source: branches/TSNE/HeuristicLab.Algorithms.DataAnalysis/3.4/TSNE/TSNE.cs @ 14512

#region License Information
/* HeuristicLab
 * Copyright (C) 2002-2016 Heuristic and Evolutionary Algorithms Laboratory (HEAL)
 *
 * This file is part of HeuristicLab.
 *
 * HeuristicLab is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * HeuristicLab is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with HeuristicLab. If not, see <http://www.gnu.org/licenses/>.
 */

//Code is based on an implementation from Laurens van der Maaten

/*
*
* Copyright (c) 2014, Laurens van der Maaten (Delft University of Technology)
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
* 1. Redistributions of source code must retain the above copyright
*    notice, this list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright
*    notice, this list of conditions and the following disclaimer in the
*    documentation and/or other materials provided with the distribution.
* 3. All advertising materials mentioning features or use of this software
*    must display the following acknowledgement:
*    This product includes software developed by the Delft University of Technology.
* 4. Neither the name of the Delft University of Technology nor the names of
*    its contributors may be used to endorse or promote products derived from
*    this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY LAURENS VAN DER MAATEN ''AS IS'' AND ANY EXPRESS
* OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
* OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
* EVENT SHALL LAURENS VAN DER MAATEN BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
* PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
* BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
* IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY
* OF SUCH DAMAGE.
*
*/
#endregion

using System;
using System.Collections.Generic;
using System.Linq;
using HeuristicLab.Analysis;
using HeuristicLab.Common;
using HeuristicLab.Core;
using HeuristicLab.Data;
using HeuristicLab.Optimization;
using HeuristicLab.Persistence.Default.CompositeSerializers.Storable;
using HeuristicLab.Random;

namespace HeuristicLab.Algorithms.DataAnalysis {
  [StorableClass]
  public class TSNE<T> : Item, ITSNE<T> where T : class, IDeepCloneable {

    private const string IterationResultName = "Iteration";
    private const string ErrorResultName = "Error";
    private const string ErrorPlotResultName = "ErrorPlot";
    private const string ScatterPlotResultName = "Scatterplot";
    private const string DataResultName = "Projected Data";

    #region Properties
    [Storable]
    private IDistance<T> distance;
    [Storable]
    private int maxIter;
    [Storable]
    private int stopLyingIter;
    [Storable]
    private int momSwitchIter;
    [Storable]
    double momentum;
    [Storable]
    private double finalMomentum;
    [Storable]
    private double eta;
    [Storable]
    private IRandom random;
    [Storable]
    private ResultCollection results;
    [Storable]
    private Dictionary<string, List<int>> dataRowLookup;
    [Storable]
    private Dictionary<string, ScatterPlotDataRow> dataRows;
    #endregion

    #region Stopping 
    public volatile bool Running;
    #endregion

    #region HLConstructors & Cloning
    [StorableConstructor]
    protected TSNE(bool deserializing) : base(deserializing) { }
    protected TSNE(TSNE<T> original, Cloner cloner) : base(original, cloner) {
      distance = cloner.Clone(original.distance);
      maxIter = original.maxIter;
      stopLyingIter = original.stopLyingIter;
      momSwitchIter = original.momSwitchIter;
      momentum = original.momentum;
      finalMomentum = original.finalMomentum;
      eta = original.eta;
      random = cloner.Clone(random);
      results = cloner.Clone(results);
      dataRowLookup = original.dataRowLookup.ToDictionary(entry => entry.Key, entry => entry.Value.Select(x => x).ToList());
      dataRows = original.dataRows.ToDictionary(entry => entry.Key, entry => cloner.Clone(entry.Value));
    }
    public override IDeepCloneable Clone(Cloner cloner) { return new TSNE<T>(this, cloner); }
    public TSNE(IDistance<T> distance, IRandom random, ResultCollection results = null, int maxIter = 1000, int stopLyingIter = 250, int momSwitchIter = 250, double momentum = .5, double finalMomentum = .8, double eta = 200.0, Dictionary<string, List<int>> dataRowLookup = null, Dictionary<string, ScatterPlotDataRow> dataRows = null) {
      this.distance = distance;
      this.maxIter = maxIter;
      this.stopLyingIter = stopLyingIter;
      this.momSwitchIter = momSwitchIter;
      this.momentum = momentum;
      this.finalMomentum = finalMomentum;
      this.eta = eta;
      this.random = random;
      this.results = results;
      this.dataRowLookup = dataRowLookup;
      if (dataRows != null)
        this.dataRows = dataRows;
      else { this.dataRows = new Dictionary<string, ScatterPlotDataRow>(); }
    }
    #endregion

