/*
* 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.
*/
/*
* C45PruneableClassifierTreeG.java
* Copyright (C) 1999 University of Waikato, Hamilton, New Zealand
* Copyright (C) 2007 Geoff Webb & Janice Boughton
*
*/
package weka.classifiers.trees.j48;
import weka.core.Capabilities;
import weka.core.Instances;
import weka.core.Instance;
import weka.core.RevisionUtils;
import weka.core.Utils;
import weka.core.Capabilities.Capability;
import java.util.ArrayList;
import java.util.Collections;
/**
* Class for handling a tree structure that can
* be pruned using C4.5 procedures and have nodes grafted on.
*
* @author Janice Boughton (based on code by Eibe Frank)
* @version $Revision: 5535 $
*/
public class C45PruneableClassifierTreeG extends ClassifierTree{
/** for serialization */
static final long serialVersionUID = 66981207374331964L;
/** True if the tree is to be pruned. */
boolean m_pruneTheTree = false;
/** The confidence factor for pruning. */
float m_CF = 0.25f;
/** Is subtree raising to be performed? */
boolean m_subtreeRaising = true;
/** Cleanup after the tree has been built. */
boolean m_cleanup = true;
/** flag for using relabelling when grafting */
boolean m_relabel = false;
/** binomial probability critical value */
double m_BiProbCrit = 1.64;
boolean m_Debug = false;
/**
* Constructor for pruneable tree structure. Stores reference
* to associated training data at each node.
*
* @param toSelectLocModel selection method for local splitting model
* @param pruneTree true if the tree is to be pruned
* @param cf the confidence factor for pruning
* @param raiseTree
* @param cleanup
* @throws Exception if something goes wrong
*/
public C45PruneableClassifierTreeG(ModelSelection toSelectLocModel,
boolean pruneTree,float cf,
boolean raiseTree,
boolean relabel, boolean cleanup)
throws Exception {
super(toSelectLocModel);
m_pruneTheTree = pruneTree;
m_CF = cf;
m_subtreeRaising = raiseTree;
m_cleanup = cleanup;
m_relabel = relabel;
}
/**
* Returns default capabilities of the classifier tree.
*
* @return the capabilities of this classifier tree
*/
public Capabilities getCapabilities() {
Capabilities result = super.getCapabilities();
result.disableAll();
// attributes
result.enable(Capability.NOMINAL_ATTRIBUTES);
result.enable(Capability.NUMERIC_ATTRIBUTES);
result.enable(Capability.MISSING_VALUES);
// class
result.enable(Capability.NOMINAL_CLASS);
result.enable(Capability.MISSING_CLASS_VALUES);
// instances
result.setMinimumNumberInstances(0);
return result;
}
/**
* Constructor for pruneable tree structure. Used to create new nodes
* in the tree during grafting.
*
* @param toSelectLocModel selection method for local splitting model
* @param data the dta used to produce split model
* @param gs the split model
* @param prune true if the tree is to be pruned
* @param cf the confidence factor for pruning
* @param raise
* @param isLeaf if this node is a leaf or not
* @param relabel whether relabeling occured
* @param cleanup
* @throws Exception if something goes wrong
*/
public C45PruneableClassifierTreeG(ModelSelection toSelectLocModel,
Instances data, ClassifierSplitModel gs,
boolean prune, float cf, boolean raise,
boolean isLeaf, boolean relabel,
boolean cleanup) {
super(toSelectLocModel);
m_relabel = relabel;
m_cleanup = cleanup;
m_localModel = gs;
m_train = data;
m_test = null;
m_isLeaf = isLeaf;
if(gs.distribution().total() > 0)
m_isEmpty = false;
else
m_isEmpty = true;
m_pruneTheTree = prune;
m_CF = cf;
m_subtreeRaising = raise;
}
/**
* Method for building a pruneable classifier tree.
*
* @param datathe data for building the tree
* @throws Exception if something goes wrong
*/
public void buildClassifier(Instances data) throws Exception {
// can classifier tree handle the data?
getCapabilities().testWithFail(data);
// remove instances with missing class
data = new Instances(data);
data.deleteWithMissingClass();
buildTree(data, m_subtreeRaising);
collapse();
if (m_pruneTheTree) {
prune();
}
doGrafting(data);
if (m_cleanup) {
cleanup(new Instances(data, 0));
}
}
/**
* Collapses a tree to a node if training error doesn't increase.
