[4] | 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 | * RELEASE INFORMATION (December 27, 2004) |
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| 19 | * |
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| 20 | * FCBF algorithm: |
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| 21 | * Template obtained from Weka |
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| 22 | * Developed for Weka by Zheng Alan Zhao |
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| 23 | * December 27, 2004 |
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| 24 | * |
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| 25 | * FCBF algorithm is a feature selection method based on Symmetrical Uncertainty Measurement for |
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| 26 | * relevance redundancy analysis. The details of FCBF algorithm are in: |
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| 27 | * |
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| 28 | <!-- technical-plaintext-start --> |
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| 29 | * Lei Yu, Huan Liu: Feature Selection for High-Dimensional Data: A Fast Correlation-Based Filter Solution. In: Proceedings of the Twentieth International Conference on Machine Learning, 856-863, 2003. |
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| 30 | <!-- technical-plaintext-end --> |
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| 31 | * |
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| 32 | * |
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| 33 | * CONTACT INFORMATION |
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| 34 | * |
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| 35 | * For algorithm implementation: |
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| 36 | * Zheng Zhao: zhaozheng at asu.edu |
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| 37 | * |
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| 38 | * For the algorithm: |
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| 39 | * Lei Yu: leiyu at asu.edu |
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| 40 | * Huan Liu: hliu at asu.edu |
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| 41 | * |
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| 42 | * Data Mining and Machine Learning Lab |
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| 43 | * Computer Science and Engineering Department |
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| 44 | * Fulton School of Engineering |
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| 45 | * Arizona State University |
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| 46 | * Tempe, AZ 85287 |
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| 47 | * |
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| 48 | * FCBFSearch.java |
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| 49 | * |
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| 50 | * Copyright (C) 2004 Data Mining and Machine Learning Lab, |
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| 51 | * Computer Science and Engineering Department, |
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| 52 | * Fulton School of Engineering, |
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| 53 | * Arizona State University |
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| 54 | * |
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| 55 | */ |
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| 56 | |
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| 57 | |
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| 58 | package weka.attributeSelection; |
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| 59 | |
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| 60 | import weka.core.Instances; |
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| 61 | import weka.core.Option; |
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| 62 | import weka.core.OptionHandler; |
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| 63 | import weka.core.Range; |
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| 64 | import weka.core.RevisionUtils; |
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| 65 | import weka.core.TechnicalInformation; |
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| 66 | import weka.core.TechnicalInformation.Type; |
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| 67 | import weka.core.TechnicalInformation.Field; |
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| 68 | import weka.core.TechnicalInformationHandler; |
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| 69 | import weka.core.Utils; |
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| 70 | |
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| 71 | import java.util.Enumeration; |
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| 72 | import java.util.Vector; |
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| 73 | |
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| 74 | /** |
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| 75 | <!-- globalinfo-start --> |
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| 76 | * FCBF : <br/> |
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| 77 | * <br/> |
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| 78 | * Feature selection method based on correlation measureand relevance&redundancy analysis. Use in conjunction with an attribute set evaluator (SymmetricalUncertAttributeEval).<br/> |
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| 79 | * <br/> |
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| 80 | * For more information see:<br/> |
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| 81 | * <br/> |
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| 82 | * Lei Yu, Huan Liu: Feature Selection for High-Dimensional Data: A Fast Correlation-Based Filter Solution. In: Proceedings of the Twentieth International Conference on Machine Learning, 856-863, 2003. |
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| 83 | * <p/> |
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| 84 | <!-- globalinfo-end --> |
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| 85 | * |
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| 86 | <!-- technical-bibtex-start --> |
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| 87 | * BibTeX: |
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| 88 | * <pre> |
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| 89 | * @inproceedings{Yu2003, |
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| 90 | * author = {Lei Yu and Huan Liu}, |
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| 91 | * booktitle = {Proceedings of the Twentieth International Conference on Machine Learning}, |
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| 92 | * pages = {856-863}, |
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| 93 | * publisher = {AAAI Press}, |
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| 94 | * title = {Feature Selection for High-Dimensional Data: A Fast Correlation-Based Filter Solution}, |
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| 95 | * year = {2003} |
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| 96 | * } |
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| 97 | * </pre> |
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| 98 | * <p/> |
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| 99 | <!-- technical-bibtex-end --> |
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| 100 | * |
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| 101 | <!-- options-start --> |
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| 102 | * Valid options are: <p/> |
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| 103 | * |
