public List<Triple> getUnshieldedCollidersFromGraph(Graph graph) {
List<Triple> colliders = new ArrayList<>();
List<Node> nodes = graph.getNodes();
for (Node b : nodes) {
List<Node> adjacentNodes = graph.getAdjacentNodes(b);
if (adjacentNodes.size() < 2) {
continue;
}
ChoiceGenerator cg = new ChoiceGenerator(adjacentNodes.size(), 2);
int[] combination;
while ((combination = cg.next()) != null) {
Node a = adjacentNodes.get(combination[0]);
Node c = adjacentNodes.get(combination[1]);
// Skip triples that are shielded.
if (graph.isAdjacentTo(a, c)) {
continue;
}
if (graph.isDefCollider(a, b, c)) {
colliders.add(new Triple(a, b, c));
}
}
}
return colliders;
}
////////////////////////////////////////////////
// collect in rTupleList all unshielded tuples
////////////////////////////////////////////////
private List<Node[]> getRTuples() {
List<Node[]> rTuples = new ArrayList<Node[]>();
List<Node> nodes = graph.getNodes();
for (Node j : nodes) {
List<Node> adjacentNodes = graph.getAdjacentNodes(j);
if (adjacentNodes.size() < 2) {
continue;
}
ChoiceGenerator cg = new ChoiceGenerator(adjacentNodes.size(), 2);
int[] combination;
while ((combination = cg.next()) != null) {
Node i = adjacentNodes.get(combination[0]);
Node k = adjacentNodes.get(combination[1]);
// Skip triples that are shielded.
if (!graph.isAdjacentTo(i, k)) {
Node[] newTuple = {i, j, k};
rTuples.add(newTuple);
}
}
}
return (rTuples);
}
/**
* Step C of PC; orients colliders using specified sepset. That is, orients x *-* y *-* z as x *->
* y <-* z just in case y is in Sepset({x, z}).
*/
public Map<Triple, Double> findCollidersUsingSepsets(
SepsetProducer sepsetProducer, Graph graph, boolean verbose, IKnowledge knowledge) {
TetradLogger.getInstance().log("details", "Starting Collider Orientation:");
Map<Triple, Double> colliders = new HashMap<>();
System.out.println("Looking for colliders");
List<Node> nodes = graph.getNodes();
for (Node b : nodes) {
List<Node> adjacentNodes = graph.getAdjacentNodes(b);
if (adjacentNodes.size() < 2) {
continue;
}
ChoiceGenerator cg = new ChoiceGenerator(adjacentNodes.size(), 2);
int[] combination;
while ((combination = cg.next()) != null) {
Node a = adjacentNodes.get(combination[0]);
Node c = adjacentNodes.get(combination[1]);
// Skip triples that are shielded.
if (graph.isAdjacentTo(a, c)) {
continue;
}
List<Node> sepset = sepsetProducer.getSepset(a, c);
if (sepset == null) continue;
// if (sepsetProducer.getPValue() < 0.5) continue;
if (!sepset.contains(b)) {
if (verbose) {
// boolean dsep = this.dsep.isIndependent(a, c);
// System.out.println("QQQ p = " + independenceTest.getPValue() +
// " " + dsep);
System.out.println(
"\nCollider orientation <" + a + ", " + b + ", " + c + "> sepset = " + sepset);
}
colliders.put(new Triple(a, b, c), sepsetProducer.getPValue());
TetradLogger.getInstance()
.log("colliderOrientations", SearchLogUtils.colliderOrientedMsg(a, b, c, sepset));
}
}
}
TetradLogger.getInstance().log("details", "Finishing Collider Orientation.");
System.out.println("Done finding colliders");
return colliders;
}
public static boolean meekR1Locally2(
Graph graph, Knowledge knowledge, IndependenceTest test, int depth) {
List<Node> nodes = graph.getNodes();
boolean changed = true;
while (changed) {
changed = false;
for (Node a : nodes) {
List<Node> adjacentNodes = graph.getAdjacentNodes(a);
if (adjacentNodes.size() < 2) {
continue;
}
ChoiceGenerator cg = new ChoiceGenerator(adjacentNodes.size(), 2);
int[] combination;
while ((combination = cg.next()) != null) {
Node b = adjacentNodes.get(combination[0]);
Node c = adjacentNodes.get(combination[1]);
// Skip triples that are shielded.
