Examples with Knowledge2 edu.cmu.tetrad.data.Knowledge2 used on opensource projects

Example 71 with Knowledge2

use of edu.cmu.tetrad.data.Knowledge2 in project tetrad by cmu-phil.

the class VcpcAltRunner method execute.

// ===================PUBLIC METHODS OVERRIDING ABSTRACT================//
public void execute() {
    IKnowledge knowledge = (IKnowledge) getParams().get("knowledge", new Knowledge2());
    Parameters searchParams = getParams();
    Parameters params = searchParams;
    VcpcAlt VcpcAlt = new VcpcAlt(getIndependenceTest());
    VcpcAlt.setKnowledge(knowledge);
    VcpcAlt.setAggressivelyPreventCycles(this.isAggressivelyPreventCycles());
    VcpcAlt.setDepth(params.getInt("depth", -1));
    Graph graph = VcpcAlt.search();
    if (getSourceGraph() != null) {
        GraphUtils.arrangeBySourceGraph(graph, getSourceGraph());
    } else if (knowledge.isDefaultToKnowledgeLayout()) {
        SearchGraphUtils.arrangeByKnowledgeTiers(graph, knowledge);
    } else {
        GraphUtils.circleLayout(graph, 200, 200, 150);
    }
    setResultGraph(graph);
}

Example 72 with Knowledge2

use of edu.cmu.tetrad.data.Knowledge2 in project tetrad by cmu-phil.

the class VcpcRunner method execute.

// ===================PUBLIC METHODS OVERRIDING ABSTRACT================//
public void execute() {
    IKnowledge knowledge = (IKnowledge) getParams().get("knowledge", new Knowledge2());
    Parameters searchParams = getParams();
    Parameters params = searchParams;
    Vcpc vcpc = new Vcpc(getIndependenceTest());
    vcpc.setKnowledge(knowledge);
    vcpc.setAggressivelyPreventCycles(this.isAggressivelyPreventCycles());
    vcpc.setDepth(params.getInt("depth", -1));
    if (independenceFactsModel != null) {
        vcpc.setFacts(independenceFactsModel.getFacts());
    }
    Graph graph = vcpc.search();
    if (getSourceGraph() != null) {
        GraphUtils.arrangeBySourceGraph(graph, getSourceGraph());
    } else if (knowledge.isDefaultToKnowledgeLayout()) {
        SearchGraphUtils.arrangeByKnowledgeTiers(graph, knowledge);
    } else {
        GraphUtils.circleLayout(graph, 200, 200, 150);
    }
    setResultGraph(graph);
    setVcpcFields(vcpc);
}

Example 73 with Knowledge2

use of edu.cmu.tetrad.data.Knowledge2 in project tetrad by cmu-phil.

the class FasDci method search.

// ==========================PUBLIC METHODS===========================//
/**
 * Discovers all adjacencies in data.  The procedure is to remove edges in the graph which connect pairs of
 * variables which are independent conditional on some other set of variables in the graph (the "sepset"). These are
 * removed in tiers.  First, edges which are independent conditional on zero other variables are removed, then edges
 * which are independent conditional on one other variable are removed, then two, then three, and so on, until no
 * more edges can be removed from the graph.  The edges which remain in the graph after this procedure are the
 * adjacencies in the data.
 *
 * @return a SepSet, which indicates which variables are independent conditional on which other variables
 */
public SepsetMapDci search() {
    this.logger.log("info", "Starting Fast Adjacency Search (DCI).");
    // Remove edges forbidden both ways.
    Set<Edge> edges = graph.getEdges();
    for (Edge _edge : edges) {
        String name1 = _edge.getNode1().getName();
        String name2 = _edge.getNode2().getName();
        if (knowledge.isForbidden(name1, name2) && knowledge.isForbidden(name2, name1)) {
            graph.removeEdge(_edge);
            this.logger.log("edgeRemoved", "Removed " + _edge + " because it was " + "forbidden by background knowledge.");
        }
    }
    // this.logger.info("Depth = " + ((depth == Integer
    // .MAX_VALUE) ? "Unlimited" : Integer.toString(depth)));
    SepsetMapDci sepset = new SepsetMapDci();
    int _depth = depth;
    if (_depth == -1) {
        _depth = 1000;
    }
    for (int d = 0; d <= _depth; d++) {
        boolean more = searchAtDepth(graph, independenceTest, new Knowledge2(), sepset, d);
        if (!more) {
            break;
        }
    }
    // verifySepsetIntegrity(sepset);
    this.logger.log("info", "Finishing Fast Adjacency Search.");
    return sepset;
}

Example 74 with Knowledge2

use of edu.cmu.tetrad.data.Knowledge2 in project tetrad by cmu-phil.

the class TestKnowledge method test2.

@Test
public final void test2() {
    List<Node> nodes1 = new ArrayList<>();
    for (int i = 0; i < 100; i++) {
        nodes1.add(new ContinuousVariable("X" + (i + 1)));
    }
    Graph g = GraphUtils.randomGraph(nodes1, 0, 100, 3, 3, 3, false);
    List<Node> nodes = g.getNodes();
    List<String> names = new ArrayList<>();
    for (Node node : nodes) names.add(node.getName());
    Knowledge2 knowledge = new Knowledge2(names);
    knowledge.addToTier(0, "X1*");
    knowledge.addToTier(1, "X2*");
    knowledge.setRequired("X4*,X6*", "X5*");
    knowledge.setRequired("X6*", "X5*");
    assertTrue(knowledge.isForbidden("X20", "X10"));
    assertTrue(knowledge.isRequired("X6", "X5"));
}

Example 75 with Knowledge2

use of edu.cmu.tetrad.data.Knowledge2 in project tetrad by cmu-phil.

the class TestDagInPatternIterator method test5.

@Test
public void test5() {
    RandomUtil.getInstance().setSeed(34828384L);
    List<Node> nodes1 = new ArrayList<>();
    for (int i = 0; i < 3; i++) {
        nodes1.add(new ContinuousVariable("X" + (i + 1)));
    }
    Dag dag1 = new Dag(GraphUtils.randomGraph(nodes1, 0, 3, 30, 15, 15, false));
    Graph pattern = SearchGraphUtils.patternForDag(dag1);
    List<Node> nodes = pattern.getNodes();
    // Make random knowedge.
    int numTiers = 6;
    IKnowledge knowledge = new Knowledge2();
    for (Node node : nodes) {
        int tier = RandomUtil.getInstance().nextInt(numTiers);
        if (tier < 2)
            continue;
        knowledge.addToTier(tier, node.getName());
    }
    if (!knowledge.isViolatedBy(pattern)) {
        DagInPatternIterator iterator1 = new DagInPatternIterator(pattern);
        Graph dag0 = null;
        while (iterator1.hasNext()) {
            Graph dag = iterator1.next();
            if (!knowledge.isViolatedBy(dag)) {
                dag0 = dag;
            }
        }
        if (dag0 == null) {
            fail("Inconsistent knowledge.");
        }
    }
    if (!knowledge.isViolatedBy(pattern)) {
        DagInPatternIterator iterator2 = new DagInPatternIterator(pattern, knowledge);
        while (iterator2.hasNext()) {
            Graph dag = iterator2.next();
            if (knowledge.isViolatedBy(dag)) {
                throw new IllegalArgumentException("Knowledge violated");
            }
        }
    }
    DagInPatternIterator iterator3 = new DagInPatternIterator(pattern);
    int count = 0;
    while (iterator3.hasNext()) {
        iterator3.next();
        count++;
    }
    assertEquals(6, count);
}