/** Get a graph and direct only the unshielded colliders. */
  public static void basicPattern(Graph graph) {
    Set<Edge> undirectedEdges = new HashSet<Edge>();

    NEXT_EDGE:
    for (Edge edge : graph.getEdges()) {
      Node head = null, tail = null;

      if (edge.getEndpoint1() == Endpoint.ARROW && edge.getEndpoint2() == Endpoint.TAIL) {
        head = edge.getNode1();
        tail = edge.getNode2();
      } else if (edge.getEndpoint2() == Endpoint.ARROW && edge.getEndpoint1() == Endpoint.TAIL) {
        head = edge.getNode2();
        tail = edge.getNode1();
      }

      if (head != null) {
        for (Node node : graph.getParents(head)) {
          if (node != tail && !graph.isAdjacentTo(tail, node)) {
            continue NEXT_EDGE;
          }
        }

        undirectedEdges.add(edge);
      }
    }

    for (Edge nextUndirected : undirectedEdges) {
      Node node1 = nextUndirected.getNode1(), node2 = nextUndirected.getNode2();

      graph.removeEdge(nextUndirected);
      graph.addUndirectedEdge(node1, node2);
    }
  }
Example #2
0
  public Graph orient() {
    Graph skeleton = GraphUtils.undirectedGraph(getPattern());
    Graph graph = new EdgeListGraph(skeleton.getNodes());

    List<Node> nodes = skeleton.getNodes();
    //        Collections.shuffle(nodes);

    if (isR1Done()) {
      ruleR1(skeleton, graph, nodes);
    }

    for (Edge edge : skeleton.getEdges()) {
      if (!graph.isAdjacentTo(edge.getNode1(), edge.getNode2())) {
        graph.addUndirectedEdge(edge.getNode1(), edge.getNode2());
      }
    }

    if (isR2Done()) {
      ruleR2(skeleton, graph);
    }

    if (isMeekDone()) {
      new MeekRules().orientImplied(graph);
    }

    return graph;
  }
  /**
   * Transforms a maximally directed pattern (PDAG) represented in graph <code>g</code> into an
   * arbitrary DAG by modifying <code>g</code> itself. Based on the algorithm described in
   * Chickering (2002) "Optimal structure identification with greedy search" Journal of Machine
   * Learning Research. R. Silva, June 2004
   */
  public static void pdagToDag(Graph g) {
    Graph p = new EdgeListGraph(g);
    List<Edge> undirectedEdges = new ArrayList<Edge>();

    for (Edge edge : g.getEdges()) {
      if (edge.getEndpoint1() == Endpoint.TAIL
          && edge.getEndpoint2() == Endpoint.TAIL
          && !undirectedEdges.contains(edge)) {
        undirectedEdges.add(edge);
      }
    }
    g.removeEdges(undirectedEdges);
    List<Node> pNodes = p.getNodes();

    do {
      Node x = null;

      for (Node pNode : pNodes) {
        x = pNode;

        if (p.getChildren(x).size() > 0) {
          continue;
        }

        Set<Node> neighbors = new HashSet<Node>();

        for (Edge edge : p.getEdges()) {
          if (edge.getNode1() == x || edge.getNode2() == x) {
            if (edge.getEndpoint1() == Endpoint.TAIL && edge.getEndpoint2() == Endpoint.TAIL) {
              if (edge.getNode1() == x) {
                neighbors.add(edge.getNode2());
              } else {
                neighbors.add(edge.getNode1());
              }
            }
          }
        }
        if (neighbors.size() > 0) {
          Collection<Node> parents = p.getParents(x);
          Set<Node> all = new HashSet<Node>(neighbors);
          all.addAll(parents);
          if (!GraphUtils.isClique(all, p)) {
            continue;
          }
        }

        for (Node neighbor : neighbors) {
          Node node1 = g.getNode(neighbor.getName());
          Node node2 = g.getNode(x.getName());

          g.addDirectedEdge(node1, node2);
        }
        p.removeNode(x);
        break;
      }
      pNodes.remove(x);
    } while (pNodes.size() > 0);
  }
Example #4
0
 public void setParameterValue(Edge edge, double value) {
   if (Edges.isDirectedEdge(edge)) {
     setEdgeCoefficient(edge.getNode1(), edge.getNode2(), value);
   } else if (Edges.isBidirectedEdge(edge)) {
     setErrorCovariance(edge.getNode1(), edge.getNode2(), value);
   } else {
     throw new IllegalArgumentException(
         "Only directed and bidirected edges are supported: " + edge);
   }
 }
Example #5
0
  public TimeLagGraphWrapper(GraphWrapper graphWrapper) {
    if (graphWrapper == null) {
      throw new NullPointerException("No graph wrapper.");
    }