    public double[,] Run(T[] data, int newDimensions, double perplexity, double theta) {
      var currentMomentum = momentum;
      var noDatapoints = data.Length;
      if (noDatapoints - 1 < 3 * perplexity) throw new ArgumentException("Perplexity too large for the number of data points!");
      SetUpResults(data);
      Running = true;
      var exact = Math.Abs(theta) < double.Epsilon;
      var newData = new double[noDatapoints, newDimensions];
      var dY = new double[noDatapoints, newDimensions];
      var uY = new double[noDatapoints, newDimensions];
      var gains = new double[noDatapoints, newDimensions];
      for (var i = 0; i < noDatapoints; i++) for (var j = 0; j < newDimensions; j++) gains[i, j] = 1.0;
      double[,] p = null;
      int[] rowP = null;
      int[] colP = null;
      double[] valP = null;
      var rand = new NormalDistributedRandom(random, 0, 1);

      //Calculate Similarities
      if (exact) p = CalculateExactSimilarites(data, perplexity);
      else CalculateApproximateSimilarities(data, perplexity, out rowP, out colP, out valP);

      // Lie about the P-values
      if (exact) for (var i = 0; i < noDatapoints; i++) for (var j = 0; j < noDatapoints; j++) p[i, j] *= 12.0;
      else for (var i = 0; i < rowP[noDatapoints]; i++) valP[i] *= 12.0;

      // Initialize solution (randomly)
      for (var i = 0; i < noDatapoints; i++) for (var j = 0; j < newDimensions; j++) newData[i, j] = rand.NextDouble() * .0001;

      // Perform main training loop
      for (var iter = 0; iter < maxIter && Running; iter++) {
        if (exact) ComputeExactGradient(p, newData, noDatapoints, newDimensions, dY);
        else ComputeGradient(rowP, colP, valP, newData, noDatapoints, newDimensions, dY, theta);
        // Update gains
        for (var i = 0; i < noDatapoints; i++) for (var j = 0; j < newDimensions; j++) gains[i, j] = Math.Sign(dY[i, j]) != Math.Sign(uY[i, j]) ? gains[i, j] + .2 : gains[i, j] * .8;
        for (var i = 0; i < noDatapoints; i++) for (var j = 0; j < newDimensions; j++) if (gains[i, j] < .01) gains[i, j] = .01;
        // Perform gradient update (with momentum and gains)
        for (var i = 0; i < noDatapoints; i++) for (var j = 0; j < newDimensions; j++) uY[i, j] = currentMomentum * uY[i, j] - eta * gains[i, j] * dY[i, j];
        for (var i = 0; i < noDatapoints; i++) for (var j = 0; j < newDimensions; j++) newData[i, j] = newData[i, j] + uY[i, j];
        // Make solution zero-mean
        ZeroMean(newData);
        // Stop lying about the P-values after a while, and switch momentum
        if (iter == stopLyingIter) {
          if (exact) for (var i = 0; i < noDatapoints; i++) for (var j = 0; j < noDatapoints; j++) p[i, j] /= 12.0;
          else for (var i = 0; i < rowP[noDatapoints]; i++) valP[i] /= 12.0;
        }
        if (iter == momSwitchIter) currentMomentum = finalMomentum;

