Beispiel #1
0
  public static Graph erdosRenyiGraph(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 = RandomUtil.getInstance().nextInt(n);
      int i2 = RandomUtil.getInstance().nextInt(n);

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

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

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

      graph.addEdge(edge);
    }

    return graph;
  }
  public GraphIndex(Graph graph) {
    LOG.info("Indexing graph...");

    for (String feedId : graph.getFeedIds()) {
      for (Agency agency : graph.getAgencies(feedId)) {
        Map<String, Agency> agencyForId = agenciesForFeedId.getOrDefault(feedId, new HashMap<>());
        agencyForId.put(agency.getId(), agency);
        this.agenciesForFeedId.put(feedId, agencyForId);
      }
    }

    Collection<Edge> edges = graph.getEdges();
    /* We will keep a separate set of all vertices in case some have the same label.
     * Maybe we should just guarantee unique labels. */
    Set<Vertex> vertices = Sets.newHashSet();
    for (Edge edge : edges) {
      vertices.add(edge.getFromVertex());
      vertices.add(edge.getToVertex());
      if (edge instanceof TablePatternEdge) {
        TablePatternEdge patternEdge = (TablePatternEdge) edge;
        TripPattern pattern = patternEdge.getPattern();
        patternForId.put(pattern.code, pattern);
      }
    }
    for (Vertex vertex : vertices) {
      vertexForId.put(vertex.getLabel(), vertex);
      if (vertex instanceof TransitStop) {
        TransitStop transitStop = (TransitStop) vertex;
        Stop stop = transitStop.getStop();
        stopForId.put(stop.getId(), stop);
        stopVertexForStop.put(stop, transitStop);
        stopsForParentStation.put(stop.getParentStation(), stop);
      }
    }
    for (TransitStop stopVertex : stopVertexForStop.values()) {
      Envelope envelope = new Envelope(stopVertex.getCoordinate());
      stopSpatialIndex.insert(envelope, stopVertex);
    }
    for (TripPattern pattern : patternForId.values()) {
      patternsForFeedId.put(pattern.getFeedId(), pattern);
      patternsForRoute.put(pattern.route, pattern);

      for (Trip trip : pattern.getTrips()) {
        patternForTrip.put(trip, pattern);
        tripForId.put(trip.getId(), trip);
      }
      for (Stop stop : pattern.getStops()) {
        patternsForStop.put(stop, pattern);
      }
    }
    for (Route route : patternsForRoute.asMap().keySet()) {
      routeForId.put(route.getId(), route);
    }

    // Copy these two service indexes from the graph until we have better ones.
    calendarService = graph.getCalendarService();
    serviceCodes = graph.serviceCodes;
    this.graph = graph;
    LOG.info("Done indexing graph.");
  }
  protected Graph<String, DefaultWeightedEdge> createWithBias(boolean negate) {
    Graph<String, DefaultWeightedEdge> g;
    double bias = 1;
    if (negate) {
      // negative-weight edges are being tested, so only a directed graph
      // makes sense
      g = new SimpleDirectedWeightedGraph<String, DefaultWeightedEdge>(DefaultWeightedEdge.class);
      bias = -1;
    } else {
      // by default, use an undirected graph
      g = new SimpleWeightedGraph<String, DefaultWeightedEdge>(DefaultWeightedEdge.class);
    }

    g.addVertex(V1);
    g.addVertex(V2);
    g.addVertex(V3);
    g.addVertex(V4);
    g.addVertex(V5);

    e12 = Graphs.addEdge(g, V1, V2, bias * 2);

    e13 = Graphs.addEdge(g, V1, V3, bias * 3);

    e24 = Graphs.addEdge(g, V2, V4, bias * 5);

    e34 = Graphs.addEdge(g, V3, V4, bias * 20);

    e45 = Graphs.addEdge(g, V4, V5, bias * 5);

    e15 = Graphs.addEdge(g, V1, V5, bias * 100);

    return g;
  }
Beispiel #4
0
  private boolean existsUnblockedSemiDirectedPath(Node from, Node to, List<Node> cond, Graph G) {
    Queue<Node> Q = new LinkedList<Node>();
    Set<Node> V = new HashSet<Node>();
    Q.offer(from);
    V.add(from);

    while (!Q.isEmpty()) {
      Node t = Q.remove();
      if (t == to) return true;

      for (Node u : G.getAdjacentNodes(t)) {
        Edge edge = G.getEdge(t, u);
        Node c = Edges.traverseSemiDirected(t, edge);
        if (c == null) continue;
        if (cond.contains(c)) continue;
        if (c == to) return true;