if (graph.isAdjacentTo(b, c)) {
continue;
}
if (graph.getEndpoint(b, a) == Endpoint.ARROW && graph.isUndirectedFromTo(a, c)) {
if (existsLocalSepsetWithoutDet(b, a, c, test, graph, depth)) {
continue;
}
if (isArrowpointAllowed(a, c, knowledge)) {
graph.setEndpoint(a, c, Endpoint.ARROW);
TetradLogger.getInstance()
.edgeOriented(SearchLogUtils.edgeOrientedMsg("Meek R1", graph.getEdge(a, c)));
changed = true;
}
} else if (graph.getEndpoint(c, a) == Endpoint.ARROW && graph.isUndirectedFromTo(a, b)) {
if (existsLocalSepsetWithoutDet(b, a, c, test, graph, depth)) {
continue;
}
if (isArrowpointAllowed(a, b, knowledge)) {
graph.setEndpoint(a, b, Endpoint.ARROW);
TetradLogger.getInstance()
.edgeOriented(SearchLogUtils.edgeOrientedMsg("Meek R1", graph.getEdge(a, b)));
changed = true;
}
}
}
}
}
return changed;
}
/**
* Performs step C of the algorithm, as indicated on page xxx of CPS, with the modification that
* X--W--Y is oriented as X-->W<--Y if W is *determined by* the sepset of (X, Y), rather than W
* just being *in* the sepset of (X, Y).
*/
public static void pcdOrientC(
SepsetMap set, IndependenceTest test, Knowledge knowledge, Graph graph) {
TetradLogger.getInstance().log("info", "Staring Collider Orientation:");
List<Node> nodes = graph.getNodes();
for (Node y : nodes) {
List<Node> adjacentNodes = graph.getAdjacentNodes(y);
if (adjacentNodes.size() < 2) {
continue;
}
ChoiceGenerator cg = new ChoiceGenerator(adjacentNodes.size(), 2);
int[] combination;
while ((combination = cg.next()) != null) {
Node x = adjacentNodes.get(combination[0]);
Node z = adjacentNodes.get(combination[1]);
// Skip triples that are shielded.
if (graph.isAdjacentTo(x, z)) {
continue;
}
List<Node> sepset = set.get(x, z);
if (sepset == null) {
continue;
}
List<Node> augmentedSet = new LinkedList<Node>(sepset);
augmentedSet.add(y);
if (test.determines(sepset, y)) {
continue;
}
//
if (!test.splitDetermines(sepset, x, z) && test.splitDetermines(augmentedSet, x, z)) {
continue;
}
if (!isArrowpointAllowed(x, y, knowledge) || !isArrowpointAllowed(z, y, knowledge)) {
continue;
}
graph.setEndpoint(x, y, Endpoint.ARROW);
graph.setEndpoint(z, y, Endpoint.ARROW);
TetradLogger.getInstance()
.log("colliderOriented", SearchLogUtils.colliderOrientedMsg(x, y, z));
}
}
TetradLogger.getInstance().log("info", "Finishing Collider Orientation.");
}
/** Meek's rule R3. If a--b, a--c, a--d, c-->b, c-->b, then orient a-->b. */
public static boolean meekR3(Graph graph, Knowledge knowledge) {
List<Node> nodes = graph.getNodes();
boolean changed = false;
for (Node a : nodes) {
List<Node> adjacentNodes = graph.getAdjacentNodes(a);
if (adjacentNodes.size() < 3) {
continue;
}
for (Node b : adjacentNodes) {
List<Node> otherAdjacents = new LinkedList<Node>(adjacentNodes);
otherAdjacents.remove(b);
if (!graph.isUndirectedFromTo(a, b)) {
continue;
}
ChoiceGenerator cg = new ChoiceGenerator(otherAdjacents.size(), 2);
int[] combination;
