public SVDModel(ExampleSet exampleSet, double[] singularValues, Matrix vMatrix) {
super(exampleSet);
this.vMatrix = vMatrix;
this.singularValues = singularValues;
this.keepAttributes = false;
this.attributeNames = new String[exampleSet.getAttributes().size()];
int counter = 0;
for (Attribute attribute : exampleSet.getAttributes()) {
attributeNames[counter] = attribute.getName();
counter++;
}
// compute cumulative values
cumulativeSingularValueProportion = new double[singularValues.length];
// insert cumulative sum of singular values
singularValuesSum = 0.0d;
for (int i = 0; i < singularValues.length; i++) {
singularValuesSum += singularValues[i];
cumulativeSingularValueProportion[i] = singularValuesSum;
}
// now reduce to proportion
for (int i = 0; i < singularValues.length; i++) {
cumulativeSingularValueProportion[i] /= singularValuesSum;
}
}
public PCAModel(ExampleSet eSet, double[] eigenvalues, double[][] eigenvectors) {
super(eSet);
this.keepAttributes = false;
this.attributeNames = new String[eSet.getAttributes().size()];
this.means = new double[eSet.getAttributes().size()];
int counter = 0;
eSet.recalculateAllAttributeStatistics(); // ensures that the statistics were created
for (Attribute attribute : eSet.getAttributes()) {
attributeNames[counter] = attribute.getName();
means[counter] = eSet.getStatistics(attribute, Statistics.AVERAGE);
counter++;
}
this.eigenVectors = new ArrayList<Eigenvector>(eigenvalues.length);
for (int i = 0; i < eigenvalues.length; i++) {
double[] currentEigenVector = new double[eSet.getAttributes().size()];
for (int j = 0; j < currentEigenVector.length; j++) {
currentEigenVector[j] = eigenvectors[j][i];
}
this.eigenVectors.add(new Eigenvector(currentEigenVector, eigenvalues[i]));
}
// order the eigenvectors by the eigenvalues
Collections.sort(this.eigenVectors);
calculateCumulativeVariance();
}
/**
* Creates attribute meta data that represents the attribute that will be generated for the
* provided arguments.
*
* @return the {@link AttributeMetaData} for the provided arguments
*/
public static AttributeMetaData generateAttributeMetaData(
ExampleSet exampleSet, String name, ExpressionType expressionType) {
AttributeMetaData newAttribute = null;
Attribute existingAtt = exampleSet.getAttributes().get(name);
int ontology = expressionType.getAttributeType();
if (ontology == Ontology.BINOMINAL) {
newAttribute = new AttributeMetaData(name, Ontology.BINOMINAL);
HashSet<String> values = new HashSet<>();
values.add("false");
values.add("true");
newAttribute.setValueSet(values, SetRelation.EQUAL);
} else {
newAttribute = new AttributeMetaData(name, ontology);
}
// restore role if attribute existed already
if (existingAtt != null) {
newAttribute.setRole(exampleSet.getAttributes().getRole(existingAtt).getSpecialName());
}
return newAttribute;
}
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;
}
@Override
public ExampleSet applyOnFiltered(ExampleSet exampleSet) throws OperatorException {
boolean round = getParameterAsBoolean(PARAMETER_ROUND);
List<Attribute> newAttributes = new LinkedList<Attribute>();
Iterator<Attribute> a = exampleSet.getAttributes().iterator();
while (a.hasNext()) {
Attribute attribute = a.next();
if ((Ontology.ATTRIBUTE_VALUE_TYPE.isA(attribute.getValueType(), Ontology.NUMERICAL))
&& (!Ontology.ATTRIBUTE_VALUE_TYPE.isA(attribute.getValueType(), Ontology.INTEGER))) {
Attribute newAttribute =
AttributeFactory.createAttribute(attribute.getName(), Ontology.INTEGER);
newAttributes.add(newAttribute);
exampleSet.getExampleTable().addAttribute(newAttribute);
for (Example example : exampleSet) {
double originalValue = example.getValue(attribute);
if (Double.isNaN(originalValue)) {
example.setValue(newAttribute, Double.NaN);
} else {
long newValue = round ? Math.round(originalValue) : (long) originalValue;
example.setValue(newAttribute, newValue);
