private Set<Integer> unionPure(Set<Set<Integer>> pureClusters) {
    Set<Integer> unionPure = new HashSet<Integer>();

    for (Set<Integer> cluster : pureClusters) {
      unionPure.addAll(cluster);
    }

    return unionPure;
  }
  private Set<Integer> triple(int n1, int n2, int n3) {
    Set<Integer> triple = new HashSet<Integer>();
    triple.add(n1);
    triple.add(n2);
    triple.add(n3);

    if (triple.size() < 3)
      throw new IllegalArgumentException(
          "Triple elements must be unique: <" + n1 + ", " + n2 + ", " + n3 + ">");

    return triple;
  }
  private boolean quartetVanishes(Set<Integer> quartet) {
    if (quartet.size() != 4)
      throw new IllegalArgumentException("Expecting a quartet, size = " + quartet.size());

    Iterator<Integer> iter = quartet.iterator();
    int x = iter.next();
    int y = iter.next();
    int z = iter.next();
    int w = iter.next();

    return testVanishing(x, y, z, w);
  }
  private Set<Integer> quartet(int x, int y, int z, int w) {
    Set<Integer> set = new HashSet<Integer>();
    set.add(x);
    set.add(y);
    set.add(z);
    set.add(w);

    if (set.size() < 4)
      throw new IllegalArgumentException(
          "Quartet elements must be unique: <" + x + ", " + y + ", " + z + ", " + w + ">");

    return set;
  }
  private Graph convertToGraph(Set<Set<Integer>> allClusters) {
    Set<Set<Node>> _clustering = new HashSet<Set<Node>>();

    for (Set<Integer> cluster : allClusters) {
      Set<Node> nodes = new HashSet<Node>();

      for (int i : cluster) {
        nodes.add(variables.get(i));
      }

      _clustering.add(nodes);
    }

    return convertSearchGraphNodes(_clustering);
  }
  private boolean clique(Set<Integer> cluster, Map<Node, Set<Node>> adjacencies) {
    List<Integer> _cluster = new ArrayList<Integer>(cluster);

    for (int i = 0; i < cluster.size(); i++) {
      for (int j = i + 1; j < cluster.size(); j++) {
        Node nodei = variables.get(_cluster.get(i));
        Node nodej = variables.get(_cluster.get(j));

        if (!adjacencies.get(nodei).contains(nodej)) {
          return false;
        }
      }
    }

    return true;
  }
  private boolean pure(Set<Integer> quartet, List<Integer> variables) {
    if (quartetVanishes(quartet)) {
      for (int o : variables) {
        if (quartet.contains(o)) continue;

        for (int p : quartet) {
          Set<Integer> _quartet = new HashSet<Integer>(quartet);
          _quartet.remove(p);
          _quartet.add(o);

          if (!quartetVanishes(_quartet)) {
            return false;
          }
        }
      }

      return significant(new ArrayList<Integer>(quartet));
    }

    return false;
  }
Esempio n. 8
0
  @Test
  public void test1() {
    GeneralizedSemPm pm = makeTypicalPm();

    print(pm);

    Node x1 = pm.getNode("X1");
    Node x2 = pm.getNode("X2");
    Node x3 = pm.getNode("X3");
    Node x4 = pm.getNode("X4");
    Node x5 = pm.getNode("X5");

    SemGraph graph = pm.getGraph();

    List<Node> variablesNodes = pm.getVariableNodes();
    print(variablesNodes);

    List<Node> errorNodes = pm.getErrorNodes();
    print(errorNodes);

    try {
      pm.setNodeExpression(x1, "cos(B1) + E_X1");
      print(pm);

      String b1 = "B1";
      String b2 = "B2";
      String b3 = "B3";

      Set<Node> nodes = pm.getReferencingNodes(b1);

      assertTrue(nodes.contains(x1));
      assertTrue(!nodes.contains(x2) && !nodes.contains(x2));

