private Graph condense(Graph mimStructure, Graph mimbuildStructure) {
// System.out.println("Uncondensed: " + mimbuildStructure);
Map<Node, Node> substitutions = new HashMap<Node, Node>();
for (Node node : mimbuildStructure.getNodes()) {
for (Node _node : mimStructure.getNodes()) {
if (node.getName().startsWith(_node.getName())) {
substitutions.put(node, _node);
break;
}
substitutions.put(node, node);
}
}
HashSet<Node> nodes = new HashSet<Node>(substitutions.values());
Graph graph = new EdgeListGraph(new ArrayList<Node>(nodes));
for (Edge edge : mimbuildStructure.getEdges()) {
Node node1 = substitutions.get(edge.getNode1());
Node node2 = substitutions.get(edge.getNode2());
if (node1 == node2) continue;
if (graph.isAdjacentTo(node1, node2)) continue;
graph.addEdge(new Edge(node1, node2, edge.getEndpoint1(), edge.getEndpoint2()));
}
// System.out.println("Condensed: " + graph);
return graph;
}
/** Returns true iif the given set forms a clique in the given graph. */
private static boolean isClique(List<Node> nodes, Graph graph) {
for (int i = 0; i < nodes.size() - 1; i++) {
for (int j = i + 1; j < nodes.size(); j++) {
if (!graph.isAdjacentTo(nodes.get(i), nodes.get(j))) {
return false;
}
}
}
return true;
}
/**
* Forward equivalence search.
*
* @param graph The graph in the state prior to the forward equivalence search.
*/
private void fes(Graph graph, List<Node> nodes) {
TetradLogger.getInstance().log("info", "** FORWARD EQUIVALENCE SEARCH");
lookupArrows = new HashMap<OrderedPair, Set<Arrow>>();
initializeArrowsForward(nodes);
while (!sortedArrows.isEmpty()) {
Arrow arrow = sortedArrows.first();
sortedArrows.remove(arrow);
Node x = arrow.getX();
Node y = arrow.getY();
clearArrow(x, y);
if (graph.isAdjacentTo(x, y)) {
continue;
}
if (!validInsert(x, y, arrow.getHOrT(), arrow.getNaYX(), graph)) {
continue;
}
List<Node> t = arrow.getHOrT();
double bump = arrow.getBump();
Set<Edge> edges = graph.getEdges();
insert(x, y, t, graph, bump);
score += bump;
rebuildPattern(graph);
// Try to avoid duplicating scoring calls. First clear out all of the edges that need to be
// changed,
// then change them, checking to see if they're already been changed. I know, roundabout, but
// there's
// a performance boost.
for (Edge edge : graph.getEdges()) {
if (!edges.contains(edge)) {
reevaluateForward(graph, nodes, edge.getNode1(), edge.getNode2());
}
}
storeGraph(graph);
}
}
/** Get all nodes that are connected to Y by an undirected edge and not adjacent to X. */
private static List<Node> getTNeighbors(Node x, Node y, Graph graph) {
List<Edge> yEdges = graph.getEdges(y);
List<Node> tNeighbors = new ArrayList<Node>();
for (Edge edge : yEdges) {
if (!Edges.isUndirectedEdge(edge)) {
continue;
}
Node z = edge.getDistalNode(y);
if (graph.isAdjacentTo(z, x)) {
continue;
}
tNeighbors.add(z);
}
return tNeighbors;
}
/**
* Find all nodes that are connected to Y by an undirected edge that are adjacent to X (that is,
* by undirected or directed edge).
