/*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
*/
/*
* BayesianLogisticRegression.java
* Copyright (C) 2008 Illinois Institute of Technology
*
*/
package weka.classifiers.bayes;
import weka.classifiers.Classifier;
import weka.classifiers.bayes.blr.GaussianPriorImpl;
import weka.classifiers.bayes.blr.LaplacePriorImpl;
import weka.classifiers.bayes.blr.Prior;
import weka.core.Attribute;
import weka.core.Capabilities;
import weka.core.Instance;
import weka.core.Instances;
import weka.core.Option;
import weka.core.OptionHandler;
import weka.core.RevisionUtils;
import weka.core.SelectedTag;
import weka.core.SerializedObject;
import weka.core.Tag;
import weka.core.TechnicalInformation;
import weka.core.TechnicalInformationHandler;
import weka.core.Utils;
import weka.core.Capabilities.Capability;
import weka.core.TechnicalInformation.Field;
import weka.core.TechnicalInformation.Type;
import weka.filters.Filter;
import weka.filters.unsupervised.attribute.Normalize;
import java.util.Enumeration;
import java.util.Random;
import java.util.StringTokenizer;
import java.util.Vector;
/**
<!-- globalinfo-start -->
* Implements Bayesian Logistic Regression for both Gaussian and Laplace Priors.<br/>
* <br/>
* For more information, see<br/>
* <br/>
* Alexander Genkin, David D. Lewis, David Madigan (2004). Large-scale bayesian logistic regression for text categorization. URL http://www.stat.rutgers.edu/~madigan/PAPERS/shortFat-v3a.pdf.
* <p/>
<!-- globalinfo-end -->
*
<!-- technical-bibtex-start -->
* BibTeX:
* <pre>
* @techreport{Genkin2004,
* author = {Alexander Genkin and David D. Lewis and David Madigan},
* institution = {DIMACS},
* title = {Large-scale bayesian logistic regression for text categorization},
* year = {2004},
* URL = {http://www.stat.rutgers.edu/\~madigan/PAPERS/shortFat-v3a.pdf}
* }
* </pre>
* <p/>
<!-- technical-bibtex-end -->
*
*
* @author Navendu Garg (gargnav at iit dot edu)
* @version $Revision: 1.3 $
*/
public class BayesianLogisticRegression extends Classifier
implements OptionHandler, TechnicalInformationHandler {
static final long serialVersionUID = -8013478897911757631L;
/** Log-likelihood values to be used to choose the best hyperparameter. */
public static double[] LogLikelihood;
/** Set of values to be used as hyperparameter values during Cross-Validation. */
public static double[] InputHyperparameterValues;
/** DEBUG Mode*/
boolean debug = false;
/** Choose whether to normalize data or not */
public boolean NormalizeData = false;
/** Tolerance criteria for the stopping criterion. */
public double Tolerance = 0.0005;
/** Threshold for binary classification of probabilisitic estimate*/
public double Threshold = 0.5;
/** Distributions available */
public static final int GAUSSIAN = 1;
public static final int LAPLACIAN = 2;
public static final Tag[] TAGS_PRIOR = {
new Tag(GAUSSIAN, "Gaussian"),
new Tag(LAPLACIAN, "Laplacian")
};
/** Distribution Prior class */
public int PriorClass = GAUSSIAN;
/** NumFolds for CV based Hyperparameters selection*/
public int NumFolds = 2;
/** Methods for selecting the hyperparameter value */
public static final int NORM_BASED = 1;
public static final int CV_BASED = 2;
public static final int SPECIFIC_VALUE = 3;
public static final Tag[] TAGS_HYPER_METHOD = {
new Tag(NORM_BASED, "Norm-based"),
new Tag(CV_BASED, "CV-based"),
new Tag(SPECIFIC_VALUE, "Specific value")
};
/** Hyperparameter selection method */
public int HyperparameterSelection = NORM_BASED;
/** The class index from the training data */
public int ClassIndex = -1;
/** Best hyperparameter for test phase */
public double HyperparameterValue = 0.27;
/** CV Hyperparameter Range */
public String HyperparameterRange = "R:0.01-316,3.16";
/** Maximum number of iterations */
public int maxIterations = 100;
/**Iteration counter */
public int iterationCounter = 0;
/** Array for storing coefficients of Bayesian regression model. */
public double[] BetaVector;
/** Array to store Regression Coefficient updates. */
public double[] DeltaBeta;
/** Trust Region Radius Update*/
public double[] DeltaUpdate;
/** Trust Region Radius*/
public double[] Delta;
/** Array to store Hyperparameter values for each feature. */
public double[] Hyperparameters;
/** R(i)= BetaVector X x(i) X y(i).