*/
public final void collapse(){
double errorsOfSubtree;
double errorsOfTree;
int i;
if (!m_isLeaf){
errorsOfSubtree = getTrainingErrors();
errorsOfTree = localModel().distribution().numIncorrect();
if (errorsOfSubtree >= errorsOfTree-1E-3){
// Free adjacent trees
m_sons = null;
m_isLeaf = true;
// Get NoSplit Model for tree.
m_localModel = new NoSplit(localModel().distribution());
}else
for (i=0;i<m_sons.length;i++)
son(i).collapse();
}
}
/**
* Prunes a tree using C4.5's pruning procedure.
*
* @throws Exception if something goes wrong
*/
public void prune() throws Exception {
double errorsLargestBranch;
double errorsLeaf;
double errorsTree;
int indexOfLargestBranch;
C45PruneableClassifierTreeG largestBranch;
int i;
if (!m_isLeaf){
// Prune all subtrees.
for (i=0;i<m_sons.length;i++)
son(i).prune();
// Compute error for largest branch
indexOfLargestBranch = localModel().distribution().maxBag();
if (m_subtreeRaising) {
errorsLargestBranch = son(indexOfLargestBranch).
getEstimatedErrorsForBranch((Instances)m_train);
} else {
errorsLargestBranch = Double.MAX_VALUE;
}
// Compute error if this Tree would be leaf
errorsLeaf =
getEstimatedErrorsForDistribution(localModel().distribution());
// Compute error for the whole subtree
errorsTree = getEstimatedErrors();
// Decide if leaf is best choice.
if (Utils.smOrEq(errorsLeaf,errorsTree+0.1) &&
Utils.smOrEq(errorsLeaf,errorsLargestBranch+0.1)){
// Free son Trees
m_sons = null;
m_isLeaf = true;
// Get NoSplit Model for node.
m_localModel = new NoSplit(localModel().distribution());
return;
}
// Decide if largest branch is better choice
// than whole subtree.
if (Utils.smOrEq(errorsLargestBranch,errorsTree+0.1)){
largestBranch = son(indexOfLargestBranch);
m_sons = largestBranch.m_sons;
m_localModel = largestBranch.localModel();
m_isLeaf = largestBranch.m_isLeaf;
newDistribution(m_train);
prune();
}
}
}
/**
* Returns a newly created tree.
*
* @param data the data to work with
* @return the new tree
* @throws Exception if something goes wrong
*/
protected ClassifierTree getNewTree(Instances data) throws Exception {
C45PruneableClassifierTreeG newTree =
new C45PruneableClassifierTreeG(m_toSelectModel, m_pruneTheTree, m_CF,
m_subtreeRaising, m_relabel, m_cleanup);
// ATBOP Modification // m_subtreeRaising, m_cleanup);
newTree.buildTree((Instances)data, m_subtreeRaising);
return newTree;
}
/**
* Computes estimated errors for tree.
*
* @return the estimated errors
*/
private double getEstimatedErrors(){
double errors = 0;
int i;
if (m_isLeaf)
return getEstimatedErrorsForDistribution(localModel().distribution());
else{
for (i=0;i<m_sons.length;i++)
errors = errors+son(i).getEstimatedErrors();
return errors;
}
}
/**
* Computes estimated errors for one branch.
*
* @param data the data to work with
* @return the estimated errors
* @throws Exception if something goes wrong
*/
private double getEstimatedErrorsForBranch(Instances data)
throws Exception {
Instances [] localInstances;
double errors = 0;
int i;
if (m_isLeaf)
return getEstimatedErrorsForDistribution(new Distribution(data));
else{
Distribution savedDist = localModel().m_distribution;
localModel().resetDistribution(data);
localInstances = (Instances[])localModel().split(data);
localModel().m_distribution = savedDist;
for (i=0;i<m_sons.length;i++)
errors = errors+
son(i).getEstimatedErrorsForBranch(localInstances[i]);
return errors;
}
}
/**
* Computes estimated errors for leaf.
*
* @param theDistribution the distribution to use
* @return the estimated errors
*/
private double getEstimatedErrorsForDistribution(Distribution
theDistribution){
if (Utils.eq(theDistribution.total(),0))
return 0;
else
return theDistribution.numIncorrect()+
Stats.addErrs(theDistribution.total(),
theDistribution.numIncorrect(),m_CF);
}
/**
* Computes errors of tree on training data.
