/** Sets the variable in a given tier to the specified list. */
public void setTier(int tier, List<String> vars) {
ensureTiers(tier);
Set<MyNode> _tier = tierSpecs.get(tier);
if (_tier != null) _tier.clear();
for (String var : vars) {
addToTier(tier, var);
}
}
private Set<Set<Integer>> finishESeeds(Set<Set<Integer>> ESeeds) {
log("Growing Effect Seeds.", true);
Set<Set<Integer>> grown = new HashSet<Set<Integer>>();
List<Integer> _variables = new ArrayList<Integer>();
for (int i = 0; i < variables.size(); i++) _variables.add(i);
// Lax grow phase with speedup.
if (algType == AlgType.lax) {
Set<Integer> t = new HashSet<Integer>();
int count = 0;
int total = ESeeds.size();
do {
if (!ESeeds.iterator().hasNext()) {
break;
}
Set<Integer> cluster = ESeeds.iterator().next();
Set<Integer> _cluster = new HashSet<Integer>(cluster);
if (extraShuffle) {
Collections.shuffle(_variables);
}
for (int o : _variables) {
if (_cluster.contains(o)) continue;
List<Integer> _cluster2 = new ArrayList<Integer>(_cluster);
int rejected = 0;
int accepted = 0;
ChoiceGenerator gen = new ChoiceGenerator(_cluster2.size(), 2);
int[] choice;
while ((choice = gen.next()) != null) {
int n1 = _cluster2.get(choice[0]);
int n2 = _cluster2.get(choice[1]);
t.clear();
t.add(n1);
t.add(n2);
t.add(o);
if (!ESeeds.contains(t)) {
rejected++;
} else {
accepted++;
}
}
if (rejected > accepted) {
continue;
}
_cluster.add(o);
// if (!(avgSumLnP(new ArrayList<Integer>(_cluster)) > -10)) {
// _cluster.remove(o);
// }
}
// This takes out all pure clusters that are subsets of _cluster.
ChoiceGenerator gen2 = new ChoiceGenerator(_cluster.size(), 3);
int[] choice2;
List<Integer> _cluster3 = new ArrayList<Integer>(_cluster);
while ((choice2 = gen2.next()) != null) {
int n1 = _cluster3.get(choice2[0]);
int n2 = _cluster3.get(choice2[1]);
int n3 = _cluster3.get(choice2[2]);
t.clear();
t.add(n1);
t.add(n2);
t.add(n3);
ESeeds.remove(t);
}
if (verbose) {
System.out.println(
"Grown "
+ (++count)
+ " of "
+ total
+ ": "
+ variablesForIndices(new ArrayList<Integer>(_cluster)));
}
grown.add(_cluster);
} while (!ESeeds.isEmpty());
}
// Lax grow phase without speedup.
if (algType == AlgType.laxWithSpeedup) {
int count = 0;
int total = ESeeds.size();
// Optimized lax version of grow phase.
for (Set<Integer> cluster : new HashSet<Set<Integer>>(ESeeds)) {
Set<Integer> _cluster = new HashSet<Integer>(cluster);
if (extraShuffle) {
Collections.shuffle(_variables);
}
for (int o : _variables) {
if (_cluster.contains(o)) continue;
List<Integer> _cluster2 = new ArrayList<Integer>(_cluster);
int rejected = 0;
int accepted = 0;
//
ChoiceGenerator gen = new ChoiceGenerator(_cluster2.size(), 2);
int[] choice;
while ((choice = gen.next()) != null) {
int n1 = _cluster2.get(choice[0]);
int n2 = _cluster2.get(choice[1]);
Set<Integer> triple = triple(n1, n2, o);
if (!ESeeds.contains(triple)) {
rejected++;
} else {
accepted++;
}
}
//
if (rejected > accepted) {
continue;
}
// System.out.println("Adding " + o + " to " + cluster);
_cluster.add(o);
}
for (Set<Integer> c : new HashSet<Set<Integer>>(ESeeds)) {
if (_cluster.containsAll(c)) {
ESeeds.remove(c);
}
}
if (verbose) {
System.out.println("Grown " + (++count) + " of " + total + ": " + _cluster);
}
grown.add(_cluster);
}
}
// Strict grow phase.