        if (!V.contains(c)) {
          V.add(c);
          Q.offer(c);
        }
      }
    }

    return false;
  }
  /**
   * Generates AdjacencyListGraph based on the values in the input file.
   *
   * @requires twitterStream is properly initialized
   * @param twitterStream initialized input stream for reading twitter file
   * @return generated graph based on input file
   */
  private static Graph readTwitterFile(FileInputStream twitterStream) {
    final int U1_INDEX = 0;
    final int U2_INDEX = 1;
    try {
      Graph g = new AdjacencyListGraph();
      BufferedReader twitterReader = new BufferedReader(new InputStreamReader(twitterStream));
      String line;
      while ((line = twitterReader.readLine()) != null) {

        // eliminate any unnecessary whitespace
        String[] columns = line.trim().replaceAll("\\s+", "").split("->");

        // first column is user 1
        // second column is user 2
        Vertex u1 = new Vertex(columns[U1_INDEX]);
        Vertex u2 = new Vertex(columns[U2_INDEX]);
        // System.out.println(columns[0]+","+columns[1]);
        g.addVertex(u1);
        g.addVertex(u2);
        g.addEdge(u1, u2);
        // System.out.println(line);
      }
      twitterReader.close();
      return g;
    } catch (Exception e) { // if something somehow goes wrong
      throw new RuntimeException(e);
    }
  }
  Graph create(Collection<? extends Deployer> deployers) {
    // S ← Set of all nodes with no incoming edges
    List<Deployer> s = new ArrayList<Deployer>();
    Map<String, Collection<Deployer>> inputCache = new HashMap<String, Collection<Deployer>>();
    // Map<Deployer, Set<Edge>> edgeCache = new IdentityHashMap<Deployer, Set<Edge>>();
    Map edgeCache = new IdentityHashMap<Deployer, Set<?>>();
    Set<String> outputs = new HashSet<String>();
    Map<String, Collection<Deployer>> outputCache = new HashMap<String, Collection<Deployer>>();
    for (Deployer deployer : deployers) {
      process(deployer, s, inputCache, edgeCache, outputs, outputCache);
    }

    processTransientDeployers(s, inputCache, outputCache, edgeCache);

    Graph graph = new Graph();
    for (Deployer d : deployers) {
      graph.addNode(d.toString());
    }

    for (Map.Entry entry : (Set<Map.Entry>) edgeCache.entrySet()) {
      System.out.println(entry);
      Set<Object> edges = (Set<Object>) entry.getValue();
      for (Object edge : edges) {
        String fromNode = fromNode(edge);
        String edgeLabel = edgeLabel(edge);
        String toNode = toNode(edge);
        graph.addEdge(fromNode, toNode, edgeLabel);
      }
    }
    System.out.println(graph.edges.size());
    return graph;
  }
  /** 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);
    }
  }
  /**
   * Creates a new iterator for the specified graph. Iteration will start at the specified start
   * vertex. If the specified start vertex is <code>
   * null</code>, Iteration will start at an arbitrary graph vertex.
   *
   * @param g the graph to be iterated.
   * @param startVertex the vertex iteration to be started.
   * @throws IllegalArgumentException if <code>g==null</code> or does not contain <code>startVertex
   *     </code>
   */
  public CrossComponentIterator(Graph<V, E> g, V startVertex) {
    super();

    if (g == null) {
      throw new IllegalArgumentException("graph must not be null");
    }
    graph = g;

    specifics = createGraphSpecifics(g);
    vertexIterator = g.vertexSet().iterator();
    setCrossComponentTraversal(startVertex == null);

    reusableEdgeEvent = new FlyweightEdgeEvent<V, E>(this, null);
    reusableVertexEvent = new FlyweightVertexEvent<V>(this, null);

    if (startVertex == null) {
      // pick a start vertex if graph not empty
      if (vertexIterator.hasNext()) {
        this.startVertex = vertexIterator.next();
      } else {
        this.startVertex = null;
      }
    } else if (g.containsVertex(startVertex)) {
      this.startVertex = startVertex;
    } else {
      throw new IllegalArgumentException("graph must contain the start vertex");
    }
  }
  private void init(Graph<V, E> g, Set<V> vertexSet, Set<E> edgeSet) {
    // create a map between vertex value to its order(1st,2nd,etc)
    // "CAT"=1 "DOG"=2 "RHINO"=3

    this.mapVertexToOrder = new HashMap<V, Integer>(vertexSet.size());

    int counter = 0;
    for (V vertex : vertexSet) {
      mapVertexToOrder.put(vertex, new Integer(counter));
      counter++;
    }

