/**
* Process the file and cluster.
*
* @param outputFile The output file.
* @param clusters The number of clusters.
* @param theAnalyst The analyst to use.
* @param iterations The number of iterations to use.
*/
public void process(
final File outputFile,
final int clusters,
final EncogAnalyst theAnalyst,
final int iterations) {
final PrintWriter tw =
this.prepareOutputFile(
outputFile, analyst.getScript().getNormalize().countActiveFields() - 1, 1);
resetStatus();
final KMeansClustering cluster = new KMeansClustering(clusters, this.data);
cluster.iteration(iterations);
int clusterNum = 0;
for (final MLCluster cl : cluster.getClusters()) {
for (final MLData item : cl.getData()) {
final int clsIndex = item.size();
final LoadedRow lr = new LoadedRow(this.getFormat(), item.getData(), 1);
lr.getData()[clsIndex] = "" + clusterNum;
writeRow(tw, lr);
}
clusterNum++;
}
reportDone(false);
tw.close();
}
/** Utility method to switch from MLData to List<Double> */
public static List<Double> doubleListFromNeuralOutput(MLData neuralOutput) {
List<Double> result = new ArrayList<Double>(neuralOutput.size());
for (double value : neuralOutput.getData()) {
result.add(value);
}
return result;
}
@Override
protected void putPrediction(MLData output, Map<StateParameter, Double> nextState) {
int i = 0;
for (StateParameter stateParameter : StateParameter.values())
if (stateParameter != width && stateParameter != height)
nextState.put(stateParameter, output.getData(i++));
}
/**
* Format neural data as a list of numbers.
*
* @param data The neural data to format.
* @return The formatted neural data.
*/
public static String formatNeuralData(final MLData data) {
final StringBuilder result = new StringBuilder();
for (int i = 0; i < data.size(); i++) {
if (i != 0) {
result.append(',');
}
result.append(Format.formatDouble(data.getData(i), 4));
}
return result.toString();
}
/**
* Calculate the Euclidean distance for the specified output neuron and the input vector. This is
* the square root of the squares of the differences between the weight and input vectors.
*
* @param matrix The matrix to get the weights from.
* @param input The input vector.
* @param outputNeuron The neuron we are calculating the distance for.
* @return The Euclidean distance.
*/
public double calculateEuclideanDistance(
final Matrix matrix, final MLData input, final int outputNeuron) {
double result = 0;
// Loop over all input data.
for (int i = 0; i < input.size(); i++) {
final double diff = input.getData(i) - matrix.get(outputNeuron, i);
result += diff * diff;
}
return BoundMath.sqrt(result);
}
/**
* Determine the classes for the specified input.
*
* @param input The input.
* @return An array of class indexes.
*/
public int[] determineClasses(MLData input) {
int[] result = new int[input.size()];
for (int i = 0; i < input.size(); i++) {
BayesianEvent event = this.events.get(i);
int classIndex = event.matchChoiceToRange(input.getData(i));
result[i] = classIndex;
}
return result;
}
public static double calculateRegressionError(MLRegression method, MLDataSet data) {
final ErrorCalculation errorCalculation = new ErrorCalculation();
if (method instanceof MLContext) ((MLContext) method).clearContext();
for (final MLDataPair pair : data) {
final MLData actual = method.compute(pair.getInput());
errorCalculation.updateError(
actual.getData(), pair.getIdeal().getData(), pair.getSignificance());
}
return errorCalculation.calculate();
}
public double[] converteEntradaEmTabuleiro(MLData entrada, boolean mantemNormalizacao) {
double[] entradas = entrada.getData();
double[] tabuleiro = new double[9];
for (int i = 0; i < 9; i++) {
if (entradas[i] > 0) tabuleiro[i] = mantemNormalizacao ? entradas[i] : Caractere.X.getValor();
else if (entradas[i + 9] < 0)
tabuleiro[i] = mantemNormalizacao ? entradas[i + 9] : Caractere.O.getValor();
}
return tabuleiro;
}
@Override
public MLData compute(MLData input) {
if (input.size() != this.inputCount) {
throw new EncogError("Invalid input size, must be " + inputCount);
}
double[] sum = new double[1];
sum[0] += this.weights[0];
for (int i = 0; i < input.size(); i++) {
sum[0] += this.weights[i + 1] * Math.pow(input.getData(i), i + 1);
}
return new BasicMLData(sum);
}
public double computeProbability(MLData input) {
// copy the input to evidence
int inputIndex = 0;
for (int i = 0; i < this.events.size(); i++) {
BayesianEvent event = this.events.get(i);
EventState state = this.query.getEventState(event);
if (state.getEventType() == EventType.Evidence) {
state.setValue((int) input.getData(inputIndex++));
}
}
// execute the query
this.query.execute();
return this.query.getProbability();
}
/** {@inheritDoc} */
@Override
public String denormalizeColumn(ColumnDefinition colDef, MLData data, int dataColumn) {
double value = data.getData(dataColumn);
final double result =
((colDef.getLow() - colDef.getHigh()) * value
- this.normalizedHigh * colDef.getLow()
+ colDef.getHigh() * this.normalizedLow)
/ (this.normalizedLow - this.normalizedHigh);
// typically caused by a number that should not have been normalized
// (i.e. normalization or actual range is infinitely small.
if (Double.isNaN(result)) {
return "" + (((this.normalizedHigh - this.normalizedLow) / 2) + this.normalizedLow);
}
return "" + result;
}
/**
* The main method.
