/*
* 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.
*/
/*
* SimpleMI.java
* Copyright (C) 2005 University of Waikato, Hamilton, New Zealand
*/
package weka.classifiers.mi;
import weka.classifiers.SingleClassifierEnhancer;
import weka.core.Attribute;
import weka.core.Capabilities;
import weka.core.Instance;
import weka.core.Instances;
import weka.core.MultiInstanceCapabilitiesHandler;
import weka.core.Option;
import weka.core.OptionHandler;
import weka.core.RevisionUtils;
import weka.core.SelectedTag;
import weka.core.Tag;
import weka.core.Utils;
import weka.core.Capabilities.Capability;
import java.util.Enumeration;
import java.util.Vector;
/**
<!-- globalinfo-start -->
* Reduces MI data into mono-instance data.
* <p/>
<!-- globalinfo-end -->
*
<!-- options-start -->
* Valid options are: <p/>
*
* <pre> -M [1|2|3]
* The method used in transformation:
* 1.arithmatic average; 2.geometric centor;
* 3.using minimax combined features of a bag (default: 1)
*
* Method 3:
* Define s to be the vector of the coordinate-wise maxima
* and minima of X, ie.,
* s(X)=(minx1, ..., minxm, maxx1, ...,maxxm), transform
* the exemplars into mono-instance which contains attributes
* s(X)</pre>
*
* <pre> -D
* If set, classifier is run in debug mode and
* may output additional info to the console</pre>
*
* <pre> -W
* Full name of base classifier.
* (default: weka.classifiers.rules.ZeroR)</pre>
*
* <pre>
* Options specific to classifier weka.classifiers.rules.ZeroR:
* </pre>
*
* <pre> -D
* If set, classifier is run in debug mode and
* may output additional info to the console</pre>
*
<!-- options-end -->
*
* @author Eibe Frank (eibe@cs.waikato.ac.nz)
* @author Xin Xu (xx5@cs.waikato.ac.nz)
* @author Lin Dong (ld21@cs.waikato.ac.nz)
* @version $Revision: 1.6 $
*/
public class SimpleMI
extends SingleClassifierEnhancer
implements OptionHandler, MultiInstanceCapabilitiesHandler {
/** for serialization */
static final long serialVersionUID = 9137795893666592662L;
/** arithmetic average */
public static final int TRANSFORMMETHOD_ARITHMETIC = 1;
/** geometric average */
public static final int TRANSFORMMETHOD_GEOMETRIC = 2;
/** using minimax combined features of a bag */
public static final int TRANSFORMMETHOD_MINIMAX = 3;
/** the transformation methods */
public static final Tag[] TAGS_TRANSFORMMETHOD = {
new Tag(TRANSFORMMETHOD_ARITHMETIC, "arithmetic average"),
new Tag(TRANSFORMMETHOD_GEOMETRIC, "geometric average"),
new Tag(TRANSFORMMETHOD_MINIMAX, "using minimax combined features of a bag")
};
/** the method used in transformation */
protected int m_TransformMethod = TRANSFORMMETHOD_ARITHMETIC;
/**
* Returns a string describing this filter
*
* @return a description of the filter suitable for
* displaying in the explorer/experimenter gui
*/
public String globalInfo() {
return "Reduces MI data into mono-instance data.";
}
/**
* Returns an enumeration describing the available options.
*
* @return an enumeration of all the available options.
*/
public Enumeration listOptions() {
Vector result = new Vector();
result.addElement(new Option(
"\tThe method used in transformation:\n"
+ "\t1.arithmatic average; 2.geometric centor;\n"
+ "\t3.using minimax combined features of a bag (default: 1)\n\n"
+ "\tMethod 3:\n"
+ "\tDefine s to be the vector of the coordinate-wise maxima\n"
+ "\tand minima of X, ie., \n"
+ "\ts(X)=(minx1, ..., minxm, maxx1, ...,maxxm), transform\n"
+ "\tthe exemplars into mono-instance which contains attributes\n"
+ "\ts(X)",
"M", 1, "-M [1|2|3]"));
Enumeration enu = super.listOptions();
while (enu.hasMoreElements()) {
result.addElement(enu.nextElement());
}
return result.elements();
}
/**
* Parses a given list of options. <p/>
*
<!-- options-start -->
* Valid options are: <p/>
*
* <pre> -M [1|2|3]
* The method used in transformation:
* 1.arithmatic average; 2.geometric centor;
* 3.using minimax combined features of a bag (default: 1)
*
* Method 3:
* Define s to be the vector of the coordinate-wise maxima
* and minima of X, ie.,
* s(X)=(minx1, ..., minxm, maxx1, ...,maxxm), transform
* the exemplars into mono-instance which contains attributes
* s(X)</pre>
*
* <pre> -D
* If set, classifier is run in debug mode and
* may output additional info to the console</pre>
*
* <pre> -W
* Full name of base classifier.
