[29] | 1 | /* |
---|
| 2 | * This program is free software; you can redistribute it and/or modify |
---|
| 3 | * it under the terms of the GNU General Public License as published by |
---|
| 4 | * the Free Software Foundation; either version 2 of the License, or |
---|
| 5 | * (at your option) any later version. |
---|
| 6 | * |
---|
| 7 | * This program is distributed in the hope that it will be useful, |
---|
| 8 | * but WITHOUT ANY WARRANTY; without even the implied warranty of |
---|
| 9 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
---|
| 10 | * GNU General Public License for more details. |
---|
| 11 | * |
---|
| 12 | * You should have received a copy of the GNU General Public License |
---|
| 13 | * along with this program; if not, write to the Free Software |
---|
| 14 | * Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA. |
---|
| 15 | */ |
---|
| 16 | |
---|
| 17 | /* |
---|
| 18 | * CVParameterSelection.java |
---|
| 19 | * Copyright (C) 1999 University of Waikato, Hamilton, New Zealand |
---|
| 20 | * |
---|
| 21 | */ |
---|
| 22 | |
---|
| 23 | package weka.classifiers.meta; |
---|
| 24 | |
---|
| 25 | import weka.classifiers.Evaluation; |
---|
| 26 | import weka.classifiers.RandomizableSingleClassifierEnhancer; |
---|
| 27 | import weka.core.Capabilities; |
---|
| 28 | import weka.core.Drawable; |
---|
| 29 | import weka.core.FastVector; |
---|
| 30 | import weka.core.Instance; |
---|
| 31 | import weka.core.Instances; |
---|
| 32 | import weka.core.Option; |
---|
| 33 | import weka.core.OptionHandler; |
---|
| 34 | import weka.core.RevisionHandler; |
---|
| 35 | import weka.core.RevisionUtils; |
---|
| 36 | import weka.core.Summarizable; |
---|
| 37 | import weka.core.TechnicalInformation; |
---|
| 38 | import weka.core.TechnicalInformationHandler; |
---|
| 39 | import weka.core.Utils; |
---|
| 40 | import weka.core.TechnicalInformation.Field; |
---|
| 41 | import weka.core.TechnicalInformation.Type; |
---|
| 42 | |
---|
| 43 | import java.io.Serializable; |
---|
| 44 | import java.io.StreamTokenizer; |
---|
| 45 | import java.io.StringReader; |
---|
| 46 | import java.util.Enumeration; |
---|
| 47 | import java.util.Random; |
---|
| 48 | import java.util.Vector; |
---|
| 49 | |
---|
| 50 | /** |
---|
| 51 | <!-- globalinfo-start --> |
---|
| 52 | * Class for performing parameter selection by cross-validation for any classifier.<br/> |
---|
| 53 | * <br/> |
---|
| 54 | * For more information, see:<br/> |
---|
| 55 | * <br/> |
---|
| 56 | * R. Kohavi (1995). Wrappers for Performance Enhancement and Oblivious Decision Graphs. Department of Computer Science, Stanford University. |
---|
| 57 | * <p/> |
---|
| 58 | <!-- globalinfo-end --> |
---|
| 59 | * |
---|
| 60 | <!-- technical-bibtex-start --> |
---|
| 61 | * BibTeX: |
---|
| 62 | * <pre> |
---|
| 63 | * @phdthesis{Kohavi1995, |
---|
| 64 | * address = {Department of Computer Science, Stanford University}, |
---|
| 65 | * author = {R. Kohavi}, |
---|
| 66 | * school = {Stanford University}, |
---|
| 67 | * title = {Wrappers for Performance Enhancement and Oblivious Decision Graphs}, |
---|
| 68 | * year = {1995} |
---|
| 69 | * } |
---|
| 70 | * </pre> |
---|
| 71 | * <p/> |
---|
| 72 | <!-- technical-bibtex-end --> |
---|
| 73 | * |
---|
| 74 | <!-- options-start --> |
---|
| 75 | * Valid options are: <p/> |
---|
| 76 | * |
---|
| 77 | * <pre> -X <number of folds> |
---|
| 78 | * Number of folds used for cross validation (default 10).</pre> |
---|
| 79 | * |
---|
| 80 | * <pre> -P <classifier parameter> |
---|
| 81 | * Classifier parameter options. |
---|
| 82 | * eg: "N 1 5 10" Sets an optimisation parameter for the |
---|
| 83 | * classifier with name -N, with lower bound 1, upper bound |
---|
| 84 | * 5, and 10 optimisation steps. The upper bound may be the |
---|
| 85 | * character 'A' or 'I' to substitute the number of |
---|
| 86 | * attributes or instances in the training data, |
---|
| 87 | * respectively. This parameter may be supplied more than |
---|
| 88 | * once to optimise over several classifier options |
---|
| 89 | * simultaneously.</pre> |
---|
| 90 | * |
---|
| 91 | * <pre> -S <num> |
---|
| 92 | * Random number seed. |
---|
| 93 | * (default 1)</pre> |
---|
| 94 | * |
---|
| 95 | * <pre> -D |
---|
| 96 | * If set, classifier is run in debug mode and |
---|
| 97 | * may output additional info to the console</pre> |
---|
| 98 | * |
---|