* This an intermediate value with respect to vector BETA, input values and corresponding class labels*/
public double[] R;
/** This vector is used to store the increments on the R(i). It is also used to determining the stopping criterion.*/
public double[] DeltaR;
/**
* This variable is used to keep track of change in
* the value of delta summation of r(i).
*/
public double Change;
/**
* Bayesian Logistic Regression returns the probability of a given instance will belong to a certain
* class (p(y=+1|Beta,X). To obtain a binary value the Threshold value is used.
* <pre>
* p(y=+1|Beta,X)>Threshold ? 1 : -1
* </pre>
*/
/** Filter interface used to point to weka.filters.unsupervised.attribute.Normalize object
*
*/
public Filter m_Filter;
/** Dataset provided to do Training/Test set.*/
protected Instances m_Instances;
/** Prior class object interface*/
protected Prior m_PriorUpdate;
public String globalInfo() {
return "Implements Bayesian Logistic Regression "
+ "for both Gaussian and Laplace Priors.\n\n"
+ "For more information, see\n\n"
+ getTechnicalInformation();
}
/**
* <pre>
* (1)Initialize m_Beta[j] to 0.
* (2)Initialize m_DeltaUpdate[j].
* </pre>
*
* */
public void initialize() throws Exception {
int numOfAttributes;
int numOfInstances;
int i;
int j;
Change = 0.0;
//Manipulate Data
if (NormalizeData) {
m_Filter = new Normalize();
m_Filter.setInputFormat(m_Instances);
m_Instances = Filter.useFilter(m_Instances, m_Filter);
}
//Set the intecept coefficient.
Attribute att = new Attribute("(intercept)");
Instance instance;
m_Instances.insertAttributeAt(att, 0);
for (i = 0; i < m_Instances.numInstances(); i++) {
instance = m_Instances.instance(i);
instance.setValue(0, 1.0);
}
//Get the number of attributes
numOfAttributes = m_Instances.numAttributes();
numOfInstances = m_Instances.numInstances();
ClassIndex = m_Instances.classIndex();
iterationCounter = 0;
//Initialize Arrays.
switch (HyperparameterSelection) {
case 1:
HyperparameterValue = normBasedHyperParameter();
if (debug) {
System.out.println("Norm-based Hyperparameter: " + HyperparameterValue);
}
break;
case 2:
HyperparameterValue = CVBasedHyperparameter();
if (debug) {
System.out.println("CV-based Hyperparameter: " + HyperparameterValue);
}
break;
}
BetaVector = new double[numOfAttributes];
Delta = new double[numOfAttributes];
DeltaBeta = new double[numOfAttributes];
Hyperparameters = new double[numOfAttributes];
DeltaUpdate = new double[numOfAttributes];
for (j = 0; j < numOfAttributes; j++) {
BetaVector[j] = 0.0;
Delta[j] = 1.0;
DeltaBeta[j] = 0.0;
DeltaUpdate[j] = 0.0;
//TODO: Change the way it takes values.