* (default: weka.classifiers.rules.ZeroR)</pre>
*
* <pre>
* Options specific to classifier weka.classifiers.rules.ZeroR:
* </pre>
*
* <pre> -D
* If set, classifier is run in debug mode and
* may output additional info to the console</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 {
setDebug(Utils.getFlag('D', options));
String methodString = Utils.getOption('M', options);
if (methodString.length() != 0) {
setTransformMethod(
new SelectedTag(
Integer.parseInt(methodString), TAGS_TRANSFORMMETHOD));
} else {
setTransformMethod(
new SelectedTag(
TRANSFORMMETHOD_ARITHMETIC, TAGS_TRANSFORMMETHOD));
}
super.setOptions(options);
}
/**
* Gets the current settings of the Classifier.
*
* @return an array of strings suitable for passing to setOptions
*/
public String[] getOptions() {
Vector result;
String[] options;
int i;
result = new Vector();
result.add("-M");
result.add("" + m_TransformMethod);
options = super.getOptions();
for (i = 0; i < options.length; i++)
result.add(options[i]);
return (String[]) result.toArray(new String[result.size()]);
}
/**
* Returns the tip text for this property
*
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String transformMethodTipText() {
return "The method used in transformation.";
}
/**
* Set the method used in transformation.
*
* @param newMethod the index of method to use.
*/
public void setTransformMethod(SelectedTag newMethod) {
if (newMethod.getTags() == TAGS_TRANSFORMMETHOD)
m_TransformMethod = newMethod.getSelectedTag().getID();
}
/**
* Get the method used in transformation.
*
* @return the index of method used.
*/
public SelectedTag getTransformMethod() {
return new SelectedTag(m_TransformMethod, TAGS_TRANSFORMMETHOD);
}
/**
* Implements MITransform (3 type of transformation) 1.arithmatic average;
* 2.geometric centor; 3.merge minima and maxima attribute value together
*
* @param train the multi-instance dataset (with relational attribute)
* @return the transformed dataset with each bag contain mono-instance
* (without relational attribute) so that any classifier not for MI dataset
* can be applied on it.
* @throws Exception if the transformation fails
*/
public Instances transform(Instances train) throws Exception{
Attribute classAttribute = (Attribute) train.classAttribute().copy();
Attribute bagLabel = (Attribute) train.attribute(0);
double labelValue;
Instances newData = train.attribute(1).relation().stringFreeStructure();
//insert a bag label attribute at the begining
newData.insertAttributeAt(bagLabel, 0);
//insert a class attribute at the end
newData.insertAttributeAt(classAttribute, newData.numAttributes());
newData.setClassIndex(newData.numAttributes()-1);
Instances mini_data = newData.stringFreeStructure();
Instances max_data = newData.stringFreeStructure();
Instance newInst = new Instance (newData.numAttributes());
Instance mini_Inst = new Instance (mini_data.numAttributes());
Instance max_Inst = new Instance (max_data.numAttributes());
newInst.setDataset(newData);
mini_Inst.setDataset(mini_data);
max_Inst.setDataset(max_data);
double N= train.numInstances( );//number of bags
for(int i=0; i<N; i++){
int attIdx =1;
Instance bag = train.instance(i); //retrieve the bag instance
labelValue= bag.value(0);
if (m_TransformMethod != TRANSFORMMETHOD_MINIMAX)
newInst.setValue(0, labelValue);
else {
mini_Inst.setValue(0, labelValue);
max_Inst.setValue(0, labelValue);
}
Instances data = bag.relationalValue(1); // retrieve relational value for each bag
for(int j=0; j<data.numAttributes( ); j++){
double value;
if(m_TransformMethod == TRANSFORMMETHOD_ARITHMETIC){
value = data.meanOrMode(j);
newInst.setValue(attIdx++, value);
}
else if (m_TransformMethod == TRANSFORMMETHOD_GEOMETRIC){
double[] minimax = minimax(data, j);
value = (minimax[0]+minimax[1])/2.0;
newInst.setValue(attIdx++, value);
}
else { //m_TransformMethod == TRANSFORMMETHOD_MINIMAX
double[] minimax = minimax(data, j);
mini_Inst.setValue(attIdx, minimax[0]);//minima value
max_Inst.setValue(attIdx, minimax[1]);//maxima value
attIdx++;
}
}
if (m_TransformMethod == TRANSFORMMETHOD_MINIMAX) {
if (!bag.classIsMissing())
max_Inst.setClassValue(bag.classValue()); //set class value
mini_data.add(mini_Inst);
max_data.add(max_Inst);
}
else{
if (!bag.classIsMissing())
newInst.setClassValue(bag.classValue()); //set class value
newData.add(newInst);
}
}
if (m_TransformMethod == TRANSFORMMETHOD_MINIMAX) {
mini_data.setClassIndex(-1);
mini_data.deleteAttributeAt(mini_data.numAttributes()-1); //delete class attribute for the minima data
max_data.deleteAttributeAt(0); // delete the bag label attribute for the maxima data
newData = Instances.mergeInstances(mini_data, max_data); //merge minima and maxima data
newData.setClassIndex(newData.numAttributes()-1);
}
return newData;
}
/**
* Get the minimal and maximal value of a certain attribute in a certain data
*
* @param data the data
* @param attIndex the index of the attribute
* @return the double array containing in entry 0 for min and 1 for max.