| 99 | * <pre> -W |
---|
| 100 | * Full name of base classifier. |
---|
| 101 | * (default: weka.classifiers.rules.ZeroR)</pre> |
---|
| 102 | * |
---|
| 103 | * <pre> |
---|
| 104 | * Options specific to classifier weka.classifiers.rules.ZeroR: |
---|
| 105 | * </pre> |
---|
| 106 | * |
---|
| 107 | * <pre> -D |
---|
| 108 | * If set, classifier is run in debug mode and |
---|
| 109 | * may output additional info to the console</pre> |
---|
| 110 | * |
---|
| 111 | <!-- options-end --> |
---|
| 112 | * |
---|
| 113 | * Options after -- are passed to the designated sub-classifier. <p> |
---|
| 114 | * |
---|
| 115 | * @author Len Trigg (trigg@cs.waikato.ac.nz) |
---|
| 116 | * @version $Revision: 5928 $ |
---|
| 117 | */ |
---|
| 118 | public class CVParameterSelection |
---|
| 119 | extends RandomizableSingleClassifierEnhancer |
---|
| 120 | implements Drawable, Summarizable, TechnicalInformationHandler { |
---|
| 121 | |
---|
| 122 | /** for serialization */ |
---|
| 123 | static final long serialVersionUID = -6529603380876641265L; |
---|
| 124 | |
---|
| 125 | /** |
---|
| 126 | * A data structure to hold values associated with a single |
---|
| 127 | * cross-validation search parameter |
---|
| 128 | */ |
---|
| 129 | protected class CVParameter |
---|
| 130 | implements Serializable, RevisionHandler { |
---|
| 131 | |
---|
| 132 | /** for serialization */ |
---|
| 133 | static final long serialVersionUID = -4668812017709421953L; |
---|
| 134 | |
---|
| 135 | /** Char used to identify the option of interest */ |
---|
| 136 | private char m_ParamChar; |
---|
| 137 | |
---|
| 138 | /** Lower bound for the CV search */ |
---|
| 139 | private double m_Lower; |
---|
| 140 | |
---|
| 141 | /** Upper bound for the CV search */ |
---|
| 142 | private double m_Upper; |
---|
| 143 | |
---|
| 144 | /** Number of steps during the search */ |
---|
| 145 | private double m_Steps; |
---|
| 146 | |
---|
| 147 | /** The parameter value with the best performance */ |
---|
| 148 | private double m_ParamValue; |
---|
| 149 | |
---|
| 150 | /** True if the parameter should be added at the end of the argument list */ |
---|
| 151 | private boolean m_AddAtEnd; |
---|
| 152 | |
---|
| 153 | /** True if the parameter should be rounded to an integer */ |
---|
| 154 | private boolean m_RoundParam; |
---|
| 155 | |
---|
| 156 | /** |
---|
| 157 | * Constructs a CVParameter. |
---|
| 158 | * |
---|
| 159 | * @param param the parameter definition |
---|
| 160 | * @throws Exception if construction of CVParameter fails |
---|
| 161 | */ |
---|
| 162 | public CVParameter(String param) throws Exception { |
---|
| 163 | |
---|
| 164 | // Tokenize the string into it's parts |
---|
| 165 | StreamTokenizer st = new StreamTokenizer(new StringReader(param)); |
---|
| 166 | if (st.nextToken() != StreamTokenizer.TT_WORD) { |
---|
| 167 | throw new Exception("CVParameter " + param |
---|
| 168 | + ": Character parameter identifier expected"); |
---|
| 169 | } |
---|
| 170 | m_ParamChar = st.sval.charAt(0); |
---|
| 171 | if (st.nextToken() != StreamTokenizer.TT_NUMBER) { |
---|
| 172 | throw new Exception("CVParameter " + param |
---|
| 173 | + ": Numeric lower bound expected"); |
---|
| 174 | } |
---|
| 175 | m_Lower = st.nval; |
---|
| 176 | if (st.nextToken() == StreamTokenizer.TT_NUMBER) { |
---|
| 177 | m_Upper = st.nval; |
---|
| 178 | if (m_Upper < m_Lower) { |
---|
| 179 | throw new Exception("CVParameter " + param |
---|
| 180 | + ": Upper bound is less than lower bound"); |
---|
| 181 | } |
---|
| 182 | } else if (st.ttype == StreamTokenizer.TT_WORD) { |
---|
| 183 | if (st.sval.toUpperCase().charAt(0) == 'A') { |
---|
| 184 | m_Upper = m_Lower - 1; |
---|
| 185 | } else if (st.sval.toUpperCase().charAt(0) == 'I') { |
---|
| 186 | m_Upper = m_Lower - 2; |
---|
| 187 | } else { |
---|
| 188 | throw new Exception("CVParameter " + param |
---|
| 189 | + ": Upper bound must be numeric, or 'A' or 'N'"); |
---|
| 190 | } |
---|
| 191 | } else { |
---|
| 192 | throw new Exception("CVParameter " + param |
---|
| 193 | + ": Upper bound must be numeric, or 'A' or 'N'"); |
---|
| 194 | } |
---|
| 195 | if (st.nextToken() != StreamTokenizer.TT_NUMBER) { |
---|
| 196 | throw new Exception("CVParameter " + param |
---|
| 197 | + ": Numeric number of steps expected"); |
---|
| 198 | } |
---|
| 199 | m_Steps = st.nval; |
---|
| 200 | if (st.nextToken() == StreamTokenizer.TT_WORD) { |