    TimeLagGraph graph = new TimeLagGraph();

    Graph _graph = graphWrapper.getGraph();

    for (Node node : _graph.getNodes()) {
      Node _node = node.like(node.getName() + ":0");
      _node.setNodeType(node.getNodeType());
      graph.addNode(_node);
    }

    for (Edge edge : _graph.getEdges()) {
      if (!Edges.isDirectedEdge(edge)) {
        throw new IllegalArgumentException();
      }

      Node from = edge.getNode1();
      Node to = edge.getNode2();

      Node _from = graph.getNode(from.getName(), 1);
      Node _to = graph.getNode(to.getName(), 0);

      graph.addDirectedEdge(_from, _to);
    }

    this.graph = graph;
  }
Example #6
0
  private Graph condense(Graph mimStructure, Graph mimbuildStructure) {
    //        System.out.println("Uncondensed: " + mimbuildStructure);

    Map<Node, Node> substitutions = new HashMap<Node, Node>();

    for (Node node : mimbuildStructure.getNodes()) {
      for (Node _node : mimStructure.getNodes()) {
        if (node.getName().startsWith(_node.getName())) {
          substitutions.put(node, _node);
          break;
        }

        substitutions.put(node, node);
      }
    }

    HashSet<Node> nodes = new HashSet<Node>(substitutions.values());
    Graph graph = new EdgeListGraph(new ArrayList<Node>(nodes));

    for (Edge edge : mimbuildStructure.getEdges()) {
      Node node1 = substitutions.get(edge.getNode1());
      Node node2 = substitutions.get(edge.getNode2());

      if (node1 == node2) continue;

      if (graph.isAdjacentTo(node1, node2)) continue;

      graph.addEdge(new Edge(node1, node2, edge.getEndpoint1(), edge.getEndpoint2()));
    }

    //        System.out.println("Condensed: " + graph);

    return graph;
  }
Example #7
0
  public boolean containsParameter(Edge edge) {
    if (Edges.isBidirectedEdge(edge)) {
      edge =
          Edges.bidirectedEdge(
              semGraph.getExogenous(edge.getNode1()), semGraph.getExogenous(edge.getNode2()));
    }

    return edgeParameters.keySet().contains(edge);
  }
Example #8
0
  private void calcStats() {
    //        Graph resultGraph = getAlgorithmRunner().getResultGraph();
    IGesRunner runner = (IGesRunner) getAlgorithmRunner();

    if (runner.getTopGraphs().isEmpty()) {
      throw new IllegalArgumentException(
          "No patterns were recorded. Please adjust the number of " + "patterns to store.");
    }

    Graph resultGraph = runner.getTopGraphs().get(runner.getIndex()).getGraph();

    if (getAlgorithmRunner().getDataModel() instanceof DataSet) {

      // resultGraph may be the output of a PC search.
      // Such graphs sometimes contain doubly directed edges.

      // /We converte such edges to directed edges here.
      // For the time being an orientation is arbitrarily selected.
      Set<Edge> allEdges = resultGraph.getEdges();

      for (Edge edge : allEdges) {
        if (edge.getEndpoint1() == Endpoint.ARROW && edge.getEndpoint2() == Endpoint.ARROW) {
          // Option 1 orient it from node1 to node2
          resultGraph.setEndpoint(edge.getNode1(), edge.getNode2(), Endpoint.ARROW);

          // Option 2 remove such edges:
          resultGraph.removeEdge(edge);
        }
      }

      Pattern pattern = new Pattern(resultGraph);
      PatternToDag ptd = new PatternToDag(pattern);
      Graph dag = ptd.patternToDagMeekRules();

      DataSet dataSet = (DataSet) getAlgorithmRunner().getDataModel();
      String report;

      if (dataSet.isContinuous()) {
        report = reportIfContinuous(dag, dataSet);
      } else if (dataSet.isDiscrete()) {
        report = reportIfDiscrete(dag, dataSet);
      } else {
        throw new IllegalArgumentException("");
      }

      JScrollPane dagWorkbenchScroll = dagWorkbenchScroll(dag);
      modelStatsText.setLineWrap(true);
      modelStatsText.setWrapStyleWord(true);
      modelStatsText.setText(report);

      removeStatsTabs();
      tabbedPane.addTab("DAG in pattern", dagWorkbenchScroll);
      tabbedPane.addTab("DAG Model Statistics", modelStatsText);
    }
  }
Example #9
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 #10
0
  public static Graph weightedRandomGraph(int n, int e) {
    List<Node> nodes = new ArrayList<Node>();
    for (int i = 0; i < n; i++) nodes.add(new GraphNode("X" + i));

