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

Example 6 with ChoiceGenerator

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

the class GFciMax method modifiedR0.

// Due to Spirtes.
public void modifiedR0(Graph fgesGraph) {
    graph.reorientAllWith(Endpoint.CIRCLE);
    fciOrientbk(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 7 with ChoiceGenerator

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

the class FgesD method calculateArrowsForward.

// Calculates the new arrows for an a->b edge.
private void calculateArrowsForward(Node a, Node b) {
    if (mode == Mode.heuristicSpeedup && !effectEdgesGraph.isAdjacentTo(a, b))
        return;
    if (adjacencies != null && !adjacencies.isAdjacentTo(a, b))
        return;
    this.neighbors.put(b, getNeighbors(b));
    if (a == b)
        throw new IllegalArgumentException();
    if (existsKnowledge()) {
        if (getKnowledge().isForbidden(a.getName(), b.getName())) {
            return;
        }
    }
    Set<Node> naYX = getNaYX(a, b);
    if (!isClique(naYX))
        return;
    List<Node> TNeighbors = getTNeighbors(a, b);
    Set<Set<Node>> previousCliques = new HashSet<>();
    previousCliques.add(new HashSet<Node>());
    Set<Set<Node>> newCliques = new HashSet<>();
    FOR: for (int i = 0; i <= TNeighbors.size(); i++) {
        final ChoiceGenerator gen = new ChoiceGenerator(TNeighbors.size(), i);
        int[] choice;
        while ((choice = gen.next()) != null) {
            Set<Node> T = GraphUtils.asSet(choice, TNeighbors);
            Set<Node> union = new HashSet<>(naYX);
            union.addAll(T);
            boolean foundAPreviousClique = false;
            for (Set<Node> clique : previousCliques) {
                if (union.containsAll(clique)) {
                    foundAPreviousClique = true;
                    break;
                }
            }
            if (!foundAPreviousClique) {
                break FOR;
            }
            if (!isClique(union))
                continue;
            newCliques.add(union);
            double bump = insertEval(a, b, T, naYX, hashIndices);
            if (bump > 0) {
                addArrow(a, b, naYX, T, bump);
            }
        // if (mode == Mode.heuristicSpeedup && union.isEmpty() && score.isEffectEdge(bump) &&
        // !effectEdgesGraph.isAdjacentTo(a, b) && graph.getParents(b).isEmpty()) {
        // effectEdgesGraph.addUndirectedEdge(a, b);
        // }
        }
        previousCliques = newCliques;
        newCliques = new HashSet<>();
    }
}

Example 8 with ChoiceGenerator

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

the class FgesD method calculateArrowsBackward.

// Calculates the arrows for the removal in the backward direction.
private void calculateArrowsBackward(Node a, Node b) {
    if (existsKnowledge()) {
        if (!getKnowledge().noEdgeRequired(a.getName(), b.getName())) {
            return;
        }
    }
    Set<Node> naYX = getNaYX(a, b);
    List<Node> _naYX = new ArrayList<>(naYX);
    final int _depth = _naYX.size();
    for (int i = 0; i <= _depth; i++) {
        final ChoiceGenerator gen = new ChoiceGenerator(_naYX.size(), i);
        int[] choice;
        while ((choice = gen.next()) != null) {
            Set<Node> diff = GraphUtils.asSet(choice, _naYX);
            Set<Node> h = new HashSet<>(_naYX);
            h.removeAll(diff);
            if (existsKnowledge()) {
                if (!validSetByKnowledge(b, h)) {
                    continue;
                }
            }
            double bump = deleteEval(a, b, diff, naYX, hashIndices);
            if (bump > 0.0) {
                addArrow(a, b, naYX, h, bump);
            }
        }
    }
}

Example 9 with ChoiceGenerator

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

the class FgesOld method calculateArrowsForward.

// Calculates the new arrows for an a->b edge.
private void calculateArrowsForward(Node a, Node b) {
    if (isHeuristicSpeedup() && !effectEdgesGraph.isAdjacentTo(a, b))
        return;
    if (adjacencies != null && !adjacencies.isAdjacentTo(a, b))
        return;
    this.neighbors.put(b, getNeighbors(b));
    if (existsKnowledge()) {
        if (getKnowledge().isForbidden(a.getName(), b.getName())) {
            return;
        }
    }
    Set<Node> naYX = getNaYX(a, b);
    if (!GraphUtils.isClique(naYX, this.graph))
        return;
    List<Node> TNeighbors = getTNeighbors(a, b);
    final int _depth = Math.min(TNeighbors.size(), depth == -1 ? 1000 : depth);
    Set<Set<Node>> previousCliques = new HashSet<>();
    previousCliques.add(new HashSet<Node>());
    Set<Set<Node>> newCliques = new HashSet<>();
    FOR: for (int i = 0; i <= _depth; i++) {
        final ChoiceGenerator gen = new ChoiceGenerator(TNeighbors.size(), i);
        int[] choice;
        while ((choice = gen.next()) != null) {
            Set<Node> T = GraphUtils.asSet(choice, TNeighbors);
            Set<Node> union = new HashSet<>(naYX);
            union.addAll(T);
            boolean foundAPreviousClique = false;
            for (Set<Node> clique : previousCliques) {
                if (union.containsAll(clique)) {
                    foundAPreviousClique = true;
                    break;
                }
            }
            if (!foundAPreviousClique) {
                break FOR;
            }
            if (!GraphUtils.isClique(union, this.graph))
                continue;
            newCliques.add(union);
            double bump = insertEval(a, b, T, naYX, hashIndices);
            if (bump > 0.0) {
                addArrow(a, b, naYX, T, bump);
            }
            if (isHeuristicSpeedup() && union.isEmpty() && fgesScore.isEffectEdge(bump) && !effectEdgesGraph.isAdjacentTo(a, b) && graph.getParents(b).isEmpty()) {
                effectEdgesGraph.addUndirectedEdge(a, b);
            }
        }
        previousCliques = newCliques;
        newCliques = new HashSet<>();
    }
}

Example 10 with ChoiceGenerator

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

the class GFci method modifiedR0.

// Due to Spirtes.
public void modifiedR0(Graph fgesGraph) {
    graph.reorientAllWith(Endpoint.CIRCLE);
    fciOrientbk(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);
                }
            }
        }
    }
}