---|
| 201 | if (st.sval.toUpperCase().charAt(0) == 'R') { |
---|
| 202 | m_RoundParam = true; |
---|
| 203 | } |
---|
| 204 | } |
---|
| 205 | } |
---|
| 206 | |
---|
| 207 | /** |
---|
| 208 | * Returns a CVParameter as a string. |
---|
| 209 | * |
---|
| 210 | * @return the CVParameter as string |
---|
| 211 | */ |
---|
| 212 | public String toString() { |
---|
| 213 | |
---|
| 214 | String result = m_ParamChar + " " + m_Lower + " "; |
---|
| 215 | switch ((int)(m_Lower - m_Upper + 0.5)) { |
---|
| 216 | case 1: |
---|
| 217 | result += "A"; |
---|
| 218 | break; |
---|
| 219 | case 2: |
---|
| 220 | result += "I"; |
---|
| 221 | break; |
---|
| 222 | default: |
---|
| 223 | result += m_Upper; |
---|
| 224 | break; |
---|
| 225 | } |
---|
| 226 | result += " " + m_Steps; |
---|
| 227 | if (m_RoundParam) { |
---|
| 228 | result += " R"; |
---|
| 229 | } |
---|
| 230 | return result; |
---|
| 231 | } |
---|
| 232 | |
---|
| 233 | /** |
---|
| 234 | * Returns the revision string. |
---|
| 235 | * |
---|
| 236 | * @return the revision |
---|
| 237 | */ |
---|
| 238 | public String getRevision() { |
---|
| 239 | return RevisionUtils.extract("$Revision: 5928 $"); |
---|
| 240 | } |
---|
| 241 | } |
---|
| 242 | |
---|
| 243 | /** |
---|
| 244 | * The base classifier options (not including those being set |
---|
| 245 | * by cross-validation) |
---|
| 246 | */ |
---|
| 247 | protected String [] m_ClassifierOptions; |
---|
| 248 | |
---|
| 249 | /** The set of all classifier options as determined by cross-validation */ |
---|
| 250 | protected String [] m_BestClassifierOptions; |
---|
| 251 | |
---|
| 252 | /** The set of all options at initialization time. So that getOptions |
---|
| 253 | can return this. */ |
---|
| 254 | protected String [] m_InitOptions; |
---|
| 255 | |
---|
| 256 | /** The cross-validated performance of the best options */ |
---|
| 257 | protected double m_BestPerformance; |
---|
| 258 | |
---|
| 259 | /** The set of parameters to cross-validate over */ |
---|
| 260 | protected FastVector m_CVParams = new FastVector(); |
---|
| 261 | |
---|
| 262 | /** The number of attributes in the data */ |
---|
| 263 | protected int m_NumAttributes; |
---|
| 264 | |
---|
| 265 | /** The number of instances in a training fold */ |
---|
| 266 | protected int m_TrainFoldSize; |
---|
| 267 | |
---|
| 268 | /** The number of folds used in cross-validation */ |
---|
| 269 | protected int m_NumFolds = 10; |
---|
| 270 | |
---|
| 271 | /** |
---|
| 272 | * Create the options array to pass to the classifier. The parameter |
---|
| 273 | * values and positions are taken from m_ClassifierOptions and |
---|
| 274 | * m_CVParams. |
---|
| 275 | * |
---|
| 276 | * @return the options array |
---|
| 277 | */ |
---|
| 278 | protected String [] createOptions() { |
---|
| 279 | |
---|
| 280 | String [] options = new String [m_ClassifierOptions.length |
---|
| 281 | + 2 * m_CVParams.size()]; |
---|
| 282 | int start = 0, end = options.length; |
---|
| 283 | |
---|
| 284 | // Add the cross-validation parameters and their values |
---|
| 285 | for (int i = 0; i < m_CVParams.size(); i++) { |
---|
| 286 | CVParameter cvParam = (CVParameter)m_CVParams.elementAt(i); |
---|
| 287 | double paramValue = cvParam.m_ParamValue; |
---|
| 288 | if (cvParam.m_RoundParam) { |
---|
| 289 | // paramValue = (double)((int) (paramValue + 0.5)); |
---|
| 290 | paramValue = Math.rint(paramValue); |
---|
| 291 | } |
---|
| 292 | if (cvParam.m_AddAtEnd) { |
---|
| 293 | options[--end] = "" + |
---|
| 294 | Utils.doubleToString(paramValue,4); |
---|
| 295 | options[--end] = "-" + cvParam.m_ParamChar; |
---|
| 296 | } else { |
---|
| 297 | options[start++] = "-" + cvParam.m_ParamChar; |
---|
| 298 | options[start++] = "" |
---|
| 299 | + Utils.doubleToString(paramValue,4); |
---|
| 300 | } |
---|
| 301 | } |
---|
| 302 | // Add the static parameters |
---|
| 303 | System.arraycopy(m_ClassifierOptions, 0, |
---|
| 304 | options, start, |
---|
| 305 | m_ClassifierOptions.length); |
---|
| 306 | |
---|
| 307 | return options; |
---|
| 308 | } |
---|
| 309 | |
---|
| 310 | /** |
---|
| 311 | * Finds the best parameter combination. (recursive for each parameter |
---|
| 312 | * being optimised). |
---|
| 313 | * |
---|
| 314 | * @param depth the index of the parameter to be optimised at this level |
---|
| 315 | * @param trainData the data the search is based on |
---|
