Example #1
0
  private void bes(Graph graph) {
    TetradLogger.getInstance().log("info", "** BACKWARD EQUIVALENCE SEARCH");

    initializeArrowsBackward(graph);

    while (!sortedArrows.isEmpty()) {
      Arrow arrow = sortedArrows.first();
      sortedArrows.remove(arrow);

      Node x = arrow.getX();
      Node y = arrow.getY();

      clearArrow(x, y);

      if (!validDelete(arrow.getHOrT(), arrow.getNaYX(), graph)) {
        continue;
      }

      List<Node> h = arrow.getHOrT();
      double bump = arrow.getBump();

      delete(x, y, h, graph, bump);
      score += bump;
      rebuildPattern(graph);

      storeGraph(graph);

      initializeArrowsBackward(
          graph); // Rebuilds Arrows from scratch each time. Fast enough for backwards.
    }
  }
Example #2
0
  private void calculateArrowsForward(Node x, Node y, Graph graph) {
    clearArrow(x, y);

    if (!knowledgeEmpty()) {
      if (getKnowledge().isForbidden(x.getName(), y.getName())) {
        return;
      }
    }

    List<Node> naYX = getNaYX(x, y, graph);
    List<Node> t = getTNeighbors(x, y, graph);

    DepthChoiceGenerator gen = new DepthChoiceGenerator(t.size(), t.size());
    int[] choice;

    while ((choice = gen.next()) != null) {
      List<Node> s = GraphUtils.asList(choice, t);

      if (!knowledgeEmpty()) {
        if (!validSetByKnowledge(y, s)) {
          continue;
        }
      }

      double bump = insertEval(x, y, s, naYX, graph);

      if (bump > 0.0) {
        Arrow arrow = new Arrow(bump, x, y, s, naYX);
        sortedArrows.add(arrow);
        addLookupArrow(x, y, arrow);
      }
    }
  }
Example #3
0
  /**
   * Forward equivalence search.
   *
   * @param graph The graph in the state prior to the forward equivalence search.
   */
  private void fes(Graph graph, List<Node> nodes) {
    TetradLogger.getInstance().log("info", "** FORWARD EQUIVALENCE SEARCH");

    lookupArrows = new HashMap<OrderedPair, Set<Arrow>>();

    initializeArrowsForward(nodes);

    while (!sortedArrows.isEmpty()) {
      Arrow arrow = sortedArrows.first();
      sortedArrows.remove(arrow);

      Node x = arrow.getX();
      Node y = arrow.getY();

      clearArrow(x, y);

      if (graph.isAdjacentTo(x, y)) {
        continue;
      }

      if (!validInsert(x, y, arrow.getHOrT(), arrow.getNaYX(), graph)) {
        continue;
      }

      List<Node> t = arrow.getHOrT();
      double bump = arrow.getBump();

      Set<Edge> edges = graph.getEdges();

      insert(x, y, t, graph, bump);
      score += bump;
      rebuildPattern(graph);

      // Try to avoid duplicating scoring calls. First clear out all of the edges that need to be
      // changed,
      // then change them, checking to see if they're already been changed. I know, roundabout, but
      // there's
      // a performance boost.
      for (Edge edge : graph.getEdges()) {
        if (!edges.contains(edge)) {
          reevaluateForward(graph, nodes, edge.getNode1(), edge.getNode2());
        }
      }

      storeGraph(graph);
    }
  }
Example #4
0
  private void clearArrow(Node x, Node y) {
    final OrderedPair<Node> pair = new OrderedPair<Node>(x, y);
    final Set<Arrow> lookupArrows = this.lookupArrows.get(pair);

    if (lookupArrows != null) {
      sortedArrows.removeAll(lookupArrows);
    }

    this.lookupArrows.remove(pair);
  }
Example #5
0
  private void storeGraph(Graph graph) {
    if (numPatternsToStore < 1) return;

    if (topGraphs.isEmpty() || score > topGraphs.first().getScore()) {
      Graph graphCopy = new EdgeListGraphSingleConnections(graph);

      topGraphs.add(new ScoredGraph(graphCopy, score));

      if (topGraphs.size() > getNumPatternsToStore()) {
        topGraphs.remove(topGraphs.first());
      }
    }
  }
Example #6
0
  // Invalid if then nodes or graph changes.
  private void calculateArrowsBackward(Node x, Node y, Graph graph) {
    if (x == y) {
      return;
    }

    if (!graph.isAdjacentTo(x, y)) {
      return;
    }

    if (!knowledgeEmpty()) {
      if (!getKnowledge().noEdgeRequired(x.getName(), y.getName())) {
        return;
      }
    }