*/
private static List<Node> getNaYX(Node x, Node y, Graph graph) {
List<Edge> yEdges = graph.getEdges(y);
List<Node> nayx = new ArrayList<Node>();
for (Edge edge : yEdges) {
if (!Edges.isUndirectedEdge(edge)) {
continue;
}
Node z = edge.getDistalNode(y);
if (!graph.isAdjacentTo(z, x)) {
continue;
}
nayx.add(z);
}
return nayx;
}
// Invalid if then nodes or graph changes.
private void calculateArrowsBackward(Node x, Node y, Graph graph) {
if (x == y) {
return;
}
if (!graph.isAdjacentTo(x, y)) {
return;
}
if (!knowledgeEmpty()) {
if (!getKnowledge().noEdgeRequired(x.getName(), y.getName())) {
return;
}
}
List<Node> naYX = getNaYX(x, y, graph);
clearArrow(x, y);
List<Node> _naYX = new ArrayList<Node>(naYX);
DepthChoiceGenerator gen = new DepthChoiceGenerator(_naYX.size(), _naYX.size());
int[] choice;
while ((choice = gen.next()) != null) {
List<Node> H = GraphUtils.asList(choice, _naYX);
if (!knowledgeEmpty()) {
if (!validSetByKnowledge(y, H)) {
continue;
}
}
double bump = deleteEval(x, y, H, naYX, graph);
if (bump > 0.0) {
Arrow arrow = new Arrow(bump, x, y, H, naYX);
sortedArrows.add(arrow);
addLookupArrow(x, y, arrow);
}
}
}
private void addRequiredEdges(Graph graph) {
if (true) return;
if (knowledgeEmpty()) return;
for (Iterator<KnowledgeEdge> it = getKnowledge().requiredEdgesIterator(); it.hasNext(); ) {
KnowledgeEdge next = it.next();
Node nodeA = graph.getNode(next.getFrom());
Node nodeB = graph.getNode(next.getTo());
if (!graph.isAncestorOf(nodeB, nodeA)) {
graph.removeEdges(nodeA, nodeB);
graph.addDirectedEdge(nodeA, nodeB);
TetradLogger.getInstance()
.log("insertedEdges", "Adding edge by knowledge: " + graph.getEdge(nodeA, nodeB));
}
}
for (Edge edge : graph.getEdges()) {
final String A = edge.getNode1().getName();
final String B = edge.getNode2().getName();
if (knowledge.isForbidden(A, B)) {
Node nodeA = edge.getNode1();
Node nodeB = edge.getNode2();
if (nodeA != null
&& nodeB != null
&& graph.isAdjacentTo(nodeA, nodeB)
&& !graph.isChildOf(nodeA, nodeB)) {
if (!graph.isAncestorOf(nodeA, nodeB)) {
graph.removeEdges(nodeA, nodeB);
graph.addDirectedEdge(nodeB, nodeA);
TetradLogger.getInstance()
.log("insertedEdges", "Adding edge by knowledge: " + graph.getEdge(nodeB, nodeA));
}
}
if (!graph.isChildOf(nodeA, nodeB)
&& getKnowledge().isForbidden(nodeA.getName(), nodeB.getName())) {
if (!graph.isAncestorOf(nodeA, nodeB)) {
graph.removeEdges(nodeA, nodeB);
graph.addDirectedEdge(nodeB, nodeA);
TetradLogger.getInstance()
.log("insertedEdges", "Adding edge by knowledge: " + graph.getEdge(nodeB, nodeA));
}
}
} else if (knowledge.isForbidden(B, A)) {
Node nodeA = edge.getNode2();
Node nodeB = edge.getNode1();
if (nodeA != null
&& nodeB != null
&& graph.isAdjacentTo(nodeA, nodeB)
&& !graph.isChildOf(nodeA, nodeB)) {
if (!graph.isAncestorOf(nodeA, nodeB)) {
graph.removeEdges(nodeA, nodeB);
graph.addDirectedEdge(nodeB, nodeA);
TetradLogger.getInstance()
.log("insertedEdges", "Adding edge by knowledge: " + graph.getEdge(nodeB, nodeA));
}
}
if (!graph.isChildOf(nodeA, nodeB)
&& getKnowledge().isForbidden(nodeA.getName(), nodeB.getName())) {
if (!graph.isAncestorOf(nodeA, nodeB)) {
graph.removeEdges(nodeA, nodeB);
graph.addDirectedEdge(nodeB, nodeA);
TetradLogger.getInstance()
