/**
* Iterates over all models and returns the class with maximum likelihood.
*
* @param origExampleSet the set of examples to be classified
*/
@Override
public ExampleSet performPrediction(ExampleSet origExampleSet, Attribute predictedLabel)
throws OperatorException {
final String attributePrefix = "AdaBoostModelPrediction";
final int numLabels = predictedLabel.getMapping().size();
final Attribute[] specialAttributes = new Attribute[numLabels];
OperatorProgress progress = null;
if (getShowProgress() && getOperator() != null && getOperator().getProgress() != null) {
progress = getOperator().getProgress();
progress.setTotal(100);
}
for (int i = 0; i < numLabels; i++) {
specialAttributes[i] =
com.rapidminer.example.Tools.createSpecialAttribute(
origExampleSet, attributePrefix + i, Ontology.NUMERICAL);
if (progress != null) {
progress.setCompleted((int) (25.0 * (i + 1) / numLabels));
}
}
Iterator<Example> reader = origExampleSet.iterator();
int progressCounter = 0;
while (reader.hasNext()) {
Example example = reader.next();
for (int i = 0; i < specialAttributes.length; i++) {
example.setValue(specialAttributes[i], 0);
}
if (progress != null && ++progressCounter % OPERATOR_PROGRESS_STEPS == 0) {
progress.setCompleted((int) (25.0 * progressCounter / origExampleSet.size()) + 25);
}
}
reader = origExampleSet.iterator();
for (int modelNr = 0; modelNr < this.getNumberOfModels(); modelNr++) {
Model model = this.getModel(modelNr);
ExampleSet exampleSet = (ExampleSet) origExampleSet.clone();
exampleSet = model.apply(exampleSet);
this.updateEstimates(exampleSet, modelNr, specialAttributes);
PredictionModel.removePredictedLabel(exampleSet);
if (progress != null) {
progress.setCompleted((int) (25.0 * (modelNr + 1) / this.getNumberOfModels()) + 50);
}
}
// Turn prediction weights into confidences and a crisp predcition:
this.evaluateSpecialAttributes(origExampleSet, specialAttributes);
// Clean up attributes:
for (int i = 0; i < numLabels; i++) {
origExampleSet.getAttributes().remove(specialAttributes[i]);
origExampleSet.getExampleTable().removeAttribute(specialAttributes[i]);
if (progress != null) {
progress.setCompleted((int) (25.0 * (i + 1) / numLabels) + 75);
}
}
return origExampleSet;
}
/** @see com.rapidminer.operator.OperatorChain#doWork() */
@Override
public void doWork() throws OperatorException {
List<Operator> nested = this.getImmediateChildren();
log.info("This StreamProcess has {} nested operators", nested.size());
for (Operator op : nested) {
log.info(" op: {}", op);
if (op instanceof DataStreamOperator) {
log.info("Resetting stream-operator {}", op);
((DataStreamOperator) op).reset();
}
}
log.info("Starting some work in doWork()");
ExampleSet exampleSet = input.getData(ExampleSet.class);
log.info("input is an example set with {} examples", exampleSet.size());
int i = 0;
Iterator<Example> it = exampleSet.iterator();
while (it.hasNext()) {
Example example = it.next();
log.info("Processing example {}", i);
DataObject datum = StreamUtils.wrap(example);
log.info("Wrapped data-object is: {}", datum);
dataStream.deliver(datum);
getSubprocess(0).execute();
inApplyLoop();
i++;
}
// super.doWork();
log.info("doWork() is finished.");
}
private static Map<Integer, MeanVariance> createMeanVariances(
com.rapidminer.example.ExampleSet exampleSet) {
double[] sum = new double[exampleSet.getAttributes().size()];
double[] squaredSum = new double[sum.length];
Iterator<com.rapidminer.example.Example> reader = exampleSet.iterator();
while (reader.hasNext()) {
com.rapidminer.example.Example example = reader.next();
int a = 0;
for (Attribute attribute : exampleSet.getAttributes()) {
double value = example.getValue(attribute);
sum[a] += value;
squaredSum[a] += value * value;
a++;
}
}
Map<Integer, MeanVariance> meanVariances = new HashMap<Integer, MeanVariance>();
for (int a = 0; a < sum.length; a++) {
sum[a] /= exampleSet.size();
squaredSum[a] /= exampleSet.size();
meanVariances.put(a, new MeanVariance(sum[a], squaredSum[a] - (sum[a] * sum[a])));
}
return meanVariances;
}
/**
* Computes Kendall's tau-b rank correlation statistic, ignoring examples containing missing
* values, with approximate comparisons.