    Graph graph = new EdgeListGraph(nodes);

    for (int e0 = 0; e0 < e; e0++) {
      int i1 = weightedRandom(nodes, graph);
      //            int i2 = RandomUtil.getInstance().nextInt(n);
      int i2 = weightedRandom(nodes, graph);

      if (!(shortestPath(nodes.get(i1), nodes.get(i2), graph) < 9)) {
        e0--;
        continue;
      }

      if (i1 == i2) {
        e0--;
        continue;
      }

      Edge edge = Edges.undirectedEdge(nodes.get(i1), nodes.get(i2));

      if (graph.containsEdge(edge)) {
        e0--;
        continue;
      }

      graph.addEdge(edge);
    }

    for (Edge edge : graph.getEdges()) {
      Node n1 = edge.getNode1();
      Node n2 = edge.getNode2();

      if (!graph.isAncestorOf(n2, n1)) {
        graph.removeEdge(edge);
        graph.addDirectedEdge(n1, n2);
      } else {
        graph.removeEdge(edge);
        graph.addDirectedEdge(n2, n1);
      }
    }

    return graph;
  }
Example #11
0
  private void ruleR2(Graph skeleton, Graph graph) {
    Set<Edge> edgeList1 = skeleton.getEdges();
    //        Collections.shuffle(edgeList1);

    for (Edge adj : edgeList1) {
      Node x = adj.getNode1();
      Node y = adj.getNode2();

      if (!isR2Orient2Cycles() && isTwoCycle(graph, x, y)) {
        continue;
      }

      if (!isTwoCycle(graph, x, y) && !isUndirected(graph, x, y)) {
        continue;
      }

      resolveOneEdgeMax(graph, x, y, isStrongR2(), new EdgeListGraph(graph));
    }
  }
Example #12
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 #13
0
  private Graph pickDag(Graph graph) {
    SearchGraphUtils.basicPattern(graph, false);
    addRequiredEdges(graph);
    boolean containsUndirected;

    do {
      containsUndirected = false;

      for (Edge edge : graph.getEdges()) {
        if (Edges.isUndirectedEdge(edge)) {
          containsUndirected = true;
          graph.removeEdge(edge);
          Edge _edge = Edges.directedEdge(edge.getNode1(), edge.getNode2());
          graph.addEdge(_edge);
        }
      }

      meekOrient(graph, getKnowledge());
    } while (containsUndirected);

    return graph;
  }
Example #14
0
  /**
   * @return The edge coefficient matrix of the model, a la SemIm. Note that this will normally need
   *     to be transposed, since [a][b] is the edge coefficient for a-->b, not b-->a. Sorry.
   *     History. THESE ARE PARAMETERS OF THE MODEL--THE ONLY PARAMETERS.
   */
  public TetradMatrix edgeCoef() {
    List<Node> variableNodes = getVariableNodes();

    TetradMatrix edgeCoef = new TetradMatrix(variableNodes.size(), variableNodes.size());

    for (Edge edge : edgeParameters.keySet()) {
      if (Edges.isBidirectedEdge(edge)) {
        continue;
      }

      Node a = edge.getNode1();
      Node b = edge.getNode2();

      int aindex = variableNodes.indexOf(a);
      int bindex = variableNodes.indexOf(b);

      double coef = edgeParameters.get(edge);

      edgeCoef.set(aindex, bindex, coef);
    }

    return edgeCoef;
  }
  /**
   * Transforms a DAG represented in graph <code>graph</code> into a maximally directed pattern
   * (PDAG) by modifying <code>g</code> itself. Based on the algorithm described in Chickering
   * (2002) "Optimal structure identification with greedy search" Journal of Machine Learning
   * Research. It works for both BayesNets and SEMs. R. Silva, June 2004
   */
  public static void dagToPdag(Graph graph) {
    // do topological sort on the nodes
    Graph graphCopy = new EdgeListGraph(graph);
    Node orderedNodes[] = new Node[graphCopy.getNodes().size()];
    int count = 0;
    while (graphCopy.getNodes().size() > 0) {
      Set<Node> exogenousNodes = new HashSet<Node>();

      for (Node next : graphCopy.getNodes()) {
        if (graphCopy.isExogenous(next)) {
          exogenousNodes.add(next);
          orderedNodes[count++] = graph.getNode(next.getName());
        }
      }

