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

Example 21 with ChoiceGenerator

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

the class Vcpc method getPopulationTripleType.

public CpcTripleType getPopulationTripleType(Node x, Node y, Node z, IndependenceTest test, int depth, Graph graph, boolean verbose) {
    if (facts == null)
        throw new NullPointerException("Need independence facts as a parent");
    // JOE HERE ARE THE INDEPENDENCE FACTS
    System.out.println("NameS" + facts.getVariableNames());
    int numSepsetsContainingY = 0;
    int numSepsetsNotContainingY = 0;
    List<Node> _nodes = graph.getAdjacentNodes(x);
    _nodes.remove(z);
    TetradLogger.getInstance().log("adjacencies", "Adjacents for " + x + "--" + y + "--" + z + " = " + _nodes);
    int _depth = depth;
    if (_depth == -1) {
        _depth = 1000;
    }
    _depth = Math.min(_depth, _nodes.size());
    while (true) {
        for (int d = 0; d <= _depth; d++) {
            ChoiceGenerator cg = new ChoiceGenerator(_nodes.size(), d);
            int[] choice;
            while ((choice = cg.next()) != null) {
                List<Node> cond = GraphUtils.asList(choice, _nodes);
                if (facts.isIndependent(x, z, cond)) {
                    // if (verbose) {
                    System.out.println("Indep Fact said: " + x + " _||_ " + z + " | " + cond);
                    if (cond.contains(y)) {
                        numSepsetsContainingY++;
                    } else {
                        numSepsetsNotContainingY++;
                    }
                } else {
                    System.out.println("This is not Indep by facts: " + x + " _||_ " + z + " | " + cond);
                }
                // 
                if (numSepsetsContainingY > 0 && numSepsetsNotContainingY > 0) {
                    return CpcTripleType.AMBIGUOUS;
                }
            }
        }
        _nodes = graph.getAdjacentNodes(z);
        _nodes.remove(x);
        TetradLogger.getInstance().log("adjacencies", "Adjacents for " + x + "--" + y + "--" + z + " = " + _nodes);
        _depth = depth;
        if (_depth == -1) {
            _depth = 1000;
        }
        _depth = Math.min(_depth, _nodes.size());
        for (int d = 0; d <= _depth; d++) {
            ChoiceGenerator cg = new ChoiceGenerator(_nodes.size(), d);
            int[] choice;
            while ((choice = cg.next()) != null) {
                List<Node> cond = GraphUtils.asList(choice, _nodes);
                if (test.isIndependent(x, z, cond)) {
                    if (cond.contains(y)) {
                        numSepsetsContainingY++;
                    } else {
                        numSepsetsNotContainingY++;
                    }
                }
                if (numSepsetsContainingY > 0 && numSepsetsNotContainingY > 0) {
                    return CpcTripleType.AMBIGUOUS;
                }
            }
        }
        break;
    }
    if (numSepsetsContainingY > 0) {
        return CpcTripleType.NONCOLLIDER;
    } else {
        if (verbose) {
            System.out.println("Orienting " + x + "-->" + y + "<-" + z);
        }
        return CpcTripleType.COLLIDER;
    }
}

Example 22 with ChoiceGenerator

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

the class Vcpc method orientUnshieldedTriples.