      Set<String> referencedParameters = pm.getReferencedParameters(x3);

      print("Parameters referenced by X3 are: " + referencedParameters);

      assertTrue(referencedParameters.contains(b1) && referencedParameters.contains(b2));
      assertTrue(!(referencedParameters.contains(b1) && referencedParameters.contains(b3)));

      Node e_x3 = pm.getNode("E_X3");
      //
      for (Node node : pm.getNodes()) {
        Set<Node> referencingNodes = pm.getReferencingNodes(node);
        print("Nodes referencing " + node + " are: " + referencingNodes);
      }

      for (Node node : pm.getVariableNodes()) {
        Set<Node> referencingNodes = pm.getReferencedNodes(node);
        print("Nodes referenced by " + node + " are: " + referencingNodes);
      }

      Set<Node> referencingX3 = pm.getReferencingNodes(x3);
      assertTrue(referencingX3.contains(x4));
      assertTrue(!referencingX3.contains(x5));

      Set<Node> referencedByX3 = pm.getReferencedNodes(x3);
      assertTrue(
          referencedByX3.contains(x1)
              && referencedByX3.contains(x2)
              && referencedByX3.contains(e_x3)
              && !referencedByX3.contains(x4));

      pm.setNodeExpression(x5, "a * E^X2 + X4 + E_X5");

      Node e_x5 = pm.getErrorNode(x5);

      graph.setShowErrorTerms(true);
      assertTrue(e_x5.equals(graph.getExogenous(x5)));

      pm.setNodeExpression(e_x5, "Beta(3, 5)");

      print(pm);

      assertEquals("Split(-1.5,-.5,.5,1.5)", pm.getParameterExpressionString(b1));
      pm.setParameterExpression(b1, "N(0, 2)");
      assertEquals("N(0, 2)", pm.getParameterExpressionString(b1));

      GeneralizedSemIm im = new GeneralizedSemIm(pm);

      print(im);

      DataSet dataSet = im.simulateDataAvoidInfinity(10, false);

      print(dataSet);

    } catch (ParseException e) {
      e.printStackTrace();
    }
  }
Esempio n. 9
0
  @Test
  public void test4() {
    // For X3

    Map<String, String[]> templates = new HashMap<>();

    templates.put(
        "NEW(b) + NEW(b) + NEW(c) + NEW(c) + NEW(c)", new String[] {"X1", "X2", "X3", "X4", "X5"});
    templates.put("NEW(X1) + NEW(b) + NEW(c) + NEW(c) + NEW(c)", new String[] {});
    templates.put("$", new String[] {});
    templates.put("TSUM($)", new String[] {"X1", "X2", "X3", "X4", "X5"});
    templates.put("TPROD($)", new String[] {"X1", "X2", "X3", "X4", "X5"});
    templates.put("TPROD($) + X2", new String[] {"X1", "X2", "X3", "X4", "X5"});
    templates.put("TPROD($) + TSUM($)", new String[] {"X1", "X2", "X3", "X4", "X5"});
    templates.put("tan(TSUM(NEW(a)*$))", new String[] {"X1", "X2", "X3", "X4", "X5"});
    templates.put("Normal(0, 1)", new String[] {"X1", "X2", "X3", "X4", "X5"});
    templates.put("Normal(m, s)", new String[] {"X1", "X2", "X3", "X4", "X5"});
    templates.put("Normal(NEW(m), s)", new String[] {"X1", "X2", "X3", "X4", "X5"});
    templates.put("Normal(NEW(m), NEW(s)) + m1 + s6", new String[] {"X1", "X2", "X3", "X4", "X5"});
    templates.put("TSUM($) + a", new String[] {"X1", "X2", "X3", "X4", "X5"});
    templates.put("TSUM($) + TSUM($) + TSUM($) + 1", new String[] {"X1", "X2", "X3", "X4", "X5"});

    for (String template : templates.keySet()) {
      GeneralizedSemPm semPm = makeTypicalPm();
      print(semPm.getGraph().toString());