      graphCopy.removeNodes(new ArrayList<Node>(exogenousNodes));
    }
    // ordered edges - improvised, inefficient implementation
    count = 0;
    Edge edges[] = new Edge[graph.getNumEdges()];
    boolean edgeOrdered[] = new boolean[graph.getNumEdges()];
    Edge orderedEdges[] = new Edge[graph.getNumEdges()];

    for (Edge edge : graph.getEdges()) {
      edges[count++] = edge;
    }

    for (int i = 0; i < edges.length; i++) {
      edgeOrdered[i] = false;
    }

    while (count > 0) {
      for (Node orderedNode : orderedNodes) {
        for (int k = orderedNodes.length - 1; k >= 0; k--) {
          for (int q = 0; q < edges.length; q++) {
            if (!edgeOrdered[q]
                && edges[q].getNode1() == orderedNodes[k]
                && edges[q].getNode2() == orderedNode) {
              edgeOrdered[q] = true;
              orderedEdges[orderedEdges.length - count] = edges[q];
              count--;
            }
          }
        }
      }
    }

    // label edges
    boolean compelledEdges[] = new boolean[graph.getNumEdges()];
    boolean reversibleEdges[] = new boolean[graph.getNumEdges()];
    for (int i = 0; i < graph.getNumEdges(); i++) {
      compelledEdges[i] = false;
      reversibleEdges[i] = false;
    }
    for (int i = 0; i < graph.getNumEdges(); i++) {
      if (compelledEdges[i] || reversibleEdges[i]) {
        continue;
      }
      Node x = orderedEdges[i].getNode1();
      Node y = orderedEdges[i].getNode2();
      for (int j = 0; j < orderedEdges.length; j++) {
        if (orderedEdges[j].getNode2() == x && compelledEdges[j]) {
          Node w = orderedEdges[j].getNode1();
          if (!graph.isParentOf(w, y)) {
            for (int k = 0; k < orderedEdges.length; k++) {
              if (orderedEdges[k].getNode2() == y) {
                compelledEdges[k] = true;
                break;
              }
            }
          } else {
            for (int k = 0; k < orderedEdges.length; k++) {
              if (orderedEdges[k].getNode1() == w && orderedEdges[k].getNode2() == y) {
                compelledEdges[k] = true;
                break;
              }
            }
          }
        }
        if (compelledEdges[i]) {
          break;
        }
      }
      if (compelledEdges[i]) {
        continue;
      }
      boolean foundZ = false;

      for (Edge orderedEdge : orderedEdges) {
        Node z = orderedEdge.getNode1();
        if (z != x && orderedEdge.getNode2() == y && !graph.isParentOf(z, x)) {
          compelledEdges[i] = true;
          for (int k = i + 1; k < graph.getNumEdges(); k++) {
            if (orderedEdges[k].getNode2() == y && !reversibleEdges[k]) {
              compelledEdges[k] = true;
            }
          }
          foundZ = true;
          break;
        }
      }

      if (!foundZ) {
        reversibleEdges[i] = true;

        for (int j = i + 1; j < orderedEdges.length; j++) {
          if (!compelledEdges[j] && orderedEdges[j].getNode2() == y) {
            reversibleEdges[j] = true;
          }
        }
      }
    }

    // undirect edges that are reversible
    for (int i = 0; i < reversibleEdges.length; i++) {
      if (reversibleEdges[i]) {
        graph.setEndpoint(orderedEdges[i].getNode1(), orderedEdges[i].getNode2(), Endpoint.TAIL);
        graph.setEndpoint(orderedEdges[i].getNode2(), orderedEdges[i].getNode1(), Endpoint.TAIL);
      }
    }
  }
Example #16
0
  /**
   * @param edge a->b or a<->b.
   * @return the range of the covariance parameter for a->b or a<->b.
   */
  public ParameterRange getParameterRange(Edge edge) {
    if (Edges.isBidirectedEdge(edge)) {
      edge =
          Edges.bidirectedEdge(
              semGraph.getExogenous(edge.getNode1()), semGraph.getExogenous(edge.getNode2()));
    }

    if (!(edgeParameters.keySet().contains(edge))) {
      throw new IllegalArgumentException("Not an edge in this model: " + edge);
    }

    double initial = edgeParameters.get(edge);

    if (initial == Double.NEGATIVE_INFINITY) {
      initial = Double.MIN_VALUE;
    } else if (initial == Double.POSITIVE_INFINITY) {
      initial = Double.MAX_VALUE;
    }

    double value = initial;