}
}
a.remove();
}
}
for (Attribute attribute : newAttributes) exampleSet.getAttributes().addRegular(attribute);
return exampleSet;
}
/** Trains a model using an ExampleSet from the input. Uses the method learn(ExampleSet). */
@Override
public void doWork() throws OperatorException {
ExampleSet exampleSet = exampleSetInput.getData(ExampleSet.class);
// some checks
if (exampleSet.getAttributes().getLabel() == null) {
throw new UserError(this, 105, new Object[0]);
}
if (exampleSet.getAttributes().size() == 0) {
throw new UserError(this, 106, new Object[0]);
}
// check capabilities and produce errors if they are not fulfilled
CapabilityCheck check =
new CapabilityCheck(
this,
Tools.booleanValue(
ParameterService.getParameterValue(
CapabilityProvider.PROPERTY_RAPIDMINER_GENERAL_CAPABILITIES_WARN),
true));
check.checkLearnerCapabilities(this, exampleSet);
Model model = learn(exampleSet);
modelOutput.deliver(model);
exampleSetOutput.deliver(exampleSet);
}
@Override
public ExampleSet apply(ExampleSet exampleSet) throws OperatorException {
String firstName = getParameterAsString(PARAMETER_FIRST_ATTRIBUTE);
String secondName = getParameterAsString(PARAMETER_SECOND_ATTRIBUTE);
AttributeRole firstRole = exampleSet.getAttributes().getRole(firstName);
AttributeRole secondRole = exampleSet.getAttributes().getRole(secondName);
if (firstRole == null) {
throw new AttributeNotFoundError(this, PARAMETER_FIRST_ATTRIBUTE, firstName);
}
if (secondRole == null) {
throw new AttributeNotFoundError(this, PARAMETER_SECOND_ATTRIBUTE, secondName);
}
String firstRoleName = firstRole.getSpecialName();
String secondRoleName = secondRole.getSpecialName();
firstRole.changeToRegular();
secondRole.changeToRegular();
firstRole.setSpecial(secondRoleName);
secondRole.setSpecial(firstRoleName);
return exampleSet;
}
@Override
public Model learn(ExampleSet exampleSet) throws OperatorException {
Kernel kernel = getKernel();
kernel.init(exampleSet);
double initLearnRate = getParameterAsDouble(PARAMETER_LEARNING_RATE);
NominalMapping labelMapping = exampleSet.getAttributes().getLabel().getMapping();
String classNeg = labelMapping.getNegativeString();
String classPos = labelMapping.getPositiveString();
double classValueNeg = labelMapping.getNegativeIndex();
int numberOfAttributes = exampleSet.getAttributes().size();
HyperplaneModel model = new HyperplaneModel(exampleSet, classNeg, classPos, kernel);
model.init(new double[numberOfAttributes], 0);
for (int round = 0; round <= getParameterAsInt(PARAMETER_ROUNDS); round++) {
double learnRate = getLearnRate(round, getParameterAsInt(PARAMETER_ROUNDS), initLearnRate);
Attributes attributes = exampleSet.getAttributes();
for (Example example : exampleSet) {
double prediction = model.predict(example);
if (prediction != example.getLabel()) {
double direction = (example.getLabel() == classValueNeg) ? -1 : 1;
// adapting intercept
model.setIntercept(model.getIntercept() + learnRate * direction);
// adapting coefficients
double coefficients[] = model.getCoefficients();
int i = 0;
for (Attribute attribute : attributes) {
coefficients[i] += learnRate * direction * example.getValue(attribute);
i++;
}
}
}
}
return model;
}
private BasicNetwork getNetwork(ExampleSet exampleSet) throws OperatorException {
BasicNetwork network = new BasicNetwork();
// input layer
network.addLayer(new FeedforwardLayer(exampleSet.getAttributes().size()));
// hidden layers
log("No hidden layers defined. Using default hidden layers.");
int layerSize = getParameterAsInt(PARAMETER_DEFAULT_HIDDEN_LAYER_SIZE);
if (layerSize <= 0) layerSize = getDefaultLayerSize(exampleSet);
for (int p = 0; p < getParameterAsInt(PARAMETER_DEFAULT_NUMBER_OF_HIDDEN_LAYERS); p++) {
network.addLayer(new FeedforwardLayer(layerSize));
}
// output layer
if (exampleSet.getAttributes().getLabel().isNominal()) {
network.addLayer(new FeedforwardLayer(new ActivationSigmoid(), 1));