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

      for (String name : templates.get(template)) {
        shouldWork.add(semPm.getNode(name));
      }

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

      for (int i = 0; i < semPm.getNodes().size(); i++) {
        print("-----------");
        print(semPm.getNodes().get(i).toString());
        print("Trying template: " + template);
        String _template = template;

        Node node = semPm.getNodes().get(i);

        try {
          _template = TemplateExpander.getInstance().expandTemplate(_template, semPm, node);
        } catch (Exception e) {
          print("Couldn't expand template: " + template);
          continue;
        }

        try {
          semPm.setNodeExpression(node, _template);
          print("Set formula " + _template + " for " + node);

          if (semPm.getVariableNodes().contains(node)) {
            works.add(node);
          }

        } catch (Exception e) {
          print("Couldn't set formula " + _template + " for " + node);
        }
      }

      for (String parameter : semPm.getParameters()) {
        print("-----------");
        print(parameter);
        print("Trying template: " + template);
        String _template = template;

        try {
          _template = TemplateExpander.getInstance().expandTemplate(_template, semPm, null);
        } catch (Exception e) {
          print("Couldn't expand template: " + template);
          continue;
        }

        try {
          semPm.setParameterExpression(parameter, _template);
          print("Set formula " + _template + " for " + parameter);
        } catch (Exception e) {
          print("Couldn't set formula " + _template + " for " + parameter);
        }
      }

      assertEquals(shouldWork, works);
    }
  }
  private Set<Set<Integer>> finishESeeds(Set<Set<Integer>> ESeeds) {
    log("Growing Effect Seeds.", true);
    Set<Set<Integer>> grown = new HashSet<Set<Integer>>();

    List<Integer> _variables = new ArrayList<Integer>();
    for (int i = 0; i < variables.size(); i++) _variables.add(i);

    // Lax grow phase with speedup.
    if (algType == AlgType.lax) {
      Set<Integer> t = new HashSet<Integer>();
      int count = 0;
      int total = ESeeds.size();

      do {
        if (!ESeeds.iterator().hasNext()) {
          break;
        }

        Set<Integer> cluster = ESeeds.iterator().next();
        Set<Integer> _cluster = new HashSet<Integer>(cluster);

        if (extraShuffle) {
          Collections.shuffle(_variables);
        }

        for (int o : _variables) {
          if (_cluster.contains(o)) continue;

          List<Integer> _cluster2 = new ArrayList<Integer>(_cluster);
          int rejected = 0;
          int accepted = 0;

          ChoiceGenerator gen = new ChoiceGenerator(_cluster2.size(), 2);
          int[] choice;

          while ((choice = gen.next()) != null) {
            int n1 = _cluster2.get(choice[0]);
            int n2 = _cluster2.get(choice[1]);

            t.clear();
            t.add(n1);
            t.add(n2);
            t.add(o);

            if (!ESeeds.contains(t)) {
              rejected++;
            } else {
              accepted++;
            }
          }

          if (rejected > accepted) {
            continue;
          }

          _cluster.add(o);

          //                    if (!(avgSumLnP(new ArrayList<Integer>(_cluster)) > -10)) {
          //                        _cluster.remove(o);
          //                    }
        }

        // This takes out all pure clusters that are subsets of _cluster.
        ChoiceGenerator gen2 = new ChoiceGenerator(_cluster.size(), 3);
        int[] choice2;
        List<Integer> _cluster3 = new ArrayList<Integer>(_cluster);

        while ((choice2 = gen2.next()) != null) {
          int n1 = _cluster3.get(choice2[0]);
          int n2 = _cluster3.get(choice2[1]);
          int n3 = _cluster3.get(choice2[2]);

          t.clear();
          t.add(n1);
          t.add(n2);
          t.add(n3);

          ESeeds.remove(t);
        }

        if (verbose) {
          System.out.println(
              "Grown "
                  + (++count)
                  + " of "
                  + total
                  + ": "
                  + variablesForIndices(new ArrayList<Integer>(_cluster)));
        }
        grown.add(_cluster);
      } while (!ESeeds.isEmpty());
    }