    // create a friendlier representation of an edge
    // by order, like 2nd->3rd instead of B->A
    // use the map to convert vertex to order
    // on directed graph, edge A->B must be (A,B)
    // on undirected graph, edge A-B can be (A,B) or (B,A)

    this.labelsEdgesSet = new HashSet<LabelsEdge>(edgeSet.size());
    for (E edge : edgeSet) {
      V sourceVertex = g.getEdgeSource(edge);
      Integer sourceOrder = mapVertexToOrder.get(sourceVertex);
      int sourceLabel = sourceOrder.intValue();
      int targetLabel = (mapVertexToOrder.get(g.getEdgeTarget(edge))).intValue();

      LabelsEdge lablesEdge = new LabelsEdge(sourceLabel, targetLabel);
      this.labelsEdgesSet.add(lablesEdge);

      if (g instanceof UndirectedGraph<?, ?>) {
        LabelsEdge oppositeEdge = new LabelsEdge(targetLabel, sourceLabel);
        this.labelsEdgesSet.add(oppositeEdge);
      }
    }
  }
Beispiel #10
0
  private Graph changeLatentNames(Graph full, Clusters measurements, List<String> latentVarList) {
    Graph g2 = null;

    try {
      g2 = (Graph) new MarshalledObject(full).get();
    } catch (IOException e) {
      e.printStackTrace();
    } catch (ClassNotFoundException e) {
      e.printStackTrace();
    }

    for (int i = 0; i < measurements.getNumClusters(); i++) {
      List<String> d = measurements.getCluster(i);
      String latentName = latentVarList.get(i);

      for (Node node : full.getNodes()) {
        if (!(node.getNodeType() == NodeType.LATENT)) {
          continue;
        }

        List<Node> _children = full.getChildren(node);

        _children.removeAll(ReidentifyVariables.getLatents(full));

        List<String> childNames = getNames(_children);

        if (new HashSet<String>(childNames).equals(new HashSet<String>(d))) {
          g2.getNode(node.getName()).setName(latentName);
        }
      }
    }

    return g2;
  }
Beispiel #11
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  /**
   * @param vertexNumber the number which identifies the vertex v in this order.
   * @return the identifying numbers of all vertices which are connected to v by an edge incoming to
   *     v.
   */
  public int[] getInEdges(int vertexNumber) {
    if (cacheEdges && (incomingEdges[vertexNumber] != null)) {
      return incomingEdges[vertexNumber];
    }

    V v = getVertex(vertexNumber);
    Set<E> edgeSet;

    if (graph instanceof DirectedGraph<?, ?>) {
      edgeSet = ((DirectedGraph<V, E>) graph).incomingEdgesOf(v);
    } else {
      edgeSet = graph.edgesOf(v);
    }

    int[] vertexArray = new int[edgeSet.size()];
    int i = 0;

    for (E edge : edgeSet) {
      V source = graph.getEdgeSource(edge), target = graph.getEdgeTarget(edge);
      vertexArray[i++] = mapVertexToOrder.get(source.equals(v) ? target : source);
    }

    if (cacheEdges) {
      incomingEdges[vertexNumber] = vertexArray;
    }

    return vertexArray;
  }
Beispiel #12
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  public List<Triple> getUnshieldedCollidersFromGraph(Graph graph) {
    List<Triple> colliders = new ArrayList<>();

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

    for (Node b : nodes) {
      List<Node> adjacentNodes = graph.getAdjacentNodes(b);

      if (adjacentNodes.size() < 2) {
        continue;
      }

      ChoiceGenerator cg = new ChoiceGenerator(adjacentNodes.size(), 2);
      int[] combination;

      while ((combination = cg.next()) != null) {
        Node a = adjacentNodes.get(combination[0]);
        Node c = adjacentNodes.get(combination[1]);