Hyperparameters[j] = HyperparameterValue;
}
DeltaR = new double[numOfInstances];
R = new double[numOfInstances];
for (i = 0; i < numOfInstances; i++) {
DeltaR[i] = 0.0;
R[i] = 0.0;
}
//Set the Prior interface to the appropriate prior implementation.
if (PriorClass == GAUSSIAN) {
m_PriorUpdate = new GaussianPriorImpl();
} else {
m_PriorUpdate = new LaplacePriorImpl();
}
}
/**
* This method tests what kind of data this classifier can handle.
* return Capabilities
*/
public Capabilities getCapabilities() {
Capabilities result = super.getCapabilities();
// attributes
result.enable(Capability.NUMERIC_ATTRIBUTES);
result.enable(Capability.BINARY_ATTRIBUTES);
// class
result.enable(Capability.BINARY_CLASS);
// instances
result.setMinimumNumberInstances(0);
return result;
}
/**
* <ul>
* <li>(1) Set the data to the class attribute m_Instances.</li>
* <li>(2)Call the method initialize() to initialize the values.</li>
* </ul>
* @param data training data
* @exception Exception if classifier can't be built successfully.
*/
public void buildClassifier(Instances data) throws Exception {
Instance instance;
int i;
int j;
// can classifier handle the data?
getCapabilities().testWithFail(data);
//(1) Set the data to the class attribute m_Instances.
m_Instances = new Instances(data);
//(2)Call the method initialize() to initialize the values.
initialize();
do {
//Compute the prior Trust Region Radius Update;
for (j = 0; j < m_Instances.numAttributes(); j++) {
if (j != ClassIndex) {
DeltaUpdate[j] = m_PriorUpdate.update(j, m_Instances, BetaVector[j],
Hyperparameters[j], R, Delta[j]);
//limit step to trust region.
DeltaBeta[j] = Math.min(Math.max(DeltaUpdate[j], 0 - Delta[j]),
Delta[j]);
//Update the
for (i = 0; i < m_Instances.numInstances(); i++) {
instance = m_Instances.instance(i);
if (instance.value(j) != 0) {
DeltaR[i] = DeltaBeta[j] * instance.value(j) * classSgn(instance.classValue());
R[i] += DeltaR[i];
}
}
//Updated Beta values.
BetaVector[j] += DeltaBeta[j];
//Update size of trust region.
Delta[j] = Math.max(2 * Math.abs(DeltaBeta[j]), Delta[j] / 2.0);
}
}
} while (!stoppingCriterion());
m_PriorUpdate.computelogLikelihood(BetaVector, m_Instances);
m_PriorUpdate.computePenalty(BetaVector, Hyperparameters);
}
/**
* This class is used to mask the internal class labels.
*
* @param value internal class label
* @return
* <pre>
* <ul><li>
* -1 for internal class label 0
* </li>
* <li>
* +1 for internal class label 1
* </li>
* </ul>
* </pre>
*/
public static double classSgn(double value) {
if (value == 0.0) {
return -1.0;
} else {
return 1.0;
}
}
/**
* Returns an instance of a TechnicalInformation object, containing
* detailed information about the technical background of this class,
* e.g., paper reference or book this class is based on.
*
* @return the technical information about this class
*/
public TechnicalInformation getTechnicalInformation() {
TechnicalInformation result = null;
result = new TechnicalInformation(Type.TECHREPORT);
result.setValue(Field.AUTHOR, "Alexander Genkin and David D. Lewis and David Madigan");
result.setValue(Field.YEAR, "2004");
result.setValue(Field.TITLE, "Large-scale bayesian logistic regression for text categorization");
result.setValue(Field.INSTITUTION, "DIMACS");
result.setValue(Field.URL, "http://www.stat.rutgers.edu/~madigan/PAPERS/shortFat-v3a.pdf");
return result;
}
/**
* This is a convient function that defines and upper bound
* (Delta>0) for values of r(i) reachable by updates in the
* trust region.
*
* r BetaVector X x(i)y(i).
