Examples with ChoiceGenerator edu.cmu.tetrad.util.ChoiceGenerator used on opensource projects

Example 61 with ChoiceGenerator

use of edu.cmu.tetrad.util.ChoiceGenerator in project tetrad by cmu-phil.

the class Mbfs method orientUnshieldedTriples.

private void orientUnshieldedTriples(IKnowledge knowledge, Graph graph, IndependenceTest test, int depth, List<Node> nodes) {
    logger.log("info", "Starting Collider Orientation:");
    colliderTriples = new HashSet<>();
    noncolliderTriples = new HashSet<>();
    ambiguousTriples = new HashSet<>();
    if (nodes == null) {
        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) {
            if (Thread.currentThread().isInterrupted()) {
                break;
            }
            Node x = adjacentNodes.get(combination[0]);
            Node z = adjacentNodes.get(combination[1]);
            if (graph.isAdjacentTo(x, z)) {
                continue;
            }
            allTriples.add(new Triple(x, y, z));
            TripleType type = getTripleType(graph, x, y, z, test, depth);
            if (type == TripleType.COLLIDER) {
                if (colliderAllowed(x, y, z, knowledge)) {
                    graph.setEndpoint(x, y, Endpoint.ARROW);
                    graph.setEndpoint(z, y, Endpoint.ARROW);
                    logger.log("tripleClassifications", "Collider oriented: " + Triple.pathString(graph, x, y, z));
                }
                colliderTriples.add(new Triple(x, y, z));
            } else if (type == TripleType.AMBIGUOUS) {
                Triple triple = new Triple(x, y, z);
                ambiguousTriples.add(triple);
                graph.addAmbiguousTriple(triple.getX(), triple.getY(), triple.getZ());
                logger.log("tripleClassifications", "tripleClassifications: " + Triple.pathString(graph, x, y, z));
            } else {
                noncolliderTriples.add(new Triple(x, y, z));
                logger.log("tripleClassifications", "tripleClassifications: " + Triple.pathString(graph, x, y, z));
            }
        }
    }
    logger.log("info", "Finishing Collider Orientation.");
}

Example 62 with ChoiceGenerator

use of edu.cmu.tetrad.util.ChoiceGenerator in project tetrad by cmu-phil.

the class Mbfs method prune.

/**
 * Tries node remove the edge node---from using adjacent nodes of node 'from', then tries node remove each other
 * edge adjacent node 'from' using remaining edges adjacent node 'from.' If the edge 'node' is removed, the method
 * immediately returns.
 *
 * @param node  The node about which pruning it to take place.
 * @param graph The getModel search graph, to be modified by pruning.
 * @param depth The maximum number of conditioning variables.
 */
private void prune(Node node, Graph graph, int depth) {
    logger.log("pruning", "Trying to remove edges adjacent to node " + node + ", depth = " + depth + ".");
    // Otherwise, try removing all other edges adjacent node node. Return
    // true if more edges could be removed at the next depth.
    List<Node> a = new LinkedList<>(graph.getAdjacentNodes(node));
    NEXT_EDGE: for (Node y : a) {
        List<Node> adjNode = new LinkedList<>(graph.getAdjacentNodes(node));
        adjNode.remove(y);
        adjNode = possibleParents(node, adjNode);
        if (adjNode.size() < depth) {
            continue;
        }
        ChoiceGenerator cg = new ChoiceGenerator(adjNode.size(), depth);
        int[] choice;
        while ((choice = cg.next()) != null) {
            if (Thread.currentThread().isInterrupted()) {
                break;
            }
            List<Node> condSet = GraphUtils.asList(choice, adjNode);
            if (independent(node, y, condSet) && !edgeRequired(node, y)) {
                graph.removeEdge(node, y);
                // The target itself must not be removed.
                if (graph.getEdges(y).isEmpty() && y != getTarget()) {
                    graph.removeNode(y);
                }
                continue NEXT_EDGE;
            }
        }
    }
    int numAdjacents = graph.getAdjacentNodes(node).size();
    noteMaxAtDepth(depth, numAdjacents, node);
}

Example 63 with ChoiceGenerator

use of edu.cmu.tetrad.util.ChoiceGenerator in project tetrad by cmu-phil.

the class MeekRulesPattern method meekR3.

/**
 * Meek's rule R3. If a--b, a--c, a--d, c-->b, d-->b, then orient a-->b.
 */
public boolean meekR3(Graph graph, IKnowledge IKnowledge) {
    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<>(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 (!isUnshieldedNoncollider(c, a, d, graph)) {
                    continue;
                }
                if (graph.isDirectedFromTo(c, b) && graph.isDirectedFromTo(d, b)) {
                    if (isArrowpointAllowed(a, b, IKnowledge) && !createsCycle(a, b, graph)) {
                        graph.setEndpoint(a, b, Endpoint.ARROW);
                        this.logger.log("impliedOrientation", SearchLogUtils.edgeOrientedMsg("Meek R3", graph.getEdge(a, b)));
                        changed = true;
                        meekR2(graph, IKnowledge);
                        break;
                    }
                }
            }
        }
    }
    return changed;
}

