public int predictState(int from_state, int number_of_steps) {
long lStartTime = System.currentTimeMillis();
int from_bin = getBinNumber((float) from_state);
SimpleMatrix result = new SimpleMatrix(transition_matrix);
for (int i = 1; i < number_of_steps; i++) result = result.mult(transition_matrix);
SimpleMatrix row_result = result.extractVector(true, from_bin);
// row_result.print();
double maxVal = row_result.get(0, 0);
int maxValIndex = 0;
for (int i = 1; i < row_result.numCols(); i++) {
if (row_result.get(0, i) >= maxVal) {
maxVal = row_result.get(0, i);
maxValIndex = i;
}
}
long lEndTime = System.currentTimeMillis();
logger.info(
("From: "
+ from_state
+ " In NumberOfSteps: "
+ number_of_steps
+ " MaxProbabilityBin: "
+ maxValIndex
+ " MostProbablyTo: "
+ getOrgValFromBinNumber(maxValIndex)));
logger.info(("Time taken for prediction = " + (lEndTime - lStartTime)));
return getOrgValFromBinNumber(maxValIndex);
}
// ecuatia Rosenbrock
// x(i) is coded with 8 bits
public double fitness(SimpleMatrix cromosom) {
int value = 0;
int n = cromosom.numRows();
double x1, x2;
for (int i = 0; i < n - 1; i++) {
x1 = cromosom.get(i);
x2 = cromosom.get(i + 1);
value += (100 * Math.pow(x2 - Math.pow(x1, 2), 2) + Math.pow(x1 - 1, 2));
}
return value;
}
public static List<Cluster> ReassignCentrids(
List<Cluster> kCentroids,
SimpleMatrix distanceMatrix,
SimpleMatrix dataSet,
int[] featureSet) {
List<Cluster> kCentroids_l = kCentroids;
int[] clusterLoc = new int[dataSet.numRows()];
for (int iRows = 0; iRows < dataSet.numRows(); iRows++) {
int clusterNo = 1;
double minvalue = distanceMatrix.get(iRows, 1);
for (int iCentroid = 0; iCentroid < kCentroids_l.size(); iCentroid++) {
// System.out.println(iRows+" "+iCentroid);
if (distanceMatrix.get(iRows, iCentroid) < minvalue) {
clusterNo = iCentroid;
minvalue = distanceMatrix.get(iRows, iCentroid);
}
}
clusterLoc[iRows] = clusterNo;
}
// Backup Centroids anc clear current centroids
for (int i = 0; i < kCentroids_l.size(); i++) {
kCentroids_l.get(i).backup();
kCentroids_l.get(i).noPoints = 0;
Arrays.fill(kCentroids_l.get(i).currPoints, -1);
Arrays.fill(kCentroids_l.get(i).intIndex, -1);
// System.out.println("Clusters Backed Up!");
}
// printKCentroids(kCentroids_l);
for (int i = 0; i < clusterLoc.length; i++) {
int insLoc = kCentroids_l.get(clusterLoc[i]).noPoints;
// System.out.println("Getting element"+dataSet.get(i, 0));
kCentroids_l.get(clusterLoc[i]).currPoints[insLoc] = (int) dataSet.get(i, 0);
kCentroids_l.get(clusterLoc[i]).intIndex[insLoc] = i;
kCentroids_l.get(clusterLoc[i]).noPoints++;
}
// System.out.println(Arrays.toString(clusterLoc));
// Now Calculate the best representative and give as new centroid values
for (int i = 0; i < kCentroids.size(); i++) {
for (int j = 0; j < featureSet.length; j++) {
double tempAvg = 0;
int[] travVector = kCentroids_l.get(i).intIndex;
for (int k = 0; k < travVector.length; k++) {
if (travVector[k] != -1) {
tempAvg = tempAvg + dataSet.get(travVector[k], featureSet[j]);
}
}
kCentroids.get(i).clusterCenter.set(0, featureSet[j], tempAvg / kCentroids.get(i).noPoints);
}
}
return kCentroids_l;
}
@Override
public double[][] predict(List<PredictionPaper> testDocs) {
String testData = "lda/test.dat";
createLdaInputTest(testData, testDocs);