*
* @param eSet the example set
* @param a the first attribute to correlate
* @param b the second attribute to correlate
* @param fuzz values within +/- fuzz may be considered tied
* @return Kendall's tau-b rank correlation
* @throws OperatorException
*/
public static double tau_b(ExampleSet eSet, Attribute a, Attribute b, double fuzz)
throws OperatorException {
ExampleSet e = extract(eSet, a, b); // reduced example set
FuzzyComp fc = new FuzzyComp(fuzz);
int c = 0; // concordant pairs
int d = 0; // discordant pairs
int ta = 0; // pairs tied on a (only)
int tb = 0; // pairs tied on b (only)
int tc = 0; // pairs tied on both a and b
int n = 0; // number of times iterator i is bumped
Iterator<Example> i = e.iterator();
while (i.hasNext()) {
// iterate through all possible pairs
Example z1 = i.next();
n++;
double x = z1.getValue(a);
double y = z1.getValue(b);
if (b.isNominal() && a != null) {
String yString = b.getMapping().mapIndex((int) y);
y = a.getMapping().getIndex(yString);
}
Iterator<Example> j = e.iterator();
for (int k = 0; k < n; k++) j.next(); // increment j to match i
while (j.hasNext()) {
// move on to subsequent examples
Example z2 = j.next();
double xx = z2.getValue(a);
double yy = z2.getValue(b);
if (b.isNominal() && a != null) {
String yyString = b.getMapping().mapIndex((int) yy);
yy = a.getMapping().getIndex(yyString);
}
int xc = fc.compare(x, xx);
int yc = fc.compare(y, yy);
if (xc == 0) {
if (yc == 0) tc++; // tied on both attributes
else ta++; // tied only on a
} else if (yc == 0) tb++; // tied only on b
else if (xc == yc) c++; // concordant pair
else d++; // discordant pair
}
}
double num = c - d;
double den = Math.sqrt((c + d + ta) * (c + d + tb));
if (den != 0) return num / den;
else return 0;
}
/** Creates a new evolutionary SVM optimization. */
public ClassificationEvoOptimization(
ExampleSet exampleSet, // training data
Kernel kernel,
double c, // SVM paras
int initType, // start population creation type para
int maxIterations,
int generationsWithoutImprovement,
int popSize, // GA paras
int selectionType,
double tournamentFraction,
boolean keepBest, // selection paras
int mutationType, // type of mutation
double crossoverProb,
boolean showConvergencePlot,
boolean showPopulationPlot,
ExampleSet holdOutSet,
RandomGenerator random,
LoggingHandler logging,
Operator executingOperator) {
super(
EvoSVM.createBoundArray(0.0d, exampleSet.size()),
EvoSVM.determineMax(c, kernel, exampleSet, selectionType, exampleSet.size()),
popSize,
exampleSet.size(),
initType,
maxIterations,
generationsWithoutImprovement,
selectionType,
tournamentFraction,
keepBest,
mutationType,
Double.NaN,
crossoverProb,
showConvergencePlot,
showPopulationPlot,
random,
logging,
executingOperator);
this.exampleSet = exampleSet;
this.holdOutSet = holdOutSet;
this.populationSize = popSize;
this.kernel = kernel;
this.c = getMax(0);
// label values
this.ys = new double[exampleSet.size()];
Iterator<Example> reader = exampleSet.iterator();
int index = 0;
Attribute label = exampleSet.getAttributes().getLabel();
while (reader.hasNext()) {
Example example = reader.next();
ys[index++] = example.getLabel() == label.getMapping().getPositiveIndex() ? 1.0d : -1.0d;
}
// optimization function
this.optimizationFunction =
new ClassificationOptimizationFunction(selectionType == NON_DOMINATED_SORTING_SELECTION);
}
/**
* Creates a fresh example set of the given size from the RapidMiner example reader. The alpha
* values and b are zero, the label will be set if it is known.
*/
public SVMExamples(
com.rapidminer.example.ExampleSet exampleSet,
Attribute labelAttribute,
Map<Integer, MeanVariance> meanVariances) {
this(exampleSet.size(), 0.0d);
this.meanVarianceMap = meanVariances;
Iterator<com.rapidminer.example.Example> reader = exampleSet.iterator();
Attribute idAttribute = exampleSet.getAttributes().getId();
int exampleCounter = 0;
while (reader.hasNext()) {
com.rapidminer.example.Example current = reader.next();
Map<Integer, Double> attributeMap = new LinkedHashMap<Integer, Double>();
int a = 0;
for (Attribute attribute : exampleSet.getAttributes()) {
double value = current.getValue(attribute);
if (!com.rapidminer.example.Tools.isDefault(attribute.getDefault(), value)) {
attributeMap.put(a, value);
}
if ((a + 1) > dim) {
dim = (a + 1);
}
a++;
}
atts[exampleCounter] = new double[attributeMap.size()];
index[exampleCounter] = new int[attributeMap.size()];
Iterator<Map.Entry<Integer, Double>> i = attributeMap.entrySet().iterator();
int attributeCounter = 0;
while (i.hasNext()) {
Map.Entry<Integer, Double> e = i.next();
Integer indexValue = e.getKey();
Double attributeValue = e.getValue();
index[exampleCounter][attributeCounter] = indexValue.intValue();
double value = attributeValue.doubleValue();
MeanVariance meanVariance = meanVarianceMap.get(indexValue);
if (meanVariance != null) {
if (meanVariance.getVariance() == 0.0d) {
value = 0.0d;
} else {
value = (value - meanVariance.getMean()) / Math.sqrt(meanVariance.getVariance());
}
}
atts[exampleCounter][attributeCounter] = value;
attributeCounter++;
}
if (labelAttribute != null) {
double label = current.getValue(labelAttribute);
if (labelAttribute.isNominal()) {
ys[exampleCounter] = (label == labelAttribute.getMapping().getPositiveIndex() ? 1 : -1);
} else {
ys[exampleCounter] = label;
}
}
if (idAttribute != null) {
ids[exampleCounter] = current.getValueAsString(idAttribute);
}
exampleCounter++;
}
}
/**
* Computes Kendall's tau-b rank correlation statistic, ignoring examples containing missing
* values.