    // look upward for a point that fails.
    double high = value + 1;

    while (paramInBounds(edge, high)) {
      high = value + 2 * (high - value);

      if (high == Double.POSITIVE_INFINITY) {
        break;
      }
    }

    // find the boundary using binary search.
    double rangeHigh;

    if (high == Double.POSITIVE_INFINITY) {
      rangeHigh = high;
    } else {
      double low = value;

      while (high - low > 1e-10) {
        double midpoint = (high + low) / 2.0;

        if (paramInBounds(edge, midpoint)) {
          low = midpoint;
        } else {
          high = midpoint;
        }
      }

      rangeHigh = (high + low) / 2.0;
    }

    // look downard for a point that fails.
    double low = value - 1;

    while (paramInBounds(edge, low)) {
      low = value - 2 * (value - low);

      if (low == Double.NEGATIVE_INFINITY) {
        break;
      }
    }

    double rangeLow;

    if (low == Double.NEGATIVE_INFINITY) {
      rangeLow = low;
    } else {

      // find the boundary using binary search.
      high = value;

      while (high - low > 1e-10) {
        double midpoint = (high + low) / 2.0;

        if (paramInBounds(edge, midpoint)) {
          high = midpoint;
        } else {
          low = midpoint;
        }
      }

      rangeLow = (high + low) / 2.0;
    }

    if (Edges.isDirectedEdge(edge)) {
      edgeParameters.put(edge, initial);
    } else if (Edges.isBidirectedEdge(edge)) {
      edgeParameters.put(edge, initial);
    }

    return new ParameterRange(edge, value, rangeLow, rangeHigh);
  }
Example #17
0
  private void addRequiredEdges(Graph graph) {
    if (true) return;
    if (knowledgeEmpty()) return;

    for (Iterator<KnowledgeEdge> it = getKnowledge().requiredEdgesIterator(); it.hasNext(); ) {
      KnowledgeEdge next = it.next();

      Node nodeA = graph.getNode(next.getFrom());
      Node nodeB = graph.getNode(next.getTo());

      if (!graph.isAncestorOf(nodeB, nodeA)) {
        graph.removeEdges(nodeA, nodeB);
        graph.addDirectedEdge(nodeA, nodeB);
        TetradLogger.getInstance()
            .log("insertedEdges", "Adding edge by knowledge: " + graph.getEdge(nodeA, nodeB));
      }
    }
    for (Edge edge : graph.getEdges()) {
      final String A = edge.getNode1().getName();
      final String B = edge.getNode2().getName();

      if (knowledge.isForbidden(A, B)) {
        Node nodeA = edge.getNode1();
        Node nodeB = edge.getNode2();

        if (nodeA != null
            && nodeB != null
            && graph.isAdjacentTo(nodeA, nodeB)
            && !graph.isChildOf(nodeA, nodeB)) {
          if (!graph.isAncestorOf(nodeA, nodeB)) {
            graph.removeEdges(nodeA, nodeB);
            graph.addDirectedEdge(nodeB, nodeA);
            TetradLogger.getInstance()
                .log("insertedEdges", "Adding edge by knowledge: " + graph.getEdge(nodeB, nodeA));
          }
        }
        if (!graph.isChildOf(nodeA, nodeB)
            && getKnowledge().isForbidden(nodeA.getName(), nodeB.getName())) {
          if (!graph.isAncestorOf(nodeA, nodeB)) {
            graph.removeEdges(nodeA, nodeB);
            graph.addDirectedEdge(nodeB, nodeA);
            TetradLogger.getInstance()
                .log("insertedEdges", "Adding edge by knowledge: " + graph.getEdge(nodeB, nodeA));
          }
        }
      } else if (knowledge.isForbidden(B, A)) {
        Node nodeA = edge.getNode2();
        Node nodeB = edge.getNode1();

        if (nodeA != null
            && nodeB != null
            && graph.isAdjacentTo(nodeA, nodeB)
            && !graph.isChildOf(nodeA, nodeB)) {
          if (!graph.isAncestorOf(nodeA, nodeB)) {
            graph.removeEdges(nodeA, nodeB);
            graph.addDirectedEdge(nodeB, nodeA);
            TetradLogger.getInstance()
                .log("insertedEdges", "Adding edge by knowledge: " + graph.getEdge(nodeB, nodeA));
          }
        }
        if (!graph.isChildOf(nodeA, nodeB)
            && getKnowledge().isForbidden(nodeA.getName(), nodeB.getName())) {
          if (!graph.isAncestorOf(nodeA, nodeB)) {
            graph.removeEdges(nodeA, nodeB);
            graph.addDirectedEdge(nodeB, nodeA);
            TetradLogger.getInstance()
                .log("insertedEdges", "Adding edge by knowledge: " + graph.getEdge(nodeB, nodeA));
          }
        }
      }
    }
  }