// private void logTriples() {
// TetradLogger.getInstance().log("info", "\nCollider triples:");
// 
// for (Triple triple : colliderTriples) {
// TetradLogger.getInstance().log("info", "Collider: " + triple);
// }
// 
// TetradLogger.getInstance().log("info", "\nNoncollider triples:");
// 
// for (Triple triple : noncolliderTriples) {
// TetradLogger.getInstance().log("info", "Noncollider: " + triple);
// }
// 
// TetradLogger.getInstance().log("info", "\nAmbiguous triples (i.e. list of triples for which " +
// "\nthere is ambiguous data about whether they are colliders or not):");
// 
// for (Triple triple : getAmbiguousTriples()) {
// TetradLogger.getInstance().log("info", "Ambiguous: " + triple);
// }
// }
// 
// //        Original triple orientation procedure.
// private void orientUnshieldedTriples(IKnowledge knowledge,
// IndependenceTest test, int depth) {
// TetradLogger.getInstance().log("info", "Starting Collider Orientation:");
// colliderTriples = new HashSet<Triple>();
// noncolliderTriples = new HashSet<Triple>();
// ambiguousTriples = new HashSet<Triple>();
// List<Node> 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) {
// Node x = adjacentNodes.get(combination[0]);
// Node z = adjacentNodes.get(combination[1]);
// 
// if (this.graph.isAdjacentTo(x, z)) {
// continue;
// }
// getAllTriples().add(new Triple(x, y, z));
// SearchGraphUtils.CpcTripleType type = SearchGraphUtils.getCpcTripleType(x, y, z, test, depth, graph, verbose);
// //                SearchGraphUtils.CpcTripleType type = SearchGraphUtils.getCpcTripleType2(x, y, z, test, depth, graph);
// 
// if (type == SearchGraphUtils.CpcTripleType.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 == SearchGraphUtils.CpcTripleType.AMBIGUOUS) {
// Triple triple = new Triple(x, y, z);
// ambiguousTriples.add(triple);
// graph.addAmbiguousTriple(triple.getX(), triple.getY(), triple.getZ());
// Edge edge = Edges.undirectedEdge(x, z);
// definitelyNonadjacencies.add(edge);
// } else {
// noncolliderTriples.add(new Triple(x, y, z));
// }
// }
// }
// TetradLogger.getInstance().log("info", "Finishing Collider Orientation.");
// }
// // Population version.
private void orientUnshieldedTriples(IKnowledge knowledge, IndependenceTest test, int depth) {
    TetradLogger.getInstance().log("info", "Starting Collider Orientation:");
    // System.out.println("orientUnshieldedTriples 1");
    colliderTriples = new HashSet<>();
    noncolliderTriples = new HashSet<>();
    ambiguousTriples = new HashSet<>();
    List<Node> 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) {
            Node x = adjacentNodes.get(combination[0]);
            Node z = adjacentNodes.get(combination[1]);
            if (this.graph.isAdjacentTo(x, z)) {
                continue;
            }
            getAllTriples().add(new Triple(x, y, z));
            CpcTripleType type = getPopulationTripleType(x, y, z, test, depth, graph, verbose);
            if (type == CpcTripleType.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 == CpcTripleType.AMBIGUOUS) {
                Triple triple = new Triple(x, y, z);
                ambiguousTriples.add(triple);
                graph.addAmbiguousTriple(triple.getX(), triple.getY(), triple.getZ());
                Edge edge = Edges.undirectedEdge(x, z);
                definitelyNonadjacencies.add(edge);
            } else {
                noncolliderTriples.add(new Triple(x, y, z));
            }
        }
    }
    TetradLogger.getInstance().log("info", "Finishing Collider Orientation.");
}

Example 23 with ChoiceGenerator

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

the class VcpcFast method getPopulationTripleType.

public CpcTripleType getPopulationTripleType(Node x, Node y, Node z, IndependenceTest test, int depth, Graph graph, boolean verbose) {
    // if ((x.getNode().equals("X5") && z.getNode().equals("X7"))
    // || (x.getNode().equals("X7") && z.getNode().equals("X5"))) {
    // System.out.println();
    // }
    // JOE HERE ARE THE FACTS.
    setFacts(facts);
    System.out.println("NameS" + facts.getVariableNames());
    IndependenceTest test1 = new IndTestDSep(graph);
    int numSepsetsContainingY = 0;
    int numSepsetsNotContainingY = 0;
    List<Node> _nodes = graph.getAdjacentNodes(x);
    _nodes.remove(z);
    TetradLogger.getInstance().log("adjacencies", "Adjacents for " + x + "--" + y + "--" + z + " = " + _nodes);
    int _depth = depth;
    if (_depth == -1) {
        _depth = 1000;
    }
    _depth = Math.min(_depth, _nodes.size());
    while (true) {
        for (int d = 0; d <= _depth; d++) {
            ChoiceGenerator cg = new ChoiceGenerator(_nodes.size(), d);
            int[] choice;
            while ((choice = cg.next()) != null) {
                List<Node> cond = GraphUtils.asList(choice, _nodes);
                if (facts.isIndependent(x, z, cond)) {
                    // if (verbose) {
                    System.out.println("Indep Fact said: " + x + " _||_ " + z + " | " + cond);
                    if (cond.contains(y)) {
                        numSepsetsContainingY++;
                    } else {
                        numSepsetsNotContainingY++;
                    }
                } else {
                    System.out.println("This is not Indep by facts: " + x + " _||_ " + z + " | " + cond);
                }
                // 
                if (numSepsetsContainingY > 0 && numSepsetsNotContainingY > 0) {
                    return CpcTripleType.AMBIGUOUS;
                }
            }
        }
        _nodes = graph.getAdjacentNodes(z);
        _nodes.remove(x);
        TetradLogger.getInstance().log("adjacencies", "Adjacents for " + x + "--" + y + "--" + z + " = " + _nodes);
        _depth = depth;
        if (_depth == -1) {
            _depth = 1000;
        }
        _depth = Math.min(_depth, _nodes.size());
        for (int d = 0; d <= _depth; d++) {
            ChoiceGenerator cg = new ChoiceGenerator(_nodes.size(), d);
            int[] choice;
            while ((choice = cg.next()) != null) {
                List<Node> cond = GraphUtils.asList(choice, _nodes);
                if (test.isIndependent(x, z, cond)) {
                    if (cond.contains(y)) {
                        numSepsetsContainingY++;
                    } else {
                        numSepsetsNotContainingY++;
                    }
                }
                if (numSepsetsContainingY > 0 && numSepsetsNotContainingY > 0) {
                    return CpcTripleType.AMBIGUOUS;
                }
            }
        }
        break;
    }
    if (numSepsetsContainingY > 0) {
        return CpcTripleType.NONCOLLIDER;
    } else {
        if (verbose) {
            System.out.println("Orienting " + x + "-->" + y + "<-" + z);
        }
        return CpcTripleType.COLLIDER;
    }
}

