public static void Main(string[] args)
{
var data = new Sequences("nbt.1882-S6.txt");
// Now we create a hidden Markov model with arbitrary probabilities
var hmm = new HiddenMarkovModel(states: data.StateNum, symbols: data.SymbolNum);
// Create a Baum-Welch learning algorithm to teach it
var teacher = new BaumWelchLearning(hmm);
// and call its Run method to start learning
var trainSamples = data.PartOfSequences(0, 2);
double error = teacher.Run(trainSamples);
var testSamples = data.PartOfSequences(1, 2);
// Let's now check the probability of some sequences:
double prob1 = Math.Exp(hmm.Evaluate(trainSamples [0]));
double prob2 = Math.Exp(hmm.Evaluate(trainSamples [1]));
double prob3 = Math.Exp(hmm.Evaluate(trainSamples [2]));
// Now those obviously violate the form of the training set:
double prob4 = Math.Exp(hmm.Evaluate(testSamples [0]));
double prob5 = Math.Exp(hmm.Evaluate(testSamples [1]));
}
static void runArbitraryDensityHiddenMarkovModelLearningExample()
{
// Create continuous sequences.
// In the sequences below, there seems to be two states, one for values between 0 and 1 and another for values between 5 and 7.
// The states seems to be switched on every observation.
double[][] observationSequences = new double[][]
{
new double[] { 0.1, 5.2, 0.3, 6.7, 0.1, 6.0 },
new double[] { 0.2, 6.2, 0.3, 6.3, 0.1, 5.0 },
new double[] { 0.1, 7.0, 0.1, 7.0, 0.2, 5.6 },
};
// Creates a continuous hidden Markov Model with two states organized in a ergoric topology
// and an underlying univariate Normal distribution as probability density.
var hmm = new HiddenMarkovModel <NormalDistribution>(topology: new Ergodic(states: 2), emissions: new NormalDistribution());
// Configure the learning algorithms to train the sequence classifier
// until the difference in the average log-likelihood changes only by as little as 0.0001.
var trainer = new BaumWelchLearning <NormalDistribution>(hmm)
{
Tolerance = 0.0001,
Iterations = 0,
};
// Fit the model.
double averageLogLikelihood = trainer.Run(observationSequences);
Console.WriteLine("average log-likelihood for the observations = {0}", averageLogLikelihood);
// The log-probability of the sequences learned.
double logLik1 = hmm.Evaluate(new[] { 0.1, 5.2, 0.3, 6.7, 0.1, 6.0 }); // -0.12799388666109757.
double logLik2 = hmm.Evaluate(new[] { 0.2, 6.2, 0.3, 6.3, 0.1, 5.0 }); // 0.01171157434400194.
// The log-probability of an unrelated sequence.
double logLik3 = hmm.Evaluate(new[] { 1.1, 2.2, 1.3, 3.2, 4.2, 1.0 }); // -298.7465244473417.
// Transform the log-probabilities to actual probabilities.
Console.WriteLine("probability = {0}", Math.Exp(logLik1)); // 0.879.
Console.WriteLine("probability = {0}", Math.Exp(logLik2)); // 1.011.
Console.WriteLine("probability = {0}", Math.Exp(logLik3)); // 0.000.
// Ask the model to decode one of the sequences.
// The state variable will contain: { 0, 1, 0, 1, 0, 1 }.
double logLikelihood = 0.0;
int[] path = hmm.Decode(new[] { 0.1, 5.2, 0.3, 6.7, 0.1, 6.0 }, out logLikelihood);
Console.Write("log-likelihood = {0}, Viterbi path = [", logLikelihood);
foreach (int state in path)
{
Console.Write("{0},", state);
}
Console.WriteLine("]");
}
public static void Evaluate()
{
double[,] transition =
{
{ 0.7, 0.3 },
{ 0.4, 0.6 }
};
double[,] emission =
{
{ 0.1, 0.4, 0.5 },
{ 0.6, 0.3, 0.1 }
};
double[] initial = { 0.6, 0.4 };
HiddenMarkovModel hmm = new HiddenMarkovModel(transition, emission, initial);
int[] sequence = new int[] { 0, 1, 2 };
double logLikeliHood = hmm.Evaluate(sequence);
// At this point, the log-likelihood of the sequence
// occurring within the model is -3.3928721329161653.
Console.WriteLine("logLikeliHood: {0}", logLikeliHood);
}
public static double BaumWelchLearning(double[][] data)
{
// Specify a initial normal distribution for the samples.
NormalDistribution density = new NormalDistribution();
// Creates a continuous hidden Markov Model with two states organized in a forward
// topology and an underlying univariate Normal distribution as probability density.
var model = new HiddenMarkovModel <NormalDistribution>(new Ergodic(2), density);
// Configure the learning algorithms to train the sequence classifier until the
// difference in the average log-likelihood changes only by as little as 0.0001
var teacher = new BaumWelchLearning <NormalDistribution>(model)
{
Tolerance = 0.001,
Iterations = 0,
};
// Fit the model
double likelihood = teacher.Run(data);
// See the log-probability of the sequences learned
double a1 = model.Evaluate(new[] { 0.999999999999928, 0, 0.999999999999988, 0, 0.999999999999988 }); // -0.12799388666109757
return(a1);
}
public void LikelihoodTest()
{
var hmm = DiscreteHiddenMarkovModelFunctionTest.CreateModel2();
int states = hmm.States;
int symbols = hmm.Symbols;
var hcrf = new ConditionalRandomField <int>(states,
new MarkovDiscreteFunction(hmm));
var hmm0 = new HiddenMarkovModel(states, symbols);
var hcrf0 = new ConditionalRandomField <int>(states,
new MarkovDiscreteFunction(hmm0));
int[] observations = new int[] { 0, 0, 1, 1, 1, 2 };
double la = hcrf.LogLikelihood(observations, observations);
double lb = hcrf0.LogLikelihood(observations, observations);
Assert.IsTrue(la > lb);
double lc = hmm.Evaluate(observations, observations);
double ld = hmm0.Evaluate(observations, observations);
Assert.IsTrue(lc > ld);
double za = hcrf.LogPartition(observations);
double zb = hcrf0.LogPartition(observations);
la += za;
lb += zb;
Assert.AreEqual(la, lc, 1e-6);
Assert.AreEqual(lb, ld, 1e-6);
}
public void GenerateTest()
{
// Example taken from http://en.wikipedia.org/wiki/Viterbi_algorithm
double[,] transition =
{
{ 0.7, 0.3 },
{ 0.4, 0.6 }
};
double[,] emission =
{
{ 0.1, 0.4, 0.5 },
{ 0.6, 0.3, 0.1 }
};
double[] initial =
{
0.6, 0.4
};
HiddenMarkovModel hmm = new HiddenMarkovModel(transition, emission, initial);
double logLikelihood;
int[] path;
int[] samples = hmm.Generate(10, out path, out logLikelihood);
double expected = hmm.Evaluate(samples, path);
Assert.AreEqual(expected, logLikelihood);
}
public double Run(int[][] observations_db)
{
int K = observations_db.Length;
double currLogLikelihood = Double.NegativeInfinity;
for (int k = 0; k < K; ++k)
{
currLogLikelihood = LogHelper.LogSum(currLogLikelihood, mModel.Evaluate(observations_db[k]));
}
double oldLogLikelihood = -1;
double deltaLogLikelihood = -1;
int iteration = 0;
do
{
oldLogLikelihood = currLogLikelihood;
int[][] paths_db = new int[K][];
for (int k = 0; k < K; ++k)
{
paths_db[k] = mModel.Decode(observations_db[k]);
}
mMaximumLikelihoodLearner.Run(observations_db, paths_db);
currLogLikelihood = double.NegativeInfinity;
for (int k = 0; k < K; ++k)
{
currLogLikelihood = LogHelper.LogSum(currLogLikelihood, mModel.Evaluate(observations_db[k]));
}
deltaLogLikelihood = System.Math.Abs(currLogLikelihood - oldLogLikelihood);
iteration++;
}while(!ShouldTerminate(deltaLogLikelihood, iteration));
return(currLogLikelihood);
}
public void DecodeTest()
{
// Example taken from http://en.wikipedia.org/wiki/Viterbi_algorithm
// Create the transition matrix A
double[,] transition =
{
{ 0.7, 0.3 },
{ 0.4, 0.6 }
};
// Create the emission matrix B
double[,] emission =
{
{ 0.1, 0.4, 0.5 },
{ 0.6, 0.3, 0.1 }
};
// Create the initial probabilities pi
double[] initial =
{
0.6, 0.4
};
// Create a new hidden Markov model
HiddenMarkovModel hmm = new HiddenMarkovModel(transition, emission, initial);
// After that, one could, for example, query the probability
// of a sequence occurring. We will consider the sequence
int[] sequence = new int[] { 0, 1, 2 };
// And now we will evaluate its likelihood
double logLikelihood = hmm.Evaluate(sequence);
// At this point, the log-likelihood of the sequence
// occurring within the model is -3.3928721329161653.
