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

Example 51 with ChoiceGenerator

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

the class Dci method awayFromAncestorCycle.

// Does only the ancestor and cycle rules of these repeatedly until no changes
private void awayFromAncestorCycle(Graph graph) {
    while (changeFlag) {
        changeFlag = false;
        List<Node> nodes = graph.getNodes();
        for (Node B : nodes) {
            List<Node> adj = graph.getAdjacentNodes(B);
            if (adj.size() < 2) {
                continue;
            }
            ChoiceGenerator cg = new ChoiceGenerator(adj.size(), 2);
            int[] combination;
            while ((combination = cg.next()) != null) {
                Node A = adj.get(combination[0]);
                Node C = adj.get(combination[1]);
                // choice gen doesnt do diff orders, so must switch A & C around.
                awayFromAncestor(graph, A, B, C);
                awayFromAncestor(graph, C, B, A);
                awayFromCycle(graph, A, B, C);
                awayFromCycle(graph, C, B, A);
            }
        }
    }
    changeFlag = true;
}

Example 52 with ChoiceGenerator

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

the class CpcOrienter method orientUnshieldedTriples.

// public final Graph orientationForGraph(Dag trueGraph) {
// Graph graph = new EdgeListGraph(independenceTest.getVariable());
// 
// for (Edge edge : trueGraph.getEdges()) {
// Node nodeA = edge.getNode1();
// Node nodeB = edge.getNode2();
// 
// Node _nodeA = independenceTest.getVariable(nodeA.getNode());
// Node _nodeB = independenceTest.getVariable(nodeB.getNode());
// 
// graph.addUndirectedEdge(_nodeA, _nodeB);
// }
// 
// SearchGraphUtils.pcOrientbk(knowledge, graph, graph.getNodes());
// orientUnshieldedTriples(knowledge, getIndependenceTest(), depth);
// MeekRules meekRules = new MeekRules();
// meekRules.setKnowledge(knowledge);
// meekRules.orientImplied(graph);
// 
// return graph;
// }
// ==========================PRIVATE METHODS===========================//
@SuppressWarnings({ "SameParameterValue" })
private void orientUnshieldedTriples(IKnowledge knowledge, IndependenceTest test, int depth) {
    TetradLogger.getInstance().log("info", "Starting Collider Orientation:");
    colliderTriples = new HashSet<>();
    noncolliderTriples = new HashSet<>();
    ambiguousTriples = new HashSet<>();
    for (Node y : graph.getNodes()) {
        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]);
            if (this.graph.isAdjacentTo(x, z)) {
                continue;
            }
            allTriples.add(new Triple(x, y, z));
            CpcOrienter.TripleType type = getTripleType(x, y, z, test, depth);
            System.out.println(new Triple(x, y, z) + " " + type);
            if (type == CpcOrienter.TripleType.COLLIDER) {
                if (colliderAllowed(x, y, z, knowledge)) {
                    graph.setEndpoint(x, y, Endpoint.ARROW);
                    graph.setEndpoint(z, y, Endpoint.ARROW);
                    TetradLogger.getInstance().log("colliderOrientations", SearchLogUtils.colliderOrientedMsg(x, y, z));
                }
                colliderTriples.add(new Triple(x, y, z));
            } else if (type == CpcOrienter.TripleType.AMBIGUOUS) {
                Triple triple = new Triple(x, y, z);
                ambiguousTriples.add(triple);
                graph.addAmbiguousTriple(triple.getX(), triple.getY(), triple.getZ());
            } else {
                noncolliderTriples.add(new Triple(x, y, z));
            }
        }
    }
    TetradLogger.getInstance().log("info", "Finishing Collider Orientation.");
}

Example 53 with ChoiceGenerator

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

the class Ccd method doNodeCollider.

private void doNodeCollider(Graph graph, Map<Triple, Double> colliders, Map<Triple, Double> noncolliders, Node b) {
    List<Node> adjacentNodes = graph.getAdjacentNodes(b);
    if (adjacentNodes.size() < 2) {
        return;
    }
    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> adja = graph.getAdjacentNodes(a);
        double score = Double.POSITIVE_INFINITY;
        List<Node> S = null;
        DepthChoiceGenerator cg2 = new DepthChoiceGenerator(adja.size(), -1);
        int[] comb2;
        while ((comb2 = cg2.next()) != null) {
            List<Node> s = GraphUtils.asList(comb2, adja);
            independenceTest.isIndependent(a, c, s);
            double _score = independenceTest.getScore();
            if (_score < score) {
                score = _score;
                S = s;
            }
        }
        List<Node> adjc = graph.getAdjacentNodes(c);
        DepthChoiceGenerator cg3 = new DepthChoiceGenerator(adjc.size(), -1);
        int[] comb3;
        while ((comb3 = cg3.next()) != null) {
            List<Node> s = GraphUtils.asList(comb3, adjc);
            independenceTest.isIndependent(c, a, s);
            double _score = independenceTest.getScore();
            if (_score < score) {
                score = _score;
                S = s;
            }
        }
        // This could happen if there are undefined values and such.
        if (S == null) {
            continue;
        }
        if (S.contains(b)) {
            noncolliders.put(new Triple(a, b, c), score);
        } else {
            colliders.put(new Triple(a, b, c), score);
        }
    }
}

Example 54 with ChoiceGenerator

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

the class Cefs 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.
 */
private void prune(Node node, Graph graph, int depth) {
    TetradLogger.getInstance().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) {
            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 55 with ChoiceGenerator

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

the class BffBeam method getRemoveTriangleMoves.

private List<Move> getRemoveTriangleMoves(Graph graph) {
    List<Move> moves = new ArrayList<>();
    for (Node b : graph.getNodes()) {
        List<Node> adj = graph.getAdjacentNodes(b);
        if (adj.size() < 2)
            continue;
        ChoiceGenerator gen = new ChoiceGenerator(adj.size(), 2);
        int[] choice;
        while ((choice = gen.next()) != null) {
            List<Node> set = GraphUtils.asList(choice, adj);
            Node a = set.get(0);
            Node c = set.get(1);
            Edge edge1 = graph.getEdge(a, b);
            Edge edge2 = graph.getEdge(b, c);
            Edge edge3 = graph.getEdge(a, c);
            if (edge1 != null && edge2 != null && edge3 != null && edge1.pointsTowards(a) && edge3.pointsTowards(c) && edge2.pointsTowards(c)) {
                moves.add(new Move(Edges.directedEdge(b, c), Edges.directedEdge(c, a), Move.Type.SWAP));
            } else if (edge1 != null && edge2 != null && edge3 != null && edge3.pointsTowards(a) && edge1.pointsTowards(b) && edge2.pointsTowards(b)) {
                moves.add(new Move(Edges.directedEdge(b, c), Edges.directedEdge(b, a), Move.Type.SWAP));
            }
        }
    }
    return moves;
}