        Analyze(exact, iter, p, rowP, colP, valP, newData, noDatapoints, newDimensions, theta);
      }
      return newData;
    }
    public static double[,] Run<TR>(TR[] data, int newDimensions, double perplexity, double theta, IDistance<TR> distance, IRandom random) where TR : class, IDeepCloneable {
      return new TSNE<TR>(distance, random).Run(data, newDimensions, perplexity, theta);
    }
    public static double[,] Run<TR>(TR[] data, int newDimensions, double perplexity, double theta, Func<TR, TR, double> distance, IRandom random) where TR : class, IDeepCloneable {
      return new TSNE<TR>(new FuctionalDistance<TR>(distance), random).Run(data, newDimensions, perplexity, theta);
    }

    #region helpers

    private void SetUpResults(IReadOnlyCollection<T> data) {
      if (dataRowLookup == null) {
        dataRowLookup = new Dictionary<string, List<int>>();
        dataRowLookup.Add("Data", Enumerable.Range(0, data.Count).ToList());
      }
      if (results == null) return;
      if (!results.ContainsKey(IterationResultName)) results.Add(new Result(IterationResultName, new IntValue(0)));
      else ((IntValue)results[IterationResultName].Value).Value = 0;

      if (!results.ContainsKey(ErrorResultName)) results.Add(new Result(ErrorResultName, new DoubleValue(0)));
      else ((DoubleValue)results[ErrorResultName].Value).Value = 0;

      if (!results.ContainsKey(ErrorPlotResultName)) results.Add(new Result(ErrorPlotResultName, new DataTable(ErrorPlotResultName, "Development of errors during Gradiant descent")));
      else results[ErrorPlotResultName].Value = new DataTable(ErrorPlotResultName, "Development of errors during Gradiant descent");

      var plot = results[ErrorPlotResultName].Value as DataTable;
      if (plot == null) throw new ArgumentException("could not create/access Error-DataTable in Results-Collection");
      if (!plot.Rows.ContainsKey("errors")) {
        plot.Rows.Add(new DataRow("errors"));
      }
      plot.Rows["errors"].Values.Clear();
      results.Add(new Result(ScatterPlotResultName, "Plot of the projected data", new ScatterPlot(DataResultName, "")));
      results.Add(new Result(DataResultName, "Projected Data", new DoubleMatrix()));

    }
    private void Analyze(bool exact, int iter, double[,] p, int[] rowP, int[] colP, double[] valP, double[,] newData, int noDatapoints, int newDimensions, double theta) {
      if (results == null) return;
      var plot = results[ErrorPlotResultName].Value as DataTable;
      if (plot == null) throw new ArgumentException("Could not create/access Error-DataTable in Results-Collection. Was it removed by some effect?");
      var errors = plot.Rows["errors"].Values;
      var c = exact
        ? EvaluateError(p, newData, noDatapoints, newDimensions)
        : EvaluateError(rowP, colP, valP, newData, theta);
      errors.Add(c);
      ((IntValue)results[IterationResultName].Value).Value = iter + 1;
      ((DoubleValue)results[ErrorResultName].Value).Value = errors.Last();

      var ndata = Normalize(newData);
      results[DataResultName].Value = new DoubleMatrix(ndata);
      var splot = results[ScatterPlotResultName].Value as ScatterPlot;
      FillScatterPlot(ndata, splot);