.log("insertedEdges", "Adding edge by knowledge: " + graph.getEdge(nodeB, nodeA));
}
}
}
}
}
/** Do an actual deletion (Definition 13 from Chickering, 2002). */
private void delete(Node x, Node y, List<Node> subset, Graph graph, double bump) {
Edge trueEdge = null;
if (trueGraph != null) {
Node _x = trueGraph.getNode(x.getName());
Node _y = trueGraph.getNode(y.getName());
trueEdge = trueGraph.getEdge(_x, _y);
}
if (log && verbose) {
Edge oldEdge = graph.getEdge(x, y);
String label = trueGraph != null && trueEdge != null ? "*" : "";
TetradLogger.getInstance()
.log(
"deletedEdges",
(graph.getNumEdges() - 1)
+ ". DELETE "
+ oldEdge
+ " "
+ subset
+ " ("
+ bump
+ ") "
+ label);
out.println(
(graph.getNumEdges() - 1)
+ ". DELETE "
+ oldEdge
+ " "
+ subset
+ " ("
+ bump
+ ") "
+ label);
} else {
int numEdges = graph.getNumEdges() - 1;
if (numEdges % 50 == 0) out.println(numEdges);
}
graph.removeEdge(x, y);
for (Node h : subset) {
Edge oldEdge = graph.getEdge(y, h);
graph.removeEdge(y, h);
graph.addDirectedEdge(y, h);
if (log) {
TetradLogger.getInstance()
.log("directedEdges", "--- Directing " + oldEdge + " to " + graph.getEdge(y, h));
}
if (verbose) {
out.println("--- Directing " + oldEdge + " to " + graph.getEdge(y, h));
}
if (Edges.isUndirectedEdge(graph.getEdge(x, h))) {
if (!graph.isAdjacentTo(x, h))
throw new IllegalArgumentException("Not adjacent: " + x + ", " + h);
oldEdge = graph.getEdge(x, h);
graph.removeEdge(x, h);
graph.addDirectedEdge(x, h);
if (log) {
TetradLogger.getInstance()
.log("directedEdges", "--- Directing " + oldEdge + " to " + graph.getEdge(x, h));
}
if (verbose) {
out.println("--- Directing " + oldEdge + " to " + graph.getEdge(x, h));
}
}
}
}
// serial.
private void insert(Node x, Node y, List<Node> t, Graph graph, double bump) {
if (graph.isAdjacentTo(x, y)) {
return; // The initial graph may already have put this edge in the graph.
// throw new IllegalArgumentException(x + " and " + y + " are already adjacent in
// the graph.");
}
Edge trueEdge = null;
if (trueGraph != null) {
Node _x = trueGraph.getNode(x.getName());
Node _y = trueGraph.getNode(y.getName());
trueEdge = trueGraph.getEdge(_x, _y);
}
graph.addDirectedEdge(x, y);
if (log) {
String label = trueGraph != null && trueEdge != null ? "*" : "";
TetradLogger.getInstance()
.log(
"insertedEdges",
graph.getNumEdges()
+ ". INSERT "
+ graph.getEdge(x, y)
+ " "
+ t
+ " "
+ bump
+ " "
+ label);
} else {
int numEdges = graph.getNumEdges() - 1;
if (verbose) {
if (numEdges % 50 == 0) out.println(numEdges);
}
}
if (verbose) {
String label = trueGraph != null && trueEdge != null ? "*" : "";
out.println(
graph.getNumEdges()
+ ". INSERT "
+ graph.getEdge(x, y)
+ " "
+ t
+ " "
+ bump
+ " "
+ label);
} else {
int numEdges = graph.getNumEdges() - 1;
if (verbose) {
if (numEdges % 50 == 0) out.println(numEdges);
}
}
for (Node _t : t) {
Edge oldEdge = graph.getEdge(_t, y);
if (oldEdge == null) throw new IllegalArgumentException("Not adjacent: " + _t + ", " + y);
graph.removeEdge(_t, y);
graph.addDirectedEdge(_t, y);
if (log && verbose) {
TetradLogger.getInstance()
.log("directedEdges", "--- Directing " + oldEdge + " to " + graph.getEdge(_t, y));
out.println("--- Directing " + oldEdge + " to " + graph.getEdge(_t, y));
}
}
}