*
* @param eSet the example set
* @param a the first attribute to correlate
* @param b the second attribute to correlate
* @return Kendall's tau-b rank correlation
* @throws OperatorException
*/
public static double tau_b(ExampleSet eSet, Attribute a, Attribute b) throws OperatorException {
ExampleSet e = extract(eSet, a, b); // reduced example set
long c = 0; // concordant pairs
long d = 0; // discordant pairs
long ta = 0; // pairs tied on a (only)
long tb = 0; // pairs tied on b (only)
long tc = 0; // pairs tied on both a and b
int n = 0; // number of times iterator i is bumped
Iterator<Example> i = e.iterator();
while (i.hasNext()) {
// iterate through all possible pairs
Example z1 = i.next();
n++;
double x = z1.getValue(a);
double y = z1.getValue(b);
if (b.isNominal() && a != null) {
String yString = b.getMapping().mapIndex((int) y);
y = a.getMapping().getIndex(yString);
}
Iterator<Example> j = e.iterator();
for (int k = 0; k < n; k++) j.next(); // increment j to match i
while (j.hasNext()) {
// move on to subsequent examples
Example z2 = j.next();
double xx = z2.getValue(a);
double yy = z2.getValue(b);
if (b.isNominal() && a != null) {
String yyString = b.getMapping().mapIndex((int) yy);
yy = a.getMapping().getIndex(yyString);
}
if (x == xx) {
if (y == yy) tc++; // tied on both attributes
else ta++; // tied only on a
} else if (y == yy) tb++; // tied only on b
else if ((x > xx && y > yy) || (x < xx && y < yy)) c++;
// concordant pair
else d++; // discordant pair
}
}
double num = c - d;
double f1 = c + d + ta;
double f2 = c + d + tb;
double den = Math.sqrt(f1 * f2);
if (den != 0) return num / den;
else return 0;
}
public Model learn(ExampleSet exampleSet) throws OperatorException {
double value = 0.0;
double[] confidences = null;
int method = getParameterAsInt(PARAMETER_METHOD);
Attribute label = exampleSet.getAttributes().getLabel();
if ((label.isNominal()) && ((method == MEDIAN) || (method == AVERAGE))) {
logWarning(
"Cannot use method '" + METHODS[method] + "' for nominal labels: changing to 'mode'!");
method = MODE;
} else if ((!label.isNominal()) && (method == MODE)) {
logWarning(
"Cannot use method '"
+ METHODS[method]
+ "' for numerical labels: changing to 'average'!");
method = AVERAGE;
}
switch (method) {
case MEDIAN:
double[] labels = new double[exampleSet.size()];
Iterator<Example> r = exampleSet.iterator();
int counter = 0;
while (r.hasNext()) {
Example example = r.next();
labels[counter++] = example.getValue(example.getAttributes().getLabel());
}
java.util.Arrays.sort(labels);
value = labels[exampleSet.size() / 2];
break;
case AVERAGE:
exampleSet.recalculateAttributeStatistics(label);
value = exampleSet.getStatistics(label, Statistics.AVERAGE);
break;
case MODE:
exampleSet.recalculateAttributeStatistics(label);
value = exampleSet.getStatistics(label, Statistics.MODE);
confidences = new double[label.getMapping().size()];
for (int i = 0; i < confidences.length; i++) {
confidences[i] =
exampleSet.getStatistics(label, Statistics.COUNT, label.getMapping().mapIndex(i))
/ exampleSet.size();
}
break;
case CONSTANT:
value = getParameterAsDouble(PARAMETER_CONSTANT);
break;
case ATTRIBUTE:
return new AttributeDefaultModel(
exampleSet, getParameterAsString(PARAMETER_ATTRIBUTE_NAME));
default:
// cannot happen
throw new OperatorException("DefaultLearner: Unknown default method '" + method + "'!");
}
log(
"Default value is '"
+ (label.isNominal() ? label.getMapping().mapIndex((int) value) : value + "")
+ "'.");
return new DefaultModel(exampleSet, value, confidences);
}
/** returns the accuracy of the predictions for the given example set */
private double evaluatePredictions(ExampleSet exampleSet) {
Iterator<Example> reader = exampleSet.iterator();
int count = 0;
int correct = 0;
while (reader.hasNext()) {
count++;
Example example = reader.next();
if (example.getLabel() == example.getPredictedLabel()) correct++;
}
return ((double) correct) / count;
}
private void restoreOldWeights(ExampleSet exampleSet) {
if (this.oldWeights != null) { // need to reset weights
Iterator<Example> reader = exampleSet.iterator();
int i = 0;
while (reader.hasNext() && i < this.oldWeights.length) {
reader.next().setWeight(this.oldWeights[i++]);
}
} else { // need to delete the weights attribute
Attribute weight = exampleSet.getAttributes().getWeight();
exampleSet.getAttributes().remove(weight);
exampleSet.getExampleTable().removeAttribute(weight);
}
}
/**
* Computes the weighted class priors of the boolean target attribute and shifts weights so that
* the priors are equal afterwards.