    List<Node> naYX = getNaYX(x, y, graph);

    clearArrow(x, y);

    List<Node> _naYX = new ArrayList<Node>(naYX);
    DepthChoiceGenerator gen = new DepthChoiceGenerator(_naYX.size(), _naYX.size());
    int[] choice;

    while ((choice = gen.next()) != null) {
      List<Node> H = GraphUtils.asList(choice, _naYX);

      if (!knowledgeEmpty()) {
        if (!validSetByKnowledge(y, H)) {
          continue;
        }
      }

      double bump = deleteEval(x, y, H, naYX, graph);

      if (bump > 0.0) {
        Arrow arrow = new Arrow(bump, x, y, H, naYX);
        sortedArrows.add(arrow);
        addLookupArrow(x, y, arrow);
      }
    }
  }
Example #7
0
  private void initializeArrowsBackward(Graph graph) {
    sortedArrows.clear();
    lookupArrows.clear();

    for (Edge edge : graph.getEdges()) {
      Node x = edge.getNode1();
      Node y = edge.getNode2();

      if (!knowledgeEmpty()) {
        if (!getKnowledge().noEdgeRequired(x.getName(), y.getName())) {
          continue;
        }
      }

      if (Edges.isDirectedEdge(edge)) {
        calculateArrowsBackward(x, y, graph);
      } else {
        calculateArrowsBackward(x, y, graph);
        calculateArrowsBackward(y, x, graph);
      }
    }
  }
Example #8
0
  public Graph search(List<Node> nodes) {
    long startTime = System.currentTimeMillis();
    localScoreCache.clear();

    if (!dataSet().getVariables().containsAll(nodes)) {
      throw new IllegalArgumentException("All of the nodes must be in " + "the supplied data set.");
    }

    Graph graph;

    if (initialGraph == null) {
      graph = new EdgeListGraphSingleConnections(nodes);
    } else {
      initialGraph = GraphUtils.replaceNodes(initialGraph, variables);
      graph = new EdgeListGraphSingleConnections(initialGraph);
    }

    topGraphs.clear();

    buildIndexing(graph);
    addRequiredEdges(graph);
    score = 0.0;

    // Do forward search.
    fes(graph, nodes);

    // Do backward search.
    bes(graph);

    long endTime = System.currentTimeMillis();
    this.elapsedTime = endTime - startTime;
    this.logger.log("graph", "\nReturning this graph: " + graph);

    this.logger.log("info", "Elapsed time = " + (elapsedTime) / 1000. + " s");
    this.logger.flush();

    return graph;
  }
Example #9
0
  /**
   * Greedy equivalence search: Start from the empty graph, add edges till model is significant.
   * Then start deleting edges till a minimum is achieved.
   *
   * @return the resulting Pattern.
   */
  public Graph search() {

    Graph graph;

    if (initialGraph == null) {
      graph = new EdgeListGraphSingleConnections(getVariables());
    } else {
      graph = new EdgeListGraphSingleConnections(initialGraph);
    }

    fireGraphChange(graph);
    buildIndexing(graph);
    addRequiredEdges(graph);

    topGraphs.clear();

    storeGraph(graph);

    List<Node> nodes = graph.getNodes();

    long start = System.currentTimeMillis();
    score = 0.0;

    // Do forward search.
    fes(graph, nodes);

    // Do backward search.
    bes(graph);

    long endTime = System.currentTimeMillis();
    this.elapsedTime = endTime - start;
    this.logger.log("graph", "\nReturning this graph: " + graph);

    this.logger.log("info", "Elapsed time = " + (elapsedTime) / 1000. + " s");
    this.logger.flush();

    return graph;
  }