// We can also get the Viterbi path of the sequence
int[] path = hmm.Decode(sequence, out logLikelihood);
// At this point, the state path will be 1-0-0 and the
// log-likelihood will be -4.3095199438871337
Assert.AreEqual(logLikelihood, Math.Log(0.01344), 1e-10);
Assert.AreEqual(path[0], 1);
Assert.AreEqual(path[1], 0);
Assert.AreEqual(path[2], 0);
}
/// <summary>
/// Returns a dictionary of Markov probabilities for all supplied sequences
/// </summary>
/// <param name="sequences"></param>
/// <returns></returns>
public Dictionary <string, double> GetMarkovProbabilities(List <string> sequences)
{
Dictionary <string, double> probabilities = new Dictionary <string, double>();
//determine probability for each sequence
foreach (string sequence in sequences)
{
//each sequence is in the form "#-#-#...-#". We need to conver this into an array of
//integers for use in the markov model
int[] sequenceNumbers = sequence.Split('_').Select(m => Convert.ToInt32(m)).ToArray();
//store probability in dictionary for use elsewhere
probabilities[sequence] = Math.Exp(_model.Evaluate(sequenceNumbers));
}
return(probabilities);
}
static void runDiscreteDensityHiddenMarkovModelExample()
{
// Create the transition matrix A.
double[,] transition =
{
{ 0.7, 0.3 },
{ 0.4, 0.6 }
};
// Create the emission matrix B.
double[,] emission =
{
{ 0.1, 0.4, 0.5 },
{ 0.6, 0.3, 0.1 }
};
// Create the initial probabilities pi.
double[] initial =
{
0.6, 0.4
};
// Create a new hidden Markov model.
HiddenMarkovModel hmm = new HiddenMarkovModel(transition, emission, initial);
// Query the probability of a sequence occurring.
int[] sequence = new int[] { 0, 1, 2 };
// Evaluate its likelihood.
double logLikelihood = hmm.Evaluate(sequence);
// The log-likelihood of the sequence occurring within the model is -3.3928721329161653.
Console.WriteLine("log-likelihood = {0}", logLikelihood);
// Get the Viterbi path of the sequence.
int[] path = hmm.Decode(sequence, out logLikelihood);
// The state path will be 1-0-0 and the log-likelihood will be -4.3095199438871337.
Console.Write("log-likelihood = {0}, Viterbi path = [", logLikelihood);
foreach (int state in path)
{
Console.Write("{0},", state);
}
Console.WriteLine("]");
}
static void runArbitraryDensityHiddenMarkovModelExample()
{
// Create the transition matrix A.
double[,] transitions =
{
{ 0.7, 0.3 },
{ 0.4, 0.6 }
};
// Create the vector of emission densities B.
GeneralDiscreteDistribution[] emissions =
{
new GeneralDiscreteDistribution(0.1, 0.4, 0.5),
new GeneralDiscreteDistribution(0.6, 0.3, 0.1)
};
// Create the initial probabilities pi.
double[] initial =
{
0.6, 0.4
};
// Create a new hidden Markov model with discrete probabilities.
var hmm = new HiddenMarkovModel <GeneralDiscreteDistribution>(transitions, emissions, initial);
// Query the probability of a sequence occurring. We will consider the sequence.
double[] sequence = new double[] { 0, 1, 2 };
// Evaluate its likelihood.
double logLikelihood = hmm.Evaluate(sequence);
// The log-likelihood of the sequence occurring within the model is -3.3928721329161653.
Console.WriteLine("log-likelihood = {0}", logLikelihood);
// Get the Viterbi path of the sequence.
int[] path = hmm.Decode(sequence, out logLikelihood);
// The state path will be 1-0-0 and the log-likelihood will be -4.3095199438871337.
Console.Write("log-likelihood = {0}, Viterbi path = [", logLikelihood);
foreach (int state in path)
{
Console.Write("{0},", state);
}
Console.WriteLine("]");
}
public static void ViterbiLearning()
{
int[][] sequences = new int[][]
{
new int[] { 0, 1, 1, 1, 1, 0, 1, 1, 1, 1 },
new int[] { 0, 1, 1, 1, 0, 1, 1, 1, 1, 1 },
new int[] { 0, 1, 1, 1, 1, 1, 1, 1, 1, 1 },
new int[] { 0, 1, 1, 1, 1, 1 },
new int[] { 0, 1, 1, 1, 1, 1, 1 },
new int[] { 0, 1, 1, 1, 1, 1, 1, 1, 1, 1 },
new int[] { 0, 1, 1, 1, 1, 1, 1, 1, 1, 1 },
};
// Creates a new Hidden Markov Model with 3 states for
// an output alphabet of two characters (zero and one)
HiddenMarkovModel hmm = new HiddenMarkovModel(state_count: 3, symbol_count: 2);
// Try to fit the model to the data until the difference in
// the average log-likelihood changes only by as little as 0.0001
var teacher = new ViterbiLearning(hmm)
{
Tolerance = 0.0001, Iterations = 0
};
double ll = teacher.Run(sequences);
// Calculate the probability that the given
// sequences originated from the model
double l1 = hmm.Evaluate(new int[] { 0, 1 }); // 0.999
double l2 = hmm.Evaluate(new int[] { 0, 1, 1, 1 }); // 0.916
Console.WriteLine("l1: {0}", System.Math.Exp(l1));
Console.WriteLine("l2: {0}", System.Math.Exp(l2));
// Sequences which do not start with zero have much lesser probability.