*/
private void rescalePriors(ExampleSet exampleSet, double[] classPriors) {
// The weights of class i are calculated as
// (1 / #classes) / (#rel_freq_class_i)
double[] weights = new double[2];
for (int i = 0; i < weights.length; i++) {
weights[i] = 1.0d / (weights.length * (classPriors[i]));
}
Iterator<Example> exRead = exampleSet.iterator();
while (exRead.hasNext()) {
Example example = exRead.next();
example.setWeight(weights[(int) (example.getLabel())]);
}
}
/**
* Similar to prepareBatch, but for extended batches.
*
* @param extendedBatch containing the extended batch
* @return the class priors of the batch
*/
private double[] prepareExtendedBatch(ExampleSet extendedBatch) {
int[] classCount = new int[2];
Iterator<Example> reader = extendedBatch.iterator();
while (reader.hasNext()) {
Example example = reader.next();
example.setWeight(1);
classCount[(int) example.getLabel()]++;
}
double[] classPriors = new double[2];
int sum = classCount[0] + classCount[1];
classPriors[0] = ((double) classCount[0]) / sum;
classPriors[1] = ((double) classCount[1]) / sum;
return classPriors;
}
public static SplittedExampleSet splitByAttribute(
ExampleSet exampleSet, Attribute attribute, double value) {
int[] elements = new int[exampleSet.size()];
Iterator<Example> reader = exampleSet.iterator();
int i = 0;
while (reader.hasNext()) {
Example example = reader.next();
double currentValue = example.getValue(attribute);
if (currentValue <= value) elements[i++] = 0;
else elements[i++] = 1;
}
Partition partition = new Partition(elements, 2);
return new SplittedExampleSet(exampleSet, partition);
}
private void updateEstimates(ExampleSet exampleSet, int modelNr, Attribute[] specialAttributes) {
Iterator<Example> reader = exampleSet.iterator();
while (reader.hasNext()) {
Example example = reader.next();
int predicted = (int) example.getPredictedLabel();
double oldValue = example.getValue(specialAttributes[predicted]);
if (Double.isNaN(oldValue)) {
logWarning("Found NaN confidence as intermediate prediction.");
oldValue = 0;
}
if (!Double.isInfinite(oldValue)) {
example.setValue(specialAttributes[predicted], oldValue + this.getWeightForModel(modelNr));
}
}
}
protected void prepareWeights(ExampleSet exampleSet) {
Attribute weightAttr = exampleSet.getAttributes().getWeight();
if (weightAttr == null) {
this.oldWeights = null;
com.rapidminer.example.Tools.createWeightAttribute(exampleSet);
} else { // Back up old weights
this.oldWeights = new double[exampleSet.size()];
Iterator<Example> reader = exampleSet.iterator();
for (int i = 0; (reader.hasNext() && i < oldWeights.length); i++) {
Example example = reader.next();
if (example != null) {
this.oldWeights[i] = example.getWeight();
example.setWeight(1);
}
}
}
}
private void evaluateSpecialAttributes(ExampleSet exampleSet, Attribute[] specialAttributes) {
Attribute predictedLabel = exampleSet.getAttributes().getPredictedLabel();
Iterator<Example> reader = exampleSet.iterator();
while (reader.hasNext()) {
Example example = reader.next();
double sum = 0;
double[] confidences = new double[specialAttributes.length];
double bestConf = -1;
int bestLabel = 0;
for (int n = 0; n < confidences.length; n++) {
confidences[n] = example.getValue(specialAttributes[n]);
if (confidences[n] > bestConf) {
bestConf = confidences[n];
bestLabel = n;
}
}
example.setValue(
predictedLabel,
predictedLabel.getMapping().mapString(this.getLabel().getMapping().mapIndex(bestLabel)));
for (int n = 0; n < confidences.length; n++) {
confidences[n] = Math.exp(confidences[n] - bestConf);
// remember for normalization:
sum += confidences[n];
}
// Normalize and set confidence values for all classes:
if (Double.isInfinite(sum) || Double.isNaN(sum)) {
int best = (int) example.getPredictedLabel();
for (int k = 0; k < confidences.length; k++) {