while ((combination = cg.next()) != null) {
Node c = otherAdjacents.get(combination[0]);
Node d = otherAdjacents.get(combination[1]);
if (graph.isAdjacentTo(c, d)) {
continue;
}
if (!graph.isUndirectedFromTo(a, c)) {
continue;
}
if (!graph.isUndirectedFromTo(a, d)) {
continue;
}
if (graph.isDirectedFromTo(c, b) && graph.isDirectedFromTo(d, b)) {
if (isArrowpointAllowed(a, b, knowledge)) {
graph.setEndpoint(a, b, Endpoint.ARROW);
TetradLogger.getInstance()
.edgeOriented(SearchLogUtils.edgeOrientedMsg("Meek R3", graph.getEdge(a, b)));
changed = true;
break;
}
}
}
}
}
return changed;
}
/////////////////////////////////////////////////////////////////////////////
// set the sepSet of x and y to the minimal such subset of the given sepSet
// and remove the edge <x, y> if background knowledge allows
/////////////////////////////////////////////////////////////////////////////
private void setMinSepSet(List<Node> sepSet, Node x, Node y) {
// It is assumed that BK has been considered before calling this method
// (for example, setting independent1 and independent2 in ruleR0_RFCI)
/*
// background knowledge requires this edge
if (knowledge.noEdgeRequired(x.getNode(), y.getNode()))
{
return;
}
*/
List<Node> empty = Collections.emptyList();
boolean indep;
try {
indep = independenceTest.isIndependent(x, y, empty);
} catch (Exception e) {
indep = false;
}
if (indep) {
getSepsets().set(x, y, empty);
return;
}
int sepSetSize = sepSet.size();
for (int i = 1; i <= sepSetSize; i++) {
ChoiceGenerator cg = new ChoiceGenerator(sepSetSize, i);
int[] combination;
while ((combination = cg.next()) != null) {
List<Node> condSet = GraphUtils.asList(combination, sepSet);
try {
indep = independenceTest.isIndependent(x, y, condSet);
} catch (Exception e) {
indep = false;
}
if (indep) {
getSepsets().set(x, y, condSet);
return;
}
}
}
}
public static boolean existsLocalSepsetWithoutDet(
Node x, Node y, Node z, IndependenceTest test, Graph graph, int depth) {
Set<Node> __nodes = new HashSet<Node>(graph.getAdjacentNodes(x));
__nodes.addAll(graph.getAdjacentNodes(z));
__nodes.remove(x);
__nodes.remove(z);
List<Node> _nodes = new LinkedList<Node>(__nodes);
TetradLogger.getInstance()
.log("adjacencies", "Adjacents for " + x + "--" + y + "--" + z + " = " + _nodes);
int _depth = depth;
if (_depth == -1) {
_depth = 1000;
}
_depth = Math.min(_depth, _nodes.size());
for (int d = 0; d <= _depth; d++) {
if (_nodes.size() >= d) {
ChoiceGenerator cg2 = new ChoiceGenerator(_nodes.size(), d);
int[] choice;
while ((choice = cg2.next()) != null) {
List<Node> condSet = asList(choice, _nodes);
if (condSet.contains(y)) {
continue;
}
if (test.determines(condSet, y)) {
continue;
}
// LogUtils.getInstance().finest("Trying " + condSet);
if (test.isIndependent(x, z, condSet)) {
return true;
}
}
}
}
return false;
}
/**
* Step C of PC; orients colliders using specified sepset. That is, orients x *-* y *-* z as x *->
* y <-* z just in case y is in Sepset({x, z}).
