Examples with Mbfs edu.cmu.tetrad.search.Mbfs used on opensource projects

Example 1 with Mbfs

use of edu.cmu.tetrad.search.Mbfs in project tetrad by cmu-phil.

the class MbSearchEditor method addSpecialMenus.

protected void addSpecialMenus(JMenuBar menuBar) {
    JMenu test = new JMenu("Independence");
    menuBar.add(test);
    IndTestMenuItems.addIndependenceTestChoices(test, this);
    if (getAlgorithmRunner() instanceof MbfsRunner) {
        JMenu graph = new JMenu("Graph");
        JMenuItem showDags = new JMenuItem("Show DAG's Consistent with forbid_latent_common_causes");
        // JMenuItem meekOrient = new JMenuItem("Meek Orientation");
        JMenuItem gesOrient = new JMenuItem("Global Score-based Reorientation");
        JMenuItem nextGraph = new JMenuItem("Next Graph");
        JMenuItem previousGraph = new JMenuItem("Previous Graph");
        graph.add(new GraphPropertiesAction(getWorkbench()));
        graph.add(new PathsAction(getWorkbench()));
        // graph.add(new DirectedPathsAction(getWorkbench()));
        // graph.add(new TreksAction(getWorkbench()));
        // graph.add(new AllPathsAction(getWorkbench()));
        // graph.add(new NeighborhoodsAction(getWorkbench()));
        graph.addSeparator();
        // graph.add(meekOrient);
        graph.add(gesOrient);
        graph.addSeparator();
        graph.add(previousGraph);
        graph.add(nextGraph);
        graph.addSeparator();
        graph.add(showDags);
        menuBar.add(graph);
        showDags.addActionListener(new ActionListener() {

            public void actionPerformed(ActionEvent e) {
                AlgorithmRunner runner = getAlgorithmRunner();
                if (!(runner instanceof MbfsRunner)) {
                    return;
                }
                MbfsRunner mbRunner = (MbfsRunner) runner;
                final Mbfs search = mbRunner.getMbFanSearch();
                if (search == null) {
                    JOptionPane.showMessageDialog(JOptionUtils.centeringComp(), "The search was not stored.");
                    return;
                }
                MbPatternDisplay display = new MbPatternDisplay(search);
                JOptionPane.showMessageDialog(JOptionUtils.centeringComp(), display, "MB DAG's Consistent with forbid_latent_common_causes", JOptionPane.PLAIN_MESSAGE);
            }
        });
        // meekOrient.addActionListener(new ActionListener() {
        // public void actionPerformed(ActionEvent e) {
        // ImpliedOrientation rules = getAlgorithmRunner().getMeekRules();
        // rules.setKnowledge((IKnowledge) getAlgorithmRunner().getParams().get("knowledge", new Knowledge2()));
        // rules.orientImplied(getGraph());
        // getWorkbench().setGraph(getGraph());
        // }
        // });
        gesOrient.addActionListener(new ActionListener() {

            public void actionPerformed(ActionEvent e) {
                DataModel dataModel = getAlgorithmRunner().getDataModel();
                final Graph graph = SearchGraphUtils.reorient(getGraph(), dataModel, getKnowledge());
                getGraphHistory().add(graph);
                getWorkbench().setGraph(graph);
                firePropertyChange("modelChanged", null, null);
            }
        });
    }
    // if (getAlgorithmRunner().supportsKnowledge()) {
    // menuBar.add(new Knowledge2Menu(this));
    // }
    menuBar.add(new LayoutMenu(this));
}

Example 2 with Mbfs

use of edu.cmu.tetrad.search.Mbfs in project tetrad by cmu-phil.

the class TestMbfs method testGenerateDaglist.

/**
 * Tests to make sure the algorithm for generating MB DAGs from an MB Pattern works, at least for one kind of tricky
 * case.
 */
@Test
public void testGenerateDaglist() {
    Graph graph = GraphConverter.convert("T-->X1,T-->X2,X1-->X2,T-->X3,X4-->T");
    IndTestDSep test = new IndTestDSep(graph);
    Mbfs search = new Mbfs(test, -1);
    Graph resultGraph = search.search("T");
    List mbDags = MbUtils.generateMbDags(resultGraph, true, search.getTest(), search.getDepth(), search.getTarget());
    assertTrue(mbDags.size() == 9);
    assertTrue(mbDags.contains(graph));
}

Example 3 with Mbfs

use of edu.cmu.tetrad.search.Mbfs in project tetrad by cmu-phil.

the class TestMbfs method testRandom.