    // Lax grow phase without speedup.
    if (algType == AlgType.laxWithSpeedup) {
      int count = 0;
      int total = ESeeds.size();

      // Optimized lax version of grow phase.
      for (Set<Integer> cluster : new HashSet<Set<Integer>>(ESeeds)) {
        Set<Integer> _cluster = new HashSet<Integer>(cluster);

        if (extraShuffle) {
          Collections.shuffle(_variables);
        }

        for (int o : _variables) {
          if (_cluster.contains(o)) continue;

          List<Integer> _cluster2 = new ArrayList<Integer>(_cluster);
          int rejected = 0;
          int accepted = 0;
          //
          ChoiceGenerator gen = new ChoiceGenerator(_cluster2.size(), 2);
          int[] choice;

          while ((choice = gen.next()) != null) {
            int n1 = _cluster2.get(choice[0]);
            int n2 = _cluster2.get(choice[1]);

            Set<Integer> triple = triple(n1, n2, o);

            if (!ESeeds.contains(triple)) {
              rejected++;
            } else {
              accepted++;
            }
          }
          //
          if (rejected > accepted) {
            continue;
          }

          //                    System.out.println("Adding " + o  + " to " + cluster);
          _cluster.add(o);
        }

        for (Set<Integer> c : new HashSet<Set<Integer>>(ESeeds)) {
          if (_cluster.containsAll(c)) {
            ESeeds.remove(c);
          }
        }

        if (verbose) {
          System.out.println("Grown " + (++count) + " of " + total + ": " + _cluster);
        }

        grown.add(_cluster);
      }
    }

    // Strict grow phase.
    if (algType == AlgType.strict) {
      Set<Integer> t = new HashSet<Integer>();
      int count = 0;
      int total = ESeeds.size();

      do {
        if (!ESeeds.iterator().hasNext()) {
          break;
        }

        Set<Integer> cluster = ESeeds.iterator().next();
        Set<Integer> _cluster = new HashSet<Integer>(cluster);

        if (extraShuffle) {
          Collections.shuffle(_variables);
        }

        VARIABLES:
        for (int o : _variables) {
          if (_cluster.contains(o)) continue;

          List<Integer> _cluster2 = new ArrayList<Integer>(_cluster);

          ChoiceGenerator gen = new ChoiceGenerator(_cluster2.size(), 2);
          int[] choice;

          while ((choice = gen.next()) != null) {
            int n1 = _cluster2.get(choice[0]);
            int n2 = _cluster2.get(choice[1]);

            t.clear();
            t.add(n1);
            t.add(n2);
            t.add(o);

            if (!ESeeds.contains(t)) {
              continue VARIABLES;
            }

            //                        if (avgSumLnP(new ArrayList<Integer>(t)) < -10) continue
            // CLUSTER;
          }

          _cluster.add(o);
        }

        // This takes out all pure clusters that are subsets of _cluster.
        ChoiceGenerator gen2 = new ChoiceGenerator(_cluster.size(), 3);
        int[] choice2;
        List<Integer> _cluster3 = new ArrayList<Integer>(_cluster);

        while ((choice2 = gen2.next()) != null) {
          int n1 = _cluster3.get(choice2[0]);
          int n2 = _cluster3.get(choice2[1]);
          int n3 = _cluster3.get(choice2[2]);

          t.clear();
          t.add(n1);
          t.add(n2);
          t.add(n3);

          ESeeds.remove(t);
        }

        if (verbose) {
          System.out.println("Grown " + (++count) + " of " + total + ": " + _cluster);
        }
        grown.add(_cluster);
      } while (!ESeeds.isEmpty());
    }