*/
public static void orientCollidersUsingSepsets(SepsetMap set, Knowledge knowledge, Graph graph) {
TetradLogger.getInstance().log("info", "Starting Collider Orientation:");
// verifySepsetIntegrity(set, graph);
List<Node> nodes = graph.getNodes();
for (Node a : nodes) {
List<Node> adjacentNodes = graph.getAdjacentNodes(a);
if (adjacentNodes.size() < 2) {
continue;
}
ChoiceGenerator cg = new ChoiceGenerator(adjacentNodes.size(), 2);
int[] combination;
while ((combination = cg.next()) != null) {
Node b = adjacentNodes.get(combination[0]);
Node c = adjacentNodes.get(combination[1]);
// Skip triples that are shielded.
if (graph.isAdjacentTo(b, c)) {
continue;
}
List<Node> sepset = set.get(b, c);
if (sepset != null
&& !sepset.contains(a)
&& isArrowpointAllowed(b, a, knowledge)
&& isArrowpointAllowed(c, a, knowledge)) {
graph.setEndpoint(b, a, Endpoint.ARROW);
graph.setEndpoint(c, a, Endpoint.ARROW);
TetradLogger.getInstance()
.log("colliderOriented", SearchLogUtils.colliderOrientedMsg(b, a, c, sepset));
}
}
}
TetradLogger.getInstance().log("info", "Finishing Collider Orientation.");
}
/** If */
public static boolean meekR2(Graph graph, Knowledge knowledge) {
List<Node> nodes = graph.getNodes();
boolean changed = false;
for (Node a : nodes) {
List<Node> adjacentNodes = graph.getAdjacentNodes(a);
if (adjacentNodes.size() < 2) {
continue;
}
ChoiceGenerator cg = new ChoiceGenerator(adjacentNodes.size(), 2);
int[] combination;
while ((combination = cg.next()) != null) {
Node b = adjacentNodes.get(combination[0]);
Node c = adjacentNodes.get(combination[1]);
if (graph.isDirectedFromTo(b, a)
&& graph.isDirectedFromTo(a, c)
&& graph.isUndirectedFromTo(b, c)) {
if (isArrowpointAllowed(b, c, knowledge)) {
graph.setEndpoint(b, c, Endpoint.ARROW);
TetradLogger.getInstance()
.edgeOriented(SearchLogUtils.edgeOrientedMsg("Meek R2", graph.getEdge(b, c)));
}
} else if (graph.isDirectedFromTo(c, a)
&& graph.isDirectedFromTo(a, b)
&& graph.isUndirectedFromTo(c, b)) {
if (isArrowpointAllowed(c, b, knowledge)) {
graph.setEndpoint(c, b, Endpoint.ARROW);
TetradLogger.getInstance()
.edgeOriented(SearchLogUtils.edgeOrientedMsg("Meek R2", graph.getEdge(c, b)));
}
}
}
}
return changed;
}
public static void orientCollidersLocally(
Knowledge knowledge, Graph graph, IndependenceTest test, int depth, Set<Node> nodesToVisit) {
TetradLogger.getInstance().log("info", "Starting Collider Orientation:");
if (nodesToVisit == null) {
nodesToVisit = new HashSet<Node>(graph.getNodes());
}
for (Node a : nodesToVisit) {
List<Node> adjacentNodes = graph.getAdjacentNodes(a);
if (adjacentNodes.size() < 2) {
continue;
}
ChoiceGenerator cg = new ChoiceGenerator(adjacentNodes.size(), 2);
int[] combination;
while ((combination = cg.next()) != null) {
Node b = adjacentNodes.get(combination[0]);
Node c = adjacentNodes.get(combination[1]);
// Skip triples that are shielded.
if (graph.isAdjacentTo(b, c)) {
continue;
}
if (isArrowpointAllowed1(b, a, knowledge) && isArrowpointAllowed1(c, a, knowledge)) {
if (!existsLocalSepsetWith(b, a, c, test, graph, depth)) {
graph.setEndpoint(b, a, Endpoint.ARROW);
graph.setEndpoint(c, a, Endpoint.ARROW);
TetradLogger.getInstance()
.log("colliderOriented", SearchLogUtils.colliderOrientedMsg(b, a, c));
}
}
}
}
TetradLogger.getInstance().log("info", "Finishing Collider Orientation.");
}
// Finds clusters of size 4 or higher.