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| 104 | * <pre> -D <create dataset> |
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| 105 | * Specify Whether the selector generates a new dataset.</pre> |
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| 106 | * |
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| 107 | * <pre> -P <start set> |
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| 108 | * Specify a starting set of attributes. |
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| 109 | * Eg. 1,3,5-7. |
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| 110 | * Any starting attributes specified are |
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| 111 | * ignored during the ranking.</pre> |
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| 112 | * |
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| 113 | * <pre> -T <threshold> |
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| 114 | * Specify a theshold by which attributes |
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| 115 | * may be discarded from the ranking.</pre> |
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| 116 | * |
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| 117 | * <pre> -N <num to select> |
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| 118 | * Specify number of attributes to select</pre> |
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| 119 | * |
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| 120 | <!-- options-end --> |
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| 121 | * |
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| 122 | * @author Zheng Zhao: zhaozheng at asu.edu |
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| 123 | * @version $Revision: 1.7 $ |
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| 124 | */ |
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| 125 | public class FCBFSearch |
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| 126 | extends ASSearch |
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| 127 | implements RankedOutputSearch, StartSetHandler, OptionHandler, |
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| 128 | TechnicalInformationHandler { |
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| 129 | |
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| 130 | /** for serialization */ |
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| 131 | static final long serialVersionUID = 8209699587428369942L; |
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| 132 | |
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| 133 | /** Holds the starting set as an array of attributes */ |
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| 134 | private int[] m_starting; |
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| 135 | |
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| 136 | /** Holds the start set for the search as a range */ |
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| 137 | private Range m_startRange; |
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| 138 | |
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| 139 | /** Holds the ordered list of attributes */ |
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| 140 | private int[] m_attributeList; |
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| 141 | |
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| 142 | /** Holds the list of attribute merit scores */ |
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| 143 | private double[] m_attributeMerit; |
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| 144 | |
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| 145 | /** Data has class attribute---if unsupervised evaluator then no class */ |
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| 146 | private boolean m_hasClass; |
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| 147 | |
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| 148 | /** Class index of the data if supervised evaluator */ |
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| 149 | private int m_classIndex; |
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| 150 | |
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| 151 | /** The number of attribtes */ |
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| 152 | private int m_numAttribs; |
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| 153 | |
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| 154 | /** |
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| 155 | * A threshold by which to discard attributes---used by the |
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| 156 | * AttributeSelection module |
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| 157 | */ |
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| 158 | private double m_threshold; |
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| 159 | |
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| 160 | /** The number of attributes to select. -1 indicates that all attributes |
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| 161 | are to be retained. Has precedence over m_threshold */ |
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| 162 | private int m_numToSelect = -1; |
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| 163 | |
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| 164 | /** Used to compute the number to select */ |
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| 165 | private int m_calculatedNumToSelect = -1; |
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| 166 | |
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| 167 | /*-----------------add begin 2004-11-15 by alan-----------------*/ |
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| 168 | /** Used to determine whether we create a new dataset according to the selected features */ |
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| 169 | private boolean m_generateOutput = false; |
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| 170 | |
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| 171 | /** Used to store the ref of the Evaluator we use*/ |
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| 172 | private ASEvaluation m_asEval; |
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| 173 | |
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| 174 | /** Holds the list of attribute merit scores generated by FCBF */ |
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| 175 | private double[][] m_rankedFCBF; |
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| 176 | |
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| 177 | /** Hold the list of selected features*/ |
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| 178 | private double[][] m_selectedFeatures; |
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| 179 | /*-----------------add end 2004-11-15 by alan-----------------*/ |
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| 180 | |
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| 181 | /** |
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| 182 | * Returns a string describing this search method |
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| 183 | * @return a description of the search suitable for |
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| 184 | * displaying in the explorer/experimenter gui |
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| 185 | */ |
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| 186 | public String globalInfo() { |
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| 187 | return |
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| 188 | "FCBF : \n\nFeature selection method based on correlation measure" |
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| 189 | + "and relevance&redundancy analysis. " |