    }
    private void FillScatterPlot(double[,] lowDimData, ScatterPlot plot) {
      foreach (var rowName in dataRowLookup.Keys) {
        if (!plot.Rows.ContainsKey(rowName)) {
          plot.Rows.Add(dataRows.ContainsKey(rowName) ? dataRows[rowName] : new ScatterPlotDataRow(rowName, "", new List<Point2D<double>>()));
        } else plot.Rows[rowName].Points.Clear();
        plot.Rows[rowName].Points.AddRange(dataRowLookup[rowName].Select(i => new Point2D<double>(lowDimData[i, 0], lowDimData[i, 1])));
      }
    }
    private static double[,] Normalize(double[,] data) {
      var max = new double[data.GetLength(1)];
      var min = new double[data.GetLength(1)];
      var res = new double[data.GetLength(0), data.GetLength(1)];
      for (var i = 0; i < max.Length; i++) max[i] = min[i] = data[0, i];
      for (var i = 0; i < data.GetLength(0); i++)
        for (var j = 0; j < data.GetLength(1); j++) {
          var v = data[i, j];
          max[j] = Math.Max(max[j], v);
          min[j] = Math.Min(min[j], v);
        }
      for (var i = 0; i < data.GetLength(0); i++) {
        for (var j = 0; j < data.GetLength(1); j++) {
          res[i, j] = (data[i, j] - (max[j] + min[j]) / 2) / (max[j] - min[j]);
        }
      }
      return res;
    }
    private void CalculateApproximateSimilarities(T[] data, double perplexity, out int[] rowP, out int[] colP, out double[] valP) {
      // Compute asymmetric pairwise input similarities
      ComputeGaussianPerplexity(data, data.Length, out rowP, out colP, out valP, perplexity, (int)(3 * perplexity));
      // Symmetrize input similarities
      int[] sRowP, symColP;
      double[] sValP;
      SymmetrizeMatrix(rowP, colP, valP, out sRowP, out symColP, out sValP);
      rowP = sRowP;
      colP = symColP;
      valP = sValP;
      var sumP = .0;
      for (var i = 0; i < rowP[data.Length]; i++) sumP += valP[i];
      for (var i = 0; i < rowP[data.Length]; i++) valP[i] /= sumP;
    }
    private double[,] CalculateExactSimilarites(T[] data, double perplexity) {
      // Compute similarities
      var p = new double[data.Length, data.Length];
      ComputeGaussianPerplexity(data, data.Length, p, perplexity);
      // Symmetrize input similarities
      for (var n = 0; n < data.Length; n++) {
        for (var m = n + 1; m < data.Length; m++) {
          p[n, m] += p[m, n];
          p[m, n] = p[n, m];
        }
      }
      var sumP = .0;
      for (var i = 0; i < data.Length; i++) for (var j = 0; j < data.Length; j++) sumP += p[i, j];
      for (var i = 0; i < data.Length; i++) for (var j = 0; j < data.Length; j++) p[i, j] /= sumP;
      return p;
    }

    private void ComputeGaussianPerplexity(IReadOnlyList<T> x, int n, out int[] rowP, out int[] colP, out double[] valP, double perplexity, int k) {
      if (perplexity > k) throw new ArgumentException("Perplexity should be lower than K!");

      // Allocate the memory we need
      rowP = new int[n + 1];
      colP = new int[n * k];
      valP = new double[n * k];
      var curP = new double[n - 1];
      rowP[0] = 0;
      for (var i = 0; i < n; i++) rowP[i + 1] = rowP[i] + k;

      // Build ball tree on data set
      var tree = new VPTree<IDataPoint<T>>(new DataPointDistance<T>(distance));
      var objX = new List<IDataPoint<T>>();
      for (var i = 0; i < n; i++) objX.Add(new DataPoint<T>(i, x[i]));
      tree.Create(objX);

      // Loop over all points to find nearest neighbors
      var indices = new List<IDataPoint<T>>();
      var distances = new List<double>();
      for (var i = 0; i < n; i++) {

        // Find nearest neighbors
        indices.Clear();
        distances.Clear();
        tree.Search(objX[i], k + 1, out indices, out distances);

        // Initialize some variables for binary search
        var found = false;
        var beta = 1.0;
        var minBeta = -double.MaxValue;
        var maxBeta = double.MaxValue;
        const double tol = 1e-5;

        // Iterate until we found a good perplexity
        var iter = 0; double sumP = 0;
        while (!found && iter < 200) {

          // Compute Gaussian kernel row
          for (var m = 0; m < k; m++) curP[m] = Math.Exp(-beta * distances[m + 1]);