} else {
network.addLayer(new FeedforwardLayer(new ActivationLinear(), 1));
}
network.reset(
RandomGenerator.getRandomGenerator(
getParameterAsBoolean(RandomGenerator.PARAMETER_USE_LOCAL_RANDOM_SEED),
getParameterAsInt(RandomGenerator.PARAMETER_LOCAL_RANDOM_SEED)));
return network;
}
@Override
public ExampleSet apply(ExampleSet exampleSet) throws OperatorException {
String attributeName = getParameterAsString(PARAMETER_ATTRIBUTE_NAME);
Long offset = getParameterAsLong(PARMETER_TIME_OFFSET);
Attribute numericalAttribute = exampleSet.getAttributes().get(attributeName);
if (numericalAttribute == null) {
throw new UserError(this, 111, attributeName);
}
Attribute newAttribute = AttributeFactory.createAttribute(Ontology.DATE_TIME);
exampleSet.getExampleTable().addAttribute(newAttribute);
exampleSet.getAttributes().addRegular(newAttribute);
for (Example example : exampleSet) {
double value = example.getValue(numericalAttribute);
if (Double.isNaN(value)) {
example.setValue(newAttribute, value);
} else {
value += offset;
example.setValue(newAttribute, value);
}
}
if (!getParameterAsBoolean(PARAMETER_KEEP_OLD_ATTRIBUTE)) {
AttributeRole oldRole = exampleSet.getAttributes().getRole(numericalAttribute);
exampleSet.getAttributes().remove(numericalAttribute);
newAttribute.setName(attributeName);
exampleSet.getAttributes().setSpecialAttribute(newAttribute, oldRole.getSpecialName());
} else {
newAttribute.setName(attributeName + "_AS_DATE");
}
return exampleSet;
}
/**
* 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++;
}
}
private List<AggregationFunction> createAggreationFunctions(ExampleSet exampleSet)
throws OperatorException {
// load global switches
boolean ignoreMissings = getParameterAsBoolean(PARAMETER_IGNORE_MISSINGS);
boolean countOnlyDistinct = getParameterAsBoolean(PARAMETER_ONLY_DISTINCT);
// creating data structures for building aggregates
List<AggregationFunction> aggregationFunctions = new LinkedList<AggregationFunction>();
// building functions for all explicitly defined aggregation attributes
Set<Attribute> explicitlyAggregatedAttributes = new HashSet<Attribute>();
List<String[]> aggregationFunctionPairs = getParameterList(PARAMETER_AGGREGATION_ATTRIBUTES);
for (String[] aggregationFunctionPair : aggregationFunctionPairs) {
Attribute attribute = exampleSet.getAttributes().get(aggregationFunctionPair[0]);
if (attribute == null) {
throw new UserError(
this, "aggregation.aggregation_attribute_not_present", aggregationFunctionPair[0]);
}
AggregationFunction function =
AggregationFunction.createAggregationFunction(
aggregationFunctionPair[1], attribute, ignoreMissings, countOnlyDistinct);
if (!function.isCompatible()) {
throw new UserError(
this,
"aggregation.incompatible_attribute_type",
attribute.getName(),
aggregationFunctionPair[1]);
}
// adding objects for this attribute to structure
explicitlyAggregatedAttributes.add(attribute);
aggregationFunctions.add(function);
}
// building the default aggregations
if (getParameterAsBoolean(PARAMETER_USE_DEFAULT_AGGREGATION)) {
String defaultAggregationFunctionName =
getParameterAsString(PARAMETER_DEFAULT_AGGREGATION_FUNCTION);
Iterator<Attribute> iterator =
attributeSelector.getAttributeSubset(exampleSet, false).iterator();
if (getCompatibilityLevel().isAtMost(VERSION_5_2_8)) {
iterator = exampleSet.getAttributes().iterator();
}
while (iterator.hasNext()) {
Attribute attribute = iterator.next();
if (!explicitlyAggregatedAttributes.contains(attribute)) {
AggregationFunction function =
AggregationFunction.createAggregationFunction(
defaultAggregationFunctionName, attribute, ignoreMissings, countOnlyDistinct);
if (function.isCompatible()) {
aggregationFunctions.add(function);
}
}
}
}
return aggregationFunctions;
}
/*
* Extracts an example set containing just the two specified
* attributes and no missing values.