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| 190 | + "Use in conjunction with an attribute set evaluator (SymmetricalUncertAttributeEval).\n\n" |
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| 191 | + "For more information see:\n\n" |
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| 192 | + getTechnicalInformation().toString(); |
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| 193 | } |
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| 194 | |
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| 195 | /** |
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| 196 | * Returns an instance of a TechnicalInformation object, containing |
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| 197 | * detailed information about the technical background of this class, |
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| 198 | * e.g., paper reference or book this class is based on. |
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| 199 | * |
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| 200 | * @return the technical information about this class |
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| 201 | */ |
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| 202 | public TechnicalInformation getTechnicalInformation() { |
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| 203 | TechnicalInformation result; |
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| 204 | |
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| 205 | result = new TechnicalInformation(Type.INPROCEEDINGS); |
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| 206 | result.setValue(Field.AUTHOR, "Lei Yu and Huan Liu"); |
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| 207 | result.setValue(Field.TITLE, "Feature Selection for High-Dimensional Data: A Fast Correlation-Based Filter Solution"); |
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| 208 | result.setValue(Field.BOOKTITLE, "Proceedings of the Twentieth International Conference on Machine Learning"); |
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| 209 | result.setValue(Field.YEAR, "2003"); |
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| 210 | result.setValue(Field.PAGES, "856-863"); |
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| 211 | result.setValue(Field.PUBLISHER, "AAAI Press"); |
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| 212 | |
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| 213 | return result; |
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| 214 | } |
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| 215 | |
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| 216 | /** |
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| 217 | * Constructor |
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| 218 | */ |
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| 219 | public FCBFSearch () { |
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| 220 | resetOptions(); |
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| 221 | } |
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| 222 | |
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| 223 | /** |
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| 224 | * Returns the tip text for this property |
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| 225 | * @return tip text for this property suitable for |
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| 226 | * displaying in the explorer/experimenter gui |
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| 227 | */ |
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| 228 | public String numToSelectTipText() { |
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| 229 | return "Specify the number of attributes to retain. The default value " |
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| 230 | +"(-1) indicates that all attributes are to be retained. Use either " |
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| 231 | +"this option or a threshold to reduce the attribute set."; |
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| 232 | } |
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| 233 | |
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| 234 | /** |
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| 235 | * Specify the number of attributes to select from the ranked list. -1 |
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| 236 | * indicates that all attributes are to be retained. |
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| 237 | * @param n the number of attributes to retain |
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| 238 | */ |
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| 239 | public void setNumToSelect(int n) { |
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| 240 | m_numToSelect = n; |
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| 241 | } |
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| 242 | |
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| 243 | /** |
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| 244 | * Gets the number of attributes to be retained. |
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| 245 | * @return the number of attributes to retain |
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| 246 | */ |
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| 247 | public int getNumToSelect() { |
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| 248 | return m_numToSelect; |
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| 249 | } |
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| 250 | |
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| 251 | /** |
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| 252 | * Gets the calculated number to select. This might be computed |
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| 253 | * from a threshold, or if < 0 is set as the number to select then |
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| 254 | * it is set to the number of attributes in the (transformed) data. |
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| 255 | * @return the calculated number of attributes to select |
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| 256 | */ |
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| 257 | public int getCalculatedNumToSelect() { |
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| 258 | if (m_numToSelect >= 0) { |
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| 259 | m_calculatedNumToSelect = m_numToSelect; |
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| 260 | } |
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| 261 | if (m_selectedFeatures.length>0 |
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| 262 | && m_selectedFeatures.length<m_calculatedNumToSelect) |
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| 263 | { |
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| 264 | m_calculatedNumToSelect = m_selectedFeatures.length; |
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| 265 | } |
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| 266 | |
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| 267 | return m_calculatedNumToSelect; |
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| 268 | } |
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| 269 | |
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| 270 | /** |
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| 271 | * Returns the tip text for this property |
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| 272 | * @return tip text for this property suitable for |
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| 273 | * displaying in the explorer/experimenter gui |
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| 274 | */ |
