C# NMF Clustering Example

using System;
using System.Collections.Generic;

using CenterSpace.NMath.Core;
using CenterSpace.NMath.Stats;

namespace CenterSpace.NMath.Stats.Examples.CSharp
{
  /// <summary>
  /// A .NET example in C# demonstrating how to cluster the "samples" represented as columns
  /// of a matrix using a Nonnegative Matrix Factorization (NMF). Note that the output
  /// of this example may vary from run to run since the NMF algorithm uses an iterative
  /// process that starts at a random solution. Thus the factorization may converge
  /// to different results on different runs (the NMF factorization is not unique).
  /// </summary> 
  class NMFClusteringExample
  {
    static void Main(string[] args)
    {
      DateTime start = DateTime.Now;

      DoubleMatrix matData = new DoubleMatrix(100, 10, new RandGenUniform(45));

      string[] names = new string[matData.Cols];
      for (int i = 0; i < names.Length; i++)
      {
        names[i] = "a" + i;
      }
      DataFrame data = new DataFrame(matData, names);

      //Factor the matrix using defaults for all factorization settings and the divergence iterative 
      //update for computing the factorization.
      NMFClustering<NMFDivergenceUpdate> NMFClustering = new NMFClustering<NMFDivergenceUpdate>();
      NMFClustering.MaxFactorizationIterations = 20000;
      int numberOfClusters = 3;
      NMFClustering.Factor(matData, numberOfClusters);

      // Check if the iterative factorization converged before hitting the default maximum
      // number of iterations.
      if (NMFClustering.Converged)
      {
        Console.WriteLine("Factorization converged in {0} iterations.", NMFClustering.Iterations);
      }
      else
      {
        Console.WriteLine("Factorization failed to converge in {0} iterations.", NMFClustering.MaxFactorizationIterations);
      }

      // Get the connectivity matrix. The connectivity matrix is an adjancy matrix, A, such that 
      // columns of the factored matrix are in the same cluster if A[i,j] == 1 and are not in the
      // same cluster if A[i,j] == 0
      ConnectivityMatrix connectivity = NMFClustering.Connectivity;
      Console.WriteLine( "Connectivity Matrix: " );
      Console.WriteLine( connectivity.ToTabDelimited() );
      Console.WriteLine(); 

      // Print out the cluster each column belongs to using the cluster set.
      ClusterSet cs = NMFClustering.ClusterSet;
      for ( int i = 0; i < cs.N; i++ )
      {
        Console.WriteLine( "Column {0} belongs to cluster {1}", data.ColumnHeaders[i], cs[i] );
      }
      Console.WriteLine();

      // Print out the the members of each cluster using the cluster set.
      for ( int clusterNumber = 0; clusterNumber < cs.NumberOfClusters; clusterNumber++ )
      {
        int[] members = cs.Cluster( clusterNumber );
        Console.Write( "Cluster number {0} contains: ", clusterNumber );
        for ( int i = 0; i < members.Length; i++ )
        {
          Console.Write( "{0} ", data.ColumnHeaders[members[i]] );
        }
        Console.WriteLine();
      }

      Console.WriteLine();
      Console.WriteLine("Press Enter Key");
      Console.Read();
    }
  }
}