svm_predict_probability", |
---|
1508 | new Class[]{ |
---|
1509 | Class.forName(CLASS_SVMMODEL), |
---|
1510 | Array.newInstance(Class.forName(CLASS_SVMNODE), Array.getLength(x)).getClass(), |
---|
1511 | Array.newInstance(Double.TYPE, prob_estimates.length).getClass()}, |
---|
1512 | new Object[]{ |
---|
1513 | m_Model, |
---|
1514 | x, |
---|
1515 | prob_estimates})).doubleValue(); |
---|
1516 | |
---|
1517 | // Return order of probabilities to canonical weka attribute order |
---|
1518 | for (int k = 0; k < prob_estimates.length; k++) { |
---|
1519 | result[labels[k]] = prob_estimates[k]; |
---|
1520 | } |
---|
1521 | } |
---|
1522 | else { |
---|
1523 | v = ((Double) invokeMethod( |
---|
1524 | Class.forName(CLASS_SVM).newInstance(), |
---|
1525 | "svm_predict", |
---|
1526 | new Class[]{ |
---|
1527 | Class.forName(CLASS_SVMMODEL), |
---|
1528 | Array.newInstance(Class.forName(CLASS_SVMNODE), Array.getLength(x)).getClass()}, |
---|
1529 | new Object[]{ |
---|
1530 | m_Model, |
---|
1531 | x})).doubleValue(); |
---|
1532 | |
---|
1533 | if (instance.classAttribute().isNominal()) { |
---|
1534 | if (m_SVMType == SVMTYPE_ONE_CLASS_SVM) { |
---|
1535 | if (v > 0) |
---|
1536 | result[0] = 1; |
---|
1537 | else |
---|
1538 | result[0] = Double.NaN; // outlier |
---|
1539 | } |
---|
1540 | else { |
---|
1541 | result[(int) v] = 1; |
---|
1542 | } |
---|
1543 | } |
---|
1544 | else { |
---|
1545 | result[0] = v; |
---|
1546 | } |
---|
1547 | } |
---|
1548 | |
---|
1549 | return result; |
---|
1550 | } |
---|
1551 | |
---|
1552 | /** |
---|
1553 | * Returns default capabilities of the classifier. |
---|
1554 | * |
---|
1555 | * @return the capabilities of this classifier |
---|
1556 | */ |
---|
1557 | public Capabilities getCapabilities() { |
---|
1558 | Capabilities result = super.getCapabilities(); |
---|
1559 | result.disableAll(); |
---|
1560 | |
---|
1561 | // attributes |
---|
1562 | result.enable(Capability.NOMINAL_ATTRIBUTES); |
---|
1563 | result.enable(Capability.NUMERIC_ATTRIBUTES); |
---|
1564 | result.enable(Capability.DATE_ATTRIBUTES); |
---|
1565 | |
---|
1566 | // class |
---|
1567 | result.enableDependency(Capability.UNARY_CLASS); |
---|
1568 | result.enableDependency(Capability.NOMINAL_CLASS); |
---|
1569 | result.enableDependency(Capability.NUMERIC_CLASS); |
---|
1570 | result.enableDependency(Capability.DATE_CLASS); |
---|
1571 | |
---|
1572 | switch (m_SVMType) { |
---|
1573 | case SVMTYPE_C_SVC: |
---|
1574 | case SVMTYPE_NU_SVC: |
---|
1575 | result.enable(Capability.NOMINAL_CLASS); |
---|
1576 | break; |
---|
1577 | |
---|
1578 | case SVMTYPE_ONE_CLASS_SVM: |
---|
1579 | result.enable(Capability.UNARY_CLASS); |
---|
1580 | break; |
---|
1581 | |
---|
1582 | case SVMTYPE_EPSILON_SVR: |
---|
1583 | case SVMTYPE_NU_SVR: |
---|
1584 | result.enable(Capability.NUMERIC_CLASS); |
---|
1585 | result.enable(Capability.DATE_CLASS); |
---|
1586 | break; |
---|
1587 | |
---|
1588 | default: |
---|
1589 | throw new IllegalArgumentException("SVMType " + m_SVMType + " is not supported!"); |
---|
1590 | } |
---|
1591 | result.enable(Capability.MISSING_CLASS_VALUES); |
---|
1592 | |
---|
1593 | return result; |
---|
1594 | } |
---|
1595 | |
---|
1596 | /** |
---|
1597 | * builds the classifier. |
---|
1598 | * |
---|
1599 | * @param insts the training instances |
---|
1600 | * @throws Exception if libsvm classes not in classpath or libsvm |
---|
1601 | * encountered a problem |
---|
1602 | */ |
---|
1603 | public void buildClassifier(Instances insts) throws Exception { |
---|
1604 | m_Filter = null; |
---|
1605 | |
---|
1606 | if (!isPresent()) |
---|
1607 | throw new Exception("libsvm classes not in CLASSPATH!"); |
---|
1608 | |
---|
1609 | // remove instances with missing class |
---|
1610 | insts = new Instances(insts); |
---|
1611 | insts.deleteWithMissingClass(); |