* delta A parameter where sigma > 0
* @return double function value
*/
public static double bigF(double r, double sigma) {
double funcValue = 0.25;
double absR = Math.abs(r);
if (absR > sigma) {
funcValue = 1.0 / (2.0 + Math.exp(absR - sigma) + Math.exp(sigma - absR));
}
return funcValue;
}
/**
* This method implements the stopping criterion
* function.
*
* @return boolean whether to stop or not.
*/
public boolean stoppingCriterion() {
int i;
double sum_deltaR = 0.0;
double sum_R = 1.0;
boolean shouldStop;
double value = 0.0;
double delta;
//Summation of changes in R(i) vector.
for (i = 0; i < m_Instances.numInstances(); i++) {
sum_deltaR += Math.abs(DeltaR[i]); //Numerator (deltaR(i))
sum_R += Math.abs(R[i]); // Denominator (1+sum(R(i))
}
delta = Math.abs(sum_deltaR - Change);
Change = delta / sum_R;
if (debug) {
System.out.println(Change + " <= " + Tolerance);
}
shouldStop = ((Change <= Tolerance) || (iterationCounter >= maxIterations))
? true : false;
iterationCounter++;
Change = sum_deltaR;
return shouldStop;
}
/**
* This method computes the values for the logistic link function.
* <pre>f(r)=exp(r)/(1+exp(r))</pre>
*
* @return output value
*/
public static double logisticLinkFunction(double r) {
return Math.exp(r) / (1.0 + Math.exp(r));
}
/**
* Sign for a given value.
* @param r
* @return double +1 if r>0, -1 if r<0
*/
public static double sgn(double r) {
double sgn = 0.0;
if (r > 0) {
sgn = 1.0;
} else if (r < 0) {
sgn = -1.0;
}
return sgn;
}
/**
* This function computes the norm-based hyperparameters
* and stores them in the m_Hyperparameters.
*/
public double normBasedHyperParameter() {
//TODO: Implement this method.
Instance instance;
double mean = 0.0;
for (int i = 0; i < m_Instances.numInstances(); i++) {
instance = m_Instances.instance(i);
double sqr_sum = 0.0;
for (int j = 0; j < m_Instances.numAttributes(); j++) {
if (j != ClassIndex) {
sqr_sum += (instance.value(j) * instance.value(j));
}
}
//sqr_sum=Math.sqrt(sqr_sum);
mean += sqr_sum;
}
mean = mean / (double) m_Instances.numInstances();
return ((double) m_Instances.numAttributes()) / mean;
}
/**
* Classifies the given instance using the Bayesian Logistic Regression function.
*
* @param instance the test instance
* @return the classification
* @throws Exception if classification can't be done successfully
*/
public double classifyInstance(Instance instance) throws Exception {
//TODO: Implement
double sum_R = 0.0;
double classification = 0.0;
sum_R = BetaVector[0];
for (int j = 0; j < instance.numAttributes(); j++) {
if (j != (ClassIndex - 1)) {
sum_R += (BetaVector[j + 1] * instance.value(j));
}
}
sum_R = logisticLinkFunction(sum_R);
if (sum_R > Threshold) {
classification = 1.0;
} else {
classification = 0.0;
}
return classification;
}
/**
* Outputs the linear regression model as a string.
*
* @return the model as string
*/
public String toString() {
if (m_Instances == null) {
return "Bayesian logistic regression: No model built yet.";
}
StringBuffer buf = new StringBuffer();
String text = "";
switch (HyperparameterSelection) {
case 1:
text = "Norm-Based Hyperparameter Selection: ";
break;
case 2:
text = "Cross-Validation Based Hyperparameter Selection: ";
break;
case 3:
text = "Specified Hyperparameter: ";
break;
}
buf.append(text).append(HyperparameterValue).append("\n\n");
buf.append("Regression Coefficients\n");
buf.append("=========================\n\n");
for (int j = 0; j < m_Instances.numAttributes(); j++) {
if (j != ClassIndex) {
if (BetaVector[j] != 0.0) {
buf.append(m_Instances.attribute(j).name()).append(" : ")
.append(BetaVector[j]).append("\n");
}
}
}
buf.append("===========================\n\n");
buf.append("Likelihood: " + m_PriorUpdate.getLoglikelihood() + "\n\n");
buf.append("Penalty: " + m_PriorUpdate.getPenalty() + "\n\n");
buf.append("Regularized Log Posterior: " + m_PriorUpdate.getLogPosterior() +
"\n");
buf.append("===========================\n\n");
return buf.toString();
}
/**
* Method computes the best hyperparameter value by doing cross
* -validation on the training data and compute the likelihood.