*
* @return the training errors
*/
private double getTrainingErrors(){
double errors = 0;
int i;
if (m_isLeaf)
return localModel().distribution().numIncorrect();
else{
for (i=0;i<m_sons.length;i++)
errors = errors+son(i).getTrainingErrors();
return errors;
}
}
/**
* Method just exists to make program easier to read.
*
* @return the local split model
*/
private ClassifierSplitModel localModel(){
return (ClassifierSplitModel)m_localModel;
}
/**
* Computes new distributions of instances for nodes
* in tree.
*
* @param data the data to compute the distributions for
* @throws Exception if something goes wrong
*/
private void newDistribution(Instances data) throws Exception {
Instances [] localInstances;
localModel().resetDistribution(data);
m_train = data;
if (!m_isLeaf){
localInstances =
(Instances [])localModel().split(data);
for (int i = 0; i < m_sons.length; i++)
son(i).newDistribution(localInstances[i]);
} else {
// Check whether there are some instances at the leaf now!
if (!Utils.eq(data.sumOfWeights(), 0)) {
m_isEmpty = false;
}
}
}
/**
* Method just exists to make program easier to read.
*/
private C45PruneableClassifierTreeG son(int index){
return (C45PruneableClassifierTreeG)m_sons[index];
}
/**
* Initializes variables for grafting.
* sets up limits array (for numeric attributes) and calls
* the recursive function traverseTree.
*
* @param data the data for the tree
* @throws Exception if anything goes wrong
*/
public void doGrafting(Instances data) throws Exception {
// 2d array for the limits
double [][] limits = new double[data.numAttributes()][2];
// 2nd dimension: index 0 == lower limit, index 1 == upper limit
// initialise to no limit
for(int i = 0; i < data.numAttributes(); i++) {
limits[i][0] = Double.NEGATIVE_INFINITY;
limits[i][1] = Double.POSITIVE_INFINITY;
}
// use an index instead of creating new Insances objects all the time
// instanceIndex[0] == array for weights at leaf
// instanceIndex[1] == array for weights in atbop
double [][] instanceIndex = new double[2][data.numInstances()];
// initialize the weight for each instance
for(int x = 0; x < data.numInstances(); x++) {
instanceIndex[0][x] = 1;
instanceIndex[1][x] = 1; // leaf instances are in atbop
}
// first call to graft
traverseTree(data, instanceIndex, limits, this, 0, -1);
}
/**
* recursive function.
* if this node is a leaf then calls findGraft, otherwise sorts
* the two sets of instances (tracked in iindex array) and calls
* sortInstances for each of the child nodes (which then calls
* this method).
*
* @param fulldata all instances
* @param iindex array the tracks the weight of each instance in
* the atbop and at the leaf (0.0 if not present)
* @param limits array specifying current upper/lower limits for numeric atts
* @param parent the node immediately before the current one
* @param pL laplace for node, as calculated by parent (in case leaf is empty)
* @param nodeClass class of node, determined by parent (in case leaf empty)
*/
private void traverseTree(Instances fulldata, double [][] iindex,
double[][] limits, C45PruneableClassifierTreeG parent,
double pL, int nodeClass) throws Exception {
if(m_isLeaf) {
findGraft(fulldata, iindex, limits,
(ClassifierTree)parent, pL, nodeClass);
} else {
// traverse each branch
for(int i = 0; i < localModel().numSubsets(); i++) {
double [][] newiindex = new double[2][fulldata.numInstances()];
for(int x = 0; x < 2; x++)
System.arraycopy(iindex[x], 0, newiindex[x], 0, iindex[x].length);
sortInstances(fulldata, newiindex, limits, i);
}
}
}
/**
* sorts/deletes instances into/from node and atbop according to
* the test for subset, then calls traverseTree for subset's node.