          // Compute entropy of current row
          sumP = double.Epsilon;
          for (var m = 0; m < k; m++) sumP += curP[m];
          var h = .0;
          for (var m = 0; m < k; m++) h += beta * (distances[m + 1] * curP[m]);
          h = h / sumP + Math.Log(sumP);

          // Evaluate whether the entropy is within the tolerance level
          var hdiff = h - Math.Log(perplexity);
          if (hdiff < tol && -hdiff < tol) {
            found = true;
          } else {
            if (hdiff > 0) {
              minBeta = beta;
              if (maxBeta.IsAlmost(double.MaxValue) || maxBeta.IsAlmost(double.MinValue))
                beta *= 2.0;
              else
                beta = (beta + maxBeta) / 2.0;
            } else {
              maxBeta = beta;
              if (minBeta.IsAlmost(double.MinValue) || minBeta.IsAlmost(double.MaxValue))
                beta /= 2.0;
              else
                beta = (beta + minBeta) / 2.0;
            }
          }

          // Update iteration counter
          iter++;
        }

        // Row-normalize current row of P and store in matrix
        for (var m = 0; m < k; m++) curP[m] /= sumP;
        for (var m = 0; m < k; m++) {
          colP[rowP[i] + m] = indices[m + 1].Index;
          valP[rowP[i] + m] = curP[m];
        }
      }
    }
    private void ComputeGaussianPerplexity(T[] x, int n, double[,] p, double perplexity) {
      // Compute the squared Euclidean distance matrix
      var dd = ComputeDistances(x);
      // Compute the Gaussian kernel row by row

      for (var i = 0; i < n; i++) {
        // Initialize some variables
        var found = false;
        var beta = 1.0;
        var minBeta = -double.MaxValue;
        var maxBeta = double.MaxValue;
        const double tol = 1e-5;
        double sumP = 0;

        // Iterate until we found a good perplexity
        var iter = 0;
        while (!found && iter < 200) {

          // Compute Gaussian kernel row
          for (var m = 0; m < n; m++) p[i, m] = Math.Exp(-beta * dd[i][m]);
          p[i, i] = double.Epsilon;

          // Compute entropy of current row
          sumP = double.Epsilon;
          for (var m = 0; m < n; m++) sumP += p[i, m];
          var h = 0.0;
          for (var m = 0; m < n; m++) h += beta * (dd[i][m] * p[i, m]);
          h = h / sumP + Math.Log(sumP);

          // Evaluate whether the entropy is within the tolerance level
          var hdiff = h - Math.Log(perplexity);
          if (hdiff < tol && -hdiff < tol) {
            found = true;
          } else {
            if (hdiff > 0) {
              minBeta = beta;
              if (maxBeta.IsAlmost(double.MaxValue) || maxBeta.IsAlmost(double.MinValue))
                beta *= 2.0;
              else
                beta = (beta + maxBeta) / 2.0;
            } else {
              maxBeta = beta;
              if (minBeta.IsAlmost(double.MinValue) || minBeta.IsAlmost(double.MaxValue))
                beta /= 2.0;
              else
                beta = (beta + minBeta) / 2.0;
            }
          }

          // Update iteration counter
          iter++;
        }

        // Row normalize P
        for (var m = 0; m < n; m++) p[i, m] /= sumP;
      }
    }
    private double[][] ComputeDistances(T[] x) {
      return x.Select(m => x.Select(n => distance.Get(m, n)).ToArray()).ToArray();
    }
    private static void ComputeExactGradient(double[,] p, double[,] y, int n, int d, double[,] dC) {

      // Make sure the current gradient contains zeros
      for (var i = 0; i < n; i++) for (var j = 0; j < d; j++) dC[i, j] = 0.0;

      // Compute the squared Euclidean distance matrix
      var dd = new double[n, n];
      ComputeSquaredEuclideanDistance(y, n, d, dd);