private Set<Set<Integer>> findPureClusters(
List<Integer> _variables, Map<Node, Set<Node>> adjacencies) {
// System.out.println("Original variables = " + variables);
Set<Set<Integer>> clusters = new HashSet<Set<Integer>>();
List<Integer> allVariables = new ArrayList<Integer>();
for (int i = 0; i < this.variables.size(); i++) allVariables.add(i);
VARIABLES:
while (!_variables.isEmpty()) {
if (_variables.size() < 4) break;
for (int x : _variables) {
Node nodeX = variables.get(x);
List<Node> adjX = new ArrayList<Node>(adjacencies.get(nodeX));
adjX.retainAll(variablesForIndices(new ArrayList<Integer>(_variables)));
for (Node node : new ArrayList<Node>(adjX)) {
if (adjacencies.get(node).size() < 3) {
adjX.remove(node);
}
}
if (adjX.size() < 3) {
continue;
}
ChoiceGenerator gen = new ChoiceGenerator(adjX.size(), 3);
int[] choice;
while ((choice = gen.next()) != null) {
Node nodeY = adjX.get(choice[0]);
Node nodeZ = adjX.get(choice[1]);
Node nodeW = adjX.get(choice[2]);
int y = variables.indexOf(nodeY);
int w = variables.indexOf(nodeW);
int z = variables.indexOf(nodeZ);
Set<Integer> cluster = quartet(x, y, z, w);
if (!clique(cluster, adjacencies)) {
continue;
}
// Note that purity needs to be assessed with respect to all of the variables in order to
// remove all latent-measure impurities between pairs of latents.
if (pure(cluster, allVariables)) {
// Collections.shuffle(_variables);
O:
for (int o : _variables) {
if (cluster.contains(o)) continue;
cluster.add(o);
List<Integer> _cluster = new ArrayList<Integer>(cluster);
if (!clique(cluster, adjacencies)) {
cluster.remove(o);
continue O;
}
// if (!allVariablesDependent(cluster)) {
// cluster.remove(o);
// continue O;
// }
ChoiceGenerator gen2 = new ChoiceGenerator(_cluster.size(), 4);
int[] choice2;
int count = 0;
while ((choice2 = gen2.next()) != null) {
int x2 = _cluster.get(choice2[0]);
int y2 = _cluster.get(choice2[1]);
int z2 = _cluster.get(choice2[2]);
int w2 = _cluster.get(choice2[3]);
Set<Integer> quartet = quartet(x2, y2, z2, w2);
// Optimizes for large clusters.
if (quartet.contains(o)) {
if (++count > 50) continue O;
}
if (quartet.contains(o) && !pure(quartet, allVariables)) {
cluster.remove(o);
continue O;
}
}
}
System.out.println(
"Cluster found: " + variablesForIndices(new ArrayList<Integer>(cluster)));
clusters.add(cluster);
_variables.removeAll(cluster);
continue VARIABLES;
}
}
}
break;
}
return clusters;
}
// Finds clusters of size 3.
private Set<Set<Integer>> findMixedClusters(
List<Integer> remaining, Set<Integer> unionPure, Map<Node, Set<Node>> adjacencies) {
Set<Set<Integer>> threeClusters = new HashSet<Set<Integer>>();
if (unionPure.isEmpty()) {
return new HashSet<Set<Integer>>();
}
REMAINING:
while (true) {
if (remaining.size() < 3) break;
ChoiceGenerator gen = new ChoiceGenerator(remaining.size(), 3);
int[] choice;
while ((choice = gen.next()) != null) {
int y = remaining.get(choice[0]);
int z = remaining.get(choice[1]);
int w = remaining.get(choice[2]);
Set<Integer> cluster = new HashSet<Integer>();
cluster.add(y);
cluster.add(z);
cluster.add(w);
// if (!allVariablesDependent(cluster)) {
// continue;
// }
if (!clique(cluster, adjacencies)) {
continue;
}
// Check all x as a cross check; really only one should be necessary.