*
* @param fulldata all instances
* @param iindex array the tracks the weight of each instance in
* the atbop and at the leaf (0.0 if not present)
* @param limits array specifying current upper/lower limits for numeric atts
* @param subset the subset for which to sort instances into inode & iatbop
*/
private void sortInstances(Instances fulldata, double [][] iindex,
double [][] limits, int subset) throws Exception {
C45Split test = (C45Split)localModel();
// update the instances index for subset
double knownCases = 0;
double thisSubsetCount = 0;
for(int x = 0; x < iindex[0].length; x++) {
if(iindex[0][x] == 0 && iindex[1][x] == 0) // skip "discarded" instances
continue;
if(!fulldata.instance(x).isMissing(test.attIndex())) {
knownCases += iindex[0][x];
if(test.whichSubset(fulldata.instance(x)) != subset) {
if(iindex[0][x] > 0) {
// move to atbop, delete from leaf
iindex[1][x] = iindex[0][x];
iindex[0][x] = 0;
} else {
if(iindex[1][x] > 0) {
// instance is now "discarded"
iindex[1][x] = 0;
}
}
} else {
thisSubsetCount += iindex[0][x];
}
}
}
// work out proportions of weight for missing values for leaf and atbop
double lprop = (knownCases == 0) ? (1.0 / (double)test.numSubsets())
: (thisSubsetCount / (double)knownCases);
// add in the instances that have missing value for attIndex
for(int x = 0; x < iindex[0].length; x++) {
if(iindex[0][x] == 0 && iindex[1][x] == 0)
continue; // skip "discarded" instances
if(fulldata.instance(x).isMissing(test.attIndex())) {
iindex[1][x] -= (iindex[1][x] - iindex[0][x]) * (1-lprop);
iindex[0][x] *= lprop;
}
}
int nodeClass = localModel().distribution().maxClass(subset);
double pL = (localModel().distribution().perClass(nodeClass) + 1.0)
/ (localModel().distribution().total() + 2.0);
// call traerseTree method for the child node
son(subset).traverseTree(fulldata, iindex,
test.minsAndMaxs(fulldata, limits, subset), this, pL, nodeClass);
}
/**
* finds new nodes that improve accuracy and grafts them onto the tree
*
* @param fulldata the instances in whole trainset
* @param iindex records num tests each instance has failed up to this node
* @param limits the upper/lower limits for numeric attributes
* @param parent the node immediately before the current one
* @param pLaplace laplace for leaf, calculated by parent (in case leaf empty)
* @param pLeafClass class of leaf, determined by parent (in case leaf empty)
*/
private void findGraft(Instances fulldata, double [][] iindex,
double [][] limits, ClassifierTree parent, double pLaplace,
int pLeafClass) throws Exception {
// get the class for this leaf
int leafClass = (m_isEmpty)
? pLeafClass
: localModel().distribution().maxClass();
// get the laplace value for this leaf
double leafLaplace = (m_isEmpty)
? pLaplace
: laplaceLeaf(leafClass);
// sort the instances into those at the leaf, those in atbop, and discarded
Instances l = new Instances(fulldata, fulldata.numInstances());
Instances n = new Instances(fulldata, fulldata.numInstances());
int lcount = 0;
int acount = 0;
for(int x = 0; x < fulldata.numInstances(); x++) {
if(iindex[0][x] <= 0 && iindex[1][x] <= 0)
continue;
if(iindex[0][x] != 0) {
l.add(fulldata.instance(x));
l.instance(lcount).setWeight(iindex[0][x]);
// move instance's weight in iindex to same index as in l
iindex[0][lcount++] = iindex[0][x];
}
if(iindex[1][x] > 0) {
n.add(fulldata.instance(x));
n.instance(acount).setWeight(iindex[1][x]);
// move instance's weight in iindex to same index as in n
iindex[1][acount++] = iindex[1][x];
}
}
boolean graftPossible = false;
double [] classDist = new double[n.numClasses()];
for(int x = 0; x < n.numInstances(); x++) {
if(iindex[1][x] > 0 && !n.instance(x).classIsMissing())
classDist[(int)n.instance(x).classValue()] += iindex[1][x];
}
for(int cVal = 0; cVal < n.numClasses(); cVal++) {
double theLaplace = (classDist[cVal] + 1.0) / (classDist[cVal] + 2.0);
if(cVal != leafClass && (theLaplace > leafLaplace) &&
(biprob(classDist[cVal], classDist[cVal], leafLaplace)
> m_BiProbCrit)) {
graftPossible = true;
break;
}
}
if(!graftPossible) {
return;
}
// 1. Initialize to {} a set of tuples t containing potential tests
ArrayList t = new ArrayList();
// go through each attribute
for(int a = 0; a < n.numAttributes(); a++) {
if(a == n.classIndex())
continue; // skip the class
// sort instances in atbop by $a
int [] sorted = sortByAttribute(n, a);
// 2. For each continuous attribute $a:
if(n.attribute(a).isNumeric()) {
// find min and max values for this attribute at the leaf
boolean prohibited = false;
double minLeaf = Double.POSITIVE_INFINITY;
double maxLeaf = Double.NEGATIVE_INFINITY;
for(int i = 0; i < l.numInstances(); i++) {
if(l.instance(i).isMissing(a)) {
if(l.instance(i).classValue() == leafClass) {
prohibited = true;
break;
}
}
double value = l.instance(i).value(a);
if(!m_relabel || l.instance(i).classValue() == leafClass) {
if(value < minLeaf)
minLeaf = value;
if(value > maxLeaf)
maxLeaf = value;
}
}
if(prohibited) {
continue;
}
// (a) find values of
// $n: instances in atbop (already have that, actually)
// $v: a value for $a that exists for a case in the atbop, where
// $v is < the min value for $a for a case at the leaf which
// has the class $c, and $v is > the lowerlimit of $a at
// the leaf.
