private JunctionTree graphToJt(UndirectedGraph g) {
JunctionTree jt = new JunctionTree(g.vertexSet().size());
Object root = g.vertexSet().iterator().next();
jt.add(root);
for (Iterator it1 = new BreadthFirstIterator(g, root); it1.hasNext(); ) {
Object v1 = it1.next();
for (Iterator it2 = GraphHelper.neighborListOf(g, v1).iterator(); it2.hasNext(); ) {
Object v2 = it2.next();
if (jt.getParent(v1) != v2) {
jt.addNode(v1, v2);
}
}
}
return jt;
}
public void dump() {
if (jtCurrent != null) {
System.out.println("Current junction tree");
jtCurrent.dump();
} else {
System.out.println("NO current junction tree");
}
}
private void initJtCpts(FactorGraph mdl, JunctionTree jt) {
for (Iterator it = jt.getVerticesIterator(); it.hasNext(); ) {
VarSet c = (VarSet) it.next();
// DiscreteFactor ptl = createBlankFactor (c);
// jt.setCPF(c, ptl);
jt.setCPF(c, new ConstantFactor(1.0));
}
for (Iterator it = mdl.factors().iterator(); it.hasNext(); ) {
Factor ptl = (Factor) it.next();
VarSet parent = jt.findParentCluster(ptl.varSet());
assert parent != null : "Unable to find parent cluster for ptl " + ptl + "in jt " + jt;
Factor cpf = jt.getCPF(parent);
Factor newCpf = cpf.multiply(ptl);
jt.setCPF(parent, newCpf);
/* debug
if (jt.isNaN()) {
throw new RuntimeException ("Got a NaN");
}
*/
}
}
/**
* Constructs a junction tree from a given factor graph. Does not perform BP in the resulting
* graph. So this gives you the structure of a jnuction tree, but the factors don't correspond to
* the true marginals unless you call BP yourself.
*
* @param mdl Factor graph to compute JT for.
*/
public JunctionTree buildJunctionTree(FactorGraph mdl) {
jtCurrent = (JunctionTree) mdl.getInferenceCache(JunctionTreeInferencer.class);
if (jtCurrent != null) {
jtCurrent.clearCPFs();
} else {
/* The graph g is the topology of the MRF that corresponds to the factor graph mdl.
* Essentially, this means that we triangulate factor graphs by converting to an MRF first.
* I could have chosen to trianglualte the FactorGraph directly, but I didn't for historical reasons
* (I already had a version of triangulate() for MRFs, not bipartite factor graphs.)
* Note that the call to mdlToGraph() is perfectly valid for FactorGraphs that are also DirectedModels,
* and has the effect of moralizing in that case. */
UndirectedGraph g = Graphs.mdlToGraph(mdl);
triangulate(g);
jtCurrent = buildJtStructure();
mdl.setInferenceCache(JunctionTreeInferencer.class, jtCurrent);
}
initJtCpts(mdl, jtCurrent);
return jtCurrent;
}
public double dumpLogJoint(Assignment assn) {
return jtCurrent.dumpLogJoint(assn);
}
public double lookupLogJoint(Assignment assn) {
return jtCurrent.lookupLogJoint(assn);
}