double l3 = hmm.Evaluate(new int[] { 1, 1 }); // 0.000
double l4 = hmm.Evaluate(new int[] { 1, 0, 0, 0 }); // 0.000
Console.WriteLine("l3: {0}", System.Math.Exp(l3));
Console.WriteLine("l4: {0}", System.Math.Exp(l4));
// Sequences which contains few errors have higher probability
// than the ones which do not start with zero. This shows some
// of the temporal elasticity and error tolerance of the HMMs.
double l5 = hmm.Evaluate(new int[] { 0, 1, 0, 1, 1, 1, 1, 1, 1 }); // 0.034
double l6 = hmm.Evaluate(new int[] { 0, 1, 1, 1, 1, 1, 1, 0, 1 }); // 0.034
Console.WriteLine("l5: {0}", System.Math.Exp(l5));
Console.WriteLine("l6: {0}", System.Math.Exp(l6));
}
public static void BaumWelchLearning()
{
// We will try to create a Hidden Markov Model which
// can detect if a given sequence starts with a zero
// and has any number of ones after that.
int[][] sequences = new int[][]
{
new int[] { 0, 1, 1, 1, 1, 0, 1, 1, 1, 1 },
new int[] { 0, 1, 1, 1, 0, 1, 1, 1, 1, 1 },
new int[] { 0, 1, 1, 1, 1, 1, 1, 1, 1, 1 },
new int[] { 0, 1, 1, 1, 1, 1 },
new int[] { 0, 1, 1, 1, 1, 1, 1 },
new int[] { 0, 1, 1, 1, 1, 1, 1, 1, 1, 1 },
new int[] { 0, 1, 1, 1, 1, 1, 1, 1, 1, 1 },
};
// Creates a new Hidden Markov Model with 3 states for
// an output alphabet of two characters (zero and one)
HiddenMarkovModel hmm = new HiddenMarkovModel(3, 2);
// Try to fit the model to the data until the difference in
// the average log-likelihood changes only by as little as 0.0001
var teacher = new BaumWelchLearning(hmm)
{
Tolerance = 0.0001, Iterations = 0
};
double ll = teacher.Run(sequences);
double l0 = Math.Exp(hmm.Evaluate(new int[] { 1, 0 }));
// Calculate the probability that the given
// sequences originated from the model
double l1 = Math.Exp(hmm.Evaluate(new int[] { 0, 1 })); // 0.999
double l2 = Math.Exp(hmm.Evaluate(new int[] { 0, 1, 1, 1 })); // 0.916
// Sequences which do not start with zero have much lesser probability.
double l3 = Math.Exp(hmm.Evaluate(new int[] { 1, 1 })); // 0.000
double l4 = Math.Exp(hmm.Evaluate(new int[] { 1, 0, 0, 0 })); // 0.000
// Sequences which contains few errors have higher probability
// than the ones which do not start with zero. This shows some
// of the temporal elasticity and error tolerance of the HMMs.
double l5 = Math.Exp(hmm.Evaluate(new int[] { 0, 1, 0, 1, 1, 1, 1, 1, 1 })); // 0.034
double l6 = Math.Exp(hmm.Evaluate(new int[] { 0, 1, 1, 1, 1, 1, 1, 0, 1 })); // 0.034
}
public static void Viterbi()
{
// Create the transition matrix A
double[,] transition =
{
{ 0.7, 0.3 },
{ 0.4, 0.6 }
};
// Create the emission matrix B
double[,] emission =
{
{ 0.1, 0.4, 0.5 },
{ 0.6, 0.3, 0.1 }
};
// Create the initial probabilities pi
double[] initial =
{
0.6, 0.4
};
// Create a new hidden Markov model
HiddenMarkovModel hmm = new HiddenMarkovModel(transition, emission, initial);
// After that, one could, for example, query the probability
// of a sequence occurring. We will consider the sequence
int[] sequence = new int[] { 0, 1, 2 };
// And now we will evaluate its likelihood
double logLikelihood = hmm.Evaluate(sequence);
// At this point, the log-likelihood of the sequence
// occurring within the model is -3.3928721329161653.
// We can also get the Viterbi path of the sequence
int[] path = hmm.Decode(sequence, out logLikelihood);
// At this point, the state path will be 1-0-0 and the
// log-likelihood will be -4.3095199438871337
}
public static void Viterbi()
{
// Create the transition matrix A
double[,] transition =
{
{ 1.0 / 3, 1.0 / 3, 1.0 / 3 },
{ 1.0 / 3, 1.0 / 3, 1.0 / 3 },
{ 1.0 / 3, 1.0 / 3, 1.0 / 3 }
};
// Create the emission matrix B
double[,] emission =
{
{ 1.0 / 4, 1.0 / 4, 1.0 / 4, 1.0 / 4, 0, 0, 0, 0 },
{ 1.0 / 6, 1.0 / 6, 1.0 / 6, 1.0 / 6, 1.0 / 6, 1.0 / 6, 0, 0 },
{ 1.0 / 8, 1.0 / 8, 1.0 / 8, 1.0 / 8, 1.0 / 8, 1.0 / 8, 1.0 / 8, 1.0 / 8 },
};
// Create the initial probabilities pi
double[] initial =
{
0.3, 0.3, 0.4
};
//var pS = new double[] { 1.0 / 3, 1.0 / 3, 1.0 / 3 };
//var p4N = new double[] { 1.0 / 4, 1.0 / 4, 1.0 / 4, 1.0 / 4 };
//var p6N = new double[] { 1.0 / 6, 1.0 / 6, 1.0 / 6, 1.0 / 6, 1.0 / 6, 1.0 / 6 };
//var p8N = new double[] { 1.0 / 8, 1.0 / 8, 1.0 / 8, 1.0 / 8, 1.0 / 8, 1.0 / 8, 1.0 / 8, 1.0 / 8 };
//var pN = new double[][] { p4N, p6N, p8N };
HiddenMarkovModel hmm = new HiddenMarkovModel(transition, emission, initial);
int[] sequence = new int[] { 1, 6, 3 };
double logLikelihood = hmm.Evaluate(sequence);
int[] path = hmm.Decode(sequence, out logLikelihood);
}
public void LearnTest2()
{
// Declare some testing data
int[][] inputs = new int[][]
{
new int[] { 0,0,1,2 }, // Class 0
new int[] { 0,1,1,2 }, // Class 0
new int[] { 0,0,0,1,2 }, // Class 0
new int[] { 0,1,2,2,2 }, // Class 0
new int[] { 2,2,1,0 }, // Class 1
new int[] { 2,2,2,1,0 }, // Class 1
new int[] { 2,2,2,1,0 }, // Class 1
new int[] { 2,2,2,2,1 }, // Class 1
};
int[] outputs = new int[]
{
0,0,0,0, // First four sequences are of class 0
1,1,1,1, // Last four sequences are of class 1
};
// We are trying to predict two different classes
int classes = 2;
// Each sequence may have up to 3 symbols (0,1,2)
int symbols = 3;
// Nested models will have 3 states each
int[] states = new int[] { 3, 3 };
// Creates a new Hidden Markov Model Classifier with the given parameters
HiddenMarkovClassifier classifier = new HiddenMarkovClassifier(classes, states, symbols);
// Create a new learning algorithm to train the sequence classifier
var teacher = new HiddenMarkovClassifierLearning(classifier,
// Train each model until the log-likelihood changes less than 0.001
modelIndex => new BaumWelchLearning(classifier.Models[modelIndex])
{
Tolerance = 0.001,
Iterations = 0
}
);
// Enable support for sequence rejection
teacher.Rejection = true;
// Train the sequence classifier using the algorithm
double likelihood = teacher.Run(inputs, outputs);
HiddenMarkovModel threshold = classifier.Threshold;
Assert.AreEqual(6, threshold.States);
Assert.AreEqual(classifier.Models[0].Transitions[0, 0], threshold.Transitions[0, 0], 1e-10);
Assert.AreEqual(classifier.Models[0].Transitions[1, 1], threshold.Transitions[1, 1], 1e-10);
Assert.AreEqual(classifier.Models[0].Transitions[2, 2], threshold.Transitions[2, 2], 1e-10);
Assert.AreEqual(classifier.Models[1].Transitions[0, 0], threshold.Transitions[3, 3], 1e-10);
Assert.AreEqual(classifier.Models[1].Transitions[1, 1], threshold.Transitions[4, 4], 1e-10);
Assert.AreEqual(classifier.Models[1].Transitions[2, 2], threshold.Transitions[5, 5], 1e-10);
for (int i = 0; i < 3; i++)
for (int j = 3; j < 6; j++)
Assert.AreEqual(Double.NegativeInfinity, threshold.Transitions[i, j]);
for (int i = 3; i < 6; i++)
for (int j = 0; j < 3; j++)
Assert.AreEqual(Double.NegativeInfinity, threshold.Transitions[i, j]);
Assert.IsFalse(Matrix.HasNaN(threshold.Transitions));
classifier.Sensitivity = 0.5;
// Will assert the models have learned the sequences correctly.