// (note: error in original paper stated that $v must be
// smaller OR EQUAL TO the min value).
// $k: $k is a class
// that maximize L' = Laplace({$x: $x contained in cases($n)
// & value($a,$x) <= $v & value($a,$x) > lowerlim($l,$a)}, $k).
double minBestClass = Double.NaN;
double minBestLaplace = leafLaplace;
double minBestVal = Double.NaN;
double minBestPos = Double.NaN;
double minBestTotal = Double.NaN;
double [][] minBestCounts = null;
double [][] counts = new double[2][n.numClasses()];
for(int x = 0; x < n.numInstances(); x++) {
if(n.instance(sorted[x]).isMissing(a))
break; // missing are sorted to end: no more valid vals
double theval = n.instance(sorted[x]).value(a);
if(m_Debug)
System.out.println("\t " + theval);
if(theval <= limits[a][0]) {
if(m_Debug)
System.out.println("\t <= lowerlim: continuing...");
continue;
}
// note: error in paper would have this read "theVal > minLeaf)
if(theval >= minLeaf) {
if(m_Debug)
System.out.println("\t >= minLeaf; breaking...");
break;
}
counts[0][(int)n.instance(sorted[x]).classValue()]
+= iindex[1][sorted[x]];
if(x != n.numInstances() - 1) {
int z = x + 1;
while(z < n.numInstances()
&& n.instance(sorted[z]).value(a) == theval) {
z++; x++;
counts[0][(int)n.instance(sorted[x]).classValue()]
+= iindex[1][sorted[x]];
}
}
// work out the best laplace/class (for <= theval)
double total = Utils.sum(counts[0]);
for(int c = 0; c < n.numClasses(); c++) {
double temp = (counts[0][c]+1.0)/(total+2.0);
if(temp > minBestLaplace) {
minBestPos = counts[0][c];
minBestTotal = total;
minBestLaplace = temp;
minBestClass = c;
minBestCounts = copyCounts(counts);
minBestVal = (x == n.numInstances()-1)
? theval
: ((theval + n.instance(sorted[x+1]).value(a)) / 2.0);
}
}
}
// (b) add to t tuple <n,a,v,k,L',"<=">
if(!Double.isNaN(minBestVal)
&& biprob(minBestPos, minBestTotal, leafLaplace) > m_BiProbCrit) {
GraftSplit gsplit = null;
try {
gsplit = new GraftSplit(a, minBestVal, 0,
leafClass, minBestCounts);
} catch (Exception e) {
System.err.println("graftsplit error: "+e.getMessage());
System.exit(1);
}
t.add(gsplit);
}
// free space
minBestCounts = null;
// (c) find values of
// n: instances in atbop (already have that, actually)
// $v: a value for $a that exists for a case in the atbop, where
// $v is > the max value for $a for a case at the leaf which
// has the class $c, and $v is <= the upperlimit of $a at
// the leaf.
// k: k is a class
// that maximize L' = Laplace({x: x contained in cases(n)
// & value(a,x) > v & value(a,x) <= upperlim(l,a)}, k).
double maxBestClass = -1;
double maxBestLaplace = leafLaplace;
double maxBestVal = Double.NaN;
double maxBestPos = Double.NaN;
double maxBestTotal = Double.NaN;
double [][] maxBestCounts = null;
for(int c = 0; c < n.numClasses(); c++) { // zero the counts
counts[0][c] = 0;
counts[1][c] = 0; // shouldn't need to do this ...