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| 275 | public String thresholdTipText() { |
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| 276 | return "Set threshold by which attributes can be discarded. Default value " |
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| 277 | + "results in no attributes being discarded. Use either this option or " |
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| 278 | +"numToSelect to reduce the attribute set."; |
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| 279 | } |
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| 280 | |
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| 281 | /** |
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| 282 | * Set the threshold by which the AttributeSelection module can discard |
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| 283 | * attributes. |
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| 284 | * @param threshold the threshold. |
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| 285 | */ |
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| 286 | public void setThreshold(double threshold) { |
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| 287 | m_threshold = threshold; |
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| 288 | } |
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| 289 | |
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| 290 | /** |
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| 291 | * Returns the threshold so that the AttributeSelection module can |
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| 292 | * discard attributes from the ranking. |
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| 293 | * @return the threshold |
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| 294 | */ |
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| 295 | public double getThreshold() { |
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| 296 | return m_threshold; |
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| 297 | } |
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| 298 | |
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| 299 | /** |
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| 300 | * Returns the tip text for this property |
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| 301 | * @return tip text for this property suitable for |
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| 302 | * displaying in the explorer/experimenter gui |
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| 303 | */ |
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| 304 | public String generateRankingTipText() { |
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| 305 | return "A constant option. FCBF is capable of generating" |
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| 306 | +" attribute rankings."; |
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| 307 | } |
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| 308 | |
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| 309 | /** |
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| 310 | * This is a dummy set method---Ranker is ONLY capable of producing |
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| 311 | * a ranked list of attributes for attribute evaluators. |
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| 312 | * @param doRank this parameter is N/A and is ignored |
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| 313 | */ |
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| 314 | public void setGenerateRanking(boolean doRank) { |
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| 315 | } |
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| 316 | |
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| 317 | /** |
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| 318 | * This is a dummy method. Ranker can ONLY be used with attribute |
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| 319 | * evaluators and as such can only produce a ranked list of attributes |
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| 320 | * @return true all the time. |
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| 321 | */ |
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| 322 | public boolean getGenerateRanking() { |
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| 323 | return true; |
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| 324 | } |
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| 325 | |
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| 326 | /** |
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| 327 | * Returns the tip text for this property |
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| 328 | * @return tip text for this property suitable for |
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| 329 | * displaying in the explorer/experimenter gui |
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| 330 | */ |
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| 331 | |
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| 332 | public String generateDataOutputTipText() { |
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| 333 | return "Generating new dataset according to the selected features." |
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| 334 | +" "; |
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| 335 | } |
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| 336 | |
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| 337 | /** |
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| 338 | * Sets the flag, by which the AttributeSelection module decide |
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| 339 | * whether create a new dataset according to the selected features. |
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| 340 | * @param doGenerate the flag, by which the AttributeSelection module |
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| 341 | * decide whether create a new dataset according to the selected |
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| 342 | * features |
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| 343 | */ |
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| 344 | public void setGenerateDataOutput(boolean doGenerate) { |
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| 345 | this.m_generateOutput = doGenerate; |
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| 346 | |
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| 347 | } |
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| 348 | |
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| 349 | /** |
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| 350 | * Returns the flag, by which the AttributeSelection module decide |
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| 351 | * whether create a new dataset according to the selected features. |
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| 352 | * @return the flag, by which the AttributeSelection module decide |
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| 353 | * whether create a new dataset according to the selected features. |
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| 354 | */ |
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| 355 | public boolean getGenerateDataOutput() { |
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| 356 | return this.m_generateOutput; |
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| 357 | } |
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| 358 | |
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| 359 | /** |
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| 360 | * Returns the tip text for this property |
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| 361 | * @return tip text for this property suitable for |