for (int i = 0; i < inputs.Length; i++)
{
int expected = outputs[i];
int actual = classifier.Compute(inputs[i], out likelihood);
Assert.AreEqual(expected, actual);
}
int[] r0 = new int[] { 1, 1, 0, 0, 2 };
double logRejection;
int c = classifier.Compute(r0, out logRejection);
Assert.AreEqual(-1, c);
Assert.AreEqual(0.99906957195279988, logRejection);
Assert.IsFalse(double.IsNaN(logRejection));
logRejection = threshold.Evaluate(r0);
Assert.AreEqual(-4.5653702970734793, logRejection, 1e-10);
Assert.IsFalse(double.IsNaN(logRejection));
threshold.Decode(r0, out logRejection);
Assert.AreEqual(-8.21169955167614, logRejection, 1e-10);
Assert.IsFalse(double.IsNaN(logRejection));
foreach (var model in classifier.Models)
{
double[,] A = model.Transitions;
for (int i = 0; i < A.GetLength(0); i++)
{
double[] row = A.Exp().GetRow(i);
double sum = row.Sum();
Assert.AreEqual(1, sum, 1e-10);
}
}
{
double[,] A = classifier.Threshold.Transitions;
for (int i = 0; i < A.GetLength(0); i++)
{
double[] row = A.GetRow(i);
double sum = row.Exp().Sum();
Assert.AreEqual(1, sum, 1e-6);
}
}
}
public void LearnTest6()
{
Accord.Math.Tools.SetupGenerator(0);
// We will try to create a Hidden Markov Model which
// can detect if a given sequence starts with a zero
// and has any number of ones after that.
//
int[][] sequences = new int[][]
{
new int[] { 0, 1, 1, 1, 1, 0, 1, 1, 1, 1 },
new int[] { 0, 1, 1, 1, 0, 1, 1, 1, 1, 1 },
new int[] { 0, 1, 1, 1, 1, 1, 1, 1, 1, 1 },
new int[] { 0, 1, 1, 1, 1, 1 },
new int[] { 0, 1, 1, 1, 1, 1, 1 },
new int[] { 0, 1, 1, 1, 1, 1, 1, 1, 1, 1 },
new int[] { 0, 1, 1, 1, 1, 1, 1, 1, 1, 1 },
};
// Creates a new Hidden Markov Model with 3 states for
// an output alphabet of two characters (zero and one)
//
HiddenMarkovModel hmm = new HiddenMarkovModel(new Forward(3), 2);
// Try to fit the model to the data until the difference in
// the average log-likelihood changes only by as little as 0.0001
//
var teacher = new ViterbiLearning(hmm)
{
Tolerance = 0.0001, Iterations = 0
};
double ll = teacher.Run(sequences);
// Calculate the probability that the given
// sequences originated from the model
double l1 = hmm.Evaluate(new int[] { 0, 1 }); // 0.613
double l2 = hmm.Evaluate(new int[] { 0, 1, 1, 1 }); // 0.500
// Sequences which do not start with zero have much lesser probability.
double l3 = hmm.Evaluate(new int[] { 1, 1 }); // 0.186
double l4 = hmm.Evaluate(new int[] { 1, 0, 0, 0 }); // 0.003
// Sequences which contains few errors have higher probability
// than the ones which do not start with zero. This shows some
// of the temporal elasticity and error tolerance of the HMMs.
//
double l5 = hmm.Evaluate(new int[] { 0, 1, 0, 1, 1, 1, 1, 1, 1 }); // 0.033
double l6 = hmm.Evaluate(new int[] { 0, 1, 1, 1, 1, 1, 1, 0, 1 }); // 0.026
double pl = System.Math.Exp(ll);
double p1 = System.Math.Exp(l1);
double p2 = System.Math.Exp(l2);
double p3 = System.Math.Exp(l3);
double p4 = System.Math.Exp(l4);
double p5 = System.Math.Exp(l5);
double p6 = System.Math.Exp(l6);
Assert.AreEqual(1.754393540912413, pl, 1e-6);
Assert.AreEqual(0.61368718756104801, p1, 1e-6);
Assert.AreEqual(0.50049466955818356, p2, 1e-6);
Assert.AreEqual(0.18643340385264684, p3, 1e-6);
Assert.AreEqual(0.00300262431355424, p4, 1e-6);
Assert.AreEqual(0.03338686211012481, p5, 1e-6);
Assert.AreEqual(0.02659161933179825, p6, 1e-6);
Assert.IsTrue(l1 > l3 && l1 > l4);
Assert.IsTrue(l2 > l3 && l2 > l4);
}
/// <summary>
/// Runs the Maximum Likelihood learning algorithm for hidden Markov models.
/// </summary>
///
/// <param name="observations">An array of observation sequences to be used to train the model.</param>
/// <param name="paths">An array of state labels associated to each observation sequence.</param>
///
/// <returns>
/// The average log-likelihood for the observations after the model has been trained.
/// </returns>
///
/// <remarks>
/// Supervised learning problem. Given some training observation sequences O = {o1, o2, ..., oK},
/// known training state paths H = {h1, h2, ..., hK} and general structure of HMM (numbers of
/// hidden and visible states), determine HMM parameters M = (A, B, pi) that best fit training data.
