public double RunForward <TEmmisionType>(IList <IObservation> observations, IHiddenMarkovModel <TEmmisionType> model) where TEmmisionType : IDistribution
{
var alphaEstimator = new AlphaEstimator <TEmmisionType>();
_alpha = alphaEstimator.Estimate(new BasicEstimationParameters <TEmmisionType> {
Model = model, Observations = observations, Normalized = Normalized
});
var T = observations.Count;
var result = (Normalized) ? double.NaN : 0d;
// Calculate results
for (var i = 0; i < model.N; i++)
{
if (Normalized)
{
result = LogExtention.eLnSum(result, _alpha[T - 1][i]);
}
else
{
result += _alpha[T - 1][i];
}
}
return(result);
}
public double[][] Estimate(KsiGammaTransitionProbabilityMatrixParameters <TDistribution> parameters)
{
if (_estimatedTransitionProbabilityMatrix != null)
{
return(_estimatedTransitionProbabilityMatrix);
}
_estimatedTransitionProbabilityMatrix = new double[parameters.Model.N][];
for (var i = 0; i < parameters.Model.N; i++)
{
_estimatedTransitionProbabilityMatrix[i] = new double[parameters.Model.N];
for (var j = 0; j < parameters.Model.N; j++)
{
double denominator = (parameters.Model.Normalized) ? double.NaN : 0, nominator = (parameters.Model.Normalized) ? double.NaN : 0;
for (var t = 0; t < parameters.T - 1; t++)
{
if (parameters.Model.Normalized)
{
nominator = LogExtention.eLnSum(nominator, parameters.Ksi[t][i, j]);
denominator = LogExtention.eLnSum(denominator, parameters.Gamma[t][i]);
}
else
{
nominator += parameters.Ksi[t][i, j];
denominator += parameters.Gamma[t][i];
}
}
_estimatedTransitionProbabilityMatrix[i][j] = CalculateTransitionProbabilityMatrixEntry(nominator, denominator, parameters.Normalized);
}
}
return(_estimatedTransitionProbabilityMatrix);
}
public double[][] Estimate(AlphaBetaTransitionProbabiltyMatrixParameters <TDistribution> parameters)
{
if (_estimatedTransitionProbabilityMatrix != null)
{
return(_estimatedTransitionProbabilityMatrix);
}
var T = parameters.Observations.Length;
_estimatedTransitionProbabilityMatrix = new double[parameters.Model.N][];
for (var i = 0; i < parameters.Model.N; i++)
{
_estimatedTransitionProbabilityMatrix[i] = new double[parameters.Model.N];
for (var j = 0; j < parameters.Model.N; j++)
{
double nominator = (parameters.Normalized) ? double.NaN : 0.0d, denominator = (parameters.Normalized) ? double.NaN : 0.0d;
for (var t = 0; t < T - 1; t++)
{
var probability = parameters.Model.Emission[j].ProbabilityDensityFunction(parameters.Observations[t + 1]);
if (parameters.Normalized)
{
nominator = LogExtention.eLnSum(nominator, LogExtention.eLnProduct(parameters.Weights[t], LogExtention.eLnProduct(parameters.Alpha[t][i], LogExtention.eLnProduct(LogExtention.eLn(parameters.Model.TransitionProbabilityMatrix[i][j]), LogExtention.eLnProduct(LogExtention.eLn(probability), parameters.Beta[t + 1][j])))));
denominator = LogExtention.eLnSum(denominator, LogExtention.eLnProduct(parameters.Weights[t], LogExtention.eLnProduct(parameters.Alpha[t][i], parameters.Beta[t][j])));
}
else
{
nominator += parameters.Weights[t] * parameters.Alpha[t][i] * parameters.Model.TransitionProbabilityMatrix[i][j] * probability * parameters.Beta[t + 1][j];
denominator += parameters.Weights[t] * parameters.Alpha[t][i] * parameters.Beta[t][j];
}
}
_estimatedTransitionProbabilityMatrix[i][j] = CalculateTransitionProbabilityMatrixEntry(nominator, denominator, parameters.Normalized);
}
}
return(_estimatedTransitionProbabilityMatrix);
}