*
* @param eSet the source example set
* @param a the first attribute to extract
* @param b the second attribute to extract
* @return the reduced example set
*/
private static ExampleSet extract(ExampleSet eSet, Attribute a, Attribute b) {
// create a new example set containing just attributes a and b
ExampleSet e = (ExampleSet) eSet.clone();
e.getAttributes().clearRegular();
e.getAttributes().clearSpecial();
e.getAttributes().addRegular(a);
e.getAttributes().addRegular(b);
return new ConditionedExampleSet(e, new NoMissingAttributesCondition(e, null));
}
/**
* Helper method replacing <code>Model.createPredictedLabel(ExampleSet)</code> in order to lower
* memory consumption.
*/
private static void createOrReplacePredictedLabelFor(ExampleSet exampleSet, Model model) {
Attribute predictedLabel = exampleSet.getAttributes().getPredictedLabel();
if (predictedLabel != null) { // remove old predicted label
exampleSet.getAttributes().remove(predictedLabel);
exampleSet.getExampleTable().removeAttribute(predictedLabel);
}
// model.createPredictedLabel(exampleSet); // not longer necessary since
// label creation is done by model.apply(...).
}
@Override
public ExampleSet apply(ExampleSet exampleSet) throws OperatorException {
// recall: difference = minuend - subtrahend
// but the subtrahend is last on the ioobjects stack, so pop first
ExampleSet subtrahendSet = subtrahendInput.getData(ExampleSet.class);
ExampleSet minuendSet = exampleSet;
subtrahendSet.remapIds();
minuendSet.remapIds();
Attribute minuendId = minuendSet.getAttributes().getId();
Attribute subtrahendId = subtrahendSet.getAttributes().getId();
// sanity checks
if ((minuendId == null) || (subtrahendId == null)) {
throw new UserError(this, 129);
}
if (minuendId.getValueType() != subtrahendId.getValueType()) {
throw new UserError(
this,
120,
new Object[] {
subtrahendId.getName(),
Ontology.VALUE_TYPE_NAMES[subtrahendId.getValueType()],
Ontology.VALUE_TYPE_NAMES[minuendId.getValueType()]
});
}
List<Integer> indices = new LinkedList<>();
{
int i = 0;
for (Example example : minuendSet) {
double id = example.getValue(minuendId);
Example subtrahendExample = null;
if (minuendId.isNominal()) {
subtrahendExample =
subtrahendSet.getExampleFromId(
subtrahendId.getMapping().getIndex(minuendId.getMapping().mapIndex((int) id)));
} else {
subtrahendExample = subtrahendSet.getExampleFromId(id);
}
if (subtrahendExample == null) {
indices.add(i);
}
i++;
}
}
int[] indexArray = new int[indices.size()];
for (int i = 0; i < indices.size(); i++) {
indexArray[i] = indices.get(i);
}
ExampleSet minusSet = new MappedExampleSet(minuendSet, indexArray);
return minusSet;
}
@Override
public void doWork() throws OperatorException {
ExampleSet exampleSet = exampleSetInput.getData();
IEntityMapping user_mapping = new EntityMapping();
IEntityMapping item_mapping = new EntityMapping();
IRatings training_data = new Ratings();
if (exampleSet.getAttributes().getSpecial("user identification") == null) {
throw new UserError(this, 105);
}
if (exampleSet.getAttributes().getSpecial("item identification") == null) {
throw new UserError(this, 105);
}
if (exampleSet.getAttributes().getLabel() == null) {
throw new UserError(this, 105);
}
Attributes Att = exampleSet.getAttributes();
AttributeRole ur = Att.getRole("user identification");
Attribute u = ur.getAttribute();
AttributeRole ir = Att.getRole("item identification");
Attribute i = ir.getAttribute();
Attribute ui = Att.getLabel();
for (Example example : exampleSet) {
double j = example.getValue(u);
int uid = user_mapping.ToInternalID((int) j);
j = example.getValue(i);
int iid = item_mapping.ToInternalID((int) j);
double r = example.getValue(ui);
training_data.Add(uid, iid, r);
}
_slopeOne recommendAlg = new _slopeOne();
recommendAlg.user_mapping = user_mapping;
recommendAlg.item_mapping = item_mapping;
recommendAlg.SetMinRating(getParameterAsInt("Min Rating"));