        // Skip triples that are shielded.
        if (graph.isAdjacentTo(a, c)) {
          continue;
        }

        if (graph.isDefCollider(a, b, c)) {
          colliders.add(new Triple(a, b, c));
        }
      }
    }

    return colliders;
  }
Beispiel #13
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  ////////////////////////////////////////////////
  // collect in rTupleList all unshielded tuples
  ////////////////////////////////////////////////
  private List<Node[]> getRTuples() {
    List<Node[]> rTuples = new ArrayList<Node[]>();
    List<Node> nodes = graph.getNodes();

    for (Node j : nodes) {
      List<Node> adjacentNodes = graph.getAdjacentNodes(j);

      if (adjacentNodes.size() < 2) {
        continue;
      }

      ChoiceGenerator cg = new ChoiceGenerator(adjacentNodes.size(), 2);
      int[] combination;

      while ((combination = cg.next()) != null) {
        Node i = adjacentNodes.get(combination[0]);
        Node k = adjacentNodes.get(combination[1]);

        // Skip triples that are shielded.
        if (!graph.isAdjacentTo(i, k)) {
          Node[] newTuple = {i, j, k};
          rTuples.add(newTuple);
        }
      }
    }

    return (rTuples);
  }
Beispiel #14
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 public Set<Edge> getNonadjacencies() {
   Graph complete = GraphUtils.completeGraph(graph);
   Set<Edge> nonAdjacencies = complete.getEdges();
   Graph undirected = GraphUtils.undirectedGraph(graph);
   nonAdjacencies.removeAll(undirected.getEdges());
   return new HashSet<Edge>(nonAdjacencies);
 }
Beispiel #15
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 public Graph copy() {
   WeightedArcSet list = new WeightedArcSet();
   Constructor[] cons = WeightedArc.class.getDeclaredConstructors();
   for (int i = 0; i < cons.length; i++) cons[i].setAccessible(true);
   ArcLabelledNodeIterator it = graph.nodeIterator();
   while (it.hasNext()) {
     Integer aux1 = it.nextInt();
     Integer aux2 = null;
     ArcLabelledNodeIterator.LabelledArcIterator suc = it.successors();
     while ((aux2 = suc.nextInt()) != null && aux2 >= 0 && (aux2 < graph.numNodes()))
       try {
         if (commit++ % COMMIT_SIZE == 0) {
           list.commit();
         }
         WeightedArc arc = (WeightedArc) cons[0].newInstance(aux2, aux1, suc.label().getFloat());
         list.add(arc);
       } catch (Exception ex) {
         throw new Error(ex);
       }
   }
   Graph result = new Graph(list.toArray(new WeightedArc[0]));
   result.nodes.clear();
   result.nodesReverse.clear();
   for (Integer n : this.nodes.keySet()) {
     if (commit++ % COMMIT_SIZE == 0) {
       result.commit();
     }
     result.nodesReverse.put(this.nodes.get(n), n);
     result.nodes.put(n, this.nodes.get(n));
   }
   return result;
 }
Beispiel #16
0
  /**
   * Random graph. Generates randomly k directed edges out of each node. The neighbors (edge
   * targets) are chosen randomly without replacement from the nodes of the graph other than the
   * source node (i.e. no loop edge is added). If k is larger than N-1 (where N is the number of
   * nodes) then k is set to be N-1 and a complete graph is returned.
   *
   * @param g the graph to be wired
   * @param k samples to be drawn for each node
   * @param r source of randomness
   * @return returns g for convenience
   */
  public static Graph wireKOut(Graph g, int k, Random r) {

    final int n = g.size();
    if (n < 2) {
      return g;
    }
    if (n <= k) {
      k = n - 1;
    }
    int[] nodes = new int[n];
    for (int i = 0; i < nodes.length; ++i) {
      nodes[i] = i;
    }
    for (int i = 0; i < n; ++i) {
      int j = 0;
      while (j < k) {
        int newedge = j + r.nextInt(n - j);
        int tmp = nodes[j];
        nodes[j] = nodes[newedge];
        nodes[newedge] = tmp;
        if (nodes[j] != i) {
          g.setEdge(i, nodes[j]);
          j++;
        }
      }
    }
    return g;
  }
Beispiel #17
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  // ===========================SCORING METHODS===================//
  public double scoreDag(Graph graph) {
    Graph dag = new EdgeListGraphSingleConnections(graph);
    buildIndexing(graph);

    double score = 0.0;

    for (Node y : dag.getNodes()) {
      Set<Node> parents = new HashSet<Node>(dag.getParents(y));
      int nextIndex = -1;
      for (int i = 0; i < getVariables().size(); i++) {
        nextIndex = hashIndices.get(variables.get(i));
      }
      int parentIndices[] = new int[parents.size()];
      Iterator<Node> pi = parents.iterator();
      int count = 0;
      while (pi.hasNext()) {
        Node nextParent = pi.next();
        parentIndices[count++] = hashIndices.get(nextParent);
      }