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| 362 | * displaying in the explorer/experimenter gui |
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| 363 | */ |
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| 364 | public String startSetTipText() { |
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| 365 | return "Specify a set of attributes to ignore. " |
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| 366 | +" When generating the ranking, FCBF will not evaluate the attributes " |
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| 367 | +" in this list. " |
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| 368 | +"This is specified as a comma " |
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| 369 | +"seperated list off attribute indexes starting at 1. It can include " |
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| 370 | +"ranges. Eg. 1,2,5-9,17."; |
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| 371 | } |
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| 372 | |
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| 373 | /** |
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| 374 | * Sets a starting set of attributes for the search. It is the |
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| 375 | * search method's responsibility to report this start set (if any) |
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| 376 | * in its toString() method. |
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| 377 | * @param startSet a string containing a list of attributes (and or ranges), |
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| 378 | * eg. 1,2,6,10-15. |
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| 379 | * @throws Exception if start set can't be set. |
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| 380 | */ |
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| 381 | public void setStartSet (String startSet) throws Exception { |
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| 382 | m_startRange.setRanges(startSet); |
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| 383 | } |
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| 384 | |
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| 385 | /** |
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| 386 | * Returns a list of attributes (and or attribute ranges) as a String |
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| 387 | * @return a list of attributes (and or attribute ranges) |
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| 388 | */ |
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| 389 | public String getStartSet () { |
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| 390 | return m_startRange.getRanges(); |
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| 391 | } |
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| 392 | |
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| 393 | /** |
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| 394 | * Returns an enumeration describing the available options. |
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| 395 | * @return an enumeration of all the available options. |
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| 396 | **/ |
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| 397 | public Enumeration listOptions () { |
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| 398 | Vector newVector = new Vector(4); |
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| 399 | |
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| 400 | newVector.addElement(new Option( |
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| 401 | "\tSpecify Whether the selector generates a new dataset.", |
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| 402 | "D", 1, "-D <create dataset>")); |
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| 403 | |
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| 404 | newVector.addElement(new Option( |
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| 405 | "\tSpecify a starting set of attributes.\n" |
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| 406 | + "\t\tEg. 1,3,5-7.\n" |
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| 407 | + "\tAny starting attributes specified are\n" |
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| 408 | + "\tignored during the ranking.", |
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| 409 | "P", 1 , "-P <start set>")); |
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| 410 | |
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| 411 | newVector.addElement(new Option( |
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| 412 | "\tSpecify a theshold by which attributes\n" |
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| 413 | + "\tmay be discarded from the ranking.", |
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| 414 | "T", 1, "-T <threshold>")); |
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| 415 | |
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| 416 | newVector.addElement(new Option( |
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| 417 | "\tSpecify number of attributes to select", |
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| 418 | "N", 1, "-N <num to select>")); |
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| 419 | |
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| 420 | return newVector.elements(); |
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| 421 | |
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| 422 | } |
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| 423 | |
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| 424 | /** |
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| 425 | * Parses a given list of options. <p/> |
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| 426 | * |
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| 427 | <!-- options-start --> |
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| 428 | * Valid options are: <p/> |
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| 429 | * |
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| 430 | * <pre> -D <create dataset> |
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| 431 | * Specify Whether the selector generates a new dataset.</pre> |
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| 432 | * |
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| 433 | * <pre> -P <start set> |
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| 434 | * Specify a starting set of attributes. |
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| 435 | * Eg. 1,3,5-7. |
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| 436 | * Any starting attributes specified are |
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| 437 | * ignored during the ranking.</pre> |
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| 438 | * |
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| 439 | * <pre> -T <threshold> |
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| 440 | * Specify a theshold by which attributes |
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| 441 | * may be discarded from the ranking.</pre> |
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| 442 | * |
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| 443 | * <pre> -N <num to select> |
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| 444 | * Specify number of attributes to select</pre> |
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| 445 | * |
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| 446 | <!-- options-end --> |
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| 447 | * |
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| 448 | * @param options the list of options as an array of strings |