| 316 | * @param random a random number generator |
---|
| 317 | * @throws Exception if an error occurs |
---|
| 318 | */ |
---|
| 319 | protected void findParamsByCrossValidation(int depth, Instances trainData, |
---|
| 320 | Random random) |
---|
| 321 | throws Exception { |
---|
| 322 | |
---|
| 323 | if (depth < m_CVParams.size()) { |
---|
| 324 | CVParameter cvParam = (CVParameter)m_CVParams.elementAt(depth); |
---|
| 325 | |
---|
| 326 | double upper; |
---|
| 327 | switch ((int)(cvParam.m_Lower - cvParam.m_Upper + 0.5)) { |
---|
| 328 | case 1: |
---|
| 329 | upper = m_NumAttributes; |
---|
| 330 | break; |
---|
| 331 | case 2: |
---|
| 332 | upper = m_TrainFoldSize; |
---|
| 333 | break; |
---|
| 334 | default: |
---|
| 335 | upper = cvParam.m_Upper; |
---|
| 336 | break; |
---|
| 337 | } |
---|
| 338 | double increment = (upper - cvParam.m_Lower) / (cvParam.m_Steps - 1); |
---|
| 339 | for(cvParam.m_ParamValue = cvParam.m_Lower; |
---|
| 340 | cvParam.m_ParamValue <= upper; |
---|
| 341 | cvParam.m_ParamValue += increment) { |
---|
| 342 | findParamsByCrossValidation(depth + 1, trainData, random); |
---|
| 343 | } |
---|
| 344 | } else { |
---|
| 345 | |
---|
| 346 | Evaluation evaluation = new Evaluation(trainData); |
---|
| 347 | |
---|
| 348 | // Set the classifier options |
---|
| 349 | String [] options = createOptions(); |
---|
| 350 | if (m_Debug) { |
---|
| 351 | System.err.print("Setting options for " |
---|
| 352 | + m_Classifier.getClass().getName() + ":"); |
---|
| 353 | for (int i = 0; i < options.length; i++) { |
---|
| 354 | System.err.print(" " + options[i]); |
---|
| 355 | } |
---|
| 356 | System.err.println(""); |
---|
| 357 | } |
---|
| 358 | ((OptionHandler)m_Classifier).setOptions(options); |
---|
| 359 | for (int j = 0; j < m_NumFolds; j++) { |
---|
| 360 | |
---|
| 361 | // We want to randomize the data the same way for every |
---|
| 362 | // learning scheme. |
---|
| 363 | Instances train = trainData.trainCV(m_NumFolds, j, new Random(1)); |
---|
| 364 | Instances test = trainData.testCV(m_NumFolds, j); |
---|
| 365 | m_Classifier.buildClassifier(train); |
---|
| 366 | evaluation.setPriors(train); |
---|
| 367 | evaluation.evaluateModel(m_Classifier, test); |
---|
| 368 | } |
---|
| 369 | double error = evaluation.errorRate(); |
---|
| 370 | if (m_Debug) { |
---|
| 371 | System.err.println("Cross-validated error rate: " |
---|
| 372 | + Utils.doubleToString(error, 6, 4)); |
---|
| 373 | } |
---|
| 374 | if ((m_BestPerformance == -99) || (error < m_BestPerformance)) { |
---|
| 375 | |
---|
| 376 | m_BestPerformance = error; |
---|
| 377 | m_BestClassifierOptions = createOptions(); |
---|
| 378 | } |
---|
| 379 | } |
---|
| 380 | } |
---|
| 381 | |
---|
| 382 | /** |
---|
| 383 | * Returns a string describing this classifier |
---|
| 384 | * @return a description of the classifier suitable for |
---|
| 385 | * displaying in the explorer/experimenter gui |
---|
| 386 | */ |
---|
| 387 | public String globalInfo() { |
---|
| 388 | return "Class for performing parameter selection by cross-validation " |
---|
| 389 | + "for any classifier.\n\n" |
---|
| 390 | + "For more information, see:\n\n" |
---|
| 391 | + getTechnicalInformation().toString(); |
---|
| 392 | } |
---|
| 393 | |
---|
| 394 | /** |
---|
| 395 | * Returns an instance of a TechnicalInformation object, containing |
---|
| 396 | * detailed information about the technical background of this class, |
---|
| 397 | * e.g., paper reference or book this class is based on. |
---|
| 398 | * |
---|
| 399 | * @return the technical information about this class |
---|
| 400 | */ |
---|
| 401 | public TechnicalInformation getTechnicalInformation() { |
---|
| 402 | TechnicalInformation result; |
---|
| 403 | |
---|
| 404 | result = new TechnicalInformation(Type.PHDTHESIS); |
---|
| 405 | result.setValue(Field.AUTHOR, "R. Kohavi"); |
---|
| 406 | result.setValue(Field.YEAR, "1995"); |
---|
| 407 | result.setValue(Field.TITLE, "Wrappers for Performance Enhancement and Oblivious Decision Graphs"); |
---|
| 408 | result.setValue(Field.SCHOOL, "Stanford University"); |
---|
| 409 | result.setValue(Field.ADDRESS, "Department of Computer Science, Stanford University"); |
---|
| 410 | |
---|
| 411 | return result; |
---|
| 412 | } |
---|
| 413 | |
---|
| 414 | /** |
---|
| 415 | * Returns an enumeration describing the available options. |
---|
| 416 | * |
---|
