public static double POISSON(int k, double lambda, bool state)
{
if (state == false)
{
return(Poisson.PMF(lambda, k));
}
return(Poisson.CDF(lambda, k));
}
private static List <List <double> > GetStateDurationProbability(List <int> sojournMeans, int maxStateLength)
{
var stateDurationProbability = new List <List <double> >(sojournMeans.Count);
var stateCounter = 0;
foreach (var sojournMean in sojournMeans)
{
stateDurationProbability.Add(new List <double>(maxStateLength));
for (var stateDuration = 0; stateDuration < maxStateLength; stateDuration++)
{
stateDurationProbability[stateCounter].Add(Math.Log(Poisson.PMF(sojournMean, stateDuration)));
}
stateCounter++;
}
return(stateDurationProbability);
}
/// <summary>
/// BestHsmmPathViterbi helper method to calculate sojourn survival function
/// </summary>
/// <param name="maxStateLength"></param>
/// <param name="means"></param>
/// <returns></returns>
public double[][] CalculateSojourn(int maxStateLength, List <int> means)
{
double[][] sojourn = CanvasCommon.Utilities.MatrixCreate(maxStateLength + 1, maxStateLength + 2);
// Store D
for (int j = 0; j < nStates; j++)
{
for (int u = 1; u < maxStateLength + 1; u++)
{
double x = 0;
for (int v = u; v < maxStateLength + 2; v++)
{
x += Math.Log(Poisson.PMF(means[j], v));
}
sojourn[j][u] = x;
}
sojourn[j][maxStateLength] = 0;
}
return(sojourn);
}
private Dictionary <double, double> GetOverlayData(double step, Chart cherte)
{
var min = cherte.Series[0].Points.Min(x => x.XValue);
var max = cherte.Series[0].Points.Max(x => x.XValue);
var overlayData = new Dictionary <double, double>();
Func <int, double, double> g = (tb, x) =>
{
switch (tabControl.SelectedIndex)
{
case 0:
return(1);
case 1:
return(1 / (max - min));
case 2:
return(Triangular.PDF(Convert.ToDouble(tb_tre_max.Text), Convert.ToDouble(tb_tre_min.Text), Convert.ToDouble(tb_tre_moda.Text), x));
case 3:
return(Erlang.PDF(Convert.ToInt32(nUD_erl_kol_norm.Value), 1.0 / Convert.ToDouble(tb_erl_moda.Text), x));
case 4:
return(Poisson.PMF(Convert.ToDouble(tb_puas_lambd.Text), (int)x));
case 5:
return(Normal.PDF(Convert.ToDouble(tb_norm_m.Text), Convert.ToDouble(tb_norm_d.Text), x));
case 6:
return(Exponential.PDF(1.0 / Convert.ToDouble(tb_exp_m.Text), x));
default:
return(double.NaN);
}
};
for (var x = min; x <= max; x += step)
{
overlayData[x] = g(tabControl.SelectedIndex, x);
}
return(overlayData);
}
/// <summary>
/// HSMM Viterbi implementtion based on:
/// Guedon, Y. (2003), Estimating hidden semi-Markov chains from discrete sequences, Journal of
/// Computational and Graphical Statistics, Volume 12, Number 3, page 604-639 - 2003
/// </summary>
/// <param name="x"></param>
/// <param name="haploidMeans"></param>
/// <returns></returns>
public List <int> BestHsmmPathViterbi(List <List <double> > x, List <double> haploidMeans)
{
// Initialization
var length = x.Count;
var alpha = CanvasCommon.Utilities.MatrixCreate(nStates, length + 1);
var bestStateDuration = new int[nStates][];
var bestStateIndex = new int[nStates][];
for (int i = 0; i < nStates; ++i)
{
bestStateIndex[i] = new int[length];
bestStateDuration[i] = new int[length];
}
for (int j = 0; j < nStates; j++)
{
alpha[j][0] = this._stateProbabilities[j];
}
var maxStateLength = 90;
var sojournMeans = new List <int> {
10, 10, 80, 50, 50
};
var stateDurationProbability = GetStateDurationProbability(sojournMeans, maxStateLength);
var sojournLastState = CalculateSojourn(maxStateLength, sojournMeans);
double emissionSequence = 0;
double tempEmissionSequence = 0;
var bestState = 0;