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| 449 | * @throws Exception if an option is not supported |
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| 450 | * |
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| 451 | **/ |
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| 452 | public void setOptions (String[] options) |
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| 453 | throws Exception { |
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| 454 | String optionString; |
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| 455 | resetOptions(); |
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| 456 | |
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| 457 | optionString = Utils.getOption('D', options); |
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| 458 | if (optionString.length() != 0) { |
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| 459 | setGenerateDataOutput(Boolean.getBoolean(optionString)); |
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| 460 | } |
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| 461 | |
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| 462 | optionString = Utils.getOption('P', options); |
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| 463 | if (optionString.length() != 0) { |
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| 464 | setStartSet(optionString); |
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| 465 | } |
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| 466 | |
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| 467 | optionString = Utils.getOption('T', options); |
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| 468 | if (optionString.length() != 0) { |
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| 469 | Double temp; |
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| 470 | temp = Double.valueOf(optionString); |
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| 471 | setThreshold(temp.doubleValue()); |
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| 472 | } |
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| 473 | |
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| 474 | optionString = Utils.getOption('N', options); |
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| 475 | if (optionString.length() != 0) { |
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| 476 | setNumToSelect(Integer.parseInt(optionString)); |
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| 477 | } |
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| 478 | } |
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| 479 | |
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| 480 | /** |
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| 481 | * Gets the current settings of ReliefFAttributeEval. |
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| 482 | * |
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| 483 | * @return an array of strings suitable for passing to setOptions() |
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| 484 | */ |
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| 485 | public String[] getOptions () { |
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| 486 | String[] options = new String[8]; |
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| 487 | int current = 0; |
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| 488 | |
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| 489 | options[current++] = "-D"; |
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| 490 | options[current++] = ""+getGenerateDataOutput(); |
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| 491 | |
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| 492 | if (!(getStartSet().equals(""))) { |
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| 493 | options[current++] = "-P"; |
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| 494 | options[current++] = ""+startSetToString(); |
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| 495 | } |
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| 496 | |
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| 497 | options[current++] = "-T"; |
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| 498 | options[current++] = "" + getThreshold(); |
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| 499 | |
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| 500 | options[current++] = "-N"; |
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| 501 | options[current++] = ""+getNumToSelect(); |
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| 502 | |
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| 503 | while (current < options.length) { |
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| 504 | options[current++] = ""; |
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| 505 | } |
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| 506 | return options; |
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| 507 | } |
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| 508 | |
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| 509 | /** |
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| 510 | * converts the array of starting attributes to a string. This is |
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| 511 | * used by getOptions to return the actual attributes specified |
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| 512 | * as the starting set. This is better than using m_startRanges.getRanges() |
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| 513 | * as the same start set can be specified in different ways from the |
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| 514 | * command line---eg 1,2,3 == 1-3. This is to ensure that stuff that |
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| 515 | * is stored in a database is comparable. |
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| 516 | * @return a comma seperated list of individual attribute numbers as a String |
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| 517 | */ |
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| 518 | private String startSetToString() { |
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| 519 | StringBuffer FString = new StringBuffer(); |
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| 520 | boolean didPrint; |
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| 521 | |
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| 522 | if (m_starting == null) { |
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| 523 | return getStartSet(); |
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| 524 | } |
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| 525 | |
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| 526 | for (int i = 0; i < m_starting.length; i++) { |
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| 527 | didPrint = false; |
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| 528 | |
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| 529 | if ((m_hasClass == false) || |
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| 530 | (m_hasClass == true && i != m_classIndex)) { |
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| 531 | FString.append((m_starting[i] + 1)); |
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| 532 | didPrint = true; |
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| 533 | } |
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| 534 | |
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| 535 | if (i == (m_starting.length - 1)) { |
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| 536 | FString.append(""); |
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| 537 | } |
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| 538 | else { |
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| 539 | if (didPrint) { |