recommendAlg.SetMaxRating(recommendAlg.GetMinRating() + getParameterAsInt("Range"));
recommendAlg.SetRatings(training_data);
recommendAlg.Train();
exampleSetOutput.deliver(exampleSet);
exampleSetOutput1.deliver(recommendAlg);
}
// checking for example set and valid attributes
@Override
public void init(ExampleSet exampleSet) throws OperatorException {
super.init(exampleSet);
Tools.onlyNominalAttributes(exampleSet, "nominal similarities");
this.useAttribute = new boolean[exampleSet.getAttributes().size()];
int i = 0;
for (Attribute attribute : exampleSet.getAttributes()) {
if (attribute.isNominal()) {
useAttribute[i] = true;
}
i++;
}
}
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);
}
}
@Override
public void doWork() throws OperatorException {
ExampleSet exampleSet = exampleSetInput.getData(ExampleSet.class);
// only use numeric attributes
Tools.onlyNumericalAttributes(exampleSet, "KernelPCA");
Tools.onlyNonMissingValues(exampleSet, getOperatorClassName(), this);
Attributes attributes = exampleSet.getAttributes();
int numberOfExamples = exampleSet.size();
// calculating means for later zero centering
exampleSet.recalculateAllAttributeStatistics();
double[] means = new double[exampleSet.getAttributes().size()];
int i = 0;
for (Attribute attribute : exampleSet.getAttributes()) {
means[i] = exampleSet.getStatistics(attribute, Statistics.AVERAGE);
i++;
}
// kernel
Kernel kernel = Kernel.createKernel(this);
// copying zero centered exampleValues
ArrayList<double[]> exampleValues = new ArrayList<double[]>(numberOfExamples);
i = 0;
for (Example columnExample : exampleSet) {
double[] columnValues = getAttributeValues(columnExample, attributes, means);
exampleValues.add(columnValues);
i++;
}
// filling kernel matrix
Matrix kernelMatrix = new Matrix(numberOfExamples, numberOfExamples);
for (i = 0; i < numberOfExamples; i++) {
for (int j = 0; j < numberOfExamples; j++) {
kernelMatrix.set(
i, j, kernel.calculateDistance(exampleValues.get(i), exampleValues.get(j)));
}
}
// calculating eigenVectors
EigenvalueDecomposition eig = kernelMatrix.eig();
Model model = new KernelPCAModel(exampleSet, means, eig.getV(), exampleValues, kernel);
if (exampleSetOutput.isConnected()) {
exampleSetOutput.deliver(model.apply(exampleSet));
}
originalOutput.deliver(exampleSet);
modelOutput.deliver(model);
}
private NeuralDataSet getTraining(ExampleSet exampleSet) {
double[][] data = new double[exampleSet.size()][exampleSet.getAttributes().size()];
double[][] labels = new double[exampleSet.size()][1];
int index = 0;
Attribute label = exampleSet.getAttributes().getLabel();
this.attributeMin = new double[exampleSet.getAttributes().size()];
this.attributeMax = new double[attributeMin.length];
exampleSet.recalculateAllAttributeStatistics();
int a = 0;
for (Attribute attribute : exampleSet.getAttributes()) {
this.attributeMin[a] = exampleSet.getStatistics(attribute, Statistics.MINIMUM);
this.attributeMax[a] = exampleSet.getStatistics(attribute, Statistics.MAXIMUM);
a++;
}
this.labelMin = exampleSet.getStatistics(label, Statistics.MINIMUM);
this.labelMax = exampleSet.getStatistics(label, Statistics.MAXIMUM);
for (Example example : exampleSet) {
// attributes
a = 0;
for (Attribute attribute : exampleSet.getAttributes()) {
if (attributeMin[a] != attributeMax[a]) {
data[index][a] =
(example.getValue(attribute) - attributeMin[a]) / (attributeMax[a] - attributeMin[a]);
} else {
data[index][a] = example.getValue(attribute) - attributeMin[a];
}
a++;
}
// label
if (label.isNominal()) {
labels[index][0] = example.getValue(label);
} else {
if (labelMax != labelMin) {
labels[index][0] = (example.getValue(label) - labelMin) / (labelMax - labelMin);
} else {
labels[index][0] = example.getValue(label) - labelMin;
}
}
index++;
}
return new BasicNeuralDataSet(data, labels);
}
@Override
public ClusterModel generateClusterModel(ExampleSet exampleSet) throws OperatorException {
// checking and creating ids if necessary