/// </remarks>
///
public double Run(Array[] observations, int[][] paths)
{
// Convert the generic representation to a vector of multivariate sequences
double[][][] obs = observations as double[][][];
if (obs == null)
{
obs = new double[observations.Length][][];
for (int i = 0; i < observations.Length; i++)
{
obs[i] = convert(observations[i], model.Dimension);
}
}
// Grab model information
int N = observations.Length;
int states = model.States;
int[] initial = new int[states];
int[,] transitions = new int[states, states];
// 1. Count first state occurrences
for (int i = 0; i < paths.Length; i++)
{
initial[paths[i][0]]++;
}
// 2. Count all state transitions
foreach (int[] path in paths)
{
for (int j = 1; j < path.Length; j++)
{
transitions[path[j - 1], path[j]]++;
}
}
if (useWeights)
{
int totalObservations = 0;
for (int i = 0; i < obs.Length; i++)
{
totalObservations += obs[i].Length;
}
double[][] weights = new double[states][];
for (int i = 0; i < weights.Length; i++)
{
weights[i] = new double[totalObservations];
}
double[][] all = new double[totalObservations][];
for (int i = 0, c = 0; i < paths.Length; i++)
{
for (int t = 0; t < paths[i].Length; t++, c++)
{
int state = paths[i][t];
all[c] = obs[i][t];
weights[state][c] = 1;
}
}
for (int i = 0; i < model.States; i++)
{
model.Emissions[i].Fit(all, weights[i], fittingOptions);
}
}
else
{
// 3. Count emissions for each state
List <double[]>[] clusters = new List <double[]> [model.States];
for (int i = 0; i < clusters.Length; i++)
{
clusters[i] = new List <double[]>();
}
// Count symbol frequencies per state
for (int i = 0; i < paths.Length; i++)
{
for (int t = 0; t < paths[i].Length; t++)
{
int state = paths[i][t];
double[] symbol = obs[i][t];
clusters[state].Add(symbol);
}
}
// Estimate probability distributions
for (int i = 0; i < model.States; i++)
{
if (clusters[i].Count > 0)
{
model.Emissions[i].Fit(clusters[i].ToArray(), null, fittingOptions);
}
}
}
// 4. Form log-probabilities, using the Laplace
// correction to avoid zero probabilities
if (useLaplaceRule)
{
// Use Laplace's rule of succession correction
// http://en.wikipedia.org/wiki/Rule_of_succession
for (int i = 0; i < initial.Length; i++)
{
initial[i]++;
for (int j = 0; j < states; j++)
{
transitions[i, j]++;
}
}
}
// Form probabilities
int initialCount = initial.Sum();
int[] transitionCount = transitions.Sum(1);
for (int i = 0; i < initial.Length; i++)
{
model.Probabilities[i] = Math.Log(initial[i] / (double)initialCount);
}
for (int i = 0; i < transitionCount.Length; i++)
{
for (int j = 0; j < states; j++)
{
model.Transitions[i, j] = Math.Log(transitions[i, j] / (double)transitionCount[i]);
}
}
System.Diagnostics.Debug.Assert(!model.Probabilities.HasNaN());
System.Diagnostics.Debug.Assert(!model.Transitions.HasNaN());
// 5. Compute log-likelihood
double logLikelihood = Double.NegativeInfinity;
for (int i = 0; i < observations.Length; i++)
{
logLikelihood = Special.LogSum(logLikelihood, model.Evaluate(observations[i]));
}
return(logLikelihood);
}
/// <summary>
/// Runs the Maximum Likelihood learning algorithm for hidden Markov models.
/// </summary>
///
/// <param name="observations">An array of observation sequences to be used to train the model.</param>
/// <param name="paths">An array of state labels associated to each observation sequence.</param>
///
/// <returns>
/// The average log-likelihood for the observations after the model has been trained.
/// </returns>
///
/// <remarks>
/// Supervised learning problem. Given some training observation sequences O = {o1, o2, ..., oK},
/// known training state paths H = {h1, h2, ..., hK} and general structure of HMM (numbers of
/// hidden and visible states), determine HMM parameters M = (A, B, pi) that best fit training data.
/// </remarks>
///
public double Run(int[][] observations, int[][] paths)
{
// Grab model information
int N = observations.Length;
int states = model.States;
int symbols = model.Symbols;
Array.Clear(initial, 0, initial.Length);
Array.Clear(transitions, 0, transitions.Length);
Array.Clear(emissions, 0, emissions.Length);
// 1. Count first state occurrences
for (int i = 0; i < paths.Length; i++)
{
initial[paths[i][0]]++;
}
// 2. Count all state transitions
foreach (int[] path in paths)
{
for (int j = 1; j < path.Length; j++)
{
transitions[path[j - 1], path[j]]++;
}
}
// 3. Count emissions for each state
for (int i = 0; i < observations.Length; i++)
{
for (int j = 0; j < observations[i].Length; j++)
{
emissions[paths[i][j], observations[i][j]]++;
}
}
// 4. Form log-probabilities, using the Laplace
// correction to avoid zero probabilities
if (useLaplaceRule)
{
// Use Laplace's rule of succession correction
// http://en.wikipedia.org/wiki/Rule_of_succession
for (int i = 0; i < initial.Length; i++)
{
initial[i]++;
for (int j = 0; j < states; j++)
{
transitions[i, j]++;
}
for (int k = 0; k < symbols; k++)
{
emissions[i, k]++;
}
}
}
// Form probabilities
int initialCount = initial.Sum();
int[] transitionCount = transitions.Sum(1);
int[] emissionCount = emissions.Sum(1);
if (initialCount == 0)
{
initialCount = 1;
}
for (int i = 0; i < transitionCount.Length; i++)
{
if (transitionCount[i] == 0)
{
transitionCount[i] = 1;
}
}
for (int i = 0; i < emissionCount.Length; i++)
{
if (emissionCount[i] == 0)
{
emissionCount[i] = 1;
}
}
for (int i = 0; i < initial.Length; i++)
{
model.Probabilities[i] = Math.Log(initial[i] / (double)initialCount);
}
for (int i = 0; i < transitionCount.Length; i++)
{
for (int j = 0; j < states; j++)
{
model.Transitions[i, j] = Math.Log(transitions[i, j] / (double)transitionCount[i]);
}
}
for (int i = 0; i < emissionCount.Length; i++)
{
for (int j = 0; j < symbols; j++)
{
model.Emissions[i, j] = Math.Log(emissions[i, j] / (double)emissionCount[i]);
}
}
System.Diagnostics.Debug.Assert(!model.Probabilities.HasNaN());
System.Diagnostics.Debug.Assert(!model.Transitions.HasNaN());
System.Diagnostics.Debug.Assert(!model.Emissions.HasNaN());
// 5. Compute log-likelihood
double logLikelihood = Double.NegativeInfinity;
for (int i = 0; i < observations.Length; i++)
{
logLikelihood = Special.LogSum(logLikelihood, model.Evaluate(observations[i]));
}
return(logLikelihood);
}
static void Main(string[] args)
{
//// Create a model with given probabilities
//HiddenMarkovModel hmm = new HiddenMarkovModel(
//transitions: new[,] // matrix A
//{
// { 0.25, 0.25, 0.00 },
// { 0.33, 0.33, 0.33 },
// { 0.90, 0.10, 0.00 },
//},
//emissions: new[,] // matrix B
//{
// { 0.1, 0.1, 0.8 },
// { 0.6, 0.2, 0.2 },
// { 0.9, 0.1, 0.0 },
//},
//initial: new[] // vector pi
//{
// 0.25, 0.25, 0.0
//});
//// Create an observation sequence of up to 2 symbols (0 or 1)
//int[] observationSequence = new[] { 0, 1, 1, 0};
//// Decode the sequence: the path will be 1-1-1-1-2-0-1-1
//int[] stateSequence = hmm.Decode(observationSequence);
//foreach (int a in stateSequence)
//{
// System.Console.Write(a + " ");
//}
//////////////////////////////////////////////////////////////////////////////
// Create the transation matrix A
double[,] transition =
{
{ 0.3, 0.2, 0.2 },
{ 0.4, 0.3, 0.1 },
{ 0.4, 0.3, 0.1 }
};
// emission probability by kmean algo.