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| 540 | FString.append(","); |
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| 541 | } |
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| 542 | } |
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| 543 | } |
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| 544 | |
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| 545 | return FString.toString(); |
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| 546 | } |
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| 547 | |
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| 548 | /** |
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| 549 | * Kind of a dummy search algorithm. Calls a Attribute evaluator to |
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| 550 | * evaluate each attribute not included in the startSet and then sorts |
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| 551 | * them to produce a ranked list of attributes. |
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| 552 | * |
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| 553 | * @param ASEval the attribute evaluator to guide the search |
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| 554 | * @param data the training instances. |
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| 555 | * @return an array (not necessarily ordered) of selected attribute indexes |
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| 556 | * @throws Exception if the search can't be completed |
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| 557 | */ |
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| 558 | public int[] search (ASEvaluation ASEval, Instances data) |
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| 559 | throws Exception { |
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| 560 | int i, j; |
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| 561 | |
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| 562 | if (!(ASEval instanceof AttributeSetEvaluator)) { |
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| 563 | throw new Exception(ASEval.getClass().getName() |
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| 564 | + " is not an " |
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| 565 | + "Attribute Set evaluator!"); |
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| 566 | } |
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| 567 | |
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| 568 | m_numAttribs = data.numAttributes(); |
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| 569 | |
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| 570 | if (ASEval instanceof UnsupervisedAttributeEvaluator) { |
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| 571 | m_hasClass = false; |
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| 572 | } |
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| 573 | else { |
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| 574 | m_classIndex = data.classIndex(); |
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| 575 | if (m_classIndex >= 0) { |
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| 576 | m_hasClass = true; |
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| 577 | } else { |
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| 578 | m_hasClass = false; |
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| 579 | } |
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| 580 | } |
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| 581 | |
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| 582 | // get the transformed data and check to see if the transformer |
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| 583 | // preserves a class index |
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| 584 | if (ASEval instanceof AttributeTransformer) { |
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| 585 | data = ((AttributeTransformer)ASEval).transformedHeader(); |
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| 586 | if (m_classIndex >= 0 && data.classIndex() >= 0) { |
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| 587 | m_classIndex = data.classIndex(); |
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| 588 | m_hasClass = true; |
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| 589 | } |
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| 590 | } |
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| 591 | |
---|
| 592 | |
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| 593 | m_startRange.setUpper(m_numAttribs - 1); |
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| 594 | if (!(getStartSet().equals(""))) { |
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| 595 | m_starting = m_startRange.getSelection(); |
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| 596 | } |
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| 597 | |
---|
| 598 | int sl=0; |
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| 599 | if (m_starting != null) { |
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| 600 | sl = m_starting.length; |
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| 601 | } |
---|
| 602 | if ((m_starting != null) && (m_hasClass == true)) { |
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| 603 | // see if the supplied list contains the class index |
---|
| 604 | boolean ok = false; |
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| 605 | for (i = 0; i < sl; i++) { |
---|
| 606 | if (m_starting[i] == m_classIndex) { |
---|
| 607 | ok = true; |
---|
| 608 | break; |
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| 609 | } |
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| 610 | } |
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| 611 | |
---|
| 612 | if (ok == false) { |
---|
| 613 | sl++; |
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| 614 | } |
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| 615 | } |
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| 616 | else { |
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| 617 | if (m_hasClass == true) { |
---|
| 618 | sl++; |
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| 619 | } |
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| 620 | } |
---|
| 621 | |
---|
| 622 | |
---|
| 623 | m_attributeList = new int[m_numAttribs - sl]; |
---|
| 624 | m_attributeMerit = new double[m_numAttribs - sl]; |
---|
| 625 | |
---|
| 626 | // add in those attributes not in the starting (omit list) |
---|
| 627 | for (i = 0, j = 0; i < m_numAttribs; i++) { |
---|
| 628 | if (!inStarting(i)) { |
---|
| 629 | m_attributeList[j++] = i; |
---|
| 630 | } |
---|
| 631 | } |
---|
| 632 | |
---|
| 633 | this.m_asEval = ASEval; |
---|
| 634 | AttributeSetEvaluator ASEvaluator = (AttributeSetEvaluator)ASEval; |
---|
| 635 | |
---|
| 636 | for (i = 0; i < m_attributeList.length; i++) { |
---|
| 637 | m_attributeMerit[i] = ASEvaluator.evaluateAttribute(m_attributeList[i]); |
---|
| 638 | } |
---|
| 639 | |
---|
| 640 | double[][] tempRanked = rankedAttributes(); |
---|
| 641 | int[] rankedAttributes = new int[m_selectedFeatures.length]; |
---|
| 642 | |
---|
| 643 | for (i = 0; i < m_selectedFeatures.length; i++) { |
---|
| 644 | rankedAttributes[i] = (int)tempRanked[i][0]; |
---|
| 645 | } |
---|
| 646 | return rankedAttributes; |
---|
| 647 | } |
---|
| 648 | |
---|
| 649 | |
---|
| 650 | |
---|
| 651 | /** |
---|
| 652 | * Sorts the evaluated attribute list |
---|
| 653 | * |
---|
| 654 | * @return an array of sorted (highest eval to lowest) attribute indexes |
---|
| 655 | * @throws Exception of sorting can't be done. |
---|
| 656 | */ |
---|
| 657 | public double[][] rankedAttributes () |
---|
| 658 | throws Exception { |
---|
| 659 | int i, j; |
---|
| 660 | |
---|