Tools.checkAndCreateIds(exampleSet);
// generating assignment
RandomGenerator random = RandomGenerator.getRandomGenerator(this);
int clusterAssignments[] = new int[exampleSet.size()];
int k = getParameterAsInt(PARAMETER_NUMBER_OF_CLUSTERS);
for (int i = 0; i < exampleSet.size(); i++) {
clusterAssignments[i] = random.nextInt(k);
}
ClusterModel model =
new ClusterModel(
exampleSet,
k,
getParameterAsBoolean(RMAbstractClusterer.PARAMETER_ADD_AS_LABEL),
getParameterAsBoolean(RMAbstractClusterer.PARAMETER_REMOVE_UNLABELED));
model.setClusterAssignments(clusterAssignments, exampleSet);
// generating cluster attribute
if (addsClusterAttribute()) {
Attribute cluster = AttributeFactory.createAttribute("cluster", Ontology.NOMINAL);
exampleSet.getExampleTable().addAttribute(cluster);
exampleSet.getAttributes().setCluster(cluster);
int i = 0;
for (Example example : exampleSet) {
example.setValue(cluster, "cluster_" + clusterAssignments[i]);
i++;
}
}
return model;
}
/** Creates the partition builder for the given sampling type. */
private static PartitionBuilder createPartitionBuilder(
ExampleSet exampleSet, int samplingType, int seed) {
PartitionBuilder builder = null;
switch (samplingType) {
case LINEAR_SAMPLING:
builder = new SimplePartitionBuilder();
break;
case SHUFFLED_SAMPLING:
builder = new ShuffledPartitionBuilder(true, seed);
break;
case STRATIFIED_SAMPLING:
default:
Attribute label = exampleSet.getAttributes().getLabel();
if ((label != null) && (label.isNominal()))
builder = new StratifiedPartitionBuilder(exampleSet, true, seed);
else {
exampleSet
.getLog()
.logNote(
"Example set has no nominal label: using shuffled partition instead of stratified partition!");
builder = new ShuffledPartitionBuilder(true, seed);
}
break;
}
return builder;
}
@Override
public PreprocessingModel createPreprocessingModel(ExampleSet exampleSet)
throws OperatorException {
boolean sortMappings = getParameterAsBoolean(PARAMETER_SORT_MAPPING_ALPHABETICALLY);
Map<String, MappingTranslation> translations = new HashMap<String, MappingTranslation>();
exampleSet.recalculateAllAttributeStatistics();
for (Attribute attribute : exampleSet.getAttributes()) {
MappingTranslation translation =
new MappingTranslation((NominalMapping) attribute.getMapping().clone());
if (attribute.isNominal()) {
for (String value : attribute.getMapping().getValues()) {
double count = exampleSet.getStatistics(attribute, Statistics.COUNT, value);
if (count > 0) {
translation.newMapping.mapString(value);
}
}
if (translation.newMapping.size() < attribute.getMapping().size()) {
if (sortMappings) {
translation.newMapping.sortMappings();
}
translations.put(attribute.getName(), translation);
}
}
}
return new RemoveUnusedNominalValuesModel(exampleSet, translations);
}
@Override
public AttributeWeights calculateWeights(ExampleSet exampleSet) throws OperatorException {
Attributes attributes = exampleSet.getAttributes();
Attribute labelAttribute = attributes.getLabel();
boolean useSquaredCorrelation = getParameterAsBoolean(PARAMETER_SQUARED_CORRELATION);
AttributeWeights weights = new AttributeWeights(exampleSet);
getProgress().setTotal(attributes.size());
int progressCounter = 0;
int exampleSetSize = exampleSet.size();
int exampleCounter = 0;
for (Attribute attribute : attributes) {
double correlation =
MathFunctions.correlation(exampleSet, labelAttribute, attribute, useSquaredCorrelation);
weights.setWeight(attribute.getName(), Math.abs(correlation));
progressCounter++;
exampleCounter += exampleSetSize;
if (exampleCounter > PROGRESS_UPDATE_STEPS) {
exampleCounter = 0;
getProgress().setCompleted(progressCounter);
}
}
return weights;
}
@Override
public void doWork() throws OperatorException {
CentroidClusterModel model = modelInput.getData(CentroidClusterModel.class);
Attributes trainAttributes = model.getTrainingHeader().getAttributes();
String[] attributeNames = model.getAttributeNames();
