コード例 #1
0
  public int getClusterNumber(String objectID) {
    int datasetIndex = -1;

    for (int i = 0; i < m_Sequences.numInstances(); i++) {
      if (objectID.equals(m_Sequences.instance(i).stringValue(0))) datasetIndex = i;
    }

    return cluster[datasetIndex];
  }
コード例 #2
0
  /**
   * Generates a clusterer by the mean of spectral clustering algorithm.
   *
   * @param data set of instances serving as training data
   * @exception Exception if the clusterer has not been generated successfully
   */
  public void buildClusterer(Instances data) throws java.lang.Exception {
    m_Sequences = new Instances(data);
    int n = data.numInstances();
    int k = data.numAttributes();
    DoubleMatrix2D w;
    if (useSparseMatrix) w = DoubleFactory2D.sparse.make(n, n);
    else w = DoubleFactory2D.dense.make(n, n);
    double[][] v1 = new double[n][];
    for (int i = 0; i < n; i++) v1[i] = data.instance(i).toDoubleArray();
    v = DoubleFactory2D.dense.make(v1);
    double sigma_sq = sigma * sigma;
    // Sets up similarity matrix
    for (int i = 0; i < n; i++)
      for (int j = i; j < n; j++) {
        /*double dist = distnorm2(v.viewRow(i), v.viewRow(j));
        if((r == -1) || (dist < r)) {
          double sim = Math.exp(- (dist * dist) / (2 * sigma_sq));
          w.set(i, j, sim);
          w.set(j, i, sim);
        }*/
        /* String [] key = {data.instance(i).stringValue(0), data.instance(j).stringValue(0)};
        System.out.println(key[0]);
        System.out.println(key[1]);
        System.out.println(simScoreMap.containsKey(key));
        Double simValue = simScoreMap.get(key);*/

        double sim = sim_matrix[i][j];
        w.set(i, j, sim);
        w.set(j, i, sim);
      }

    // Partitions points
    int[][] p = partition(w, alpha_star);

    // Deploys results
    numOfClusters = p.length;
    cluster = new int[n];
    for (int i = 0; i < p.length; i++) for (int j = 0; j < p[i].length; j++) cluster[p[i][j]] = i;

    // System.out.println("Final partition:");
    // UtilsJS.printMatrix(p);
    // System.out.println("Cluster:\n");
    // UtilsJS.printArray(cluster);
    this.numOfClusters = cluster[Utils.maxIndex(cluster)] + 1;
    //  System.out.println("Num clusters:\t"+this.numOfClusters);
  }
コード例 #3
0
  public void buildClusterer(ArrayList<String> seqDB, double[][] sm) {
    seqList = seqDB;

    this.setSimMatrix(sm);

    Attribute seqString = new Attribute("sequence", (FastVector) null);
    FastVector attrInfo = new FastVector();
    attrInfo.addElement(seqString);
    Instances data = new Instances("data", attrInfo, 0);

    for (int i = 0; i < seqList.size(); i++) {
      Instance currentInst = new Instance(1);
      currentInst.setDataset(data);
      currentInst.setValue(0, seqList.get(i));
      data.add(currentInst);
    }

    try {
      buildClusterer(data);
    } catch (Exception e) {
      // TODO Auto-generated catch block
      e.printStackTrace();
    }
  }