}
// check smallest val for a in atbop is < upper limit
if(n.numInstances() >= 1
&& n.instance(sorted[0]).value(a) < limits[a][1]) {
for(int x = n.numInstances() - 1; x >= 0; x--) {
if(n.instance(sorted[x]).isMissing(a))
continue;
double theval = n.instance(sorted[x]).value(a);
if(m_Debug)
System.out.println("\t " + theval);
if(theval > limits[a][1]) {
if(m_Debug)
System.out.println("\t >= upperlim; continuing...");
continue;
}
if(theval <= maxLeaf) {
if(m_Debug)
System.out.println("\t < maxLeaf; breaking...");
break;
}
// increment counts
counts[1][(int)n.instance(sorted[x]).classValue()]
+= iindex[1][sorted[x]];
if(x != 0 && !n.instance(sorted[x-1]).isMissing(a)) {
int z = x - 1;
while(z >= 0 && n.instance(sorted[z]).value(a) == theval) {
z--; x--;
counts[1][(int)n.instance(sorted[x]).classValue()]
+= iindex[1][sorted[x]];
}
}
// work out best laplace for > theval
double total = Utils.sum(counts[1]);
for(int c = 0; c < n.numClasses(); c++) {
double temp = (counts[1][c]+1.0)/(total+2.0);
if(temp > maxBestLaplace ) {
maxBestPos = counts[1][c];
maxBestTotal = total;
maxBestLaplace = temp;
maxBestClass = c;
maxBestCounts = copyCounts(counts);
maxBestVal = (x == 0)
? theval
: ((theval + n.instance(sorted[x-1]).value(a)) / 2.0);
}
}
}
// (d) add to t tuple <n,a,v,k,L',">">
if(!Double.isNaN(maxBestVal)
&& biprob(maxBestPos,maxBestTotal,leafLaplace) > m_BiProbCrit) {
GraftSplit gsplit = null;
try {
gsplit = new GraftSplit(a, maxBestVal, 1,
leafClass, maxBestCounts);
} catch (Exception e) {
System.err.println("graftsplit error:" + e.getMessage());
System.exit(1);
}
t.add(gsplit);
}
}
} else { // must be a nominal attribute
// 3. for each discrete attribute a for which there is no
// test at an ancestor of l
// skip if this attribute has already been used
if(limits[a][1] == 1) {
continue;
}
boolean [] prohibit = new boolean[l.attribute(a).numValues()];
for(int aval = 0; aval < n.attribute(a).numValues(); aval++) {
for(int x = 0; x < l.numInstances(); x++) {
if((l.instance(x).isMissing(a)
|| l.instance(x).value(a) == aval)
&& (!m_relabel || (l.instance(x).classValue() == leafClass))) {
prohibit[aval] = true;
break;
}
}
}
// (a) find values of
// $n: instances in atbop (already have that, actually)
// $v: $v is a value for $a
// $k: $k is a class
// that maximize L' = Laplace({$x: $x contained in cases($n)
// & value($a,$x) = $v}, $k).
double bestVal = Double.NaN;
double bestClass = Double.NaN;
double bestLaplace = leafLaplace;
double [][] bestCounts = null;
double [][] counts = new double[2][n.numClasses()];
for(int x = 0; x < n.numInstances(); x++) {
if(n.instance(sorted[x]).isMissing(a))
continue;
// zero the counts
for(int c = 0; c < n.numClasses(); c++)
counts[0][c] = 0;
double theval = n.instance(sorted[x]).value(a);
counts[0][(int)n.instance(sorted[x]).classValue()]
+= iindex[1][sorted[x]];
if(x != n.numInstances() - 1) {
int z = x + 1;
while(z < n.numInstances()
&& n.instance(sorted[z]).value(a) == theval) {
z++; x++;
counts[0][(int)n.instance(sorted[x]).classValue()]
+= iindex[1][sorted[x]];
}
}
if(!prohibit[(int)theval]) {
// work out best laplace for > theval
double total = Utils.sum(counts[0]);
bestLaplace = leafLaplace;
bestClass = Double.NaN;
for(int c = 0; c < n.numClasses(); c++) {
double temp = (counts[0][c]+1.0)/(total+2.0);
if(temp > bestLaplace
&& biprob(counts[0][c],total,leafLaplace) > m_BiProbCrit) {
bestLaplace = temp;
bestClass = c;
bestVal = theval;
bestCounts = copyCounts(counts);
}
}
// add to graft list
if(!Double.isNaN(bestClass)) {
GraftSplit gsplit = null;
try {
gsplit = new GraftSplit(a, bestVal, 2,
leafClass, bestCounts);
} catch (Exception e) {
System.err.println("graftsplit error: "+e.getMessage());
System.exit(1);
}
t.add(gsplit);
}
}
}
// (b) add to t tuple <n,a,v,k,L',"=">
// done this already
}
}
// 4. remove from t all tuples <n,a,v,c,L,x> such that L <=
// Laplace(cases(l),c) or prob(x,n,Laplace(cases(l),c) <= 0.05
// -- checked this constraint prior to adding a tuple --
// *** step six done before step five for efficiency ***
// 6. for each <n,a,v,k,L,x> in t ordered on L from highest to lowest
// order the tuples from highest to lowest laplace
// (this actually orders lowest to highest)
Collections.sort(t);
// 5. remove from t all tuples <n,a,v,c,L,x> such that there is
// no tuple <n',a',v',k',L',x'> such that k' != c & L' < L.