Attribute[] attributes = new Attribute[attributeNames.length + 1];
for (int i = 0; i < attributeNames.length; i++) {
Attribute originalAttribute = trainAttributes.get(attributeNames[i]);
attributes[i] =
AttributeFactory.createAttribute(attributeNames[i], originalAttribute.getValueType());
if (originalAttribute.isNominal()) {
attributes[i].setMapping((NominalMapping) originalAttribute.getMapping().clone());
}
}
Attribute clusterAttribute = AttributeFactory.createAttribute("cluster", Ontology.NOMINAL);
attributes[attributes.length - 1] = clusterAttribute;
MemoryExampleTable table = new MemoryExampleTable(attributes);
for (int i = 0; i < model.getNumberOfClusters(); i++) {
double[] data = new double[attributeNames.length + 1];
System.arraycopy(model.getCentroidCoordinates(i), 0, data, 0, attributeNames.length);
data[attributeNames.length] = clusterAttribute.getMapping().mapString("cluster_" + i);
table.addDataRow(new DoubleArrayDataRow(data));
}
ExampleSet resultSet = table.createExampleSet();
resultSet.getAttributes().setSpecialAttribute(clusterAttribute, Attributes.CLUSTER_NAME);
modelOutput.deliver(model);
exampleSetOutput.deliver(resultSet);
}
public SOMModelPlotter(PlotterConfigurationModel settings, ExampleSet exampleSet, Model model) {
super(settings);
this.model = model;
this.exampleSet = exampleSet;
this.colorizer =
new SOMClassColorizer(exampleSet.getAttributes().getLabel().getMapping().size());
}
@Override
public ExampleSet read() throws OperatorException {
FileInputStream inStream = null;
try {
inStream = new FileInputStream(getParameterAsFile(PARAMETER_FASTA_FILE_NAME));
} catch (FileNotFoundException e) {
// TODO: "Fill"
}
FastaReader<DNASequence, NucleotideCompound> fastaReader =
new FastaReader<DNASequence, NucleotideCompound>(
inStream,
new GenericFastaHeaderParser<DNASequence, NucleotideCompound>(),
new DNASequenceCreator(DNACompoundSet.getDNACompoundSet()));
LinkedHashMap<String, DNASequence> b = null;
try {
b = fastaReader.process();
} catch (Exception e) {
// TODO: "Fill"
}
String data[][] = new String[0][];
if (b != null) {
data = new String[b.size()][2];
int i = 0;
for (Map.Entry<String, DNASequence> entry : b.entrySet()) {
data[i][0] = entry.getValue().getOriginalHeader();
data[i][1] = entry.getValue().getSequenceAsString();
i++;
}
}
ExampleSet outSet = ExampleSetFactory.createExampleSet(data);
outSet.getAttributes().get("att1").setName("DNA name");
outSet.getAttributes().get("att2").setName("Chain");
return outSet;
}
/** 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);
}
@Override
public void doWork() throws OperatorException {
ExampleSet exampleSet = exampleSetInput.getData();
IPosOnlyFeedback training_data = new PosOnlyFeedback();
IEntityMapping user_mapping = new EntityMapping();
IEntityMapping item_mapping = new EntityMapping();
if (exampleSet.getAttributes().getSpecial("user identification") == null) {
throw new UserError(this, 105);
}
if (exampleSet.getAttributes().getSpecial("item identification") == null) {
throw new UserError(this, 105);
}
Attributes Att = exampleSet.getAttributes();
AttributeRole ur = Att.getRole("user identification");
Attribute u = ur.getAttribute();
AttributeRole ir = Att.getRole("item identification");
Attribute i = ir.getAttribute();
for (Example example : exampleSet) {
double j = example.getValue(u);
int uid = (int) j;
j = example.getValue(i);
int iid = (int) j;
training_data.Add(user_mapping.ToInternalID(uid), item_mapping.ToInternalID(iid));
checkForStop();
}
System.out.println(training_data.GetMaxItemID() + " " + training_data.GetMaxUserID());
Random recommendAlg = new Random();
recommendAlg.SetFeedback(training_data);
recommendAlg.user_mapping = user_mapping;
recommendAlg.item_mapping = item_mapping;
recommendAlg.Train();
exampleSetOutput.deliver(exampleSet);
exampleSetOutput1.deliver(recommendAlg);
}
/**
* 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;
}