confidences[k] = 0;
}
confidences[best] = 1;
} else {
for (int k = 0; k < confidences.length; k++) {
confidences[k] /= sum;
example.setConfidence(predictedLabel.getMapping().mapIndex(k), confidences[k]);
}
}
}
}
private BayBoostModel retrainLastWeight(
BayBoostModel ensemble, ExampleSet exampleSet, Vector holdOutSet) throws OperatorException {
this.prepareExtendedBatch(exampleSet); // method fits by chance
int modelNum = ensemble.getNumberOfModels();
Vector<BayBoostBaseModelInfo> modelInfo = new Vector<BayBoostBaseModelInfo>();
double[] priors = ensemble.getPriors();
for (int i = 0; i < modelNum - 1; i++) {
Model model = ensemble.getModel(i);
ContingencyMatrix cm = ensemble.getContingencyMatrix(i);
modelInfo.add(new BayBoostBaseModelInfo(model, cm));
exampleSet = model.apply(exampleSet);
WeightedPerformanceMeasures.reweightExamples(exampleSet, cm, false);
}
Model latestModel = ensemble.getModel(modelNum - 1);
exampleSet = latestModel.apply(exampleSet);
// quite ugly:
double[] weights = new double[holdOutSet.size()];
Iterator it = holdOutSet.iterator();
int index = 0;
while (it.hasNext()) {
Example example = (Example) it.next();
weights[index++] = example.getWeight();
}
Iterator<Example> reader = exampleSet.iterator();
while (reader.hasNext()) {
reader.next().setWeight(0);
}
it = holdOutSet.iterator();
index = 0;
while (it.hasNext()) {
Example example = (Example) it.next();
example.setWeight(weights[index++]);
}
WeightedPerformanceMeasures wp = new WeightedPerformanceMeasures(exampleSet);
modelInfo.add(new BayBoostBaseModelInfo(latestModel, wp.getContingencyMatrix()));
return new BayBoostModel(exampleSet, modelInfo, priors);
}
/**
* Calculates ranks for an attribute.
*
* <p>Ranks are returned as double precision values, with 1 as the rank of the smallest value.
* Values within +/- fuzz of each other may be considered tied. Tied values receive identical
* ranks. Missing values receive rank NaN.
*
* <p>Note that application of the "fuzz" factor is dependent on the order of the observations in
* the example set. For instance, if the first three values encountered are x, x+fuzz and
* x+2*fuzz, the first two will be considered tied but the third will not, since x+2*fuzz is not
* within +/- fuzz of x.
*
* @param eSet the example set
* @param att the attribute to rank
* @param fuzz values within +/- fuzz may be considered tied
* @return a double precision array of ranks
*/
public static double[] rank(ExampleSet eSet, Attribute att, Attribute mappingAtt, double fuzz) {
TreeMap<Double, ArrayList<Integer>> map;
if (fuzz == 0.0) map = new TreeMap<Double, ArrayList<Integer>>();
else {
FuzzyComp fc = new FuzzyComp(fuzz);
map = new TreeMap<Double, ArrayList<Integer>>(fc);
}
double[] rank = new double[eSet.size()];
Iterator<Example> reader = eSet.iterator();
int i = 0; // example index
// iterate through the example set
while (reader.hasNext()) {
// get the attribute values from the next example
Example e = reader.next();
double x = e.getValue(att);
if (att.isNominal() && mappingAtt != null) {
String xString = att.getMapping().mapIndex((int) x);
x = mappingAtt.getMapping().getIndex(xString);
}
// punt if either is missing
if (Double.isNaN(x)) rank[i++] = Double.NaN;
else {
// insert x into the tree
if (!map.containsKey(x))
// new key -- create a new entry in the map
map.put(x, new ArrayList<Integer>());
map.get(x).add(i++); // add the index to the list
}
}
// convert the map to ranks
double r = 0;
for (double x : map.keySet()) {
ArrayList<Integer> y = map.get(x);
double v = r + (1.0 + y.size()) / 2.0;
for (int j : y) rank[j] = v;
r += y.size();
}
return rank;
}
public IOObject[] apply() throws OperatorException {
ExampleSet eSet = getInput(ExampleSet.class);
// only warning, removing is done by createSpecialAttribute(...)