---|
1612 | |
---|
1613 | if (!getDoNotReplaceMissingValues()) { |
---|
1614 | m_ReplaceMissingValues = new ReplaceMissingValues(); |
---|
1615 | m_ReplaceMissingValues.setInputFormat(insts); |
---|
1616 | insts = Filter.useFilter(insts, m_ReplaceMissingValues); |
---|
1617 | } |
---|
1618 | |
---|
1619 | // can classifier handle the data? |
---|
1620 | // we check this here so that if the user turns off |
---|
1621 | // replace missing values filtering, it will fail |
---|
1622 | // if the data actually does have missing values |
---|
1623 | getCapabilities().testWithFail(insts); |
---|
1624 | |
---|
1625 | if (getNormalize()) { |
---|
1626 | m_Filter = new Normalize(); |
---|
1627 | m_Filter.setInputFormat(insts); |
---|
1628 | insts = Filter.useFilter(insts, m_Filter); |
---|
1629 | } |
---|
1630 | |
---|
1631 | Vector vy = new Vector(); |
---|
1632 | Vector vx = new Vector(); |
---|
1633 | int max_index = 0; |
---|
1634 | |
---|
1635 | for (int d = 0; d < insts.numInstances(); d++) { |
---|
1636 | Instance inst = insts.instance(d); |
---|
1637 | Object x = instanceToArray(inst); |
---|
1638 | int m = Array.getLength(x); |
---|
1639 | |
---|
1640 | if (m > 0) |
---|
1641 | max_index = Math.max(max_index, ((Integer) getField(Array.get(x, m - 1), "index")).intValue()); |
---|
1642 | vx.addElement(x); |
---|
1643 | vy.addElement(new Double(inst.classValue())); |
---|
1644 | } |
---|
1645 | |
---|
1646 | // calculate actual gamma |
---|
1647 | if (getGamma() == 0) |
---|
1648 | m_GammaActual = 1.0 / max_index; |
---|
1649 | else |
---|
1650 | m_GammaActual = m_Gamma; |
---|
1651 | |
---|
1652 | // check parameter |
---|
1653 | String error_msg = (String) invokeMethod( |
---|
1654 | Class.forName(CLASS_SVM).newInstance(), |
---|
1655 | "svm_check_parameter", |
---|
1656 | new Class[]{ |
---|
1657 | Class.forName(CLASS_SVMPROBLEM), |
---|
1658 | Class.forName(CLASS_SVMPARAMETER)}, |
---|
1659 | new Object[]{ |
---|
1660 | getProblem(vx, vy), |
---|
1661 | getParameters()}); |
---|
1662 | |
---|
1663 | if (error_msg != null) |
---|
1664 | throw new Exception("Error: " + error_msg); |
---|
1665 | |
---|
1666 | // train model |
---|
1667 | m_Model = invokeMethod( |
---|
1668 | Class.forName(CLASS_SVM).newInstance(), |
---|
1669 | "svm_train", |
---|
1670 | new Class[]{ |
---|
1671 | Class.forName(CLASS_SVMPROBLEM), |
---|
1672 | Class.forName(CLASS_SVMPARAMETER)}, |
---|
1673 | new Object[]{ |
---|
1674 | getProblem(vx, vy), |
---|
1675 | getParameters()}); |
---|
1676 | |
---|
1677 | // save internal model? |
---|
1678 | if (!m_ModelFile.isDirectory()) { |
---|
1679 | invokeMethod( |
---|
1680 | Class.forName(CLASS_SVM).newInstance(), |
---|
1681 | "svm_save_model", |
---|
1682 | new Class[]{ |
---|
1683 | String.class, |
---|
1684 | Class.forName(CLASS_SVMMODEL)}, |
---|
1685 | new Object[]{ |
---|
1686 | m_ModelFile.getAbsolutePath(), |
---|
1687 | m_Model}); |
---|
1688 | } |
---|
1689 | } |
---|
1690 | |
---|
1691 | /** |
---|
1692 | * returns a string representation. |
---|
1693 | * |
---|
1694 | * @return a string representation |
---|
1695 | */ |
---|
1696 | public String toString() { |
---|
1697 | return "LibSVM wrapper, original code by Yasser EL-Manzalawy (= WLSVM)"; |
---|
1698 | } |
---|
1699 | |
---|
1700 | /** |
---|
1701 | * Returns the revision string. |
---|
1702 | * |
---|
1703 | * @return the revision |
---|
1704 | */ |
---|
1705 | public String getRevision() { |
---|
1706 | return RevisionUtils.extract("$Revision: 5928 $"); |
---|
1707 | } |
---|
1708 | |
---|
1709 | /** |
---|
1710 | * Main method for testing this class. |
---|
1711 | * |
---|
1712 | * @param args the options |
---|
1713 | */ |
---|
1714 | public static void main(String[] args) { |
---|
1715 | runClassifier(new LibSVM(), args); |
---|
1716 | } |
---|
1717 | } |
---|