*
* @param args No arguments are used.
*/
public static void main(final String args[]) {
// create a neural network, without using a factory
BasicNetwork network = new BasicNetwork();
network.addLayer(new BasicLayer(null, true, 2));
network.addLayer(new BasicLayer(new ActivationSigmoid(), true, 3));
network.addLayer(new BasicLayer(new ActivationSigmoid(), false, 1));
network.getStructure().finalizeStructure();
network.reset();
// create training data
MLDataSet trainingSet = new BasicMLDataSet(XOR_INPUT, XOR_IDEAL);
// train the neural network
final StochasticGradientDescent train = new StochasticGradientDescent(network, trainingSet);
train.setUpdateRule(new RMSPropUpdate());
int epoch = 1;
do {
train.iteration();
System.out.println("Epoch #" + epoch + " Error:" + train.getError());
epoch++;
} while (train.getError() > 0.01);
train.finishTraining();
// test the neural network
System.out.println("Neural Network Results:");
for (MLDataPair pair : trainingSet) {
final MLData output = network.compute(pair.getInput());
System.out.println(
pair.getInput().getData(0)
+ ","
+ pair.getInput().getData(1)
+ ", actual="
+ output.getData(0)
+ ",ideal="
+ pair.getIdeal().getData(0));
}
PerturbationFeatureImportanceCalc d;
Encog.getInstance().shutdown();
}
/** {@inheritDoc} */
@Override
public final void iteration() {
if (this.mustInit) {
initWeights();
}
double worstDistance = Double.NEGATIVE_INFINITY;
for (final MLDataPair pair : this.training) {
final MLData out = this.network.computeInstar(pair.getInput());
// determine winner
final int winner = EngineArray.indexOfLargest(out.getData());
// calculate the distance
double distance = 0;
for (int i = 0; i < pair.getInput().size(); i++) {
final double diff =
pair.getInput().getData(i) - this.network.getWeightsInputToInstar().get(i, winner);
distance += diff * diff;
}
distance = BoundMath.sqrt(distance);
if (distance > worstDistance) {
worstDistance = distance;
}
// train
for (int j = 0; j < this.network.getInputCount(); j++) {
final double delta =
this.learningRate
* (pair.getInput().getData(j)
- this.network.getWeightsInputToInstar().get(j, winner));
this.network.getWeightsInputToInstar().add(j, winner, delta);
}
}
setError(worstDistance);
}
public MLMethod decode(final NEATPopulation pop, final Substrate substrate, final Genome genome) {
// obtain the CPPN
final NEATCODEC neatCodec = new NEATCODEC();
final NEATNetwork cppn = (NEATNetwork) neatCodec.decode(genome);
final List<NEATLink> linkList = new ArrayList<NEATLink>();
final ActivationFunction[] afs = new ActivationFunction[substrate.getNodeCount()];
final ActivationFunction af = new ActivationSteepenedSigmoid();
// all activation functions are the same
for (int i = 0; i < afs.length; i++) {
afs[i] = af;
}
final double c = this.maxWeight / (1.0 - this.minWeight);
final MLData input = new BasicMLData(cppn.getInputCount());
// First create all of the non-bias links.
for (final SubstrateLink link : substrate.getLinks()) {
final SubstrateNode source = link.getSource();
final SubstrateNode target = link.getTarget();
int index = 0;
for (final double d : source.getLocation()) {
input.setData(index++, d);
}
for (final double d : target.getLocation()) {
input.setData(index++, d);
}
final MLData output = cppn.compute(input);
double weight = output.getData(0);
if (Math.abs(weight) > this.minWeight) {
weight = (Math.abs(weight) - this.minWeight) * c * Math.signum(weight);
linkList.add(new NEATLink(source.getId(), target.getId(), weight));
}
}
// now create biased links
input.clear();
final int d = substrate.getDimensions();
final List<SubstrateNode> biasedNodes = substrate.getBiasedNodes();
for (final SubstrateNode target : biasedNodes) {
for (int i = 0; i < d; i++) {
input.setData(d + i, target.getLocation()[i]);
}
final MLData output = cppn.compute(input);
double biasWeight = output.getData(1);
if (Math.abs(biasWeight) > this.minWeight) {
biasWeight = (Math.abs(biasWeight) - this.minWeight) * c * Math.signum(biasWeight);
linkList.add(new NEATLink(0, target.getId(), biasWeight));
}
}
// check for invalid neural network
if (linkList.size() == 0) {
return null;
}
Collections.sort(linkList);
final NEATNetwork network =
new NEATNetwork(substrate.getInputCount(), substrate.getOutputCount(), linkList, afs);
network.setActivationCycles(substrate.getActivationCycles());
return network;
}
public int winner(MLData output) {
return EngineArray.maxIndex(output.getData());
}
/** {@inheritDoc} */
@Override
public MLData compute(final MLData input) {
final MLData output = new BasicMLData(getOutputCount());
this.flat.compute(input.getData(), output.getData());
return output;
}