* The method can parse a range of values or a list of values.
* @return Best hyperparameter value with the max likelihood value on the training data.
* @throws Exception
*/
public double CVBasedHyperparameter() throws Exception {
//TODO: Method incomplete.
double start;
//TODO: Method incomplete.
double end;
//TODO: Method incomplete.
double multiplier;
int size = 0;
double[] list = null;
double MaxHypeValue = 0.0;
double MaxLikelihood = 0.0;
StringTokenizer tokenizer = new StringTokenizer(HyperparameterRange);
String rangeType = tokenizer.nextToken(":");
if (rangeType.equals("R")) {
String temp = tokenizer.nextToken();
tokenizer = new StringTokenizer(temp);
start = Double.parseDouble(tokenizer.nextToken("-"));
tokenizer = new StringTokenizer(tokenizer.nextToken());
end = Double.parseDouble(tokenizer.nextToken(","));
multiplier = Double.parseDouble(tokenizer.nextToken());
int steps = (int) (((Math.log10(end) - Math.log10(start)) / Math.log10(multiplier)) +
1);
list = new double[steps];
int count = 0;
for (double i = start; i <= end; i *= multiplier) {
list[count++] = i;
}
} else if (rangeType.equals("L")) {
Vector vec = new Vector();
while (tokenizer.hasMoreTokens()) {
vec.add(tokenizer.nextToken(","));
}
list = new double[vec.size()];
for (int i = 0; i < vec.size(); i++) {
list[i] = Double.parseDouble((String) vec.get(i));
}
} else {
//throw exception.
}
// Perform two-fold cross-validation to collect
// unbiased predictions
if (list != null) {
int numFolds = (int) NumFolds;
Random random = new Random();
m_Instances.randomize(random);
m_Instances.stratify(numFolds);
for (int k = 0; k < list.length; k++) {
for (int i = 0; i < numFolds; i++) {
Instances train = m_Instances.trainCV(numFolds, i, random);
SerializedObject so = new SerializedObject(this);
BayesianLogisticRegression blr = (BayesianLogisticRegression) so.getObject();
// blr.setHyperparameterSelection(3);
blr.setHyperparameterSelection(new SelectedTag(SPECIFIC_VALUE,
TAGS_HYPER_METHOD));
blr.setHyperparameterValue(list[k]);
// blr.setPriorClass(PriorClass);
blr.setPriorClass(new SelectedTag(PriorClass,
TAGS_PRIOR));
blr.setThreshold(Threshold);
blr.setTolerance(Tolerance);
blr.buildClassifier(train);
Instances test = m_Instances.testCV(numFolds, i);
double val = blr.getLoglikeliHood(blr.BetaVector, test);
if (debug) {
System.out.println("Fold " + i + "Hyperparameter: " + list[k]);
System.out.println("===================================");
System.out.println(" Likelihood: " + val);
}
if ((k == 0) | (val > MaxLikelihood)) {
MaxLikelihood = val;
MaxHypeValue = list[k];
}
}
}
} else {
return HyperparameterValue;
}
return MaxHypeValue;
}
/**
*
* @return likelihood for a given set of betas and instances
*/
public double getLoglikeliHood(double[] betas, Instances instances) {
m_PriorUpdate.computelogLikelihood(betas, instances);
return m_PriorUpdate.getLoglikelihood();
}
/**
* Returns an enumeration describing the available options.
*
* @return an enumeration of all the available options.