*/
public static double[] minimax(Instances data, int attIndex){
double[] rt = {Double.POSITIVE_INFINITY, Double.NEGATIVE_INFINITY};
for(int i=0; i<data.numInstances(); i++){
double val = data.instance(i).value(attIndex);
if(val > rt[1])
rt[1] = val;
if(val < rt[0])
rt[0] = val;
}
for(int j=0; j<2; j++)
if(Double.isInfinite(rt[j]))
rt[j] = Double.NaN;
return rt;
}
/**
* Returns default capabilities of the classifier.
*
* @return the capabilities of this classifier
*/
public Capabilities getCapabilities() {
Capabilities result = super.getCapabilities();
// attributes
result.enable(Capability.NOMINAL_ATTRIBUTES);
result.enable(Capability.RELATIONAL_ATTRIBUTES);
result.enable(Capability.MISSING_VALUES);
// class
result.disableAllClasses();
result.disableAllClassDependencies();
if (super.getCapabilities().handles(Capability.NOMINAL_CLASS))
result.enable(Capability.NOMINAL_CLASS);
if (super.getCapabilities().handles(Capability.BINARY_CLASS))
result.enable(Capability.BINARY_CLASS);
result.enable(Capability.MISSING_CLASS_VALUES);
// other
result.enable(Capability.ONLY_MULTIINSTANCE);
return result;
}
/**
* Returns the capabilities of this multi-instance classifier for the
* relational data.
*
* @return the capabilities of this object
* @see Capabilities
*/
public Capabilities getMultiInstanceCapabilities() {
Capabilities result = super.getCapabilities();
// attributes
result.enable(Capability.NOMINAL_ATTRIBUTES);
result.enable(Capability.NUMERIC_ATTRIBUTES);
result.enable(Capability.DATE_ATTRIBUTES);
result.enable(Capability.MISSING_VALUES);
// class
result.disableAllClasses();
result.enable(Capability.NO_CLASS);
return result;
}
/**
* Builds the classifier
*
* @param train the training data to be used for generating the
* boosted classifier.
* @throws Exception if the classifier could not be built successfully
*/
public void buildClassifier(Instances train) throws Exception {
// can classifier handle the data?
getCapabilities().testWithFail(train);
// remove instances with missing class
train = new Instances(train);
train.deleteWithMissingClass();
if (m_Classifier == null) {
throw new Exception("A base classifier has not been specified!");
}
if (getDebug())
System.out.println("Start training ...");
Instances data = transform(train);
data.deleteAttributeAt(0); // delete the bagID attribute
m_Classifier.buildClassifier(data);
if (getDebug())
System.out.println("Finish building model");
}
/**
* Computes the distribution for a given exemplar
*
* @param newBag the exemplar for which distribution is computed
* @return the distribution
* @throws Exception if the distribution can't be computed successfully
*/
public double[] distributionForInstance(Instance newBag)
throws Exception {
double [] distribution = new double[2];
Instances test = new Instances (newBag.dataset(), 0);
test.add(newBag);
test = transform(test);
test.deleteAttributeAt(0);
Instance newInst=test.firstInstance();
distribution = m_Classifier.distributionForInstance(newInst);
return distribution;
}
/**
* Gets a string describing the classifier.
*
* @return a string describing the classifer built.
*/
public String toString() {
return "SimpleMI with base classifier: \n"+m_Classifier.toString();
}
/**
* Returns the revision string.
*
* @return the revision
*/
public String getRevision() {
return RevisionUtils.extract("$Revision: 1.6 $");
}
/**
* Main method for testing this class.
*
* @param argv should contain the command line arguments to the
* scheme (see Evaluation)
*/
public static void main(String[] argv) {
runClassifier(new SimpleMI(), argv);
}
}