    // Optimized pick phase.
    log("Choosing among grown Effect Clusters.", true);

    for (Set<Integer> l : grown) {
      ArrayList<Integer> _l = new ArrayList<Integer>(l);
      Collections.sort(_l);
      if (verbose) {
        log("Grown: " + variablesForIndices(_l), false);
      }
    }

    Set<Set<Integer>> out = new HashSet<Set<Integer>>();

    List<Set<Integer>> list = new ArrayList<Set<Integer>>(grown);

    //        final Map<Set<Integer>, Double> pValues = new HashMap<Set<Integer>, Double>();
    //
    //        for (Set<Integer> o : grown) {
    //            pValues.put(o, getP(new ArrayList<Integer>(o)));
    //        }

    Collections.sort(
        list,
        new Comparator<Set<Integer>>() {
          @Override
          public int compare(Set<Integer> o1, Set<Integer> o2) {
            //                if (o1.size() == o2.size()) {
            //                    double chisq1 = pValues.get(o1);
            //                    double chisq2 = pValues.get(o2);
            //                    return Double.compare(chisq2, chisq1);
            //                }

            return o2.size() - o1.size();
          }
        });

    //        for (Set<Integer> o : list) {
    //            if (pValues.get(o) < alpha) continue;
    //            System.out.println(variablesForIndices(new ArrayList<Integer>(o)) + "  p = " +
    // pValues.get(o));
    //        }

    Set<Integer> all = new HashSet<Integer>();

    CLUSTER:
    for (Set<Integer> cluster : list) {
      //            if (pValues.get(cluster) < alpha) continue;

      for (Integer i : cluster) {
        if (all.contains(i)) continue CLUSTER;
      }

      out.add(cluster);

      //            if (getPMulticluster(out) < alpha) {
      //                out.remove(cluster);
      //                continue;
      //            }

      all.addAll(cluster);
    }

    return out;
  }
  private Void findSeeds() {
    Tetrad tetrad = null;
    List<Node> empty = new ArrayList();
    if (variables.size() < 4) {
      Set<Set<Integer>> ESeeds = new HashSet<Set<Integer>>();
    }

    Map<Node, Set<Node>> adjacencies;

    if (depth == -2) {
      adjacencies = new HashMap<Node, Set<Node>>();

      for (Node node : variables) {
        HashSet<Node> _nodes = new HashSet<Node>(variables);
        _nodes.remove(node);
        adjacencies.put(node, _nodes);
      }
    } else {
      //            System.out.println("Running PC adjacency search...");
      Graph graph = new EdgeListGraph(variables);
      Fas fas = new Fas(graph, indTest);
      fas.setVerbose(false);
      fas.setDepth(depth); // 1?
      adjacencies = fas.searchMapOnly();
      //            System.out.println("...done.");
    }

    List<Integer> allVariables = new ArrayList<Integer>();
    for (int i = 0; i < variables.size(); i++) allVariables.add(i);

    log("Finding seeds.", true);

    ChoiceGenerator gen = new ChoiceGenerator(allVariables.size(), 3);
    int[] choice;
    CHOICE:
    while ((choice = gen.next()) != null) {
      int n1 = allVariables.get(choice[0]);
      int n2 = allVariables.get(choice[1]);
      int n3 = allVariables.get(choice[2]);
      Node v1 = variables.get(choice[0]);
      Node v2 = variables.get(choice[1]);
      Node v3 = variables.get(choice[2]);

      Set<Integer> triple = triple(n1, n2, n3);

      if (!clique(triple, adjacencies)) {
        continue;
      }

      boolean EPure = true;
      boolean CPure1 = true;
      boolean CPure2 = true;
      boolean CPure3 = true;

      for (int o : allVariables) {
        if (triple.contains(o)) {
          continue;
        }