*/
public Enumeration listOptions() {
Vector newVector = new Vector();
newVector.addElement(new Option("\tShow Debugging Output\n", "D", 0, "-D"));
newVector.addElement(new Option("\tDistribution of the Prior "
+"(1=Gaussian, 2=Laplacian)"
+"\n\t(default: 1=Gaussian)"
, "P", 1,
"-P <integer>"));
newVector.addElement(new Option("\tHyperparameter Selection Method "
+"(1=Norm-based, 2=CV-based, 3=specific value)\n"
+"\t(default: 1=Norm-based)",
"H",
1,
"-H <integer>"));
newVector.addElement(new Option("\tSpecified Hyperparameter Value (use in conjunction with -H 3)\n"
+"\t(default: 0.27)",
"V",
1,
"-V <double>"));
newVector.addElement(new Option(
"\tHyperparameter Range (use in conjunction with -H 2)\n"
+"\t(format: R:start-end,multiplier OR L:val(1), val(2), ..., val(n))\n"
+"\t(default: R:0.01-316,3.16)",
"R",
1,
"-R <string>"));
newVector.addElement(new Option("\tTolerance Value\n\t(default: 0.0005)",
"Tl",
1,
"-Tl <double>"));
newVector.addElement(new Option("\tThreshold Value\n\t(default: 0.5)",
"S",
1,
"-S <double>"));
newVector.addElement(new Option("\tNumber Of Folds (use in conjuction with -H 2)\n"
+"\t(default: 2)",
"F",
1,
"-F <integer>"));
newVector.addElement(new Option("\tMax Number of Iterations\n\t(default: 100)",
"I",
1,
"-I <integer>"));
newVector.addElement(new Option("\tNormalize the data",
"N", 0, "-N"));
return newVector.elements();
}
/**
* Parses a given list of options. <p/>
*
<!-- options-start -->
* Valid options are: <p/>
*
* <pre> -D
* Show Debugging Output
* </pre>
*
* <pre> -P <integer>
* Distribution of the Prior (1=Gaussian, 2=Laplacian)
* (default: 1=Gaussian)</pre>
*
* <pre> -H <integer>
* Hyperparameter Selection Method (1=Norm-based, 2=CV-based, 3=specific value)
* (default: 1=Norm-based)</pre>
*
* <pre> -V <double>
* Specified Hyperparameter Value (use in conjunction with -H 3)
* (default: 0.27)</pre>
*
* <pre> -R <string>
* Hyperparameter Range (use in conjunction with -H 2)
* (format: R:start-end,multiplier OR L:val(1), val(2), ..., val(n))
* (default: R:0.01-316,3.16)</pre>
*
* <pre> -Tl <double>
* Tolerance Value
* (default: 0.0005)</pre>
*
* <pre> -S <double>
* Threshold Value
* (default: 0.5)</pre>
*
* <pre> -F <integer>
* Number Of Folds (use in conjuction with -H 2)
* (default: 2)</pre>
*
* <pre> -I <integer>
* Max Number of Iterations
* (default: 100)</pre>
*
* <pre> -N
* Normalize the data</pre>
*
<!-- options-end -->
*
* @param options the list of options as an array of strings
* @throws Exception if an option is not supported
*/
public void setOptions(String[] options) throws Exception {
//Debug Option
debug = Utils.getFlag('D', options);
// Set Tolerance.
String Tol = Utils.getOption("Tl", options);
if (Tol.length() != 0) {
Tolerance = Double.parseDouble(Tol);
}
//Set Threshold
String Thres = Utils.getOption('S', options);
if (Thres.length() != 0) {
Threshold = Double.parseDouble(Thres);
}
//Set Hyperparameter Type
String Hype = Utils.getOption('H', options);
if (Hype.length() != 0) {
HyperparameterSelection = Integer.parseInt(Hype);
}
//Set Hyperparameter Value
String HyperValue = Utils.getOption('V', options);
if (HyperValue.length() != 0) {
HyperparameterValue = Double.parseDouble(HyperValue);
}
// Set hyper parameter range or list.