var firstState = true;
var firstI = true;
var transition = Enumerable.Repeat(1.0, nStates).ToArray();
// Induction
for (int t = 1; t < length - 1; t++)
{
for (int j = 0; j < nStates; j++)
{
emissionSequence = 0;
firstState = true;
for (int stateDuration = 1; stateDuration < Math.Min(maxStateLength, t); stateDuration += 2)
{
firstI = true;
for (int i = 0; i < nStates; i++)
{
if (i == j)
{
continue;
}
if (Math.Log(_transition[i][j]) + alpha[i][t - stateDuration] > tempEmissionSequence || firstI)
{
tempEmissionSequence = Math.Log(_transition[i][j]) + alpha[i][t - stateDuration];
bestState = i;
firstI = false;
}
}
if (firstState || emissionSequence + stateDurationProbability[j][stateDuration] + tempEmissionSequence > alpha[j][t])
{
alpha[j][t] = emissionSequence + stateDurationProbability[j][stateDuration] + tempEmissionSequence;
bestStateDuration[j][t] = stateDuration;
bestStateIndex[j][t] = bestState;
firstState = false;
}
emissionSequence += _emission.EstimateViterbiLikelihood(x[t - stateDuration], j, haploidMeans, transition);
}
if (t + 1 <= maxStateLength)
{
if (firstState || emissionSequence + Math.Log(Poisson.PMF(sojournMeans[j], t + 1) * _stateProbabilities[j]) > alpha[j][t])
{
alpha[j][t] = emissionSequence + Math.Log(Poisson.PMF(sojournMeans[j], t + 1) * _stateProbabilities[j]);
bestStateDuration[j][t] = -1;
bestStateIndex[j][t] = -1;
}
}
alpha[j][t] += _emission.EstimateViterbiLikelihood(x[t], j, haploidMeans, transition);
}
}
for (int j = 0; j < nStates; j++)
{
emissionSequence = 0;
firstState = true;
for (int stateDuration = 1; stateDuration < maxStateLength - 1; stateDuration++)
{
firstI = true;
for (int i = 0; i < nStates; i++)
{
if (i == j)
{
continue;
}
if (Math.Log(_transition[i][j]) + alpha[i][length - 1 - stateDuration] > tempEmissionSequence || firstI)
{
tempEmissionSequence = Math.Log(_transition[i][j]) + alpha[i][length - 1 - stateDuration];
bestState = i;
firstI = false;
}
}
if (emissionSequence + Math.Log(sojournLastState[j][Math.Min(stateDuration, maxStateLength)]) + tempEmissionSequence > alpha[j][length - 1] || firstState)
{
alpha[j][length - 1] = emissionSequence + Math.Log(sojournLastState[j][Math.Min(stateDuration, maxStateLength)]) + tempEmissionSequence;
bestStateDuration[j][length - 1] = stateDuration;
bestStateIndex[j][length - 1] = bestState;
firstState = false;
}
emissionSequence += _emission.EstimateViterbiLikelihood(x[length - 1 - stateDuration], j, haploidMeans, transition);
}
if (emissionSequence + Math.Log(sojournLastState[j][Math.Min(length - 1, maxStateLength)] * _stateProbabilities[j]) > alpha[j][length - 1] || firstState)
{
alpha[j][length - 1] = emissionSequence + Math.Log(sojournLastState[j][Math.Min(length, maxStateLength)] * _stateProbabilities[j]);
bestStateDuration[j][length - 1] = -1;
bestStateIndex[j][length - 1] = -1;
}
alpha[j][length - 1] += _emission.EstimateViterbiLikelihood(x[length - 1], j, haploidMeans, transition);
}
// backtracking
List <int> finalStates = Enumerable.Repeat(2, length).ToList();
int T = length - 1;
while (bestStateIndex[bestState][T] >= 0)
{
for (int i = T; i >= T - bestStateDuration[bestState][T] + 1; i--)
{
finalStates[i] = bestState;
}
var alternativeBestState = bestState;
bestState = bestStateIndex[bestState][T];
T -= bestStateDuration[alternativeBestState][T];
}
finalStates.Reverse();
OutlierMask(finalStates);
SmallSegmentsMask(finalStates);
OversegmentationMask(finalStates);
return(finalStates);
}
public float ComputeProbabilityDensity(int value_domain)
{
return((float)Poisson.PMF(d_lambda, value_domain));
}