Example 24 with ChoiceGenerator

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

the class SepsetsMaxScore method getMaxScoreSet.

private List<Node> getMaxScoreSet(Node i, Node k) {
    double _p = 0.0;
    List<Node> _v = null;
    if (extraSepsets != null) {
        final List<Node> v = extraSepsets.get(i, k);
        if (v != null) {
            independenceTest.isIndependent(i, k, v);
            double p = independenceTest.getScore();
            if (p > _p) {
                _p = p;
                _v = v;
            }
        }
    }
    List<Node> adji = graph.getAdjacentNodes(i);
    List<Node> adjk = graph.getAdjacentNodes(k);
    adji.remove(k);
    adjk.remove(i);
    for (int d = 0; d <= Math.min((depth == -1 ? 1000 : depth), adji.size()); d++) {
        ChoiceGenerator gen = new ChoiceGenerator(adji.size(), d);
        int[] choice;
        while ((choice = gen.next()) != null) {
            List<Node> v = GraphUtils.asList(choice, adji);
            getIndependenceTest().isIndependent(i, k, v);
            double p = getIndependenceTest().getScore();
            if (p > _p) {
                _p = p;
                _v = v;
            }
        }
    }
    for (int d = 0; d <= Math.min((depth == -1 ? 1000 : depth), adjk.size()); d++) {
        ChoiceGenerator gen = new ChoiceGenerator(adjk.size(), d);
        int[] choice;
        while ((choice = gen.next()) != null) {
            List<Node> v = GraphUtils.asList(choice, adjk);
            getIndependenceTest().isIndependent(i, k, v);
            double p = getIndependenceTest().getScore();
            if (p > _p) {
                _p = p;
                _v = v;
            }
        }
    }
    this.p = _p;
    return _v;
}

Example 25 with ChoiceGenerator

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

the class SepsetsMinScore method getMinSepset.

private List<Node> getMinSepset(Node i, Node k) {
    double _p = Double.POSITIVE_INFINITY;
    List<Node> _v = null;
    List<Node> adji = graph.getAdjacentNodes(i);
    List<Node> adjk = graph.getAdjacentNodes(k);
    adji.remove(k);
    adjk.remove(i);
    for (int d = 0; d <= Math.min((depth == -1 ? 1000 : depth), Math.max(adji.size(), adjk.size())); d++) {
        if (d <= adji.size()) {
            ChoiceGenerator gen = new ChoiceGenerator(adji.size(), d);
            int[] choice;
            while ((choice = gen.next()) != null) {
                List<Node> v2 = GraphUtils.asList(choice, adji);
                getIndependenceTest().isIndependent(i, k, v2);
                double p2 = getIndependenceTest().getScore();
                if (returnNullWhenIndep) {
                    if (p2 < _p && p2 < 0) {
                        _p = p2;
                        _v = v2;
                    }
                } else {
                    if (p2 < _p) {
                        _p = p2;
                        _v = v2;
                    }
                }
            }
        }
        if (d <= adjk.size()) {
            ChoiceGenerator gen = new ChoiceGenerator(adjk.size(), d);
            int[] choice;
            while ((choice = gen.next()) != null) {
                List<Node> v2 = GraphUtils.asList(choice, adjk);
                getIndependenceTest().isIndependent(i, k, v2);
                double p2 = getIndependenceTest().getScore();
                if (returnNullWhenIndep) {
                    if (p2 < _p && p2 < 0) {
                        _p = p2;
                        _v = v2;
                    }
                } else {
                    if (p2 < _p) {
                        _p = p2;
                        _v = v2;
                    }
                }
            }
        }
    }
    this.p = _p;
    return _v;
}