String HyperparameterRange = Utils.getOption("R", options);
//Set Prior class.
String strPrior = Utils.getOption('P', options);
if (strPrior.length() != 0) {
PriorClass = Integer.parseInt(strPrior);
}
String folds = Utils.getOption('F', options);
if (folds.length() != 0) {
NumFolds = Integer.parseInt(folds);
}
String iterations = Utils.getOption('I', options);
if (iterations.length() != 0) {
maxIterations = Integer.parseInt(iterations);
}
NormalizeData = Utils.getFlag('N', options);
//TODO: Implement this method for other options.
Utils.checkForRemainingOptions(options);
}
/**
*
*/
public String[] getOptions() {
Vector result = new Vector();
//Add Debug Mode to options.
result.add("-D");
//Add Tolerance value to options
result.add("-Tl");
result.add("" + Tolerance);
//Add Threshold value to options
result.add("-S");
result.add("" + Threshold);
//Add Hyperparameter value to options
result.add("-H");
result.add("" + HyperparameterSelection);
result.add("-V");
result.add("" + HyperparameterValue);
result.add("-R");
result.add("" + HyperparameterRange);
//Add Prior Class to options
result.add("-P");
result.add("" + PriorClass);
result.add("-F");
result.add("" + NumFolds);
result.add("-I");
result.add("" + maxIterations);
result.add("-N");
return (String[]) result.toArray(new String[result.size()]);
}
/**
* Main method for testing this class.
*
* @param argv the options
*/
public static void main(String[] argv) {
runClassifier(new BayesianLogisticRegression(), argv);
}
/**
* Returns the tip text for this property
*
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String debugTipText() {
return "Turns on debugging mode.";
}
/**
*
*/
public void setDebug(boolean debugMode) {
debug = debugMode;
}
/**
* Returns the tip text for this property
*
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String hyperparameterSelectionTipText() {
return "Select the type of Hyperparameter to be used.";
}
/**
* Get the method used to select the hyperparameter
*
* @return the method used to select the hyperparameter
*/
public SelectedTag getHyperparameterSelection() {
return new SelectedTag(HyperparameterSelection,
TAGS_HYPER_METHOD);
}
/**
* Set the method used to select the hyperparameter
*
* @param newMethod the method used to set the hyperparameter
*/
public void setHyperparameterSelection(SelectedTag newMethod) {
if (newMethod.getTags() == TAGS_HYPER_METHOD) {
int c = newMethod.getSelectedTag().getID();
if (c >= 1 && c <= 3) {
HyperparameterSelection = c;
} else {
throw new IllegalArgumentException("Wrong selection type, -H value should be: "
+ "1 for norm-based, 2 for CV-based and "
+ "3 for specific value");
}
}
}
/**
* Returns the tip text for this property
*
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String priorClassTipText() {
return "The type of prior to be used.";
}
/**
* Set the type of prior to use.
*
* @param newMethod the type of prior to use.
*/
public void setPriorClass(SelectedTag newMethod) {
if (newMethod.getTags() == TAGS_PRIOR) {
int c = newMethod.getSelectedTag().getID();
if (c == GAUSSIAN || c == LAPLACIAN) {
PriorClass = c;
} else {
throw new IllegalArgumentException("Wrong selection type, -P value should be: "
+ "1 for Gaussian or 2 for Laplacian");
}
}
}
/**
* Get the type of prior to use.
*
* @return the type of prior to use
*/
public SelectedTag getPriorClass() {
return new SelectedTag(PriorClass,
TAGS_PRIOR);
}
/**
* Returns the tip text for this property
*
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String thresholdTipText() {
return "Set the threshold for classifiction. The logistic function doesn't "
+ "return a class label but an estimate of p(y=+1|B,x(i)). "
+ "These estimates need to be converted to binary class label predictions. "
+ "values above the threshold are assigned class +1.";
}
/**
* Return the threshold being used.