      if (this.isDiscrete()) {
        score += localDiscreteScore(nextIndex, parentIndices);
      } else {
        score += localSemScore(nextIndex, parentIndices);
      }
    }
    return score;
  }
Beispiel #18
0
 /** @return dfs wenn gefunden, ansonsten NULL */
 @Override
 public Graph<Integer> dfs(Node<Integer> start, Node<Integer> goal) {
   this.unvisitAllNodes();
   Graph<Integer> dfs = new ImplGraph();
   dfs.setNode(start.value());
   boolean found = this.dfs(start, goal, dfs);
   return found ? dfs : null;
 }
Beispiel #19
0
 private void populateLists(List<Vertex> verticies, List<Edge> edges) {
   for (Vertex v : graph.getVertices()) {
     verticies.add(v);
   }
   for (Edge e : graph.getEdges()) {
     edges.add(e);
   }
 }
  private Set<String> getDownstream(String mut) {
    Set<String> tfs = new HashSet<String>();
    tfs.add(mut);

    if (depth > 1) tfs.addAll(travSt.getDownstream(tfs, depth - 1));

    return travExp.getDownstream(tfs);
  }
Beispiel #21
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  /**
   * A sink star. Wires a sink star topology adding a link to 0 from all other nodes.
   *
   * @param g the graph to be wired
   * @return returns g for convenience
   */
  public static Graph wireStar(Graph g) {

    final int n = g.size();
    for (int i = 1; i < n; ++i) {
      g.setEdge(i, 0);
    }
    return g;
  }
Beispiel #22
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 public static void main(String[] args) {
   Graph g = new Graph();
   g.addEdge(0, 1);
   g.addEdge(1, 2);
   System.out.println(g.edges);
   g.removeNode(1);
   System.out.println(g.edges);
 }
Beispiel #23
0
  /**
   * Step C of PC; orients colliders using specified sepset. That is, orients x *-* y *-* z as x *->
   * y <-* z just in case y is in Sepset({x, z}).
   */
  public Map<Triple, Double> findCollidersUsingSepsets(
      SepsetProducer sepsetProducer, Graph graph, boolean verbose, IKnowledge knowledge) {
    TetradLogger.getInstance().log("details", "Starting Collider Orientation:");
    Map<Triple, Double> colliders = new HashMap<>();

    System.out.println("Looking for colliders");

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

    for (Node b : nodes) {
      List<Node> adjacentNodes = graph.getAdjacentNodes(b);

      if (adjacentNodes.size() < 2) {
        continue;
      }

      ChoiceGenerator cg = new ChoiceGenerator(adjacentNodes.size(), 2);
      int[] combination;

      while ((combination = cg.next()) != null) {
        Node a = adjacentNodes.get(combination[0]);
        Node c = adjacentNodes.get(combination[1]);

        // Skip triples that are shielded.
        if (graph.isAdjacentTo(a, c)) {
          continue;
        }

        List<Node> sepset = sepsetProducer.getSepset(a, c);

        if (sepset == null) continue;

        //                if (sepsetProducer.getPValue() < 0.5) continue;

        if (!sepset.contains(b)) {
          if (verbose) {
            //                        boolean dsep = this.dsep.isIndependent(a, c);
            //                        System.out.println("QQQ p = " + independenceTest.getPValue() +
            // " " + dsep);

            System.out.println(
                "\nCollider orientation <" + a + ", " + b + ", " + c + "> sepset = " + sepset);
          }

          colliders.put(new Triple(a, b, c), sepsetProducer.getPValue());

          TetradLogger.getInstance()
              .log("colliderOrientations", SearchLogUtils.colliderOrientedMsg(a, b, c, sepset));
        }
      }
    }

    TetradLogger.getInstance().log("details", "Finishing Collider Orientation.");

    System.out.println("Done finding colliders");

    return colliders;
  }
Beispiel #24
0
  private boolean isUndirected(Graph graph, Node x, Node y) {
    List<Edge> edges = graph.getEdges(x, y);
    if (edges.size() == 1) {
      Edge edge = graph.getEdge(x, y);
      return Edges.isUndirectedEdge(edge);
    }

    return false;
  }
Beispiel #25
0
  public int[] getEdgeNumbers(E e) {
    V v1 = graph.getEdgeSource(e), v2 = graph.getEdgeTarget(e);

    int[] edge = new int[2];
    edge[0] = mapVertexToOrder.get(v1);
    edge[1] = mapVertexToOrder.get(v2);

    return edge;
  }
  /**
   * Performs step C of the algorithm, as indicated on page xxx of CPS, with the modification that
   * X--W--Y is oriented as X-->W<--Y if W is *determined by* the sepset of (X, Y), rather than W
   * just being *in* the sepset of (X, Y).
   */
  public static void pcdOrientC(
      SepsetMap set, IndependenceTest test, Knowledge knowledge, Graph graph) {
    TetradLogger.getInstance().log("info", "Staring Collider Orientation:");

