/**
* Constructor
*
* @param nbInstances number of lines in the database
* @param lattice associated lattice
*/
public EntropyComputer(int nbInstances, Lattice lattice) {
this.lookup = new HashMap<BitSet, Double>();
this.lattice = lattice;
this.nbInstances = nbInstances;
lookup.put(new BitSet(lattice.getNbVariables()), 0.0);
this.partialEntropy = new double[this.nbInstances + 1];
double lnN = log(nbInstances);
partialEntropy[0] = 0.0;
for (int i = 1; i < partialEntropy.length; i++) {
partialEntropy[i] = i * (log(i) - lnN);
}
nbCellsEverParsed = 0;
}
/**
* Computes the partial entropy for a lattice node (set of variables)
*
* @param clique the lattice node represented by a set of integers
* @return the entropy
*/
public Double computeEntropy(BitSet clique) {
Double computedEntropy = lookup.get(clique);
if (computedEntropy != null) {
// System.out.println("cached entropy for clique "+clique+":"+clique.hashCode());
return computedEntropy;
}
// System.out.println("Getting entropy for clique "+clique+":"+clique.hashCode());
// System.out.println("computing entropy for clique "+clique);
double entropy = 0.0;
LatticeNode node = lattice.getNode(clique);
int nbCells = node.getNbCells();
nbCellsEverParsed += nbCells;
// System.out.println("matrix:"+Arrays.toString(matrix));
for (int i = 0; i < nbCells; i++) {
int O = node.getMatrixCell(i);
entropy += partialEntropy[O];
}
entropy /= nbInstances;
entropy *= -1.0;
// System.out.println("caching "+clique+"("+clique.hashCode()+"):"+entropy);
lookup.put(clique, entropy);
return entropy;
}
/** @return the number of variables in the dataset */
public int getNbVariables() {
return lattice.getNbVariables();
}
public void setProbabilities(Lattice lattice) {
for (Integer nodeID : jnodes.keySet()) {
BayesNode n = jnodes.get(nodeID);
// System.out.println("setting CPT for "+n.getName());
List<BayesNode> parents = n.getParents();
List<BayesNode> parentsAndChild = new ArrayList<BayesNode>(parents);
parentsAndChild.add(n);
int nbParents = parents.size();
// System.out.println(nbParents+" parents");
// System.out.print("numbers for jayes =[");
// for (int i = 0; i < parentsAndChild.size(); i++) {
// BayesNode nodeTmp = parentsAndChild.get(i);
// System.out.print(nodesNumber.get(nodeTmp)+",");
// }
// System.out.println("]");
BitSet numbers = new BitSet();
numbers.set(nodeID);
int[] sizes = new int[nbParents];
int nbRowsInCPT = 1;
for (int i = 0; i < parents.size(); i++) {
BayesNode parent = parents.get(i);
numbers.set(nodesNumber.get(parent));
sizes[i] = parents.get(i).getOutcomeCount();
nbRowsInCPT *= sizes[i];
}
LatticeNode latticeNode = lattice.getNode(numbers);
Map<Integer, Integer> fromNodeIDToPositionInSortedTable = new HashMap<Integer, Integer>();
Integer[] variablesNumbers = new Integer[numbers.cardinality()];
int current = 0;
for (int i = numbers.nextSetBit(0); i >= 0; i = numbers.nextSetBit(i + 1)) {
variablesNumbers[current] = i;
current++;
}
for (int i = 0; i < variablesNumbers.length; i++) {
fromNodeIDToPositionInSortedTable.put(variablesNumbers[i], i);
}
int[] counts = new int[nbRowsInCPT * n.getOutcomeCount()];
int[] indexes4lattice = new int[parentsAndChild.size()];
int[] indexes4Jayes = new int[parentsAndChild.size()];
// System.out.println(counts.length +" cases");
// System.out.println("numbers for lattice "+Arrays.toString(variablesNumbers));
for (int c = 0; c < counts.length; c++) {
// System.out.println("case "+c);
int index = c;
// find indexes
for (int i = indexes4Jayes.length - 1; i > 0; i--) {
BayesNode associatedNode = parentsAndChild.get(i);
int dim = associatedNode.getOutcomeCount();
indexes4Jayes[i] = index % dim;
index /= dim;
}
indexes4Jayes[0] = index;
// System.out.println("indexes jayes = "+Arrays.toString(indexes4Jayes));
for (int i = 0; i < indexes4Jayes.length; i++) {
BayesNode nodeInPositionI = parentsAndChild.get(i);
// System.out.println(nodeInPositionI);
// System.out.println(fromNodeIDToPositionInSortedTable);
int nodeInPositionIID = nodesNumber.get(nodeInPositionI);
int indexInSortedTable = fromNodeIDToPositionInSortedTable.get(nodeInPositionIID);
indexes4lattice[indexInSortedTable] = indexes4Jayes[i];
}
// System.out.println("indexes lattice = "+Arrays.toString(indexes4lattice));
int count = latticeNode.getMatrixCell(indexes4lattice);
counts[c] = count;
}
// System.out.println(Arrays.toString(counts));
// System.out.println("total="+sumAllCounts);
double mTerm = 0.5;
double[] probas1D = new double[n.getOutcomeCount() * nbRowsInCPT];
for (int s = 0; s < probas1D.length; s += n.getOutcomeCount()) {
double sumOfCounts = 0.0;
for (int j = 0; j < n.getOutcomeCount(); j++) {
sumOfCounts += counts[s + j] + mTerm;
}
for (int j = 0; j < n.getOutcomeCount(); j++) {
probas1D[s + j] = (counts[s + j] + mTerm) / sumOfCounts;
}
}
// System.out.println(Arrays.toString(probas1D));
n.setProbabilities(probas1D);
}
System.out.println("Compiling network for inference...");
inferer = new JunctionTreeAlgorithm();
inferer.setNetwork(jbn);
evidence = new HashMap<BayesNode, String>();
System.out.println("Compiled.");
}