Attribute idAttribute = eSet.getAttributes().getId();
if (idAttribute != null) {
logWarning("Overwriting old id attribute!");
}
// create new id attribute
boolean nominalIds = getParameterAsBoolean(PARAMETER_CREATE_NOMINAL_IDS);
idAttribute =
Tools.createSpecialAttribute(
eSet, Attributes.ID_NAME, nominalIds ? Ontology.NOMINAL : Ontology.INTEGER);
// set IDs
int currentId = 1;
Iterator<Example> r = eSet.iterator();
while (r.hasNext()) {
Example example = r.next();
example.setValue(
idAttribute,
nominalIds ? idAttribute.getMapping().mapString("id_" + currentId) : currentId);
currentId++;
checkForStop();
}
// initialize example visualizer
Operator visualizer = null;
try {
visualizer = OperatorService.createOperator(ExampleVisualizationOperator.class);
} catch (OperatorCreationException e) {
logNote("Cannot initialize example visualizer, skipping...");
}
if (visualizer != null) visualizer.apply(new IOContainer(eSet));
return new IOObject[] {eSet};
}
@Override
public ExampleSet performPrediction(ExampleSet exampleSet, Attribute predictedLabel)
throws OperatorException {
Attribute label = this.getLabel();
final int posLabel = label.getMapping().getPositiveIndex();
final int negLabel = label.getMapping().getNegativeIndex();
final String posLabelS = label.getMapping().mapIndex(posLabel);
final String negLabelS = label.getMapping().mapIndex(negLabel);
exampleSet = model.apply(exampleSet);
Iterator<Example> reader = exampleSet.iterator();
while (reader.hasNext()) {
Example example = reader.next();
double predicted = PlattScaling.getLogOddsPosConfidence(example.getConfidence(posLabelS));
double scaledPos =
1.0d / (1.0d + Math.exp(predicted * parameters.getA() + parameters.getB()));
double scaledNeg = 1.0d - scaledPos;
example.setValue(predictedLabel, (scaledPos >= scaledNeg) ? posLabel : negLabel);
example.setConfidence(posLabelS, scaledPos);
example.setConfidence(negLabelS, scaledNeg);
}
return exampleSet;
}
@Override
protected void createMatrices() {
List<Attribute> attributes = new ArrayList<Attribute>(exampleSet.getAttributes().size());
for (Attribute attribute : exampleSet.getAttributes()) {
attributes.add((Attribute) attribute.clone());
}
MemoryExampleTable table = new MemoryExampleTable(attributes);
for (int x = 0; x < dimensions[0]; x++) {
for (int y = 0; y < dimensions[1]; y++) {
DataRow row = new DoubleArrayDataRow(net.getNodeWeights(new int[] {x, y}));
table.addDataRow(row);
}
}
ExampleSet set = table.createExampleSet();
this.classificationMatrix = new double[dimensions[0]][dimensions[1]];
try {
set = model.apply(set);
Iterator<Example> exampleIterator = set.iterator();
for (int x = 0; x < dimensions[0]; x++) {
for (int y = 0; y < dimensions[1]; y++) {
Example example = exampleIterator.next();
classificationMatrix[x][y] =
example.getValue(example.getAttributes().getPredictedLabel());
}
}
} catch (OperatorException e) {
// LogService.getGlobal().log("Cannot use Model for prediction of node label: " +
// e.getMessage(), LogService.WARNING);
LogService.getRoot()
.log(
Level.WARNING,
"com.rapidminer.operator.visualization.SOMModelPlotter.using_model_for_prediction_error"
+ e.getMessage());
}
super.createMatrices();
}
/**
* Constructs a <code>Model</code> repeatedly running a weak learner, reweighting the training
* example set accordingly, and combining the hypothesis using the available weighted performance
* values.
*/
public Model learn(ExampleSet exampleSet) throws OperatorException {
this.runVector = new RunVector();
BayBoostModel ensembleNewBatch = null;
BayBoostModel ensembleExtBatch = null;
final Vector<BayBoostBaseModelInfo> modelInfo = new Vector<BayBoostBaseModelInfo>(); // for
// models
// and
// their
// probability
// estimates
Vector<BayBoostBaseModelInfo> modelInfo2 = new Vector<BayBoostBaseModelInfo>();
this.currentIteration = 0;
int firstOpenBatch = 1;
// prepare the stream control attribute
final Attribute streamControlAttribute;
{
Attribute attr = null;
if ((attr = exampleSet.getAttributes().get(STREAM_CONTROL_ATTRIB_NAME)) == null)
streamControlAttribute =
com.rapidminer.example.Tools.createSpecialAttribute(
exampleSet, STREAM_CONTROL_ATTRIB_NAME, Ontology.INTEGER);
else {
streamControlAttribute = attr;
logWarning(
"Attribute with the (reserved) name of the stream control attribute exists. It is probably an old version created by this operator. Trying to recycle it... ");
// Resetting the stream control attribute values by overwriting
// them with 0 avoids (unlikely)
// problems in case the same ExampleSet is passed to this
// operator over and over again:
Iterator<Example> e = exampleSet.iterator();
while (e.hasNext()) {
e.next().setValue(streamControlAttribute, 0);