Utils.runCommand(
"lib/lda-c-dist/lda inf "
+ " lib/lda-c-dist/settings.txt "
+ "lda/final "
+ testData
+ " lda/output",
false);
double[][] gammasMatrix = Utils.readMatrix("lda/output-gamma.dat", false);
double alpha = Utils.readAlpha("lda/final.other");
for (int i = 0; i < gammasMatrix.length; i++) {
for (int j = 0; j < gammasMatrix[i].length; j++) {
gammasMatrix[i][j] -= alpha;
}
}
SimpleMatrix gammas = new SimpleMatrix(gammasMatrix);
SimpleMatrix beta = new SimpleMatrix(betaMatrix);
SimpleMatrix probabilities = gammas.mult(beta);
double[][] result = new double[probabilities.numRows()][probabilities.numCols()];
for (int row = 0; row < probabilities.numRows(); row++) {
for (int col = 0; col < probabilities.numCols(); col++) {
result[row][col] = probabilities.get(row, col);
}
}
return result;
}
// ecuatia sferei
// sum from i=1 to m of x(i)^2
// x(i) is coded with 8 bits
public double fitness(SimpleMatrix cromosom) {
int value = 0;
int n = cromosom.numCols();
for (int i = 0; i < n; i++) {
value += Math.pow(cromosom.get(i), 2);
}
return value;
}
public void trainMarkovChainModel(double[] input) {
int input_size = input.length;
int from_state, to_state;
Integer[] count = new Integer[num_of_states];
for (int i = 0; i < num_of_states; i++) count[i] = 0;
// Loop through the input and record the number of transitions
for (int i = 0; i < input_size - 2; i++) {
from_state = getBinNumber(input[i]);
to_state = getBinNumber(input[i + 1]);
// Increment entry by 1
// transition_matrix[from_state][to_state]++;
transition_matrix.set(from_state, to_state, transition_matrix.get(from_state, to_state) + 1);
count[from_state]++;
// COMMENT THIS
logger.info(
"FromVal:"
+ input[i]
+ " FromBin: "
+ from_state
+ " ToVal:"
+ input[i + 1]
+ " ToBin: "
+ to_state
+ " TransitionCount: "
+ transition_matrix.get(from_state, to_state)
+ " TotalCount: "
+ count[from_state]);
}
// Calculate the transition probability matrix
for (int i = 0; i < num_of_states; i++) {
for (int j = 0; j < num_of_states; j++) {
if (count[i] == 0) {
// transition_matrix[i][j]
transition_matrix.set(i, j, 0);
} else {
// transition_matrix[i][j]/=count[i];
transition_matrix.set(i, j, transition_matrix.get(i, j) / count[i]);
}
}
}
}
// ecuatia Rastrigin
// x(i) is coded with 8 bits
public double fitness(SimpleMatrix cromosom) {
int value = 0;
int n = cromosom.numCols();
double x1;
for (int i = 0; i < n; i++) {
x1 = cromosom.get(i);
value += (x1 * x1 - 10 * Math.cos(Math.PI * x1) + 10);
}
return value;
}
// ecuatia Griewank
// x(i) is coded with 8 bits
public double fitness(SimpleMatrix cromosom) {
int sum = 0, product = 1;
int n = cromosom.numCols();
double x1;
for (int i = 0; i < n; i++) {
x1 = cromosom.get(i);
sum += x1 * x1;
product *= Math.cos(x1 / Math.sqrt(i + 1));
}
return 1 / 4000 * sum - product + 1;
}
public static boolean detectConvergence(
List<Cluster> kCentroids, int[] featureSet, double tolerance) {
int iCentroids = kCentroids.size();
boolean toReturn = true;
for (int i = 0; i < iCentroids; i++) {
toReturn = true;
SimpleMatrix current = kCentroids.get(i).clusterCenter.copy();
SimpleMatrix previous = kCentroids.get(i).clusterPrevious.copy();
for (int j = 0; j < featureSet.length; j++) {
toReturn = true;