for(int x = 0; x < t.size(); x++) {
GraftSplit gs = (GraftSplit)t.get(x);
if(gs.maxClassForSubsetOfInterest() != leafClass) {
break; // reached a graft with class != leafClass, so stop deleting
} else {
t.remove(x);
x--;
}
}
// if no potential grafts were found, do nothing and return
if(t.size() < 1) {
return;
}
// create the distributions for each graft
for(int x = t.size()-1; x >= 0; x--) {
GraftSplit gs = (GraftSplit)t.get(x);
try {
gs.buildClassifier(l);
gs.deleteGraftedCases(l); // so they don't go down the other branch
} catch (Exception e) {
System.err.println("graftsplit build error: " + e.getMessage());
}
}
// add this stuff to the tree
((C45PruneableClassifierTreeG)parent).setDescendents(t, this);
}
/**
* sorts the int array in ascending order by attribute indexed
* by a in dataset data.
* @param the data the indices represent
* @param the index of the attribute to sort by
* @return array of sorted indicies
*/
private int [] sortByAttribute(Instances data, int a) {
double [] attList = data.attributeToDoubleArray(a);
int [] temp = Utils.sort(attList);
return temp;
}
/**
* deep copy the 2d array of counts
*
* @param src the array to copy
* @return a copy of src
*/
private double [][] copyCounts(double [][] src) {
double [][] newArr = new double[src.length][0];
for(int x = 0; x < src.length; x++) {
newArr[x] = new double[src[x].length];
for(int y = 0; y < src[x].length; y++) {
newArr[x][y] = src[x][y];
}
}
return newArr;
}
/**
* Help method for computing class probabilities of
* a given instance.
*
* @throws Exception if something goes wrong
*/
private double getProbsLaplace(int classIndex, Instance instance, double weight)
throws Exception {
double [] weights;
double prob = 0;
int treeIndex;
int i,j;
if (m_isLeaf) {
return weight * localModel().classProbLaplace(classIndex, instance, -1);
} else {
treeIndex = localModel().whichSubset(instance);
if (treeIndex == -1) {
weights = localModel().weights(instance);
for (i = 0; i < m_sons.length; i++) {
if (!son(i).m_isEmpty) {
if (!son(i).m_isLeaf) {
prob += son(i).getProbsLaplace(classIndex, instance,
weights[i] * weight);
} else {
prob += weight * weights[i] *
localModel().classProbLaplace(classIndex, instance, i);
}
}
}
return prob;
} else {
if (son(treeIndex).m_isLeaf) {
return weight * localModel().classProbLaplace(classIndex, instance,
treeIndex);
} else {
return son(treeIndex).getProbsLaplace(classIndex,instance,weight);
}
}
}
}
/**
* Help method for computing class probabilities of
* a given instance.
*
* @throws Exception if something goes wrong
*/
private double getProbs(int classIndex, Instance instance, double weight)
throws Exception {
double [] weights;
double prob = 0;
int treeIndex;
int i,j;
if (m_isLeaf) {
return weight * localModel().classProb(classIndex, instance, -1);
} else {
treeIndex = localModel().whichSubset(instance);
if (treeIndex == -1) {
weights = localModel().weights(instance);
for (i = 0; i < m_sons.length; i++) {
if (!son(i).m_isEmpty) {
prob += son(i).getProbs(classIndex, instance,
weights[i] * weight);
}
}
return prob;
} else {
if (son(treeIndex).m_isEmpty) {
return weight * localModel().classProb(classIndex, instance,
treeIndex);
} else {
return son(treeIndex).getProbs(classIndex, instance, weight);
}
}
}
}
/**
* add the grafted nodes at originalLeaf's position in tree.
* a recursive function that terminates when t is empty.