}
}
}
// and the weight attribute
if (exampleSet.getAttributes().getWeight() == null) {
this.prepareWeights(exampleSet);
}
boolean estimateFavoursExtBatch = true;
// *** The main loop, one iteration per batch: ***
Iterator<Example> reader = exampleSet.iterator();
while (reader.hasNext()) {
// increment batch number, collect batch and evaluate performance of
// current model on batch
double[] classPriors =
this.prepareBatch(++this.currentIteration, reader, streamControlAttribute);
ConditionedExampleSet trainingSet =
new ConditionedExampleSet(
exampleSet, new BatchFilterCondition(streamControlAttribute, this.currentIteration));
final EstimatedPerformance estPerf;
// Step 1: apply the ensemble model to the current batch (prediction
// phase), evaluate and store result
if (ensembleExtBatch != null) {
// apply extended batch model first:
trainingSet = (ConditionedExampleSet) ensembleExtBatch.apply(trainingSet);
this.performance = evaluatePredictions(trainingSet); // unweighted
// performance;
// then apply new batch model:
trainingSet = (ConditionedExampleSet) ensembleNewBatch.apply(trainingSet);
double newBatchPerformance = evaluatePredictions(trainingSet);
// heuristic: use extended batch model for predicting
// unclassified instances
if (estimateFavoursExtBatch == true)
estPerf =
new EstimatedPerformance("accuracy", this.performance, trainingSet.size(), false);
else
estPerf =
new EstimatedPerformance("accuracy", newBatchPerformance, trainingSet.size(), false);
// final double[] ensembleWeights;
// continue with the better model:
if (newBatchPerformance > this.performance) {
this.performance = newBatchPerformance;
firstOpenBatch = Math.max(1, this.currentIteration - 1);
// ensembleWeights = ensembleNewBatch.getModelWeights();
} else {
modelInfo.clear();
modelInfo.addAll(modelInfo2);
// ensembleWeights = ensembleExtBatch.getModelWeights();
}
} else if (ensembleNewBatch != null) {
trainingSet = (ConditionedExampleSet) ensembleNewBatch.apply(trainingSet);
this.performance = evaluatePredictions(trainingSet);
firstOpenBatch = Math.max(1, this.currentIteration - 1);
estPerf = new EstimatedPerformance("accuracy", this.performance, trainingSet.size(), false);
} else estPerf = null; // no model ==> no prediction performance
if (estPerf != null) {
PerformanceVector perf = new PerformanceVector();
perf.addAveragable(estPerf);
this.runVector.addVector(perf);
}
// *** retraining phase ***
// Step 2: First reconstruct the initial weighting, if necessary.
if (this.getParameterAsBoolean(PARAMETER_RESCALE_LABEL_PRIORS) == true) {
this.rescalePriors(trainingSet, classPriors);
}
estimateFavoursExtBatch = true;
// Step 3: Find better weights for existing models and continue
// training
if (modelInfo.size() > 0) {
modelInfo2 = new Vector<BayBoostBaseModelInfo>();
for (BayBoostBaseModelInfo bbbmi : modelInfo) {
modelInfo2.add(bbbmi); // BayBoostBaseModelInfo objects
// cannot be changed, no deep copy
// required
}
// separate hold out set
final double holdOutRatio = this.getParameterAsDouble(PARAMETER_FRACTION_HOLD_OUT_SET);
Vector<Example> holdOutExamples = new Vector<Example>();
if (holdOutRatio > 0) {
RandomGenerator random = RandomGenerator.getRandomGenerator(this);
Iterator<Example> randBatchReader = trainingSet.iterator();
while (randBatchReader.hasNext()) {
Example example = randBatchReader.next();
if (random.nextDoubleInRange(0, 1) <= holdOutRatio) {
example.setValue(streamControlAttribute, 0);
holdOutExamples.add(example);
}
}
// TODO: create new example set
// trainingSet.updateCondition();
}
// model 1: train one more base classifier
boolean trainingExamplesLeft = this.adjustBaseModelWeights(trainingSet, modelInfo);
if (trainingExamplesLeft) {
// "trainingExamplesLeft" needs to be checked to avoid
// exceptions.
// Anyway, learning does not make sense, otherwise.
if (!this.trainAdditionalModel(trainingSet, modelInfo)) {}
}
ensembleNewBatch = new BayBoostModel(exampleSet, modelInfo, classPriors);
// model 2: remove last classifier, extend batch, train on
// extended batch
ExampleSet extendedBatch = // because of the ">=" condition it
// is sufficient to remember the
// opening batch
new ConditionedExampleSet(
exampleSet, new BatchFilterCondition(streamControlAttribute, firstOpenBatch));
classPriors = this.prepareExtendedBatch(extendedBatch);
if (this.getParameterAsBoolean(PARAMETER_RESCALE_LABEL_PRIORS) == true) {
this.rescalePriors(extendedBatch, classPriors);
}
modelInfo2.remove(modelInfo2.size() - 1);
trainingExamplesLeft = this.adjustBaseModelWeights(extendedBatch, modelInfo2);
// If no training examples are left: no need and chance to
// continue training.