| 417 | * @return an enumeration of all the available options. |
---|
| 418 | */ |
---|
| 419 | public Enumeration listOptions() { |
---|
| 420 | |
---|
| 421 | Vector newVector = new Vector(2); |
---|
| 422 | |
---|
| 423 | newVector.addElement(new Option( |
---|
| 424 | "\tNumber of folds used for cross validation (default 10).", |
---|
| 425 | "X", 1, "-X <number of folds>")); |
---|
| 426 | newVector.addElement(new Option( |
---|
| 427 | "\tClassifier parameter options.\n" |
---|
| 428 | + "\teg: \"N 1 5 10\" Sets an optimisation parameter for the\n" |
---|
| 429 | + "\tclassifier with name -N, with lower bound 1, upper bound\n" |
---|
| 430 | + "\t5, and 10 optimisation steps. The upper bound may be the\n" |
---|
| 431 | + "\tcharacter 'A' or 'I' to substitute the number of\n" |
---|
| 432 | + "\tattributes or instances in the training data,\n" |
---|
| 433 | + "\trespectively. This parameter may be supplied more than\n" |
---|
| 434 | + "\tonce to optimise over several classifier options\n" |
---|
| 435 | + "\tsimultaneously.", |
---|
| 436 | "P", 1, "-P <classifier parameter>")); |
---|
| 437 | |
---|
| 438 | |
---|
| 439 | Enumeration enu = super.listOptions(); |
---|
| 440 | while (enu.hasMoreElements()) { |
---|
| 441 | newVector.addElement(enu.nextElement()); |
---|
| 442 | } |
---|
| 443 | return newVector.elements(); |
---|
| 444 | } |
---|
| 445 | |
---|
| 446 | |
---|
| 447 | /** |
---|
| 448 | * Parses a given list of options. <p/> |
---|
| 449 | * |
---|
| 450 | <!-- options-start --> |
---|
| 451 | * Valid options are: <p/> |
---|
| 452 | * |
---|
| 453 | * <pre> -X <number of folds> |
---|
| 454 | * Number of folds used for cross validation (default 10).</pre> |
---|
| 455 | * |
---|
| 456 | * <pre> -P <classifier parameter> |
---|
| 457 | * Classifier parameter options. |
---|
| 458 | * eg: "N 1 5 10" Sets an optimisation parameter for the |
---|
| 459 | * classifier with name -N, with lower bound 1, upper bound |
---|
| 460 | * 5, and 10 optimisation steps. The upper bound may be the |
---|
| 461 | * character 'A' or 'I' to substitute the number of |
---|
| 462 | * attributes or instances in the training data, |
---|
| 463 | * respectively. This parameter may be supplied more than |
---|
| 464 | * once to optimise over several classifier options |
---|
| 465 | * simultaneously.</pre> |
---|
| 466 | * |
---|
| 467 | * <pre> -S <num> |
---|
| 468 | * Random number seed. |
---|
| 469 | * (default 1)</pre> |
---|
| 470 | * |
---|
| 471 | * <pre> -D |
---|
| 472 | * If set, classifier is run in debug mode and |
---|
| 473 | * may output additional info to the console</pre> |
---|
| 474 | * |
---|
| 475 | * <pre> -W |
---|
| 476 | * Full name of base classifier. |
---|
| 477 | * (default: weka.classifiers.rules.ZeroR)</pre> |
---|
| 478 | * |
---|
| 479 | * <pre> |
---|
| 480 | * Options specific to classifier weka.classifiers.rules.ZeroR: |
---|
| 481 | * </pre> |
---|
| 482 | * |
---|
| 483 | * <pre> -D |
---|
| 484 | * If set, classifier is run in debug mode and |
---|
| 485 | * may output additional info to the console</pre> |
---|
| 486 | * |
---|
| 487 | <!-- options-end --> |
---|
| 488 | * |
---|
| 489 | * Options after -- are passed to the designated sub-classifier. <p> |
---|
| 490 | * |
---|
| 491 | * @param options the list of options as an array of strings |
---|
| 492 | * @throws Exception if an option is not supported |
---|
| 493 | */ |
---|
| 494 | public void setOptions(String[] options) throws Exception { |
---|
| 495 | |
---|
| 496 | String foldsString = Utils.getOption('X', options); |
---|
| 497 | if (foldsString.length() != 0) { |
---|
| 498 | setNumFolds(Integer.parseInt(foldsString)); |
---|
| 499 | } else { |
---|
| 500 | setNumFolds(10); |
---|
| 501 | } |
---|
| 502 | |
---|
| 503 | String cvParam; |
---|
| 504 | m_CVParams = new FastVector(); |
---|
| 505 | do { |
---|
| 506 | cvParam = Utils.getOption('P', options); |
---|
| 507 | if (cvParam.length() != 0) { |
---|
| 508 | addCVParameter(cvParam); |
---|
| 509 | } |
---|
| 510 | } while (cvParam.length() != 0); |
---|
| 511 | |
---|
| 512 | super.setOptions(options); |
---|
| 513 | } |
---|
| 514 | |
---|
| 515 | /** |
---|
| 516 | * Gets the current settings of the Classifier. |
---|
| 517 | * |
---|
| 518 | * @return an array of strings suitable for passing to setOptions |
---|
| 519 | */ |
---|
| 520 | public String [] getOptions() { |