        Node v4 = variables.get(o);
        tetrad = new Tetrad(v1, v2, v3, v4);

        if (deltaTest.getPValue(tetrad) > alpha) {
          EPure = false;
          if (indTest.isDependent(v1, v4, empty)) {
            CPure1 = false;
          }
          if (indTest.isDependent(v2, v4, empty)) {
            CPure2 = false;
          }
        }
        tetrad = new Tetrad(v1, v3, v2, v4);
        if (deltaTest.getPValue(tetrad) > alpha) {
          EPure = false;
          if (indTest.isDependent(v3, v4, empty)) {
            CPure3 = false;
          }
        }

        if (!(EPure || CPure1 || CPure2 || CPure3)) {
          continue CHOICE;
        }
      }

      HashSet<Integer> _cluster = new HashSet<Integer>(triple);

      if (verbose) {
        log("++" + variablesForIndices(new ArrayList<Integer>(triple)), false);
      }

      if (EPure) {
        ESeeds.add(_cluster);
      }
      if (!EPure) {
        if (CPure1) {
          Set<Integer> _cluster1 = new HashSet<Integer>(n2, n3);
          _cluster1.addAll(CSeeds.get(n1));
          CSeeds.set(n1, _cluster1);
        }
        if (CPure2) {
          Set<Integer> _cluster2 = new HashSet<Integer>(n1, n3);
          _cluster2.addAll(CSeeds.get(n2));
          CSeeds.set(n2, _cluster2);
        }
        if (CPure3) {
          Set<Integer> _cluster3 = new HashSet<Integer>(n1, n2);
          _cluster3.addAll(CSeeds.get(n3));
          CSeeds.set(n3, _cluster3);
        }
      }
    }
    return null;
  }
 private Set<List<Set<Integer>>> combineClusters(
     Set<Set<Integer>> ESeeds, List<Set<Integer>> CSeeds) {
   Set<Set<Integer>> EClusters = finishESeeds(ESeeds);
   Set<Integer> Cs = new HashSet();
   for (int i = 0; i < variables.size(); i++) Cs.add(i);
   Set<Integer> Es = new HashSet();
   for (Set<Integer> ECluster : EClusters) Es.addAll(ECluster);
   Cs.removeAll(Es);
   List<List<Set<Integer>>> Clusters = new ArrayList();
   for (Set<Integer> ECluster : EClusters) {
     List<Set<Integer>> newCluster = new ArrayList<Set<Integer>>();
     newCluster.add(1, ECluster);
     Clusters.add(newCluster);
   }
   List<Set<Integer>> EClustersArray = new ArrayList<Set<Integer>>();
   for (Set<Integer> ECluster : EClusters) EClustersArray.add(ECluster);
   for (Integer c : Cs) {
     int match = -1;
     int overlap = 0;
     boolean pass = false;
     for (int i = 0; i < EClusters.size(); i++) {
       Set<Integer> ECluster = EClustersArray.get(i);
       Set<Integer> intersection = ECluster;
       intersection.retainAll(CSeeds.get(c));
       int _overlap = intersection.size();
       if (_overlap > overlap) {
         overlap = _overlap;
         match = i;
         if (overlap / ECluster.size() > CIparameter) {
           pass = true;
         }
       }
     }
     if (pass) {
       List<Set<Integer>> modCluster = new ArrayList<Set<Integer>>();
       Set<Integer> newCs = Clusters.get(match).get(0);
       newCs.add(c);
       modCluster.add(newCs);
       modCluster.add(EClustersArray.get(match));
       Clusters.set(match, modCluster);
     }
   }
   Set<List<Set<Integer>>> ClusterSet = new HashSet<List<Set<Integer>>>(Clusters);
   return ClusterSet;
 }
  //  Finds clusters of size 3.
  private Set<Set<Integer>> findMixedClusters(
      List<Integer> remaining, Set<Integer> unionPure, Map<Node, Set<Node>> adjacencies) {
    Set<Set<Integer>> threeClusters = new HashSet<Set<Integer>>();

    if (unionPure.isEmpty()) {
      return new HashSet<Set<Integer>>();
    }

    REMAINING:
    while (true) {
      if (remaining.size() < 3) break;