Example 64 with ChoiceGenerator

use of edu.cmu.tetrad.util.ChoiceGenerator in project tetrad by cmu-phil.

the class MeekRulesPattern method meekR1Locally.

public boolean meekR1Locally(Graph graph, IKnowledge IKnowledge) {
    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]);
            // Skip triples that are shielded.
            if (graph.isAdjacentTo(b, c)) {
                continue;
            }
            if (graph.getEndpoint(b, a) == Endpoint.ARROW && graph.isUndirectedFromTo(a, c)) {
                if (!isUnshieldedNoncollider(b, a, c, graph)) {
                    continue;
                }
                if (isArrowpointAllowed(a, c, IKnowledge) && !createsCycle(a, c, graph)) {
                    graph.setEndpoint(a, c, Endpoint.ARROW);
                    this.logger.log("impliedOrientation", SearchLogUtils.edgeOrientedMsg("Meek R1 triangle (" + b + "-->" + a + "---" + c + ")", graph.getEdge(a, c)));
                    changed = true;
                    meekR2(graph, IKnowledge);
                }
            } else if (graph.getEndpoint(c, a) == Endpoint.ARROW && graph.isUndirectedFromTo(a, b)) {
                if (!isUnshieldedNoncollider(b, a, c, graph)) {
                    continue;
                }
                if (isArrowpointAllowed(a, b, IKnowledge) && !createsCycle(a, b, graph)) {
                    graph.setEndpoint(a, b, Endpoint.ARROW);
                    this.logger.log("impliedOrientation", SearchLogUtils.edgeOrientedMsg("Meek R1 triangle (" + c + "-->" + a + "---" + b + ")", graph.getEdge(a, b)));
                    changed = true;
                    meekR2(graph, IKnowledge);
                }
            }
        }
    }
    return changed;
}

Example 65 with ChoiceGenerator

use of edu.cmu.tetrad.util.ChoiceGenerator in project tetrad by cmu-phil.

the class PurifyTetradBased method listCrossConstructPValues.

private List<Double> listCrossConstructPValues(List<int[]> clustering, boolean[] eliminated, double cutoff) {
    List<Double> allPValues = new ArrayList<>();
    boolean countable = false;
    for (int p1 = 0; p1 < clustering.size(); p1++) {
        for (int p2 = p1 + 1; p2 < clustering.size(); p2++) {
            int[] cluster1 = clustering.get(p1);
            int[] cluster2 = clustering.get(p2);
            if (cluster1.length >= 3 && cluster2.length >= 1) {
                ChoiceGenerator gen1 = new ChoiceGenerator(cluster1.length, 3);
                int[] choice1;
                while ((choice1 = gen1.next()) != null) {
                    ChoiceGenerator gen2 = new ChoiceGenerator(cluster2.length, 1);
                    int[] choice2;
                    while ((choice2 = gen2.next()) != null) {
                        List<Integer> crossCluster = new ArrayList<>();
                        for (int i : choice1) crossCluster.add(cluster1[i]);
                        for (int i : choice2) crossCluster.add(cluster2[i]);
                        List<Double> pValues = listPValues(crossCluster, eliminated, cutoff);
                        if (pValues != null) {
                            countable = true;
                            allPValues.addAll(pValues);
                        }
                    }
                }
            }
            if (cluster2.length >= 3 && cluster1.length >= 1) {
                ChoiceGenerator gen1 = new ChoiceGenerator(cluster2.length, 3);
                int[] choice1;
                while ((choice1 = gen1.next()) != null) {
                    ChoiceGenerator gen2 = new ChoiceGenerator(cluster1.length, 1);
                    int[] choice2;
                    while ((choice2 = gen2.next()) != null) {
                        List<Integer> crossCluster = new ArrayList<>();
                        for (int i : choice1) crossCluster.add(cluster2[i]);
                        for (int i : choice2) crossCluster.add(cluster1[i]);
                        List<Double> pValues = listPValues(crossCluster, eliminated, cutoff);
                        if (pValues != null) {
                            countable = true;
                            allPValues.addAll(pValues);
                        }
                    }
                }
            }
            if (cluster1.length >= 2 && cluster2.length >= 2) {
                ChoiceGenerator gen1 = new ChoiceGenerator(cluster1.length, 2);
                int[] choice1;
                while ((choice1 = gen1.next()) != null) {
                    ChoiceGenerator gen2 = new ChoiceGenerator(cluster2.length, 2);
                    int[] choice2;
                    while ((choice2 = gen2.next()) != null) {
                        List<Integer> crossCluster = new ArrayList<>();
                        for (int i : choice1) crossCluster.add(cluster1[i]);
                        for (int i : choice2) crossCluster.add(cluster2[i]);
                        List<Double> pValues = listPValues2by2(crossCluster, eliminated, cutoff);
                        if (pValues != null) {
                            countable = true;
                            allPValues.addAll(pValues);
                        }
                    }
                }
            }
        }
    }
    return countable ? allPValues : null;
}