if (algType == AlgType.strict) {
Set<Integer> t = new HashSet<Integer>();
int count = 0;
int total = ESeeds.size();
do {
if (!ESeeds.iterator().hasNext()) {
break;
}
Set<Integer> cluster = ESeeds.iterator().next();
Set<Integer> _cluster = new HashSet<Integer>(cluster);
if (extraShuffle) {
Collections.shuffle(_variables);
}
VARIABLES:
for (int o : _variables) {
if (_cluster.contains(o)) continue;
List<Integer> _cluster2 = new ArrayList<Integer>(_cluster);
ChoiceGenerator gen = new ChoiceGenerator(_cluster2.size(), 2);
int[] choice;
while ((choice = gen.next()) != null) {
int n1 = _cluster2.get(choice[0]);
int n2 = _cluster2.get(choice[1]);
t.clear();
t.add(n1);
t.add(n2);
t.add(o);
if (!ESeeds.contains(t)) {
continue VARIABLES;
}
// if (avgSumLnP(new ArrayList<Integer>(t)) < -10) continue
// CLUSTER;
}
_cluster.add(o);
}
// This takes out all pure clusters that are subsets of _cluster.
ChoiceGenerator gen2 = new ChoiceGenerator(_cluster.size(), 3);
int[] choice2;
List<Integer> _cluster3 = new ArrayList<Integer>(_cluster);
while ((choice2 = gen2.next()) != null) {
int n1 = _cluster3.get(choice2[0]);
int n2 = _cluster3.get(choice2[1]);
int n3 = _cluster3.get(choice2[2]);
t.clear();
t.add(n1);
t.add(n2);
t.add(n3);
ESeeds.remove(t);
}
if (verbose) {
System.out.println("Grown " + (++count) + " of " + total + ": " + _cluster);
}
grown.add(_cluster);
} while (!ESeeds.isEmpty());
}
// Optimized pick phase.
log("Choosing among grown Effect Clusters.", true);
for (Set<Integer> l : grown) {
ArrayList<Integer> _l = new ArrayList<Integer>(l);
Collections.sort(_l);
if (verbose) {
log("Grown: " + variablesForIndices(_l), false);
}
}
Set<Set<Integer>> out = new HashSet<Set<Integer>>();
List<Set<Integer>> list = new ArrayList<Set<Integer>>(grown);
// final Map<Set<Integer>, Double> pValues = new HashMap<Set<Integer>, Double>();
//
// for (Set<Integer> o : grown) {
// pValues.put(o, getP(new ArrayList<Integer>(o)));
// }
Collections.sort(
list,
new Comparator<Set<Integer>>() {
@Override
public int compare(Set<Integer> o1, Set<Integer> o2) {
// if (o1.size() == o2.size()) {
// double chisq1 = pValues.get(o1);
// double chisq2 = pValues.get(o2);
// return Double.compare(chisq2, chisq1);
// }
return o2.size() - o1.size();
}
});
// for (Set<Integer> o : list) {
// if (pValues.get(o) < alpha) continue;
// System.out.println(variablesForIndices(new ArrayList<Integer>(o)) + " p = " +
// pValues.get(o));
// }
Set<Integer> all = new HashSet<Integer>();
CLUSTER:
for (Set<Integer> cluster : list) {
// if (pValues.get(cluster) < alpha) continue;
for (Integer i : cluster) {
if (all.contains(i)) continue CLUSTER;
}
out.add(cluster);
// if (getPMulticluster(out) < alpha) {
// out.remove(cluster);
// continue;
// }
all.addAll(cluster);
}
return out;
}