| 661 | if (m_attributeList == null || m_attributeMerit == null) { |
---|
| 662 | throw new Exception("Search must be performed before a ranked " |
---|
| 663 | + "attribute list can be obtained"); |
---|
| 664 | } |
---|
| 665 | |
---|
| 666 | int[] ranked = Utils.sort(m_attributeMerit); |
---|
| 667 | // reverse the order of the ranked indexes |
---|
| 668 | double[][] bestToWorst = new double[ranked.length][2]; |
---|
| 669 | |
---|
| 670 | for (i = ranked.length - 1, j = 0; i >= 0; i--) { |
---|
| 671 | bestToWorst[j++][0] = ranked[i]; |
---|
| 672 | //alan: means in the arrary ranked, varialbe is from ranked as from small to large |
---|
| 673 | } |
---|
| 674 | |
---|
| 675 | // convert the indexes to attribute indexes |
---|
| 676 | for (i = 0; i < bestToWorst.length; i++) { |
---|
| 677 | int temp = ((int)bestToWorst[i][0]); |
---|
| 678 | bestToWorst[i][0] = m_attributeList[temp]; //for the index |
---|
| 679 | bestToWorst[i][1] = m_attributeMerit[temp]; //for the value of the index |
---|
| 680 | } |
---|
| 681 | |
---|
| 682 | if (m_numToSelect > bestToWorst.length) { |
---|
| 683 | throw new Exception("More attributes requested than exist in the data"); |
---|
| 684 | } |
---|
| 685 | |
---|
| 686 | this.FCBFElimination(bestToWorst); |
---|
| 687 | |
---|
| 688 | if (m_numToSelect <= 0) { |
---|
| 689 | if (m_threshold == -Double.MAX_VALUE) { |
---|
| 690 | m_calculatedNumToSelect = m_selectedFeatures.length; |
---|
| 691 | } else { |
---|
| 692 | determineNumToSelectFromThreshold(m_selectedFeatures); |
---|
| 693 | } |
---|
| 694 | } |
---|
| 695 | /* if (m_numToSelect > 0) { |
---|
| 696 | determineThreshFromNumToSelect(bestToWorst); |
---|
| 697 | } */ |
---|
| 698 | |
---|
| 699 | return m_selectedFeatures; |
---|
| 700 | } |
---|
| 701 | |
---|
| 702 | private void determineNumToSelectFromThreshold(double [][] ranking) { |
---|
| 703 | int count = 0; |
---|
| 704 | for (int i = 0; i < ranking.length; i++) { |
---|
| 705 | if (ranking[i][1] > m_threshold) { |
---|
| 706 | count++; |
---|
| 707 | } |
---|
| 708 | } |
---|
| 709 | m_calculatedNumToSelect = count; |
---|
| 710 | } |
---|
| 711 | |
---|
| 712 | private void determineThreshFromNumToSelect(double [][] ranking) |
---|
| 713 | throws Exception { |
---|
| 714 | if (m_numToSelect > ranking.length) { |
---|
| 715 | throw new Exception("More attributes requested than exist in the data"); |
---|
| 716 | } |
---|
| 717 | |
---|
| 718 | if (m_numToSelect == ranking.length) { |
---|
| 719 | return; |
---|
| 720 | } |
---|
| 721 | |
---|
| 722 | m_threshold = (ranking[m_numToSelect-1][1] + |
---|
| 723 | ranking[m_numToSelect][1]) / 2.0; |
---|
| 724 | } |
---|
| 725 | |
---|
| 726 | /** |
---|
| 727 | * returns a description of the search as a String |
---|
| 728 | * @return a description of the search |
---|
| 729 | */ |
---|
| 730 | public String toString () { |
---|
| 731 | StringBuffer BfString = new StringBuffer(); |
---|
| 732 | BfString.append("\tAttribute ranking.\n"); |
---|
| 733 | |
---|
| 734 | if (m_starting != null) { |
---|
| 735 | BfString.append("\tIgnored attributes: "); |
---|
| 736 | |
---|
| 737 | BfString.append(startSetToString()); |
---|
| 738 | BfString.append("\n"); |
---|
| 739 | } |
---|
| 740 | |
---|
| 741 | if (m_threshold != -Double.MAX_VALUE) { |
---|
| 742 | BfString.append("\tThreshold for discarding attributes: " |
---|
| 743 | + Utils.doubleToString(m_threshold,8,4)+"\n"); |
---|
| 744 | } |
---|
| 745 | |
---|
| 746 | BfString.append("\n\n"); |
---|
| 747 | |
---|
| 748 | BfString.append(" J || SU(j,Class) || I || SU(i,j). \n"); |
---|
| 749 | |
---|
| 750 | for (int i=0; i<m_rankedFCBF.length; i++) |
---|
| 751 | { |
---|
| 752 | BfString.append(Utils.doubleToString(m_rankedFCBF[i][0]+1,6,0)+" ; " |
---|
| 753 | +Utils.doubleToString(m_rankedFCBF[i][1],12,7)+" ; "); |
---|
| 754 | if (m_rankedFCBF[i][2] == m_rankedFCBF[i][0]) |
---|
| 755 | { |
---|
| 756 | BfString.append(" *\n"); |
---|
| 757 | } |
---|
| 758 | else |
---|
| 759 | { |
---|
| 760 | BfString.append(Utils.doubleToString(m_rankedFCBF[i][2] + 1,5,0) + " ; " |
---|
| 761 | + m_rankedFCBF[i][3] + "\n"); |
---|
| 762 | } |
---|
| 763 | } |
---|
| 764 | |
---|
| 765 | return BfString.toString(); |
---|
| 766 | } |
---|
| 767 | |
---|
| 768 | |
---|
| 769 | /** |
---|
| 770 | * Resets stuff to default values |
---|
| 771 | */ |
---|
| 772 | protected void resetOptions () { |
---|
| 773 | m_starting = null; |
---|
| 774 | m_startRange = new Range(); |
---|
| 775 | m_attributeList = null; |
---|
| 776 | m_attributeMerit = null; |
---|
| 777 | m_threshold = -Double.MAX_VALUE; |
---|
| 778 | } |
---|
| 779 | |
---|
| 780 | |
---|
| 781 | private boolean inStarting (int feat) { |
---|
| 782 | // omit the class from the evaluation |
---|
| 783 | if ((m_hasClass == true) && (feat == m_classIndex)) { |
---|
| 784 | return true; |
---|
| 785 | } |
---|
| 786 | |
---|
| 787 | if (m_starting == null) { |
---|
| 788 | return false; |
---|
| 789 | } |
---|
| 790 | |
---|
| 791 | for (int i = 0; i < m_starting.length; i++) { |
---|
| 792 | if (m_starting[i] == feat) { |
---|
| 793 | return true; |
---|
| 794 | } |
---|
| 795 | } |
---|
| 796 | |
---|
| 797 | return false; |
---|
| 798 | } |
---|
| 799 | |
---|
| 800 | private void FCBFElimination(double[][]rankedFeatures) |
---|
| 801 | throws Exception { |
---|
| 802 | |
---|
| 803 | int i,j; |
---|
| 804 | |
---|
| 805 | m_rankedFCBF = new double[m_attributeList.length][4]; |
---|
| 806 | int[] attributes = new int[1]; |
---|
| 807 | int[] classAtrributes = new int[1]; |
---|
| 808 | |
---|
| 809 | int numSelectedAttributes = 0; |
---|
| 810 | |
---|
| 811 | int startPoint = 0; |
---|
| 812 | double tempSUIJ = 0; |
---|
| 813 | |
---|
| 814 | AttributeSetEvaluator ASEvaluator = (AttributeSetEvaluator)m_asEval; |
---|
| 815 | |
---|
| 816 | for (i = 0; i < rankedFeatures.length; i++) { |
---|
| 817 | m_rankedFCBF[i][0] = rankedFeatures[i][0]; |
---|
| 818 | m_rankedFCBF[i][1] = rankedFeatures[i][1]; |
---|
| 819 | m_rankedFCBF[i][2] = -1; |
---|
| 820 | } |
---|
| 821 | |
---|
| 822 | while (startPoint < rankedFeatures.length) |
---|
| 823 | { |
---|
| 824 | if (m_rankedFCBF[startPoint][2] != -1) |
---|
| 825 | { |
---|
| 826 | startPoint++; |
---|
| 827 | continue; |
---|
| 828 | } |
---|
| 829 | |
---|
| 830 | m_rankedFCBF[startPoint][2] = m_rankedFCBF[startPoint][0]; |
---|
| 831 | numSelectedAttributes++; |
---|
| 832 | |
---|
| 833 | for (i = startPoint + 1; i < m_attributeList.length; i++) |
---|
| 834 | { |
---|
| 835 | if (m_rankedFCBF[i][2] != -1) |
---|
| 836 | { |
---|
| 837 | continue; |
---|
| 838 | } |
---|
| 839 | attributes[0] = (int) m_rankedFCBF[startPoint][0]; |
---|
| 840 | classAtrributes[0] = (int) m_rankedFCBF[i][0]; |
---|
| 841 | tempSUIJ = ASEvaluator.evaluateAttribute(attributes, classAtrributes); |
---|
| 842 | if (m_rankedFCBF[i][1] < tempSUIJ || Math.abs(tempSUIJ-m_rankedFCBF[i][1])<1E-8) |
---|
| 843 | { |
---|
| 844 | m_rankedFCBF[i][2] = m_rankedFCBF[startPoint][0]; |
---|
| 845 | m_rankedFCBF[i][3] = tempSUIJ; |
---|
| 846 | } |
---|
| 847 | } |
---|
| 848 | startPoint++; |
---|
| 849 | } |
---|
| 850 | |
---|
| 851 | m_selectedFeatures = new double[numSelectedAttributes][2]; |
---|
| 852 | |
---|
| 853 | for (i = 0, j = 0; i < m_attributeList.length; i++) |
---|
| 854 | { |
---|
| 855 | if (m_rankedFCBF[i][2] == m_rankedFCBF[i][0]) |
---|
| 856 | { |
---|
| 857 | m_selectedFeatures[j][0] = m_rankedFCBF[i][0]; |
---|
| 858 | m_selectedFeatures[j][1] = m_rankedFCBF[i][1]; |
---|
| 859 | j++; |
---|
| 860 | } |
---|
| 861 | } |
---|
| 862 | } |
---|
| 863 | |
---|
| 864 | /** |
---|
| 865 | * Returns the revision string. |
---|
| 866 | * |
---|
| 867 | * @return the revision |
---|
| 868 | */ |
---|
| 869 | public String getRevision() { |
---|
| 870 | return RevisionUtils.extract("$Revision: 1.7 $"); |
---|
| 871 | } |
---|
| 872 | } |
---|