public double[][] Estimate(AdvancedEstimationParameters <TDistribution> parameters)
{
if (_gamma != null)
{
return(_gamma);
}
var denominator = new double[parameters.Observations.Count];
for (var t = 0; t < parameters.Observations.Count; t++)
{
denominator[t] = (parameters.Normalized) ? double.NaN : 0d;
for (var i = 0; i < parameters.Model.N; i++)
{
if (parameters.Normalized)
{
denominator[t] = LogExtention.eLnSum(denominator[t], LogExtention.eLnProduct(parameters.Alpha[t][i], parameters.Beta[t][i]));
}
else
{
denominator[t] += parameters.Alpha[t][i] * parameters.Beta[t][i];
}
}
}
try
{
_gamma = new double[parameters.Observations.Count][];
for (var t = 0; t < parameters.Observations.Count; t++)
{
_gamma[t] = new double[parameters.Model.N];
for (var i = 0; i < parameters.Model.N; i++)
{
if (parameters.Normalized)
{
_gamma[t][i] = LogExtention.eLnProduct(LogExtention.eLnProduct(parameters.Alpha[t][i], parameters.Beta[t][i]), -denominator[t]);
}
else
{
_gamma[t][i] = (parameters.Alpha[t][i] * parameters.Beta[t][i]) / denominator[t];
}
}
}
}
catch (Exception)
{
for (var t = 0; t < parameters.Observations.Count; t++)
{
for (var i = 0; i < parameters.Model.N; i++)
{
Debug.WriteLine("Gamma [{0}][{1}] : alpha : {2} , beta : {3} , denominator : {4} : gamma {5} ", t, i, parameters.Alpha[t][i], parameters.Beta[t][i], denominator[t], _gamma[t][i]);
}
}
throw;
}
return(_gamma);
}
public double[][] Estimate(BasicEstimationParameters <TDistribution> parameters)
{
if (_beta != null)
{
return(_beta);
}
var T = parameters.Observations.Count;
try
{
_beta = new double[T][];
_beta[T - 1] = new double[parameters.Model.N];
for (var i = 0; i < parameters.Model.N; i++)
{
_beta[T - 1][i] = (parameters.Normalized) ? 0d : 1d;
}
for (var t = T - 2; t >= 0; t--)
{
_beta[t] = new double[parameters.Model.N];
for (var i = 0; i < parameters.Model.N; i++)
{
_beta[t][i] = (parameters.Normalized) ? double.NaN : 0d;
for (var j = 0; j < parameters.Model.N; j++)
{
var o = EstimatorUtilities.GetProbability(parameters.Model.Emission[j], parameters.Observations, t + 1);
if (parameters.Normalized)
{
_beta[t][i] = LogExtention.eLnSum(_beta[t][i],
LogExtention.eLnProduct(LogExtention.eLn(parameters.Model.TransitionProbabilityMatrix[i][j]),
LogExtention.eLnProduct(LogExtention.eLn(o), _beta[t + 1][j])));
}
else
{
_beta[t][i] += parameters.Model.TransitionProbabilityMatrix[i][j] * o * _beta[t + 1][j];
}
}
}
}
}
catch (Exception)
{
for (var t = T - 2; t >= 0; t--)
{
for (var i = 0; i < parameters.Model.N; i++)
{
for (var j = 0; j < parameters.Model.N; j++)
{
Debug.WriteLine("[{0}][{1}] : beta : {2}", t, i, _beta[t][i]);
}
}
}
throw;
}
return(_beta);
}
public void eLnSum_YGreaterThanX_eLnSumReturned()
{
var x = 1d;
var y = 2d;
var result = LogExtention.eLnSum(x, y);
Assert.AreEqual(y + LogExtention.eLn(1 + Math.Exp(x - y)), result);
}
public void eLnSum_XGreaterThanY_eLnSumReturned()
{
var x = 2d;
var y = 1d;
var result = LogExtention.eLnSum(x, y);
Assert.AreEqual(x + LogExtention.eLn(1 + Math.Exp(y - x)), result);
}
public void eLnSum_YisNaN_XReturned()
{
var x = 1d;
var y = double.NaN;
var result = LogExtention.eLnSum(x, y);
Assert.AreEqual(x, result);
}
public double[][,] Estimate(AdvancedEstimationParameters <TDistribution> parameters)
{
if (_ksi != null)
{
return(_ksi);
}
var denominator = new double[parameters.Observations.Count];
for (var t = 0; t < parameters.Observations.Count - 1; t++)
{