boolean allX = true;
for (int x : unionPure) {
Set<Integer> _cluster = new HashSet<Integer>(cluster);
_cluster.add(x);
if (!quartetVanishes(_cluster) || !significant(new ArrayList<Integer>(_cluster))) {
allX = false;
break;
}
}
if (allX) {
threeClusters.add(cluster);
unionPure.addAll(cluster);
remaining.removeAll(cluster);
System.out.println(
"3-cluster found: " + variablesForIndices(new ArrayList<Integer>(cluster)));
continue REMAINING;
}
}
break;
}
return threeClusters;
}
private Void findSeeds() {
Tetrad tetrad = null;
List<Node> empty = new ArrayList();
if (variables.size() < 4) {
Set<Set<Integer>> ESeeds = new HashSet<Set<Integer>>();
}
Map<Node, Set<Node>> adjacencies;
if (depth == -2) {
adjacencies = new HashMap<Node, Set<Node>>();
for (Node node : variables) {
HashSet<Node> _nodes = new HashSet<Node>(variables);
_nodes.remove(node);
adjacencies.put(node, _nodes);
}
} else {
// System.out.println("Running PC adjacency search...");
Graph graph = new EdgeListGraph(variables);
Fas fas = new Fas(graph, indTest);
fas.setVerbose(false);
fas.setDepth(depth); // 1?
adjacencies = fas.searchMapOnly();
// System.out.println("...done.");
}
List<Integer> allVariables = new ArrayList<Integer>();
for (int i = 0; i < variables.size(); i++) allVariables.add(i);
log("Finding seeds.", true);
ChoiceGenerator gen = new ChoiceGenerator(allVariables.size(), 3);
int[] choice;
CHOICE:
while ((choice = gen.next()) != null) {
int n1 = allVariables.get(choice[0]);
int n2 = allVariables.get(choice[1]);
int n3 = allVariables.get(choice[2]);
Node v1 = variables.get(choice[0]);
Node v2 = variables.get(choice[1]);
Node v3 = variables.get(choice[2]);
Set<Integer> triple = triple(n1, n2, n3);
if (!clique(triple, adjacencies)) {
continue;
}
boolean EPure = true;
boolean CPure1 = true;
boolean CPure2 = true;
boolean CPure3 = true;
for (int o : allVariables) {
if (triple.contains(o)) {
continue;
}
Node v4 = variables.get(o);
tetrad = new Tetrad(v1, v2, v3, v4);
if (deltaTest.getPValue(tetrad) > alpha) {
EPure = false;
if (indTest.isDependent(v1, v4, empty)) {
CPure1 = false;
}
if (indTest.isDependent(v2, v4, empty)) {
CPure2 = false;
}
}
tetrad = new Tetrad(v1, v3, v2, v4);
if (deltaTest.getPValue(tetrad) > alpha) {
EPure = false;
if (indTest.isDependent(v3, v4, empty)) {
CPure3 = false;
}
}
if (!(EPure || CPure1 || CPure2 || CPure3)) {
continue CHOICE;
}
}
HashSet<Integer> _cluster = new HashSet<Integer>(triple);
if (verbose) {
log("++" + variablesForIndices(new ArrayList<Integer>(triple)), false);
}
if (EPure) {
ESeeds.add(_cluster);
}
if (!EPure) {
if (CPure1) {
Set<Integer> _cluster1 = new HashSet<Integer>(n2, n3);
_cluster1.addAll(CSeeds.get(n1));
CSeeds.set(n1, _cluster1);
}
if (CPure2) {
Set<Integer> _cluster2 = new HashSet<Integer>(n1, n3);
_cluster2.addAll(CSeeds.get(n2));
CSeeds.set(n2, _cluster2);
}
if (CPure3) {
Set<Integer> _cluster3 = new HashSet<Integer>(n1, n2);
_cluster3.addAll(CSeeds.get(n3));
CSeeds.set(n3, _cluster3);
}
}
}
return null;
}
public static CpcTripleType getCpcTripleType(
Node x, Node y, Node z, IndependenceTest test, int depth, Graph graph) {
// System.out.println("getCpcTripleType 1");
boolean existsSepsetContainingY = false;
boolean existsSepsetNotContainingY = false;
Set<Node> __nodes = new HashSet<Node>(graph.getAdjacentNodes(x));
__nodes.remove(z);
// System.out.println("getCpcTripleType 2");
List<Node> _nodes = new LinkedList<Node>(__nodes);