      // Compute Q-matrix and normalization sum
      var q = new double[n, n];
      var sumQ = .0;
      for (var n1 = 0; n1 < n; n1++) {
        for (var m = 0; m < n; m++) {
          if (n1 == m) continue;
          q[n1, m] = 1 / (1 + dd[n1, m]);
          sumQ += q[n1, m];
        }
      }

      // Perform the computation of the gradient
      for (var n1 = 0; n1 < n; n1++) {
        for (var m = 0; m < n; m++) {
          if (n1 == m) continue;
          var mult = (p[n1, m] - q[n1, m] / sumQ) * q[n1, m];
          for (var d1 = 0; d1 < d; d1++) {
            dC[n1, d1] += (y[n1, d1] - y[m, d1]) * mult;
          }
        }
      }
    }
    private static void ComputeSquaredEuclideanDistance(double[,] x, int n, int d, double[,] dd) {
      var dataSums = new double[n];
      for (var i = 0; i < n; i++) {
        for (var j = 0; j < d; j++) {
          dataSums[i] += x[i, j] * x[i, j];
        }
      }
      for (var i = 0; i < n; i++) {
        for (var m = 0; m < n; m++) {
          dd[i, m] = dataSums[i] + dataSums[m];
        }
      }
      for (var i = 0; i < n; i++) {
        dd[i, i] = 0.0;
        for (var m = i + 1; m < n; m++) {
          dd[i, m] = 0.0;
          for (var j = 0; j < d; j++) {
            dd[i, m] += (x[i, j] - x[m, j]) * (x[i, j] - x[m, j]);
          }
          dd[m, i] = dd[i, m];
        }
      }
    }
    private static void ComputeGradient(int[] rowP, int[] colP, double[] valP, double[,] y, int n, int d, double[,] dC, double theta) {
      var tree = new SPTree(y);
      double[] sumQ = { 0 };
      var posF = new double[n, d];
      var negF = new double[n, d];
      tree.ComputeEdgeForces(rowP, colP, valP, n, posF);
      var row = new double[d];
      for (int n1 = 0; n1 < n; n1++) {
        Buffer.BlockCopy(negF, (sizeof(double) * n1 * d), row, 0, d);
        tree.ComputeNonEdgeForces(n1, theta, row, sumQ);
      }

      // Compute final t-SNE gradient
      for (var i = 0; i < n; i++)
        for (var j = 0; j < d; j++) {
          dC[i, j] = posF[i, j] - negF[i, j] / sumQ[0];
        }
    }
    private static double EvaluateError(double[,] p, double[,] y, int n, int d) {
      // Compute the squared Euclidean distance matrix
      var dd = new double[n, n];
      var q = new double[n, n];
      ComputeSquaredEuclideanDistance(y, n, d, dd);

      // Compute Q-matrix and normalization sum
      var sumQ = double.Epsilon;
      for (var n1 = 0; n1 < n; n1++) {
        for (var m = 0; m < n; m++) {
          if (n1 != m) {
            q[n1, m] = 1 / (1 + dd[n1, m]);
            sumQ += q[n1, m];
          } else q[n1, m] = double.Epsilon;
        }
      }
      for (var i = 0; i < n; i++) for (var j = 0; j < n; j++) q[i, j] /= sumQ;

      // Sum t-SNE error
      var c = .0;
      for (var i = 0; i < n; i++)
        for (var j = 0; j < n; j++) {
          c += p[i, j] * Math.Log((p[i, j] + float.Epsilon) / (q[i, j] + float.Epsilon));
        }
      return c;
    }
    private static double EvaluateError(IReadOnlyList<int> rowP, IReadOnlyList<int> colP, IReadOnlyList<double> valP, double[,] y, double theta) {
      // Get estimate of normalization term
      var n = y.GetLength(0);
      var d = y.GetLength(1);
      var tree = new SPTree(y);
      var buff = new double[d];
      double[] sumQ = { 0 };
      for (var i = 0; i < n; i++) tree.ComputeNonEdgeForces(i, theta, buff, sumQ);