denominator[t] = (parameters.Normalized) ? double.NaN : 0d;
for (var i = 0; i < parameters.Model.N; i++)
{
for (var j = 0; j < parameters.Model.N; j++)
{
var o = EstimatorUtilities.GetProbability(parameters.Model.Emission[j], parameters.Observations, t + 1);
if (parameters.Normalized)
{
denominator[t] = LogExtention.eLnSum(denominator[t], LogExtention.eLnProduct(parameters.Alpha[t][i],
LogExtention.eLnProduct(LogExtention.eLn(parameters.Model.TransitionProbabilityMatrix[i][j]),
LogExtention.eLnProduct(parameters.Beta[t + 1][j], LogExtention.eLn(o)))));
}
else
{
denominator[t] += parameters.Alpha[t][i] * parameters.Model.TransitionProbabilityMatrix[i][j] * parameters.Beta[t + 1][j] * o;
}
}
}
}
_ksi = new double[parameters.Observations.Count][, ];
for (var t = 0; t < parameters.Observations.Count - 1; t++)
{
_ksi[t] = new double[parameters.Model.N, parameters.Model.N];
for (var i = 0; i < parameters.Model.N; i++)
{
for (var j = 0; j < parameters.Model.N; j++)
{
var o = EstimatorUtilities.GetProbability(parameters.Model.Emission[j], parameters.Observations, t + 1);
if (parameters.Normalized)
{
var nominator = LogExtention.eLnProduct(parameters.Alpha[t][i],
LogExtention.eLnProduct(LogExtention.eLn(parameters.Model.TransitionProbabilityMatrix[i][j]),
LogExtention.eLnProduct(parameters.Beta[t + 1][j], LogExtention.eLn(o))));
_ksi[t][i, j] = LogExtention.eLnProduct(nominator, -denominator[t]);
}
else
{
var nominator = parameters.Alpha[t][i] * parameters.Model.TransitionProbabilityMatrix[i][j] * parameters.Beta[t + 1][j] * o;
_ksi[t][i, j] = nominator / denominator[t];
}
}
}
}
return(_ksi);
}
public double[][] Estimate(BasicEstimationParameters <TDistribution> parameters)
{
if (_alpha != null)
{
return(_alpha);
}
_alpha = new double[parameters.Observations.Count][];
_alpha[0] = new double[parameters.Model.N];
// Initialize
for (var i = 0; i < parameters.Model.N; i++)
{
var o = EstimatorUtilities.GetProbability(parameters.Model.Emission[i], parameters.Observations, 0);
_alpha[0][i] = (parameters.Normalized) ? LogExtention.eLnProduct(LogExtention.eLn(parameters.Model.Pi[i]), LogExtention.eLn(o)) : parameters.Model.Pi[i] * o;
}
// Induction
for (var t = 1; t < parameters.Observations.Count; t++)
{
_alpha[t] = new double[parameters.Model.N];
for (var j = 0; j < parameters.Model.N; j++)
{
var sum = (parameters.Normalized) ? double.NaN : 0d;
for (var i = 0; i < parameters.Model.N; i++)
{
if (parameters.Normalized)
{
sum = LogExtention.eLnSum(sum, LogExtention.eLnProduct(_alpha[t - 1][i], LogExtention.eLn(parameters.Model.TransitionProbabilityMatrix[i][j])));
}
else
{
sum += _alpha[t - 1][i] * parameters.Model.TransitionProbabilityMatrix[i][j];
}
}
var o = EstimatorUtilities.GetProbability(parameters.Model.Emission[j], parameters.Observations, t);
if (parameters.Normalized)
{
_alpha[t][j] = LogExtention.eLnProduct(sum, LogExtention.eLn(o));
}
else
{
_alpha[t][j] = sum * o;
}
}
}
return(_alpha);
}
public IDistribution Evaluate(double[] observations, double[] symbols, double[] gamma, bool logNormalized)
{
var M = symbols.Length;
var T = observations.Length;
var probabilities = new double[M];
for (var k = 0; k < M; k++)
{
double den = (logNormalized) ? double.NaN : 0, num = (logNormalized) ? double.NaN : 0;
for (var t = 0; t < T; t++)
{
if (observations[t] == symbols[k])
{
if (logNormalized)
{
num = LogExtention.eLnSum(num, gamma[t]);
}
else
{
num = num + gamma[t];
}
}
if (logNormalized)
{