---|
| 521 | |
---|
| 522 | String[] superOptions; |
---|
| 523 | |
---|
| 524 | if (m_InitOptions != null) { |
---|
| 525 | try { |
---|
| 526 | ((OptionHandler)m_Classifier).setOptions((String[])m_InitOptions.clone()); |
---|
| 527 | superOptions = super.getOptions(); |
---|
| 528 | ((OptionHandler)m_Classifier).setOptions((String[])m_BestClassifierOptions.clone()); |
---|
| 529 | } catch (Exception e) { |
---|
| 530 | throw new RuntimeException("CVParameterSelection: could not set options " + |
---|
| 531 | "in getOptions()."); |
---|
| 532 | } |
---|
| 533 | } else { |
---|
| 534 | superOptions = super.getOptions(); |
---|
| 535 | } |
---|
| 536 | String [] options = new String [superOptions.length + m_CVParams.size() * 2 + 2]; |
---|
| 537 | |
---|
| 538 | int current = 0; |
---|
| 539 | for (int i = 0; i < m_CVParams.size(); i++) { |
---|
| 540 | options[current++] = "-P"; options[current++] = "" + getCVParameter(i); |
---|
| 541 | } |
---|
| 542 | options[current++] = "-X"; options[current++] = "" + getNumFolds(); |
---|
| 543 | |
---|
| 544 | System.arraycopy(superOptions, 0, options, current, |
---|
| 545 | superOptions.length); |
---|
| 546 | |
---|
| 547 | return options; |
---|
| 548 | } |
---|
| 549 | |
---|
| 550 | /** |
---|
| 551 | * Returns (a copy of) the best options found for the classifier. |
---|
| 552 | * |
---|
| 553 | * @return the best options |
---|
| 554 | */ |
---|
| 555 | public String[] getBestClassifierOptions() { |
---|
| 556 | return (String[]) m_BestClassifierOptions.clone(); |
---|
| 557 | } |
---|
| 558 | |
---|
| 559 | /** |
---|
| 560 | * Returns default capabilities of the classifier. |
---|
| 561 | * |
---|
| 562 | * @return the capabilities of this classifier |
---|
| 563 | */ |
---|
| 564 | public Capabilities getCapabilities() { |
---|
| 565 | Capabilities result = super.getCapabilities(); |
---|
| 566 | |
---|
| 567 | result.setMinimumNumberInstances(m_NumFolds); |
---|
| 568 | |
---|
| 569 | return result; |
---|
| 570 | } |
---|
| 571 | |
---|
| 572 | /** |
---|
| 573 | * Generates the classifier. |
---|
| 574 | * |
---|
| 575 | * @param instances set of instances serving as training data |
---|
| 576 | * @throws Exception if the classifier has not been generated successfully |
---|
| 577 | */ |
---|
| 578 | public void buildClassifier(Instances instances) throws Exception { |
---|
| 579 | |
---|
| 580 | // can classifier handle the data? |
---|
| 581 | getCapabilities().testWithFail(instances); |
---|
| 582 | |
---|
| 583 | // remove instances with missing class |
---|
| 584 | Instances trainData = new Instances(instances); |
---|
| 585 | trainData.deleteWithMissingClass(); |
---|
| 586 | |
---|
| 587 | if (!(m_Classifier instanceof OptionHandler)) { |
---|
| 588 | throw new IllegalArgumentException("Base classifier should be OptionHandler."); |
---|
| 589 | } |
---|
| 590 | m_InitOptions = ((OptionHandler)m_Classifier).getOptions(); |
---|
| 591 | m_BestPerformance = -99; |
---|
| 592 | m_NumAttributes = trainData.numAttributes(); |
---|
| 593 | Random random = new Random(m_Seed); |
---|
| 594 | trainData.randomize(random); |
---|
| 595 | m_TrainFoldSize = trainData.trainCV(m_NumFolds, 0).numInstances(); |
---|
| 596 | |
---|
| 597 | // Check whether there are any parameters to optimize |
---|
| 598 | if (m_CVParams.size() == 0) { |
---|
| 599 | m_Classifier.buildClassifier(trainData); |
---|
| 600 | m_BestClassifierOptions = m_InitOptions; |
---|
| 601 | return; |
---|
| 602 | } |
---|
| 603 | |
---|
| 604 | if (trainData.classAttribute().isNominal()) { |
---|
| 605 | trainData.stratify(m_NumFolds); |
---|
| 606 | } |
---|
| 607 | m_BestClassifierOptions = null; |
---|
| 608 | |
---|
| 609 | // Set up m_ClassifierOptions -- take getOptions() and remove |
---|
| 610 | // those being optimised. |
---|
| 611 | m_ClassifierOptions = ((OptionHandler)m_Classifier).getOptions(); |
---|
| 612 | for (int i = 0; i < m_CVParams.size(); i++) { |
---|
| 613 | Utils.getOption(((CVParameter)m_CVParams.elementAt(i)).m_ParamChar, |
---|
| 614 | m_ClassifierOptions); |
---|
| 615 | } |
---|
| 616 | findParamsByCrossValidation(0, trainData, random); |
---|
| 617 | |
---|
| 618 | String [] options = (String [])m_BestClassifierOptions.clone(); |
---|
| 619 | ((OptionHandler)m_Classifier).setOptions(options); |
---|
| 620 | m_Classifier.buildClassifier(trainData); |
---|
| 621 | } |
---|
| 622 | |
---|