      // Loop over all edges to compute t-SNE error
      var c = .0;
      for (var k = 0; k < n; k++) {
        for (var i = rowP[k]; i < rowP[k + 1]; i++) {
          var q = .0;
          for (var j = 0; j < d; j++) buff[j] = y[k, j];
          for (var j = 0; j < d; j++) buff[j] -= y[colP[i], j];
          for (var j = 0; j < d; j++) q += buff[j] * buff[j];
          q = 1.0 / (1.0 + q) / sumQ[0];
          c += valP[i] * Math.Log((valP[i] + float.Epsilon) / (q + float.Epsilon));
        }
      }
      return c;
    }
    private static void SymmetrizeMatrix(IReadOnlyList<int> rowP, IReadOnlyList<int> colP, IReadOnlyList<double> valP, out int[] symRowP, out int[] symColP, out double[] symValP) {

      // Count number of elements and row counts of symmetric matrix
      var n = rowP.Count - 1;
      var rowCounts = new int[n];
      for (var j = 0; j < n; j++) {
        for (var i = rowP[j]; i < rowP[j + 1]; i++) {

          // Check whether element (col_P[i], n) is present
          var present = false;
          for (var m = rowP[colP[i]]; m < rowP[colP[i] + 1]; m++) {
            if (colP[m] == j) present = true;
          }
          if (present) rowCounts[j]++;
          else {
            rowCounts[j]++;
            rowCounts[colP[i]]++;
          }
        }
      }
      var noElem = 0;
      for (var i = 0; i < n; i++) noElem += rowCounts[i];

      // Allocate memory for symmetrized matrix
      symRowP = new int[n + 1];
      symColP = new int[noElem];
      symValP = new double[noElem];

      // Construct new row indices for symmetric matrix
      symRowP[0] = 0;
      for (var i = 0; i < n; i++) symRowP[i + 1] = symRowP[i] + rowCounts[i];

      // Fill the result matrix
      var offset = new int[n];
      for (var j = 0; j < n; j++) {
        for (var i = rowP[j]; i < rowP[j + 1]; i++) {                                  // considering element(n, colP[i])

          // Check whether element (col_P[i], n) is present
          var present = false;
          for (var m = rowP[colP[i]]; m < rowP[colP[i] + 1]; m++) {
            if (colP[m] != j) continue;
            present = true;
            if (j > colP[i]) continue; // make sure we do not add elements twice
            symColP[symRowP[j] + offset[j]] = colP[i];
            symColP[symRowP[colP[i]] + offset[colP[i]]] = j;
            symValP[symRowP[j] + offset[j]] = valP[i] + valP[m];
            symValP[symRowP[colP[i]] + offset[colP[i]]] = valP[i] + valP[m];
          }

          // If (colP[i], n) is not present, there is no addition involved
          if (!present) {
            symColP[symRowP[j] + offset[j]] = colP[i];
            symColP[symRowP[colP[i]] + offset[colP[i]]] = j;
            symValP[symRowP[j] + offset[j]] = valP[i];
            symValP[symRowP[colP[i]] + offset[colP[i]]] = valP[i];
          }

          // Update offsets
          if (present && (j > colP[i])) continue;
          offset[j]++;
          if (colP[i] != j) offset[colP[i]]++;
        }
      }

      // Divide the result by two
      for (var i = 0; i < noElem; i++) symValP[i] /= 2.0;
    }
    private static void ZeroMean(double[,] x) {
      // Compute data mean
      var n = x.GetLength(0);
      var d = x.GetLength(1);
      var mean = new double[d];
      for (var i = 0; i < n; i++) {
        for (var j = 0; j < d; j++) {
          mean[j] += x[i, j];
        }
      }
      for (var i = 0; i < d; i++) {
        mean[i] /= n;
      }
      // Subtract data mean
      for (var i = 0; i < n; i++) {
        for (var j = 0; j < d; j++) {
          x[i, j] -= mean[j];
        }
      }
    }
    #endregion
  }
}