*
* @param t the list of nodes to graft
* @param originalLeaf the leaf that the grafts are replacing
*/
public void setDescendents(ArrayList t,
C45PruneableClassifierTreeG originalLeaf) {
Instances headerInfo = new Instances(m_train, 0);
boolean end = false;
ClassifierSplitModel splitmod = null;
C45PruneableClassifierTreeG newNode;
if(t.size() > 0) {
splitmod = (ClassifierSplitModel)t.remove(t.size() - 1);
newNode = new C45PruneableClassifierTreeG(m_toSelectModel, headerInfo,
splitmod, m_pruneTheTree, m_CF, m_subtreeRaising,
false, m_relabel, m_cleanup);
} else {
// get the leaf for one of newNode's children
NoSplit kLeaf = ((GraftSplit)localModel()).getOtherLeaf();
newNode =
new C45PruneableClassifierTreeG(m_toSelectModel, headerInfo,
kLeaf, m_pruneTheTree, m_CF, m_subtreeRaising,
true, m_relabel, m_cleanup);
end = true;
}
// behave differently for parent of original leaf, since we don't
// want to destroy any of its other branches
if(m_sons != null) {
for(int x = 0; x < m_sons.length; x++) {
if(son(x).equals(originalLeaf)) {
m_sons[x] = newNode; // replace originalLeaf with newNode
}
}
} else {
// allocate space for the children
m_sons = new C45PruneableClassifierTreeG[localModel().numSubsets()];
// get the leaf for one of newNode's children
NoSplit kLeaf = ((GraftSplit)localModel()).getLeaf();
C45PruneableClassifierTreeG kNode =
new C45PruneableClassifierTreeG(m_toSelectModel, headerInfo,
kLeaf, m_pruneTheTree, m_CF, m_subtreeRaising,
true, m_relabel, m_cleanup);
// figure where to put the new node
if(((GraftSplit)localModel()).subsetOfInterest() == 0) {
m_sons[0] = kNode;
m_sons[1] = newNode;
} else {
m_sons[0] = newNode;
m_sons[1] = kNode;
}
}
if(!end)
((C45PruneableClassifierTreeG)newNode).setDescendents
(t, (C45PruneableClassifierTreeG)originalLeaf);
}
/**
* class prob with laplace correction (assumes binary class)
*/
private double laplaceLeaf(double classIndex) {
double l = (localModel().distribution().perClass((int)classIndex) + 1.0)
/ (localModel().distribution().total() + 2.0);
return l;
}
/**
* Significance test
* @param double x, double n, double r.
* @return returns the probability of obtaining x or MORE out of n
* if r proportion of n are positive.
*
* z for normal estimation of binomial probability of obtaining x
* or more out of n, if r proportion of n are positive
*/
public double biprob(double x, double n, double r) throws Exception {
return ((((x) - 0.5) - (n) * (r)) / Math.sqrt((n) * (r) * (1.0 - (r))));
}
/**
* Prints tree structure.
*/
public String toString() {
try {
StringBuffer text = new StringBuffer();
if(m_isLeaf) {
text.append(": ");
if(m_localModel instanceof GraftSplit)
text.append(((GraftSplit)m_localModel).dumpLabelG(0,m_train));
else
text.append(m_localModel.dumpLabel(0,m_train));
} else
dumpTree(0,text);
text.append("\n\nNumber of Leaves : \t"+numLeaves()+"\n");
text.append("\nSize of the tree : \t"+numNodes()+"\n");
return text.toString();
} catch (Exception e) {
return "Can't print classification tree.";
}
}
/**
* Help method for printing tree structure.
*
* @throws Exception if something goes wrong
*/
protected void dumpTree(int depth,StringBuffer text) throws Exception {
int i,j;
for(i=0;i<m_sons.length;i++) {
text.append("\n");;
for(j=0;j<depth;j++)
text.append("| ");
text.append(m_localModel.leftSide(m_train));
text.append(m_localModel.rightSide(i, m_train));
if(m_sons[i].m_isLeaf) {
text.append(": ");
if(m_localModel instanceof GraftSplit)
text.append(((GraftSplit)m_localModel).dumpLabelG(i,m_train));
else
text.append(m_localModel.dumpLabel(i,m_train));
} else
((C45PruneableClassifierTreeG)m_sons[i]).dumpTree(depth+1,text);
}
}
/**
* Returns the revision string.
*
* @return the revision
*/
public String getRevision() {
return RevisionUtils.extract("$Revision: 5535 $");
}
}