double[,] emission =
{
{ 0.55, 0.075, 0.275, 0, 0.1 }, //Dance 1
{ 0.52, 0.22, 0.16, 0, 0.1 }, //Dance 2
{ 0.357, 0.357, 0.186, 0, 0.1 } //Dance 3
};
// Create the initial probabilities pi
double[] initial =
{
0.4, 0.2, 0.4
};
// Create a new hidden Markov model
HiddenMarkovModel hmm = new HiddenMarkovModel(transition, emission, initial);
// After that, one could, for example, query the probability
// of a sequence ocurring. We will consider the sequence
int[] sequence = new int[] { 0, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1 };
// And now we will evaluate its likelihood
double logLikelihood = hmm.Evaluate(sequence);
// At this point, the log-likelihood of the sequence
// ocurring within the model is -3.3928721329161653.
// We can also get the Viterbi path of the sequence
int[] path = hmm.Decode(sequence, out logLikelihood);
// At this point, the state path will be 1-0-0 and the
// log-likelihood will be -4.3095199438871337
foreach (int a in path)
{
System.Console.Write(a + " ");
}
System.Console.ReadKey();
}
public void LearnTest7()
{
// Create continuous sequences. In the sequences below, there
// seems to be two states, one for values between 0 and 1 and
// another for values between 5 and 7. The states seems to be
// switched on every observation.
double[][] sequences = new double[][]
{
new double[] { 0.1, 5.2, 0.3, 6.7, 0.1, 6.0 },
new double[] { 0.2, 6.2, 0.3, 6.3, 0.1, 5.0 },
new double[] { 0.1, 7.0, 0.1, 7.0, 0.2, 5.6 },
};
// Specify a initial normal distribution for the samples.
var density = new NormalDistribution();
// Creates a continuous hidden Markov Model with two states organized in a forward
// topology and an underlying univariate Normal distribution as probability density.
var model = new HiddenMarkovModel <NormalDistribution>(new Forward(2), density);
// Configure the learning algorithms to train the sequence classifier until the
// difference in the average log-likelihood changes only by as little as 0.0001
var teacher = new ViterbiLearning <NormalDistribution>(model)
{
Tolerance = 0.0001,
Iterations = 0,
};
// Fit the model
double logLikelihood = teacher.Run(sequences);
// See the probability of the sequences learned
double a1 = model.Evaluate(new[] { 0.1, 5.2, 0.3, 6.7, 0.1, 6.0 }); // 0.40
double a2 = model.Evaluate(new[] { 0.2, 6.2, 0.3, 6.3, 0.1, 5.0 }); // 0.46
// See the probability of an unrelated sequence
double a3 = model.Evaluate(new[] { 1.1, 2.2, 1.3, 3.2, 4.2, 1.0 }); // 1.42
double likelihood = Math.Exp(logLikelihood);
a1 = Math.Exp(a1);
a2 = Math.Exp(a2);
a3 = Math.Exp(a3);
Assert.AreEqual(1.5418305348314281, likelihood, 1e-10);
Assert.AreEqual(0.4048936808991913, a1, 1e-10);
Assert.AreEqual(0.4656014344844673, a2, 1e-10);
Assert.AreEqual(1.4232710878429383E-48, a3, 1e-10);
Assert.IsFalse(double.IsNaN(logLikelihood));
Assert.IsFalse(double.IsNaN(a1));
Assert.IsFalse(double.IsNaN(a2));
Assert.IsFalse(double.IsNaN(a3));
Assert.AreEqual(2, model.Emissions.Length);
var state1 = (model.Emissions[0] as NormalDistribution);
var state2 = (model.Emissions[1] as NormalDistribution);
Assert.AreEqual(0.16666666666666, state1.Mean, 1e-10);
Assert.AreEqual(6.11111111111111, state2.Mean, 1e-10);
Assert.IsFalse(Double.IsNaN(state1.Mean));
Assert.IsFalse(Double.IsNaN(state2.Mean));
Assert.AreEqual(0.007499999999999, state1.Variance, 1e-10);
Assert.AreEqual(0.538611111111111, state2.Variance, 1e-10);
Assert.IsFalse(Double.IsNaN(state1.Variance));
Assert.IsFalse(Double.IsNaN(state2.Variance));
Assert.AreEqual(2, model.Transitions.GetLength(0));
Assert.AreEqual(2, model.Transitions.GetLength(1));
var A = Matrix.Exp(model.Transitions);
Assert.AreEqual(0.090, A[0, 0], 1e-3);
Assert.AreEqual(0.909, A[0, 1], 1e-3);
Assert.AreEqual(0.875, A[1, 0], 1e-3);
Assert.AreEqual(0.125, A[1, 1], 1e-3);
Assert.IsFalse(A.HasNaN());
}
public void PredictTest()
{
int[][] sequences = new int[][]
{
new int[] { 0, 3, 1, 2 },
};
HiddenMarkovModel hmm = new HiddenMarkovModel(new Forward(4), 4);
var teacher = new BaumWelchLearning(hmm)
{
Tolerance = 1e-10, Iterations = 0
};
double ll = teacher.Run(sequences);
double l11, l12, l13, l14;
int p1 = hmm.Predict(new int[] { 0 }, 1, out l11)[0];
int p2 = hmm.Predict(new int[] { 0, 3 }, 1, out l12)[0];
int p3 = hmm.Predict(new int[] { 0, 3, 1 }, 1, out l13)[0];
int p4 = hmm.Predict(new int[] { 0, 3, 1, 2 }, 1, out l14)[0];
Assert.AreEqual(3, p1);
Assert.AreEqual(1, p2);
Assert.AreEqual(2, p3);
Assert.AreEqual(2, p4);
double l21 = hmm.Evaluate(new int[] { 0, 3 });
double l22 = hmm.Evaluate(new int[] { 0, 3, 1 });
double l23 = hmm.Evaluate(new int[] { 0, 3, 1, 2 });
double l24 = hmm.Evaluate(new int[] { 0, 3, 1, 2, 2 });
Assert.AreEqual(l11, l21, 1e-10);
Assert.AreEqual(l12, l22, 1e-10);
Assert.AreEqual(l13, l23, 1e-10);
Assert.AreEqual(l14, l24, 1e-10);
Assert.IsFalse(double.IsNaN(l11));
Assert.IsFalse(double.IsNaN(l12));
Assert.IsFalse(double.IsNaN(l13));
Assert.IsFalse(double.IsNaN(l14));
Assert.IsFalse(double.IsNaN(l21));