| 623 | |
---|
| 624 | /** |
---|
| 625 | * Predicts the class distribution for the given test instance. |
---|
| 626 | * |
---|
| 627 | * @param instance the instance to be classified |
---|
| 628 | * @return the predicted class value |
---|
| 629 | * @throws Exception if an error occurred during the prediction |
---|
| 630 | */ |
---|
| 631 | public double[] distributionForInstance(Instance instance) throws Exception { |
---|
| 632 | |
---|
| 633 | return m_Classifier.distributionForInstance(instance); |
---|
| 634 | } |
---|
| 635 | |
---|
| 636 | /** |
---|
| 637 | * Adds a scheme parameter to the list of parameters to be set |
---|
| 638 | * by cross-validation |
---|
| 639 | * |
---|
| 640 | * @param cvParam the string representation of a scheme parameter. The |
---|
| 641 | * format is: <br> |
---|
| 642 | * param_char lower_bound upper_bound number_of_steps <br> |
---|
| 643 | * eg to search a parameter -P from 1 to 10 by increments of 1: <br> |
---|
| 644 | * P 1 10 11 <br> |
---|
| 645 | * @throws Exception if the parameter specifier is of the wrong format |
---|
| 646 | */ |
---|
| 647 | public void addCVParameter(String cvParam) throws Exception { |
---|
| 648 | |
---|
| 649 | CVParameter newCV = new CVParameter(cvParam); |
---|
| 650 | |
---|
| 651 | m_CVParams.addElement(newCV); |
---|
| 652 | } |
---|
| 653 | |
---|
| 654 | /** |
---|
| 655 | * Gets the scheme paramter with the given index. |
---|
| 656 | * |
---|
| 657 | * @param index the index for the parameter |
---|
| 658 | * @return the scheme parameter |
---|
| 659 | */ |
---|
| 660 | public String getCVParameter(int index) { |
---|
| 661 | |
---|
| 662 | if (m_CVParams.size() <= index) { |
---|
| 663 | return ""; |
---|
| 664 | } |
---|
| 665 | return ((CVParameter)m_CVParams.elementAt(index)).toString(); |
---|
| 666 | } |
---|
| 667 | |
---|
| 668 | /** |
---|
| 669 | * Returns the tip text for this property |
---|
| 670 | * @return tip text for this property suitable for |
---|
| 671 | * displaying in the explorer/experimenter gui |
---|
| 672 | */ |
---|
| 673 | public String CVParametersTipText() { |
---|
| 674 | return "Sets the scheme parameters which are to be set "+ |
---|
| 675 | "by cross-validation.\n"+ |
---|
| 676 | "The format for each string should be:\n"+ |
---|
| 677 | "param_char lower_bound upper_bound number_of_steps\n"+ |
---|
| 678 | "eg to search a parameter -P from 1 to 10 by increments of 1:\n"+ |
---|
| 679 | " \"P 1 10 10\" "; |
---|
| 680 | } |
---|
| 681 | |
---|
| 682 | /** |
---|
| 683 | * Get method for CVParameters. |
---|
| 684 | * |
---|
| 685 | * @return the CVParameters |
---|
| 686 | */ |
---|
| 687 | public Object[] getCVParameters() { |
---|
| 688 | |
---|
| 689 | Object[] CVParams = m_CVParams.toArray(); |
---|
| 690 | |
---|
| 691 | String params[] = new String[CVParams.length]; |
---|
| 692 | |
---|
| 693 | for(int i=0; i<CVParams.length; i++) |
---|
| 694 | params[i] = CVParams[i].toString(); |
---|
| 695 | |
---|
| 696 | return params; |
---|
| 697 | |
---|
| 698 | } |
---|
| 699 | |
---|
| 700 | /** |
---|
| 701 | * Set method for CVParameters. |
---|
| 702 | * |
---|
| 703 | * @param params the CVParameters to use |
---|
| 704 | * @throws Exception if the setting of the CVParameters fails |
---|
| 705 | */ |
---|
| 706 | public void setCVParameters(Object[] params) throws Exception { |
---|
| 707 | |
---|
| 708 | FastVector backup = m_CVParams; |
---|
| 709 | m_CVParams = new FastVector(); |
---|
| 710 | |
---|
| 711 | for(int i=0; i<params.length; i++) { |
---|
| 712 | try{ |
---|
| 713 | addCVParameter((String)params[i]); |
---|
| 714 | } |
---|
| 715 | catch(Exception ex) { m_CVParams = backup; throw ex; } |
---|
| 716 | } |
---|
| 717 | } |
---|
| 718 | |
---|
| 719 | /** |
---|
| 720 | * Returns the tip text for this property |
---|
| 721 | * @return tip text for this property suitable for |
---|
| 722 | * displaying in the explorer/experimenter gui |
---|
| 723 | */ |
---|
| 724 | public String numFoldsTipText() { |
---|
| 725 | return "Get the number of folds used for cross-validation."; |
---|
| 726 | } |
---|
| 727 | |
---|
| 728 | /** |
---|
| 729 | * Gets the number of folds for the cross-validation. |
---|
| 730 | * |
---|
| 731 | * @return the number of folds for the cross-validation |
---|
| 732 | */ |
---|
| 733 | public int getNumFolds() { |
---|
| 734 | |
---|
| 735 | return m_NumFolds; |
---|
| 736 | } |