      ChoiceGenerator gen = new ChoiceGenerator(remaining.size(), 3);
      int[] choice;

      while ((choice = gen.next()) != null) {
        int y = remaining.get(choice[0]);
        int z = remaining.get(choice[1]);
        int w = remaining.get(choice[2]);

        Set<Integer> cluster = new HashSet<Integer>();
        cluster.add(y);
        cluster.add(z);
        cluster.add(w);

        //                if (!allVariablesDependent(cluster)) {
        //                    continue;
        //                }

        if (!clique(cluster, adjacencies)) {
          continue;
        }

        // Check all x as a cross check; really only one should be necessary.
        boolean allX = true;

        for (int x : unionPure) {
          Set<Integer> _cluster = new HashSet<Integer>(cluster);
          _cluster.add(x);

          if (!quartetVanishes(_cluster) || !significant(new ArrayList<Integer>(_cluster))) {
            allX = false;
            break;
          }
        }

        if (allX) {
          threeClusters.add(cluster);
          unionPure.addAll(cluster);
          remaining.removeAll(cluster);

          System.out.println(
              "3-cluster found: " + variablesForIndices(new ArrayList<Integer>(cluster)));

          continue REMAINING;
        }
      }

      break;
    }

    return threeClusters;
  }
  // Trying to optimize the search for 4-cliques a bit.
  private Set<Set<Integer>> findPureClusters2(
      List<Integer> _variables, Map<Node, Set<Node>> adjacencies) {
    System.out.println("Original variables = " + variables);

    Set<Set<Integer>> clusters = new HashSet<Set<Integer>>();
    List<Integer> allVariables = new ArrayList<Integer>();
    Set<Node> foundVariables = new HashSet<Node>();
    for (int i = 0; i < this.variables.size(); i++) allVariables.add(i);

    for (int x : _variables) {
      Node nodeX = variables.get(x);
      if (foundVariables.contains(nodeX)) continue;

      List<Node> adjX = new ArrayList<Node>(adjacencies.get(nodeX));
      adjX.removeAll(foundVariables);

      if (adjX.size() < 3) continue;

      for (Node nodeY : adjX) {
        if (foundVariables.contains(nodeY)) continue;

        List<Node> commonXY = new ArrayList<Node>(adjacencies.get(nodeY));
        commonXY.retainAll(adjX);
        commonXY.removeAll(foundVariables);

        for (Node nodeZ : commonXY) {
          if (foundVariables.contains(nodeZ)) continue;

          List<Node> commonXZ = new ArrayList<Node>(commonXY);
          commonXZ.retainAll(adjacencies.get(nodeZ));
          commonXZ.removeAll(foundVariables);

          for (Node nodeW : commonXZ) {
            if (foundVariables.contains(nodeW)) continue;

            if (!adjacencies.get(nodeY).contains(nodeW)) {
              continue;
            }

            int y = variables.indexOf(nodeY);
            int w = variables.indexOf(nodeW);
            int z = variables.indexOf(nodeZ);

            Set<Integer> cluster = quartet(x, y, z, w);

            // Note that purity needs to be assessed with respect to all of the variables in order
            // to
            // remove all latent-measure impurities between pairs of latents.
            if (pure(cluster, allVariables)) {

              O:
              for (int o : _variables) {
                if (cluster.contains(o)) continue;
                cluster.add(o);

                if (!clique(cluster, adjacencies)) {
                  cluster.remove(o);
                  continue O;
                }

                //                                if (!allVariablesDependent(cluster)) {
                //                                    cluster.remove(o);
                //                                    continue O;
                //                                }

                List<Integer> _cluster = new ArrayList<Integer>(cluster);

                ChoiceGenerator gen2 = new ChoiceGenerator(_cluster.size(), 4);
                int[] choice2;
                int count = 0;

                while ((choice2 = gen2.next()) != null) {
                  int x2 = _cluster.get(choice2[0]);
                  int y2 = _cluster.get(choice2[1]);
                  int z2 = _cluster.get(choice2[2]);
                  int w2 = _cluster.get(choice2[3]);