    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]);

        // Skip triples that are shielded.
        if (graph.isAdjacentTo(x, z)) {
          continue;
        }

        List<Node> sepset = set.get(x, z);

        if (sepset == null) {
          continue;
        }

        List<Node> augmentedSet = new LinkedList<Node>(sepset);
        augmentedSet.add(y);

        if (test.determines(sepset, y)) {
          continue;
        }
        //
        if (!test.splitDetermines(sepset, x, z) && test.splitDetermines(augmentedSet, x, z)) {
          continue;
        }

        if (!isArrowpointAllowed(x, y, knowledge) || !isArrowpointAllowed(z, y, knowledge)) {
          continue;
        }

        graph.setEndpoint(x, y, Endpoint.ARROW);
        graph.setEndpoint(z, y, Endpoint.ARROW);

        TetradLogger.getInstance()
            .log("colliderOriented", SearchLogUtils.colliderOrientedMsg(x, y, z));
      }
    }

    TetradLogger.getInstance().log("info", "Finishing Collider Orientation.");
  }
Beispiel #27
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 private boolean localMarkovIndep(Node x, Node y, Graph pattern, IndependenceTest test) {
   List<Node> future = pattern.getDescendants(Collections.singletonList(x));
   List<Node> boundary = pattern.getAdjacentNodes(x);
   boundary.removeAll(future);
   List<Node> closure = new ArrayList<>(boundary);
   closure.add(x);
   closure.remove(y);
   if (future.contains(y) || boundary.contains(y)) return false;
   return test.isIndependent(x, y, boundary);
 }
Beispiel #28
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 public Graph transpose() {
   Graph g = copy();
   try {
     g.graph = Transform.transposeOffline(g.graph, 1000);
     g.reverse = Transform.transposeOffline(g.reverse, 1000);
   } catch (IOException ex) {
     throw new Error(ex);
   }
   return g;
 }
Beispiel #29
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  public static GraphOrder forwardGraph(Graph graph) {
    GraphOrder result = new GraphOrder();

    NodeBitMap visited = graph.createNodeBitMap();

    for (ControlSinkNode node : graph.getNodes(ControlSinkNode.class)) {
      result.visitForward(visited, node);
    }
    return result;
  }
  private double getPMulticluster(List<List<Integer>> clusters, int numRestarts) {
    if (false) {
      Graph g = new EdgeListGraph();
      List<Node> latents = new ArrayList<Node>();
      for (int i = 0; i < clusters.size(); i++) {
        GraphNode latent = new GraphNode("L" + i);
        latent.setNodeType(NodeType.LATENT);
        latents.add(latent);
        g.addNode(latent);

        List<Node> cluster = variablesForIndices(clusters.get(i));

        for (int j = 0; j < cluster.size(); j++) {
          g.addNode(cluster.get(j));
          g.addDirectedEdge(latent, cluster.get(j));
        }
      }
      SemPm pm = new SemPm(g);

      //            pm.fixOneLoadingPerLatent();

      SemOptimizerPowell semOptimizer = new SemOptimizerPowell();
      semOptimizer.setNumRestarts(numRestarts);

      SemEstimator est = new SemEstimator(cov, pm, semOptimizer);
      est.setScoreType(SemIm.ScoreType.Fgls);
      est.estimate();
      return est.getEstimatedSem().getPValue();
    } else {
      double max = Double.NEGATIVE_INFINITY;

      for (int i = 0; i < numRestarts; i++) {
        Mimbuild2 mimbuild = new Mimbuild2();

        List<List<Node>> _clusters = new ArrayList<List<Node>>();

        for (List<Integer> _cluster : clusters) {
          _clusters.add(variablesForIndices(_cluster));
        }

        List<String> names = new ArrayList<String>();

        for (int j = 0; j < clusters.size(); j++) {
          names.add("L" + j);
        }

        mimbuild.search(_clusters, names, cov);

        double c = mimbuild.getpValue();
        if (c > max) max = c;
      }

      return max;
    }
  }