---|
| 737 | |
---|
| 738 | /** |
---|
| 739 | * Sets the number of folds for the cross-validation. |
---|
| 740 | * |
---|
| 741 | * @param numFolds the number of folds for the cross-validation |
---|
| 742 | * @throws Exception if parameter illegal |
---|
| 743 | */ |
---|
| 744 | public void setNumFolds(int numFolds) throws Exception { |
---|
| 745 | |
---|
| 746 | if (numFolds < 0) { |
---|
| 747 | throw new IllegalArgumentException("Stacking: Number of cross-validation " + |
---|
| 748 | "folds must be positive."); |
---|
| 749 | } |
---|
| 750 | m_NumFolds = numFolds; |
---|
| 751 | } |
---|
| 752 | |
---|
| 753 | /** |
---|
| 754 | * Returns the type of graph this classifier |
---|
| 755 | * represents. |
---|
| 756 | * |
---|
| 757 | * @return the type of graph this classifier represents |
---|
| 758 | */ |
---|
| 759 | public int graphType() { |
---|
| 760 | |
---|
| 761 | if (m_Classifier instanceof Drawable) |
---|
| 762 | return ((Drawable)m_Classifier).graphType(); |
---|
| 763 | else |
---|
| 764 | return Drawable.NOT_DRAWABLE; |
---|
| 765 | } |
---|
| 766 | |
---|
| 767 | /** |
---|
| 768 | * Returns graph describing the classifier (if possible). |
---|
| 769 | * |
---|
| 770 | * @return the graph of the classifier in dotty format |
---|
| 771 | * @throws Exception if the classifier cannot be graphed |
---|
| 772 | */ |
---|
| 773 | public String graph() throws Exception { |
---|
| 774 | |
---|
| 775 | if (m_Classifier instanceof Drawable) |
---|
| 776 | return ((Drawable)m_Classifier).graph(); |
---|
| 777 | else throw new Exception("Classifier: " + |
---|
| 778 | m_Classifier.getClass().getName() + " " + |
---|
| 779 | Utils.joinOptions(m_BestClassifierOptions) |
---|
| 780 | + " cannot be graphed"); |
---|
| 781 | } |
---|
| 782 | |
---|
| 783 | /** |
---|
| 784 | * Returns description of the cross-validated classifier. |
---|
| 785 | * |
---|
| 786 | * @return description of the cross-validated classifier as a string |
---|
| 787 | */ |
---|
| 788 | public String toString() { |
---|
| 789 | |
---|
| 790 | if (m_InitOptions == null) |
---|
| 791 | return "CVParameterSelection: No model built yet."; |
---|
| 792 | |
---|
| 793 | String result = "Cross-validated Parameter selection.\n" |
---|
| 794 | + "Classifier: " + m_Classifier.getClass().getName() + "\n"; |
---|
| 795 | try { |
---|
| 796 | for (int i = 0; i < m_CVParams.size(); i++) { |
---|
| 797 | CVParameter cvParam = (CVParameter)m_CVParams.elementAt(i); |
---|
| 798 | result += "Cross-validation Parameter: '-" |
---|
| 799 | + cvParam.m_ParamChar + "'" |
---|
| 800 | + " ranged from " + cvParam.m_Lower |
---|
| 801 | + " to "; |
---|
| 802 | switch ((int)(cvParam.m_Lower - cvParam.m_Upper + 0.5)) { |
---|
| 803 | case 1: |
---|
| 804 | result += m_NumAttributes; |
---|
| 805 | break; |
---|
| 806 | case 2: |
---|
| 807 | result += m_TrainFoldSize; |
---|
| 808 | break; |
---|
| 809 | default: |
---|
| 810 | result += cvParam.m_Upper; |
---|
| 811 | break; |
---|
| 812 | } |
---|
| 813 | result += " with " + cvParam.m_Steps + " steps\n"; |
---|
| 814 | } |
---|
| 815 | } catch (Exception ex) { |
---|
| 816 | result += ex.getMessage(); |
---|
| 817 | } |
---|
| 818 | result += "Classifier Options: " |
---|
| 819 | + Utils.joinOptions(m_BestClassifierOptions) |
---|
| 820 | + "\n\n" + m_Classifier.toString(); |
---|
| 821 | return result; |
---|
| 822 | } |
---|
| 823 | |
---|
| 824 | /** |
---|
| 825 | * A concise description of the model. |
---|
| 826 | * |
---|
| 827 | * @return a concise description of the model |
---|
| 828 | */ |
---|
| 829 | public String toSummaryString() { |
---|
| 830 | |
---|
| 831 | String result = "Selected values: " |
---|
| 832 | + Utils.joinOptions(m_BestClassifierOptions); |
---|
| 833 | return result + '\n'; |
---|
| 834 | } |
---|
| 835 | |
---|
| 836 | /** |
---|
| 837 | * Returns the revision string. |
---|
| 838 | * |
---|
| 839 | * @return the revision |
---|
| 840 | */ |
---|
| 841 | public String getRevision() { |
---|
| 842 | return RevisionUtils.extract("$Revision: 5928 $"); |
---|
| 843 | } |
---|
| 844 | |
---|
| 845 | /** |
---|
| 846 | * Main method for testing this class. |
---|
| 847 | * |
---|
| 848 | * @param argv the options |
---|
| 849 | */ |
---|
| 850 | public static void main(String [] argv) { |
---|
| 851 | runClassifier(new CVParameterSelection(), argv); |
---|
| 852 | } |
---|
| 853 | } |
---|