                  Set<Integer> quartet = quartet(x2, y2, z2, w2);

                  // Optimizes for large clusters.
                  if (quartet.contains(o)) {
                    if (++count > 2) continue O;
                  }

                  if (quartet.contains(o) && !pure(quartet, allVariables)) {
                    cluster.remove(o);
                    continue O;
                  }
                }
              }

              System.out.println(
                  "Cluster found: " + variablesForIndices(new ArrayList<Integer>(cluster)));
              clusters.add(cluster);
              foundVariables.addAll(variablesForIndices(new ArrayList<Integer>(cluster)));
            }
          }
        }
      }
    }

    return clusters;
  }
  // Finds clusters of size 4 or higher.
  private Set<Set<Integer>> findPureClusters(
      List<Integer> _variables, Map<Node, Set<Node>> adjacencies) {
    //        System.out.println("Original variables = " + variables);

    Set<Set<Integer>> clusters = new HashSet<Set<Integer>>();
    List<Integer> allVariables = new ArrayList<Integer>();
    for (int i = 0; i < this.variables.size(); i++) allVariables.add(i);

    VARIABLES:
    while (!_variables.isEmpty()) {
      if (_variables.size() < 4) break;

      for (int x : _variables) {
        Node nodeX = variables.get(x);
        List<Node> adjX = new ArrayList<Node>(adjacencies.get(nodeX));
        adjX.retainAll(variablesForIndices(new ArrayList<Integer>(_variables)));

        for (Node node : new ArrayList<Node>(adjX)) {
          if (adjacencies.get(node).size() < 3) {
            adjX.remove(node);
          }
        }

        if (adjX.size() < 3) {
          continue;
        }

        ChoiceGenerator gen = new ChoiceGenerator(adjX.size(), 3);
        int[] choice;

        while ((choice = gen.next()) != null) {
          Node nodeY = adjX.get(choice[0]);
          Node nodeZ = adjX.get(choice[1]);
          Node nodeW = adjX.get(choice[2]);

          int y = variables.indexOf(nodeY);
          int w = variables.indexOf(nodeW);
          int z = variables.indexOf(nodeZ);

          Set<Integer> cluster = quartet(x, y, z, w);

          if (!clique(cluster, adjacencies)) {
            continue;
          }

          // Note that purity needs to be assessed with respect to all of the variables in order to
          // remove all latent-measure impurities between pairs of latents.
          if (pure(cluster, allVariables)) {

            //                        Collections.shuffle(_variables);

            O:
            for (int o : _variables) {
              if (cluster.contains(o)) continue;
              cluster.add(o);
              List<Integer> _cluster = new ArrayList<Integer>(cluster);

              if (!clique(cluster, adjacencies)) {
                cluster.remove(o);
                continue O;
              }

              //                            if (!allVariablesDependent(cluster)) {
              //                                cluster.remove(o);
              //                                continue O;
              //                            }

              ChoiceGenerator gen2 = new ChoiceGenerator(_cluster.size(), 4);
              int[] choice2;
              int count = 0;

              while ((choice2 = gen2.next()) != null) {
                int x2 = _cluster.get(choice2[0]);
                int y2 = _cluster.get(choice2[1]);
                int z2 = _cluster.get(choice2[2]);
                int w2 = _cluster.get(choice2[3]);

                Set<Integer> quartet = quartet(x2, y2, z2, w2);

                // Optimizes for large clusters.
                if (quartet.contains(o)) {
                  if (++count > 50) continue O;
                }

                if (quartet.contains(o) && !pure(quartet, allVariables)) {
                  cluster.remove(o);
                  continue O;
                }
              }
            }

            System.out.println(
                "Cluster found: " + variablesForIndices(new ArrayList<Integer>(cluster)));
            clusters.add(cluster);
            _variables.removeAll(cluster);

            continue VARIABLES;
          }
        }
      }

      break;
    }

    return clusters;
  }