*
* @return the threshold
*/
public double getThreshold() {
return Threshold;
}
/**
* Set the threshold to use.
*
* @param threshold the threshold to use
*/
public void setThreshold(double threshold) {
Threshold = threshold;
}
/**
* Returns the tip text for this property
*
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String toleranceTipText() {
return "This value decides the stopping criterion.";
}
/**
* Get the tolerance value
*
* @return the tolerance value
*/
public double getTolerance() {
return Tolerance;
}
/**
* Set the tolerance value
*
* @param tolerance the tolerance value to use
*/
public void setTolerance(double tolerance) {
Tolerance = tolerance;
}
/**
* Returns the tip text for this property
*
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String hyperparameterValueTipText() {
return "Specific hyperparameter value. Used when the hyperparameter "
+ "selection method is set to specific value";
}
/**
* Get the hyperparameter value. Used when the hyperparameter
* selection method is set to specific value
*
* @return the hyperparameter value
*/
public double getHyperparameterValue() {
return HyperparameterValue;
}
/**
* Set the hyperparameter value. Used when the hyperparameter
* selection method is set to specific value
*
* @param hyperparameterValue the value of the hyperparameter
*/
public void setHyperparameterValue(double hyperparameterValue) {
HyperparameterValue = hyperparameterValue;
}
/**
* Returns the tip text for this property
*
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String numFoldsTipText() {
return "The number of folds to use for CV-based hyperparameter selection.";
}
/**
* Return the number of folds for CV-based hyperparameter selection
*
* @return the number of CV folds
*/
public int getNumFolds() {
return NumFolds;
}
/**
* Set the number of folds to use for CV-based hyperparameter
* selection
*
* @param numFolds number of folds to select
*/
public void setNumFolds(int numFolds) {
NumFolds = numFolds;
}
/**
* Returns the tip text for this property
*
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String maxIterationsTipText() {
return "The maximum number of iterations to perform.";
}
/**
* Get the maximum number of iterations to perform
*
* @return the maximum number of iterations
*/
public int getMaxIterations() {
return maxIterations;
}
/**
* Set the maximum number of iterations to perform
*
* @param maxIterations maximum number of iterations
*/
public void setMaxIterations(int maxIterations) {
this.maxIterations = maxIterations;
}
/**
* Returns the tip text for this property
*
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String normalizeDataTipText() {
return "Normalize the data.";
}
/**
* Returns true if the data is to be normalized first
*
* @return true if the data is to be normalized
*/
public boolean isNormalizeData() {
return NormalizeData;
}
/**
* Set whether to normalize the data or not
*
* @param normalizeData true if data is to be normalized
*/
public void setNormalizeData(boolean normalizeData) {
NormalizeData = normalizeData;
}
/**
* Returns the tip text for this property
*
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String hyperparameterRangeTipText() {
return "Hyperparameter value range. In case of CV-based Hyperparameters, "
+ "you can specify the range in two ways: \n"
+ "Comma-Separated: L: 3,5,6 (This will be a list of possible values.)\n"
+ "Range: R:0.01-316,3.16 (This will take values from 0.01-316 (inclusive) "
+ "in multiplications of 3.16";
}
/**
* Get the range of hyperparameter values to consider
* during CV-based selection.
*
* @return the range of hyperparameters as a Stringe
*/
public String getHyperparameterRange() {
return HyperparameterRange;
}
/**
* Set the range of hyperparameter values to consider
* during CV-based selection
*
* @param hyperparameterRange the range of hyperparameter values
*/
public void setHyperparameterRange(String hyperparameterRange) {
HyperparameterRange = hyperparameterRange;
}
/**
* Returns true if debug is turned on.
*
* @return true if debug is turned on
*/
public boolean isDebug() {
return debug;
}
/**
* Returns the revision string.
*
* @return the revision
*/
public String getRevision() {
return RevisionUtils.extract("$Revision: 1.3 $");
}
}