@Test
public void testRandom() {
    RandomUtil.getInstance().setSeed(8388428832L);
    List<Node> nodes1 = new ArrayList<>();
    for (int i = 0; i < 10; i++) {
        nodes1.add(new ContinuousVariable("X" + (i + 1)));
    }
    Dag dag = new Dag(GraphUtils.randomGraph(nodes1, 0, 10, 5, 5, 5, false));
    IndependenceTest test = new IndTestDSep(dag);
    Mbfs search = new Mbfs(test, -1);
    List<Node> nodes = dag.getNodes();
    for (Node node : nodes) {
        Graph resultMb = search.search(node.getName());
        Graph trueMb = GraphUtils.markovBlanketDag(node, dag);
        List<Node> resultNodes = resultMb.getNodes();
        List<Node> trueNodes = trueMb.getNodes();
        Set<String> resultNames = new HashSet<>();
        for (Node resultNode : resultNodes) {
            resultNames.add(resultNode.getName());
        }
        Set<String> trueNames = new HashSet<>();
        for (Node v : trueNodes) {
            trueNames.add(v.getName());
        }
        assertTrue(resultNames.equals(trueNames));
        Set<Edge> resultEdges = resultMb.getEdges();
        for (Edge resultEdge : resultEdges) {
            if (Edges.isDirectedEdge(resultEdge)) {
                String name1 = resultEdge.getNode1().getName();
                String name2 = resultEdge.getNode2().getName();
                Node node1 = trueMb.getNode(name1);
                Node node2 = trueMb.getNode(name2);
                // possibility that the node is actually a child.
                if (node1 == null) {
                    fail("Node " + name1 + " is not in the true graph.");
                }
                if (node2 == null) {
                    fail("Node " + name2 + " is not in the true graph.");
                }
                Edge trueEdge = trueMb.getEdge(node1, node2);
                if (trueEdge == null) {
                    Node resultNode1 = resultMb.getNode(node1.getName());
                    Node resultNode2 = resultMb.getNode(node2.getName());
                    Node resultTarget = resultMb.getNode(node.getName());
                    Edge a = resultMb.getEdge(resultNode1, resultTarget);
                    Edge b = resultMb.getEdge(resultNode2, resultTarget);
                    if (a == null || b == null) {
                        continue;
                    }
                    if ((Edges.isDirectedEdge(a) && Edges.isUndirectedEdge(b)) || (Edges.isUndirectedEdge(a) && Edges.isDirectedEdge(b))) {
                        continue;
                    }
                    fail("EXTRA EDGE: Edge in result MB but not true MB = " + resultEdge);
                }
                assertEquals(resultEdge.getEndpoint1(), trueEdge.getEndpoint1());
                assertEquals(resultEdge.getEndpoint2(), trueEdge.getEndpoint2());
            }
        }
    }
}

Example 4 with Mbfs

use of edu.cmu.tetrad.search.Mbfs in project tetrad by cmu-phil.

the class MbFanSearchRunner method execute.

// =================PUBLIC METHODS OVERRIDING ABSTRACT=================//
/**
 * Executes the algorithm, producing (at least) a result workbench. Must be
 * implemented in the extending class.
 */
public void execute() {
    int pcDepth = getParams().getInt("depth", -1);
    Mbfs mbfs = new Mbfs(getIndependenceTest(), pcDepth);
    Parameters params = getParams();
    if (params instanceof Parameters) {
        mbfs.setAggressivelyPreventCycles(params.getBoolean("aggressivelyPreventCycles", false));
    }
    IKnowledge knowledge = (IKnowledge) getParams().get("knowledge", new Knowledge2());
    mbfs.setKnowledge(knowledge);
    String targetName = getParams().getString("targetName", null);
    Graph graph = mbfs.search(targetName);
    setResultGraph(graph);
    if (getSourceGraph() != null) {
        GraphUtils.arrangeBySourceGraph(graph, getSourceGraph());
    } else if (knowledge.isDefaultToKnowledgeLayout()) {
        SearchGraphUtils.arrangeByKnowledgeTiers(graph, knowledge);
    } else {
        GraphUtils.circleLayout(graph, 200, 200, 150);
    }
    this.mbfs = mbfs;
}