TetradLogger.getInstance()
.log("adjacencies", "Adjacents for " + x + "--" + y + "--" + z + " = " + _nodes);
// System.out.println("getCpcTripleType 3");
int _depth = depth;
if (_depth == -1) {
_depth = 1000;
}
_depth = Math.min(_depth, _nodes.size());
// System.out.println("getCpcTripleType 4");
for (int d = 0; d <= _depth; d++) {
// System.out.println("getCpcTripleType 5");
ChoiceGenerator cg = new ChoiceGenerator(_nodes.size(), d);
int[] choice;
while ((choice = cg.next()) != null) {
// System.out.println("getCpcTripleType 6");
List<Node> condSet = GraphUtils.asList(choice, _nodes);
// System.out.println("getCpcTripleType 7");
if (test.isIndependent(x, z, condSet)) {
if (condSet.contains(y)) {
existsSepsetContainingY = true;
} else {
existsSepsetNotContainingY = true;
}
}
}
}
// System.out.println("getCpcTripleType 8");
__nodes = new HashSet<Node>(graph.getAdjacentNodes(z));
__nodes.remove(x);
_nodes = new LinkedList<Node>(__nodes);
TetradLogger.getInstance()
.log("adjacencies", "Adjacents for " + x + "--" + y + "--" + z + " = " + _nodes);
// System.out.println("getCpcTripleType 9");
_depth = depth;
if (_depth == -1) {
_depth = 1000;
}
_depth = Math.min(_depth, _nodes.size());
// System.out.println("getCpcTripleType 10");
for (int d = 0; d <= _depth; d++) {
// System.out.println("getCpcTripleType 11");
ChoiceGenerator cg = new ChoiceGenerator(_nodes.size(), d);
int[] choice;
while ((choice = cg.next()) != null) {
List<Node> condSet = GraphUtils.asList(choice, _nodes);
if (test.isIndependent(x, z, condSet)) {
if (condSet.contains(y)) {
existsSepsetContainingY = true;
} else {
existsSepsetNotContainingY = true;
}
}
}
}
// System.out.println("getCpcTripleType 12");
if (existsSepsetContainingY == existsSepsetNotContainingY) {
return CpcTripleType.AMBIGUOUS;
} else if (!existsSepsetNotContainingY) {
return CpcTripleType.NONCOLLIDER;
} else {
return CpcTripleType.COLLIDER;
}
}
// Trying to optimize the search for 4-cliques a bit.
private Set<Set<Integer>> findPureClusters2(
List<Integer> _variables, Map<Node, Set<Node>> adjacencies) {
System.out.println("Original variables = " + variables);
Set<Set<Integer>> clusters = new HashSet<Set<Integer>>();
List<Integer> allVariables = new ArrayList<Integer>();
Set<Node> foundVariables = new HashSet<Node>();
for (int i = 0; i < this.variables.size(); i++) allVariables.add(i);
for (int x : _variables) {
Node nodeX = variables.get(x);
if (foundVariables.contains(nodeX)) continue;
List<Node> adjX = new ArrayList<Node>(adjacencies.get(nodeX));
adjX.removeAll(foundVariables);
if (adjX.size() < 3) continue;
for (Node nodeY : adjX) {
if (foundVariables.contains(nodeY)) continue;
List<Node> commonXY = new ArrayList<Node>(adjacencies.get(nodeY));
commonXY.retainAll(adjX);
commonXY.removeAll(foundVariables);
for (Node nodeZ : commonXY) {
if (foundVariables.contains(nodeZ)) continue;
List<Node> commonXZ = new ArrayList<Node>(commonXY);
commonXZ.retainAll(adjacencies.get(nodeZ));
commonXZ.removeAll(foundVariables);
for (Node nodeW : commonXZ) {
if (foundVariables.contains(nodeW)) continue;
if (!adjacencies.get(nodeY).contains(nodeW)) {
continue;
}
int y = variables.indexOf(nodeY);
int w = variables.indexOf(nodeW);
int z = variables.indexOf(nodeZ);
Set<Integer> cluster = quartet(x, y, z, w);
// Note that purity needs to be assessed with respect to all of the variables in order
// to
// remove all latent-measure impurities between pairs of latents.