Assert.IsFalse(double.IsNaN(l22));
Assert.IsFalse(double.IsNaN(l23));
Assert.IsFalse(double.IsNaN(l24));
double ln1;
int[] pn = hmm.Predict(new int[] { 0 }, 4, out ln1);
Assert.AreEqual(4, pn.Length);
Assert.AreEqual(3, pn[0]);
Assert.AreEqual(1, pn[1]);
Assert.AreEqual(2, pn[2]);
Assert.AreEqual(2, pn[3]);
double ln2 = hmm.Evaluate(new int[] { 0, 3, 1, 2, 2 });
Assert.AreEqual(ln1, ln2, 1e-10);
}
/*
* this method passes all the possible directions
* that can create a horizontal line to the HMM library
* as observations. A and B are the state and
* observation probabilities for the model
* pi is the intial state of the model
* the function returns true if the input matches any
* of the observations used to train the model
*/
bool horizontalEvalution(int [] input)
{
if(input.Length != 1){
return false;
}
int[][] sequences = new int[][]
{
new int[]{ EAST },
new int[] { WEST }
};
double [,] A = new double[8,8]
{
{0, 0, 0, 0, 0, 0, 0, 0},
{0, 0, 0, 0, 0, 0, 0, 0},
{0, 0, 0, 0, 0, 0, 0, 0},
{0, 0, 0, 0, 0, 0, 0, 0},
{0, 0, 0, 0, 0, 0, 0, 0},
{0, 0, 0, 0, 0, 0, 0, 0},
{0, 0, 0, 0, 0, 0, 0, 0},
{0, 0, 0, 0, 0, 0, 0, 0}
};
double [,] B = new double[8,8]
{
{1, 0, 0, 0, 0, 0, 0, 0},
{0, 1, 0, 0, 0, 0, 0, 0},
{0, 0, 1, 0, 0, 0, 0, 0},
{0, 0, 0, 1, 0, 0, 0, 0},
{0, 0, 0, 0, 1, 0, 0, 0},
{0, 0, 0, 0, 0, 1, 0, 0},
{0, 0, 0, 0, 0, 0, 1, 0},
{0, 0, 0, 0, 0, 0, 0, 1}
};
double [] pi = new double [] {0, 0, 0.5, 0.5, 0, 0, 0, 0};
HiddenMarkovModel model = new HiddenMarkovModel(A, B, pi);
model.Learn(sequences, 0.0001);
if(model.Evaluate(input) >= 0.5){
return true;
}else{
return false;
}
}
static void runDiscreteDensityHiddenMarkovModelLearningExample()
{
int[][] observationSequences =
{
new[] { 0, 1, 2, 3 },
new[] { 0, 0, 0,1, 1, 2, 2, 3, 3 },
new[] { 0, 0, 1,2, 2, 2, 3, 3 },
new[] { 0, 1, 2,3, 3, 3, 3 },
};
{
// Create a hidden Markov model with arbitrary probabilities.
HiddenMarkovModel hmm = new HiddenMarkovModel(states: 4, symbols: 4);
// Create a Baum-Welch learning algorithm to teach it.
BaumWelchLearning trainer = new BaumWelchLearning(hmm);
// Call its Run method to start learning.
double averageLogLikelihood = trainer.Run(observationSequences);
Console.WriteLine("average log-likelihood for the observations = {0}", averageLogLikelihood);
// Check the probability of some sequences.
double logLik1 = hmm.Evaluate(new[] { 0, 1, 2, 3 }); // 0.013294354967987107.
Console.WriteLine("probability = {0}", Math.Exp(logLik1));
double logLik2 = hmm.Evaluate(new[] { 0, 0, 1, 2, 2, 3 }); // 0.002261813011419950.
Console.WriteLine("probability = {0}", Math.Exp(logLik2));
double logLik3 = hmm.Evaluate(new[] { 0, 0, 1, 2, 3, 3 }); // 0.002908045300397080.
Console.WriteLine("probability = {0}", Math.Exp(logLik3));
// Violate the form of the training set.
double logLik4 = hmm.Evaluate(new[] { 3, 2, 1, 0 }); // 0.000000000000000000.
Console.WriteLine("probability = {0}", Math.Exp(logLik4));
double logLik5 = hmm.Evaluate(new[] { 0, 0, 1, 3, 1, 1 }); // 0.000000000113151816.
Console.WriteLine("probability = {0}", Math.Exp(logLik5));
}
{
// Create a hidden Markov model with arbitrary probabilities.
var hmm = new HiddenMarkovModel <GeneralDiscreteDistribution>(states: 4, emissions: new GeneralDiscreteDistribution(symbols: 4));
// Create a Baum-Welch learning algorithm to teach it
// until the difference in the average log-likelihood changes only by as little as 0.0001
// and the number of iterations is less than 1000.
var trainer = new BaumWelchLearning <GeneralDiscreteDistribution>(hmm)
{
Tolerance = 0.0001,
Iterations = 1000,
};
// Call its Run method to start learning.
double averageLogLikelihood = trainer.Run(observationSequences);
Console.WriteLine("average log-likelihood for the observations = {0}", averageLogLikelihood);
// Check the probability of some sequences.
double logLik1 = hmm.Evaluate(new[] { 0, 1, 2, 3 }); // 0.013294354967987107.
Console.WriteLine("probability = {0}", Math.Exp(logLik1));
double logLik2 = hmm.Evaluate(new[] { 0, 0, 1, 2, 2, 3 }); // 0.002261813011419950.
Console.WriteLine("probability = {0}", Math.Exp(logLik2));
double logLik3 = hmm.Evaluate(new[] { 0, 0, 1, 2, 3, 3 }); // 0.002908045300397080.
Console.WriteLine("probability = {0}", Math.Exp(logLik3));
// Violate the form of the training set.
double logLik4 = hmm.Evaluate(new[] { 3, 2, 1, 0 }); // 0.000000000000000000.
Console.WriteLine("probability = {0}", Math.Exp(logLik4));
double logLik5 = hmm.Evaluate(new[] { 0, 0, 1, 3, 1, 1 }); // 0.000000000113151816.
Console.WriteLine("probability = {0}", Math.Exp(logLik5));
}
}
/// <summary>
/// Gets the probability mass function (pmf) for
/// this distribution evaluated at point <c>x</c>.
/// </summary>
///
/// <param name="x">A single point in the distribution range.</param>
///
/// <returns>
/// The probability of <c>x</c> occurring
/// in the current distribution.
/// </returns>
///
/// <remarks>
/// The Probability Mass Function (PMF) describes the
/// probability that a given value <c>x</c> will occur.
