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

Example 11 with ChoiceGenerator

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

the class GFci method search.

// ========================PUBLIC METHODS==========================//
public Graph search() {
    long time1 = System.currentTimeMillis();
    List<Node> nodes = getIndependenceTest().getVariables();
    logger.log("info", "Starting FCI algorithm.");
    logger.log("info", "Independence test = " + getIndependenceTest() + ".");
    this.graph = new EdgeListGraphSingleConnections(nodes);
    Fges fges = new Fges(score);
    fges.setKnowledge(getKnowledge());
    fges.setVerbose(verbose);
    fges.setNumPatternsToStore(0);
    fges.setFaithfulnessAssumed(faithfulnessAssumed);
    fges.setMaxDegree(maxDegree);
    fges.setOut(out);
    graph = fges.search();
    Graph fgesGraph = new EdgeListGraphSingleConnections(graph);
    sepsets = new SepsetsGreedy(fgesGraph, independenceTest, null, maxDegree);
    for (Node b : nodes) {
        if (Thread.currentThread().isInterrupted()) {
            break;
        }
        List<Node> adjacentNodes = fgesGraph.getAdjacentNodes(b);
        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 a = adjacentNodes.get(combination[0]);
            Node c = adjacentNodes.get(combination[1]);
            if (graph.isAdjacentTo(a, c) && fgesGraph.isAdjacentTo(a, c)) {
                if (sepsets.getSepset(a, c) != null) {
                    graph.removeEdge(a, c);
                }
            }
        }
    }
    modifiedR0(fgesGraph);
    FciOrient fciOrient = new FciOrient(sepsets);
    fciOrient.setVerbose(verbose);
    fciOrient.setOut(out);
    fciOrient.setKnowledge(getKnowledge());
    fciOrient.setCompleteRuleSetUsed(completeRuleSetUsed);
    fciOrient.setMaxPathLength(maxPathLength);
    fciOrient.doFinalOrientation(graph);
    GraphUtils.replaceNodes(graph, independenceTest.getVariables());
    long time2 = System.currentTimeMillis();
    elapsedTime = time2 - time1;
    graph.setPag(true);
    return graph;
}

Example 12 with ChoiceGenerator

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

the class GPc method modifiedR0.

// Due to Spirtes.
public void modifiedR0(Graph fgesGraph) {
    graph.reorientAllWith(Endpoint.TAIL);
    pcOrientBk(knowledge, graph, graph.getNodes());
    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]);
            if (fgesGraph.isDefCollider(a, b, c)) {
                graph.setEndpoint(a, b, Endpoint.ARROW);
                graph.setEndpoint(c, b, Endpoint.ARROW);
            } else if (fgesGraph.isAdjacentTo(a, c) && !graph.isAdjacentTo(a, c)) {
                List<Node> sepset = sepsets.getSepset(a, c);
                if (sepset != null && !sepset.contains(b)) {
                    graph.setEndpoint(a, b, Endpoint.ARROW);
                    graph.setEndpoint(c, b, Endpoint.ARROW);
                }
            }
        }
    }
}

Example 13 with ChoiceGenerator

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

the class FciMax method doNode.

private void doNode(Graph graph, Map<Triple, Double> scores, 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;
            }
        }
        // S actually has to be non-null here, but the compiler doesn't know that.
        if (S != null && !S.contains(b)) {
            scores.put(new Triple(a, b, c), score);
        }
    }
}

Example 14 with ChoiceGenerator

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

the class FciOrientT method rulesR1R2cycle.

// Does all 3 of these rules at once instead of going through all
// triples multiple times per iteration of doFinalOrientation.
public void rulesR1R2cycle(Graph graph) {
    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.
            ruleR1(A, B, C, graph);
            ruleR1(C, B, A, graph);
            ruleR2(A, B, C, graph);
            ruleR2(C, B, A, graph);
        }
    }
}

Example 15 with ChoiceGenerator

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

the class FciOrientT method ruleR6R7.

/**
 * Implements Zhang's rules R6 and R7, applies them over the graph once. Orient single tails. R6: If A---Bo-*C then
 * A---B--*C. R7: If A--oBo-*C and A,C nonadjacent, then A--oB--*C
 */
public void ruleR6R7(Graph graph) {
    List<Node> nodes = graph.getNodes();
    for (Node b : nodes) {
        List<Node> adjacents = graph.getAdjacentNodes(b);
        if (adjacents.size() < 2)
            continue;
        ChoiceGenerator cg = new ChoiceGenerator(adjacents.size(), 2);
        for (int[] choice = cg.next(); choice != null; choice = cg.next()) {
            Node a = adjacents.get(choice[0]);
            Node c = adjacents.get(choice[1]);
            if (graph.isAdjacentTo(a, c))
                continue;
            if (!(graph.getEndpoint(b, a) == Endpoint.TAIL))
                continue;
            if (!(graph.getEndpoint(c, b) == Endpoint.CIRCLE))
                continue;
            if (graph.getEndpoint(a, b) == Endpoint.TAIL) {
                // We know A---Bo-*C: R6 applies!
                graph.setEndpoint(c, b, Endpoint.TAIL);
                logger.log("impliedOrientations", SearchLogUtils.edgeOrientedMsg("Single tails (tail)", graph.getEdge(c, b)));
                changeFlag = true;
            }
            if (graph.getEndpoint(a, b) == Endpoint.CIRCLE) {
                // if (graph.isAdjacentTo(a, c)) continue;
                logger.log("impliedOrientations", SearchLogUtils.edgeOrientedMsg("Single tails (tail)", graph.getEdge(c, b)));
                // We know A--oBo-*C and A,C nonadjacent: R7 applies!
                graph.setEndpoint(c, b, Endpoint.TAIL);
                changeFlag = true;
            }
        }
    }
}