if (pure(cluster, allVariables)) {
O:
for (int o : _variables) {
if (cluster.contains(o)) continue;
cluster.add(o);
if (!clique(cluster, adjacencies)) {
cluster.remove(o);
continue O;
}
// if (!allVariablesDependent(cluster)) {
// cluster.remove(o);
// continue O;
// }
List<Integer> _cluster = new ArrayList<Integer>(cluster);
ChoiceGenerator gen2 = new ChoiceGenerator(_cluster.size(), 4);
int[] choice2;
int count = 0;
while ((choice2 = gen2.next()) != null) {
int x2 = _cluster.get(choice2[0]);
int y2 = _cluster.get(choice2[1]);
int z2 = _cluster.get(choice2[2]);
int w2 = _cluster.get(choice2[3]);
Set<Integer> quartet = quartet(x2, y2, z2, w2);
// Optimizes for large clusters.
if (quartet.contains(o)) {
if (++count > 2) continue O;
}
if (quartet.contains(o) && !pure(quartet, allVariables)) {
cluster.remove(o);
continue O;
}
}
}
System.out.println(
"Cluster found: " + variablesForIndices(new ArrayList<Integer>(cluster)));
clusters.add(cluster);
foundVariables.addAll(variablesForIndices(new ArrayList<Integer>(cluster)));
}
}
}
}
}
return clusters;
}
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;
}
/**
* Calculates the error variance for the given error node, given all of the coefficient values in
* the model.
*
* @param error An error term in the model--i.e. a variable with NodeType.ERROR.
* @return The value of the error variance, or Double.NaN is the value is undefined.
*/
private double calculateErrorVarianceFromParams(Node error) {
error = semGraph.getNode(error.getName());
Node child = semGraph.getChildren(error).get(0);
List<Node> parents = semGraph.getParents(child);
double otherVariance = 0;
for (Node parent : parents) {
if (parent == error) continue;
double coef = getEdgeCoefficient(parent, child);
otherVariance += coef * coef;
}
if (parents.size() >= 2) {
ChoiceGenerator gen = new ChoiceGenerator(parents.size(), 2);
int[] indices;
while ((indices = gen.next()) != null) {
Node node1 = parents.get(indices[0]);
Node node2 = parents.get(indices[1]);
double coef1, coef2;
if (node1.getNodeType() != NodeType.ERROR) {
coef1 = getEdgeCoefficient(node1, child);
} else {
coef1 = 1;
}
if (node2.getNodeType() != NodeType.ERROR) {
coef2 = getEdgeCoefficient(node2, child);
} else {
coef2 = 1;
}
List<List<Node>> treks = GraphUtils.treksIncludingBidirected(semGraph, node1, node2);
double cov = 0.0;
for (List<Node> trek : treks) {
double product = 1.0;
for (int i = 1; i < trek.size(); i++) {
Node _node1 = trek.get(i - 1);
Node _node2 = trek.get(i);
Edge edge = semGraph.getEdge(_node1, _node2);
double factor;
if (Edges.isBidirectedEdge(edge)) {
factor = edgeParameters.get(edge);
} else if (!edgeParameters.containsKey(edge)) {
factor = 1;
} else if (semGraph.isParentOf(_node1, _node2)) {
factor = getEdgeCoefficient(_node1, _node2);
} else {
factor = getEdgeCoefficient(_node2, _node1);
}
product *= factor;
}
cov += product;
}
otherVariance += 2 * coef1 * coef2 * cov;
}
}
return 1.0 - otherVariance <= 0 ? Double.NaN : 1.0 - otherVariance;
}
