/** Copies the info out of the old proposition into a new proposition for the new BayesIm. */
public Proposition(VariableSource variableSource, Proposition proposition) {
this(variableSource);
if (proposition == null) {
throw new NullPointerException();
}
List<Node> variables = variableSource.getVariables();
List<Node> oldVariables = proposition.getVariableSource().getVariables();
for (int i = 0; i < variables.size(); i++) {
DiscreteVariable variable = (DiscreteVariable) variables.get(i);
int oldIndex = -1;
for (int j = 0; j < oldVariables.size(); j++) {
DiscreteVariable _variable = (DiscreteVariable) oldVariables.get(j);
if (variable.equals(_variable)) {
oldIndex = j;
break;
}
}
if (oldIndex != -1) {
for (int j = 0; j < allowedCategories[i].length; j++) {
allowedCategories[i][j] = proposition.isAllowed(oldIndex, j);
}
}
}
}
private static int nextValue(Proposition proposition, int variable, int currentIndex) {
for (int i = currentIndex + 1; i < proposition.getNumCategories(variable); i++) {
if (proposition.isAllowed(variable, i)) {
return i;
}
}
return -1;
}
/**
* Restricts this proposition to the categories for the given variable that are true in the given
* proposition.
*/
public void restrictToProposition(Proposition proposition, int variable) {
if (proposition.getVariableSource() != this.variableSource) {
throw new IllegalArgumentException(
"Can only restrict to " + "propositions for the same variable source.");
}
for (int j = 0; j < allowedCategories[variable].length; j++) {
if (!proposition.isAllowed(variable, j)) {
removeCategory(variable, j);
}
}
}
/**
* Constructs a new on-the-fly BayesIM that will calculate conditional probabilities on the fly
* from the given discrete data set, for the given Bayes PM.
*
* @param bayesPm the given Bayes PM, which specifies a directed acyclic graph for a Bayes net and
* parametrization for the Bayes net, but not actual values for the parameters.
* @param dataSet the discrete data set from which conditional probabilities should be estimated
* on the fly.
*/
public OnTheFlyMarginalCalculator(BayesPm bayesPm, DataSet dataSet)
throws IllegalArgumentException {
if (bayesPm == null) {
throw new NullPointerException();
}
if (dataSet == null) {
throw new NullPointerException();
}
// Make sure all of the variables in the PM are in the data set;
// otherwise, estimation is impossible.
BayesUtils.ensureVarsInData(bayesPm.getVariables(), dataSet);
// DataUtils.ensureVariablesExist(bayesPm, dataSet);
this.bayesPm = new BayesPm(bayesPm);
// Get the nodes from the BayesPm. This fixes the order of the nodes
// in the BayesIm, independently of any change to the BayesPm.
// (This order must be maintained.)
Graph graph = bayesPm.getDag();
this.nodes = graph.getNodes().toArray(new Node[0]);
// Initialize.
initialize();
// Create a subset of the data set with the variables of the IM, in
// the order of the IM.
List<Node> variables = getVariables();
this.dataSet = dataSet.subsetColumns(variables);
// Create a tautologous proposition for evidence.
this.evidence = new Evidence(Proposition.tautology(this));
}
/**
* @return the estimated conditional probability for the given assertion conditional on the given
* condition.
*/
public double getConditionalProb(Proposition assertion, Proposition condition) {
if (assertion.getVariableSource() != condition.getVariableSource()) {
throw new IllegalArgumentException(
"Assertion and condition must be " + "for the same Bayes IM.");
}
List<Node> assertionVars = assertion.getVariableSource().getVariables();
List<Node> dataVars = dataSet.getVariables();
assertionVars = GraphUtils.replaceNodes(assertionVars, dataVars);
if (!new HashSet<Node>(assertionVars).equals(new HashSet<Node>(dataVars))) {
throw new IllegalArgumentException(
"Assertion variable and data variables"
+ " are either different or in a different order: "
+ "\n\tAssertion vars: "
+ assertionVars
+ "\n\tData vars: "
+ dataVars);
}
int[] point = new int[dims.length];
int count1 = 0;
int count2 = 0;
this.missingValueCaseFound = false;
point:
for (int i = 0; i < numRows; i++) {
for (int j = 0; j < dims.length; j++) {
point[j] = dataSet.getInt(i, j);
if (point[j] == DiscreteVariable.MISSING_VALUE) {
continue point;
}
}
if (condition.isPermissibleCombination(point)) {
count1++;
if (assertion.isPermissibleCombination(point)) {
count2++;
}
}
}
return count2 / (double) count1;
}
/**
* Restricts this proposition to the categories for each variable that are true in the given
* proposition.
*/
public void restrictToProposition(Proposition proposition) {
if (proposition.getVariableSource() != this.variableSource) {
throw new IllegalArgumentException(
"Can only restrict to " + "propositions for the same variable source.");
}
for (int i = 0; i < allowedCategories.length; i++) {
for (int j = 0; j < allowedCategories[i].length; j++) {
if (!proposition.allowedCategories[i][j]) {
this.allowedCategories[i][j] = false;
}
}
}
}
/** @return the estimated probability of the given proposition. */
public double getProb(Proposition assertion) {
int[] point = new int[dims.length];
int count = 0;
this.missingValueCaseFound = false;
point:
for (int i = 0; i < numRows; i++) {
for (int j = 0; j < dims.length; j++) {
point[j] = dataSet.getInt(i, j);
if (point[j] == DiscreteVariable.MISSING_VALUE) {
this.missingValueCaseFound = true;
continue point;
}
}
if (assertion.isPermissibleCombination(point)) {
count++;
}
}
return count / (double) this.numRows;
}
private double getUpdatedMarginalFromModel(int variable, int category) {
Proposition evidence = getEvidence().getProposition();
int[] variableValues = new int[evidence.getNumVariables()];
for (int i = 0; i < evidence.getNumVariables(); i++) {
variableValues[i] = nextValue(evidence, i, -1);
}
variableValues[variableValues.length - 1] = -1;
double sum = 0.0;
loop:
while (true) {
for (int i = evidence.getNumVariables() - 1; i >= 0; i--) {
if (hasNextValue(evidence, i, variableValues[i])) {
variableValues[i] = nextValue(evidence, i, variableValues[i]);
for (int j = i + 1; j < evidence.getNumVariables(); j++) {
if (hasNextValue(evidence, j, -1)) {
variableValues[j] = nextValue(evidence, j, -1);
} else {
break loop;
}
}
double product = 1.0;
for (int m = 0; m < getNumNodes(); m++) {
Proposition assertion = Proposition.tautology(this);
assertion.setCategory(variable, category);
Proposition condition = new Proposition(evidence);
int[] parents = getParents(m);
for (int parent : parents) {
condition.disallowComplement(parent, variableValues[parent]);
}
if (condition.existsCombination()) {
product *= getDiscreteProbs().getConditionalProb(assertion, condition);
}
}
sum += product;
continue loop;
}
}
break;
}
return sum;
}