den = LogExtention.eLnSum(den, gamma[t]);
}
else
{
den = den + gamma[t];
}
}
probabilities[k] = 1e-10;
if (!num.EqualsToZero())
{
if (logNormalized)
{
probabilities[k] = den.EqualsToZero() ? 0.0 : LogExtention.eExp(LogExtention.eLnProduct(num, -den));
}
else
{
probabilities[k] = den.EqualsToZero() ? 0.0 : num / den;
}
}
}
return(new DiscreteDistribution(symbols, probabilities));
}
protected void EstimateTransitionProbabilityMatrix(double[][] gamma, double[][,] ksi, decimal[] observationWeights, int sequenceLength)
{
var checksum = new double[_model.N];
for (var i = 0; i < _model.N; i++)
{
_estimatedTransitionProbabilityMatrix[i] = new double[_model.N];
for (var j = 0; j < _model.N; j++)
{
double den = (_model.Normalized) ? double.NaN : 0, num = (_model.Normalized) ? double.NaN : 0;
for (var t = 0; t < sequenceLength - 1; t++)
{
var weight = GetWeightValue(t, observationWeights);
if (_model.Normalized)
{
num = LogExtention.eLnSum(num, LogExtention.eLnProduct(weight, ksi[t][i, j]));
den = LogExtention.eLnSum(den, LogExtention.eLnProduct(weight, gamma[t][i]));
}
else
{
num += weight * ksi[t][i, j];
den += weight * gamma[t][i];
}
}
if (_model.Normalized)
{
_estimatedTransitionProbabilityMatrix[i][j] = den.EqualsToZero() ? 0.0 : LogExtention.eExp(LogExtention.eLnProduct(num, -den));
}
else
{
_estimatedTransitionProbabilityMatrix[i][j] = den.EqualsToZero() ? 0.0 : num / den;
}
checksum[i] = checksum[i] + _estimatedTransitionProbabilityMatrix[i][j];
}
}
CheckTransitionProbabilityMatrix(checksum);
}
public double RunBackward <TEmmisionType>(IList <IObservation> observations, IHiddenMarkovModel <TEmmisionType> model) where TEmmisionType : IDistribution
{
var betaEstimator = new BetaEstimator <TEmmisionType>();
_beta = betaEstimator.Estimate(new BasicEstimationParameters <TEmmisionType> {
Model = model, Observations = observations, Normalized = Normalized
});
var result = (Normalized) ? double.NaN : 0d;
for (var j = 0; j < model.N; j++)
{
if (Normalized)
{
result = LogExtention.eLnSum(result,
LogExtention.eLnProduct(LogExtention.eLn(model.Pi[j]), _beta[1][j]));
}
else
{
result += model.Pi[j] * _beta[1][j];
}
}
return(result);
}
public double[][] Estimate(MixtureCoefficientEstimationParameters <TDistribution> parameters)
{
_parameters = parameters;
if (_coefficients != null)
{
return(_coefficients);
}
try
{
_coefficients = new double[parameters.Model.N][];
_denominator = new double[parameters.Model.N];
for (var i = 0; i < parameters.Model.N; i++)
{
_denominator[i] = (parameters.Model.Normalized) ? double.NaN : 0d;
for (var t = 0; t < parameters.Observations.Count; t++)
{
var weight = GetWeightValue(t, parameters.ObservationWeights);
if (parameters.Normalized)
{
_denominator[i] = LogExtention.eLnSum(LogExtention.eLnProduct(weight, parameters.Gamma[t][i]), _denominator[i]);
}
else
{
_denominator[i] += weight * parameters.Gamma[t][i];
}
}
}
for (var i = 0; i < parameters.Model.N; i++)
{
_coefficients[i] = new double[parameters.L];
for (var l = 0; l < parameters.L; l++)
{
var nominator = (parameters.Model.Normalized) ? double.NaN : 0d;
for (var t = 0; t < parameters.Observations.Count; t++)
{
var weight = GetWeightValue(t, parameters.ObservationWeights);
if (parameters.Normalized)
{
nominator = LogExtention.eLnSum(LogExtention.eLnProduct(weight, parameters.GammaComponents[t][i, l]), nominator);
}
else
{
nominator += weight * parameters.GammaComponents[t][i, l];
}
}