// System.out.println(current.get(0, featureSet[j])+" "+previous.get(0, featureSet[j])+"
// "+Math.abs(Math.abs(current.get(0, featureSet[j])) - Math.abs(previous.get(0,
// featureSet[j])))+" "+tolerance*current.get(0, featureSet[j]));
if (Math.abs(
Math.abs(current.get(0, featureSet[j])) - Math.abs(previous.get(0, featureSet[j])))
> (tolerance * current.get(0, featureSet[j]))) {
kCentroids.get(i).hasChanged = true;
// System.out.println("Changes are there");
break;
} else {
kCentroids.get(i).hasChanged = false;
}
// System.out.println(kCentroids.get(i).hasChanged);
}
// System.out.println(kCentroids.get(i).hasChanged);
// if(kCentroids.get(i).hasChanged=true) break;
}
// Check if I for true
for (int j = 0; j < iCentroids; j++) {
// System.out.println(kCentroids.get(j).hasChanged);
if (kCentroids.get(j).hasChanged) {
toReturn = false;
break;
} else {
toReturn = true;
}
}
// System.out.println("To reyurn"+toReturn);
return toReturn;
}
public Vector transform(Vector point) {
double tempX =
(matrix.get(0, 0) * point.X()) + (matrix.get(1, 0) * point.Y() + matrix.get(2, 0));
double tempY =
(matrix.get(0, 1) * point.X()) + (matrix.get(1, 1) * point.Y() + matrix.get(2, 1));
return new Vector(tempX, tempY);
}
/** Outputs the scores from the tree. Counts the tree nodes the same as setIndexLabels. */
static int outputTreeScores(PrintStream out, Tree tree, int index) {
if (tree.isLeaf()) {
return index;
}
out.print(" " + index + ":");
SimpleMatrix vector = RNNCoreAnnotations.getPredictions(tree);
for (int i = 0; i < vector.getNumElements(); ++i) {
out.print(" " + NF.format(vector.get(i)));
}
out.println();
index++;
for (Tree child : tree.children()) {
index = outputTreeScores(out, child, index);
}
return index;
}
public static SimpleMatrix compDist(
List<Cluster> kCentroids, SimpleMatrix dataSet, int[] featureSet, String distanceMetric) {
int dRows = dataSet.numRows();
int dCols = kCentroids.size();
int[] features = featureSet;
SimpleMatrix distMatrix = new SimpleMatrix(dRows, dCols);
for (int iCentroid = 0; iCentroid < dCols; iCentroid++) {
Cluster kcenter = kCentroids.get(iCentroid);
for (int iRows = 0; iRows < dRows; iRows++) {
double distTemp = 0;
for (int iFeature = 0; iFeature < features.length; iFeature++) {
double cX = kcenter.clusterCenter.get(0, features[iFeature]);
double dX = dataSet.get(iRows, features[iFeature]);
distTemp = distTemp + Math.pow(cX - dX, 2);
}
distMatrix.set(iRows, iCentroid, Math.sqrt(distTemp));
}
}
return distMatrix;
}
public static void main(String[] args) {
try {
if (args.length < 5) {
System.out.println(
"Invalid Syntax usage. \n The Syntax is KMeans inputfile distance-metric #Centroids #Iterations Tolerance featureSet crossValidation testDataSet");
}
String inputFile = args[0];
String distanceMetric = args[1];
int centroids = Integer.parseInt(args[2]);
int iterations = Integer.parseInt(args[3]);
double tolerance = Double.parseDouble(args[4]);
String inpFeatures = args[5];
String crossValidation = args[6];
String testFile = args[7];
String[] temp = inpFeatures.split(",");
int[] featureSet = new int[temp.length];
boolean hasConvered = false;
for (int i = 0; i < temp.length; i++) {
featureSet[i] = Integer.parseInt(temp[i]);
}
System.out.println("Features Considered are" + Arrays.toString(featureSet));