if (trainingExamplesLeft == false) {
ensembleExtBatch = new BayBoostModel(exampleSet, modelInfo2, classPriors);
} else {
boolean success = this.trainAdditionalModel(extendedBatch, modelInfo2);
if (success) {
ensembleExtBatch = new BayBoostModel(exampleSet, modelInfo2, classPriors);
} else {
ensembleExtBatch = null;
estimateFavoursExtBatch = false;
}
}
if (holdOutRatio > 0) {
Iterator hoEit = holdOutExamples.iterator();
while (hoEit.hasNext()) {
((Example) hoEit.next()).setValue(streamControlAttribute, this.currentIteration);
}
// TODO: create new example set
// trainingSet.updateCondition();
if (ensembleExtBatch != null) {
trainingSet = (ConditionedExampleSet) ensembleNewBatch.apply(trainingSet);
hoEit = holdOutExamples.iterator();
int errors = 0;
while (hoEit.hasNext()) {
Example example = (Example) hoEit.next();
if (example.getPredictedLabel() != example.getLabel()) errors++;
}
double newBatchErr = ((double) errors) / holdOutExamples.size();
trainingSet = (ConditionedExampleSet) ensembleExtBatch.apply(trainingSet);
hoEit = holdOutExamples.iterator();
errors = 0;
while (hoEit.hasNext()) {
Example example = (Example) hoEit.next();
if (example.getPredictedLabel() != example.getLabel()) errors++;
}
double extBatchErr = ((double) errors) / holdOutExamples.size();
estimateFavoursExtBatch = (extBatchErr <= newBatchErr);
if (estimateFavoursExtBatch) {
ensembleExtBatch =
this.retrainLastWeight(ensembleExtBatch, trainingSet, holdOutExamples);
} else
ensembleNewBatch =
this.retrainLastWeight(ensembleNewBatch, trainingSet, holdOutExamples);
} else
ensembleNewBatch =
this.retrainLastWeight(ensembleNewBatch, trainingSet, holdOutExamples);
}
} else {
this.trainAdditionalModel(trainingSet, modelInfo);
ensembleNewBatch = new BayBoostModel(exampleSet, modelInfo, classPriors);
ensembleExtBatch = null;
estimateFavoursExtBatch = false;
}
}
this.restoreOldWeights(exampleSet);
return (ensembleExtBatch == null ? ensembleNewBatch : ensembleExtBatch);
}
/** Creates an iterator over all examples. */
public Iterator<Example> iterator() {
return new AttributesExampleReader(parent.iterator(), this);
}
/** Returns a model containing all support vectors, i.e. the examples with non-zero alphas. */
private EvoSVMModel getModel(double[] alphas) {
// calculate support vectors
Iterator<Example> reader = exampleSet.iterator();
List<SupportVector> supportVectors = new ArrayList<SupportVector>();
int index = 0;
while (reader.hasNext()) {
double currentAlpha = alphas[index];
Example currentExample = reader.next();
if (currentAlpha != 0.0d) {
double[] x = new double[exampleSet.getAttributes().size()];
int a = 0;
for (Attribute attribute : exampleSet.getAttributes())
x[a++] = currentExample.getValue(attribute);
supportVectors.add(new SupportVector(x, ys[index], currentAlpha));
}
index++;
}
// calculate all sum values
double[] sum = new double[exampleSet.size()];
reader = exampleSet.iterator();
index = 0;
while (reader.hasNext()) {
Example current = reader.next();
double[] x = new double[exampleSet.getAttributes().size()];
int a = 0;
for (Attribute attribute : exampleSet.getAttributes()) x[a++] = current.getValue(attribute);
sum[index] = kernel.getSum(supportVectors, x);
index++;
}
// calculate b (from Stefan's mySVM code)
double bSum = 0.0d;
int bCounter = 0;
for (int i = 0; i < alphas.length; i++) {
if ((ys[i] * alphas[i] - c < -IS_ZERO) && (ys[i] * alphas[i] > IS_ZERO)) {
bSum += ys[i] - sum[i];
bCounter++;
} else if ((ys[i] * alphas[i] + c > IS_ZERO) && (ys[i] * alphas[i] < -IS_ZERO)) {
bSum += ys[i] - sum[i];
bCounter++;
}
}
if (bCounter == 0) {
// unlikely
bSum = 0.0d;
for (int i = 0; i < alphas.length; i++) {
if ((ys[i] * alphas[i] < IS_ZERO) && (ys[i] * alphas[i] > -IS_ZERO)) {
bSum += ys[i] - sum[i];
bCounter++;
}
}
if (bCounter == 0) {
// even unlikelier
bSum = 0.0d;
for (int i = 0; i < alphas.length; i++) {
bSum += ys[i] - sum[i];
bCounter++;
}
}
}
return new EvoSVMModel(exampleSet, supportVectors, kernel, bSum / bCounter);
}