if (parameters.Normalized)
{
_coefficients[i][l] = LogExtention.eLnProduct(nominator, -_denominator[i]);
}
else
{
_coefficients[i][l] = nominator / _denominator[i];
}
if (Math.Round(_coefficients[i].Sum(), 5) > 1)
{
Debug.WriteLine("Mixture Coeffiecients [{0},{1}] : {2}", i, l, new Vector(_coefficients[i]));
throw new ApplicationException(string.Format("Mixture Coeffiecients is greater than 1. [{0},{1}] : {2} : {3}", i, l, new Vector(_coefficients[i]), Math.Round(_coefficients[i].Sum(), 5)));
}
}
}
}
catch (Exception)
{
for (var i = 0; i < parameters.Model.N; i++)
{
for (var l = 0; l < parameters.L; l++)
{
Debug.WriteLine("Coeffiecients[{0}][{1}] : {2}", i, l, _coefficients[i][l]);
if (Math.Round(_coefficients[i].Sum(), 5) > 1)
{
Debug.WriteLine("Mixture Coeffiecients [{0},{1}] : {2}", i, l, new Vector(_coefficients[i]));
throw new ApplicationException(string.Format("Mixture Coeffiecients is greater than 1. [{0},{1}] : {2} : {3}", i, l, new Vector(_coefficients[i]), Math.Round(_coefficients[i].Sum(), 5)));
}
}
}
throw;
}
return(_coefficients);
}
public List <IState> Run(IList <IObservation> observations, IList <IState> states,
double[] startDistribution,
double[][] transitionProbabilityMatrix,
double[][] distributionWeights,
IDistribution[][] distributions)
{
var N = states.Count;
var T = observations.Count;
var K = distributionWeights[0].Length;
ComputationPath = new double[T][];
ReproducePath = new int[T][];
var mpp = new List <IState>(states.Count);
// Initialize for the first observation
ComputationPath[0] = new double[N];
ReproducePath[0] = new int[N];
mpp.Add(new State());
for (var i = 0; i < N; i++)
{
var sum = (Normalized) ? double.NaN : 0d;
for (int k = 0; k < K; k++)
{
if (Normalized)
{
sum = LogExtention.eLnSum(sum, LogExtention.eLnProduct(LogExtention.eLn(distributionWeights[i][k]), LogExtention.eLn(GetProbability(distributions[i][k], observations, 0))));
}
else
{
sum += distributionWeights[i][k] * GetProbability(distributions[i][k], observations, 0);
}
}
if (Normalized)
{
ComputationPath[0][i] = LogExtention.eLnProduct(LogExtention.eLn(startDistribution[i]), sum);
}
else
{
ComputationPath[0][i] = startDistribution[i] * sum;
}
ReproducePath[0][i] = -1;
}
// Induction
for (var t = 1; t < T; t++)
{
ComputationPath[t] = new double[N];
ReproducePath[t] = new int[N];
mpp.Add(new State());
for (var j = 0; j < N; j++)
{
// argmax + max
var max = double.NegativeInfinity; //0;
for (var i = 0; i < N; i++)
{
var value = (Normalized) ? LogExtention.eLnProduct(ComputationPath[t - 1][i], LogExtention.eLn(transitionProbabilityMatrix[i][j])) :
ComputationPath[t - 1][i] * transitionProbabilityMatrix[i][j];
if (value > max)
{
max = value;
ReproducePath[t][j] = i;
}
}
var sum = (Normalized) ? double.NaN : 0d;
for (var k = 0; k < K; k++)
{
if (Normalized)
{
sum = LogExtention.eLnSum(sum, LogExtention.eLnProduct(LogExtention.eLn(distributionWeights[j][k]), LogExtention.eLn(GetProbability(distributions[j][k], observations, 0))));
}
else
{
sum += distributionWeights[j][k] * GetProbability(distributions[j][k], observations, 0);
}
}
if (Normalized)
{
ComputationPath[t][j] = LogExtention.eLnProduct(max, sum);
}
else
{
ComputationPath[t][j] = max * sum;
}
}
}
// Calculate results (from first observation)
mpp[T - 1] = states[GetMaximumDeltaValueStateIndex(ComputationPath[T - 1])];
for (var i = T - 2; i >= 0; i--)
{
mpp[i] = states[ReproducePath[i + 1][mpp[i + 1].Index]];
}
return(mpp);
}