SimpleMatrix dataSet = new SimpleMatrix().loadCSV(inputFile);
// Cluster Parameters
int dsRows = dataSet.numRows();
int dsCol = dataSet.numCols();
// Cluster Initialization
List<Cluster> kcentroids = new ArrayList<Cluster>();
for (int i = 0; i < centroids; i++) {
int random = genRandom(0, dsRows - 1);
int[] currPoints = new int[dsRows];
int[] intIndex = new int[dsRows];
// This will have remnance of the first chosen element
Random r = new Random();
SimpleMatrix t = new SimpleMatrix().random(1, dsCol, 0, 0, r);
Cluster centers =
new Cluster(i, dataSet.extractVector(true, random), t, currPoints, intIndex);
kcentroids.add(centers);
}
// printKCentroids(kcentroids);
// dataSet.print();
SimpleMatrix distMatrix = compDist(kcentroids, dataSet, featureSet, distanceMetric);
// distMatrix.print();
// System.out.println(distMatrix.get(0, 1));
// ReassignCentrids(kcentroids, distMatrix, dataSet,featureSet);
// printKCentroids(kcentroids);
for (int k = 0; k < iterations; k++) {
System.out.println("------------------------Iteration " + k + " ------------------------");
distMatrix = compDist(kcentroids, dataSet, featureSet, distanceMetric);
// distMatrix.print();
ReassignCentrids(kcentroids, distMatrix, dataSet, featureSet);
printKCentroids(kcentroids);
hasConvered = detectConvergence(kcentroids, featureSet, tolerance);
// System.out.println(hasConvered);
if (hasConvered) {
System.out.println(
"------------------------Has Converged : Tolerance------------------------");
break;
}
}
if (!hasConvered)
System.out.println(
"------------------------Has Converged : Iterations------------------------");
if (crossValidation.equals("true")) {
SimpleMatrix test = new SimpleMatrix().loadCSV(testFile);
SimpleMatrix dist = compDist(kcentroids, test, featureSet, distanceMetric);
System.out.println("----------Associating Set Data Sets to Calculated Centroid-------");
// dist.print();
List<Cluster> kCentroids_l = kcentroids;
int[] clusterLoc = new int[test.numRows()];
for (int iRows = 0; iRows < test.numRows(); iRows++) {
int clusterNo = 1;
double minvalue = dist.get(iRows, 1);
for (int iCentroid = 0; iCentroid < kCentroids_l.size(); iCentroid++) {
// System.out.println(iRows+" "+iCentroid);
if (dist.get(iRows, iCentroid) < minvalue) {
clusterNo = iCentroid;
minvalue = dist.get(iRows, iCentroid);
}
}
clusterLoc[iRows] = clusterNo;
}
// System.out.println(Arrays.toString(clusterLoc));
for (int i = 0; i < kCentroids_l.size(); i++) {
kCentroids_l.get(i).backup();
kCentroids_l.get(i).noPoints = 0;
Arrays.fill(kCentroids_l.get(i).currPoints, -1);
Arrays.fill(kCentroids_l.get(i).intIndex, -1);
// System.out.println("Clusters Backed Up!");
}
// printKCentroids(kCentroids_l);
for (int i = 0; i < clusterLoc.length; i++) {
int insLoc = kCentroids_l.get(clusterLoc[i]).noPoints;
// System.out.println("Getting element"+dataSet.get(i, 0));
kCentroids_l.get(clusterLoc[i]).currPoints[insLoc] = (int) test.get(i, 0);
kCentroids_l.get(clusterLoc[i]).intIndex[insLoc] = i;
kCentroids_l.get(clusterLoc[i]).noPoints++;
}
printKCentroids(kCentroids_l);
}
} catch (Exception e) {
System.out.println("Unfortunately There is an error.");
e.printStackTrace();
}
}
public double fitness(SimpleMatrix cromosom) {
return Math.sin((Math.PI * cromosom.get(0)) / 256);
}