/// </remarks>
///
public override double ProbabilityMassFunction(int[] x)
{
return(Math.Exp(model.Evaluate(x)));
}
private static double testThresholdModel(int[][] inputs, int[] outputs, HiddenMarkovClassifier classifier, double likelihood)
{
HiddenMarkovModel threshold = classifier.Threshold;
Assert.AreEqual(6, threshold.States);
Assert.AreEqual(classifier.Models[0].Transitions[0, 0], threshold.Transitions[0, 0], 1e-10);
Assert.AreEqual(classifier.Models[0].Transitions[1, 1], threshold.Transitions[1, 1], 1e-10);
Assert.AreEqual(classifier.Models[0].Transitions[2, 2], threshold.Transitions[2, 2], 1e-10);
Assert.AreEqual(classifier.Models[1].Transitions[0, 0], threshold.Transitions[3, 3], 1e-10);
Assert.AreEqual(classifier.Models[1].Transitions[1, 1], threshold.Transitions[4, 4], 1e-10);
Assert.AreEqual(classifier.Models[1].Transitions[2, 2], threshold.Transitions[5, 5], 1e-10);
for (int i = 0; i < 3; i++)
{
for (int j = 3; j < 6; j++)
{
Assert.AreEqual(Double.NegativeInfinity, threshold.Transitions[i, j]);
}
}
for (int i = 3; i < 6; i++)
{
for (int j = 0; j < 3; j++)
{
Assert.AreEqual(Double.NegativeInfinity, threshold.Transitions[i, j]);
}
}
Assert.IsFalse(Matrix.HasNaN(threshold.LogTransitions));
classifier.Sensitivity = 0.5;
// Will assert the models have learned the sequences correctly.
for (int i = 0; i < inputs.Length; i++)
{
int expected = outputs[i];
int actual = classifier.Compute(inputs[i], out likelihood);
Assert.AreEqual(expected, actual);
}
int[] r0 = new int[] { 1, 1, 0, 0, 2 };
double logRejection;
int c = classifier.Compute(r0, out logRejection);
Assert.AreEqual(-1, c);
Assert.AreEqual(0.99996241769427985, logRejection, 1e-10);
logRejection = threshold.Evaluate(r0);
Assert.AreEqual(-5.5993214137039073, logRejection, 1e-10);
threshold.Decode(r0, out logRejection);
Assert.AreEqual(-9.31035541707617, logRejection, 1e-10);
foreach (var model in classifier.Models)
{
double[,] A = model.Transitions;
for (int i = 0; i < A.GetLength(0); i++)
{
double[] row = A.Exp().GetRow(i);
double sum = row.Sum();
Assert.AreEqual(1, sum, 1e-10);
}
}
{
double[,] A = classifier.Threshold.Transitions;
for (int i = 0; i < A.GetLength(0); i++)
{
double[] row = A.GetRow(i);
double sum = row.Exp().Sum();
Assert.AreEqual(1, sum, 1e-6);
}
}
return(likelihood);
}
public void LearnTest8()
{
// Create continuous sequences. In the sequence below, there
// seems to be two states, one for values equal to 1 and another
// for values equal to 2.
double[][] sequences = new double[][]
{
new double[] { 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2 }
};
// Specify a initial normal distribution for the samples.
var density = new NormalDistribution();
// Creates a continuous hidden Markov Model with two states organized in a forward
// topology and an underlying univariate Normal distribution as probability density.
var model = new HiddenMarkovModel <NormalDistribution>(new Forward(2), density);
// Configure the learning algorithms to train the sequence classifier until the
// difference in the average log-likelihood changes only by as little as 0.0001
var teacher = new ViterbiLearning <NormalDistribution>(model)
{
Tolerance = 0.0001,
Iterations = 0,
// However, we will need to specify a regularization constant as the
// variance of each state will likely be zero (all values are equal)
FittingOptions = new NormalOptions()
{
Regularization = double.Epsilon
}
};
// Fit the model
double likelihood = teacher.Run(sequences);
// See the probability of the sequences learned
double a1 = model.Evaluate(new double[] { 1, 2, 1, 2, 1, 2, 1, 2, 1 }); // exp(a1) = infinity
double a2 = model.Evaluate(new double[] { 1, 2, 1, 2, 1 }); // exp(a2) = infinity
// See the probability of an unrelated sequence
double a3 = model.Evaluate(new double[] { 1, 2, 3, 2, 1, 2, 1 }); // exp(a3) = 0
double a4 = model.Evaluate(new double[] { 1.1, 2.2, 1.3, 3.2, 4.2, 1.0 }); // exp(a4) = 0
Assert.AreEqual(double.PositiveInfinity, System.Math.Exp(likelihood));
Assert.AreEqual(3340.6878090199571, a1);
Assert.AreEqual(1855.791720669667, a2);
Assert.AreEqual(0.0, Math.Exp(a3));
Assert.AreEqual(0.0, Math.Exp(a4));
Assert.AreEqual(2, model.Emissions.Length);
var state1 = (model.Emissions[0] as NormalDistribution);
var state2 = (model.Emissions[1] as NormalDistribution);
Assert.AreEqual(1.0, state1.Mean, 1e-10);
Assert.AreEqual(2.0, state2.Mean, 1e-10);
Assert.IsFalse(Double.IsNaN(state1.Mean));
Assert.IsFalse(Double.IsNaN(state2.Mean));
Assert.IsTrue(state1.Variance < 1e-30);
Assert.IsTrue(state2.Variance < 1e-30);
var A = Matrix.Exp(model.Transitions);
Assert.AreEqual(2, A.GetLength(0));
Assert.AreEqual(2, A.GetLength(1));
Assert.AreEqual(0.0714285714285714, A[0, 0], 1e-6);
Assert.AreEqual(0.9285714285714286, A[0, 1], 1e-6);
Assert.AreEqual(0.9230769230769231, A[1, 0], 1e-6);
Assert.AreEqual(0.0769230769230769, A[1, 1], 1e-6);
}
public void LearnTest2()
{
// Declare some testing data
int[][] inputs = new int[][]
{
new int[] { 0, 0, 1, 2 }, // Class 0
new int[] { 0, 1, 1, 2 }, // Class 0
new int[] { 0, 0, 0, 1, 2 }, // Class 0
new int[] { 0, 1, 2, 2, 2 }, // Class 0
new int[] { 2, 2, 1, 0 }, // Class 1
new int[] { 2, 2, 2, 1, 0 }, // Class 1
new int[] { 2, 2, 2, 1, 0 }, // Class 1
new int[] { 2, 2, 2, 2, 1 }, // Class 1
};
int[] outputs = new int[]
{
0, 0, 0, 0, // First four sequences are of class 0
1, 1, 1, 1, // Last four sequences are of class 1
};
// We are trying to predict two different classes
int classes = 2;
// Each sequence may have up to 3 symbols (0,1,2)
int symbols = 3;
// Nested models will have 3 states each
int[] states = new int[] { 3, 3 };
// Creates a new Hidden Markov Model Classifier with the given parameters
HiddenMarkovClassifier classifier = new HiddenMarkovClassifier(classes, states, symbols);
// Create a new learning algorithm to train the sequence classifier
var teacher = new HiddenMarkovClassifierLearning(classifier,
// Train each model until the log-likelihood changes less than 0.001
modelIndex => new BaumWelchLearning(classifier.Models[modelIndex])
{
Tolerance = 0.001,
Iterations = 0
}
);
// Enable support for sequence rejection
teacher.Rejection = true;
// Train the sequence classifier using the algorithm
double likelihood = teacher.Run(inputs, outputs);
// Will assert the models have learned the sequences correctly.
for (int i = 0; i < inputs.Length; i++)
{
int expected = outputs[i];
int actual = classifier.Compute(inputs[i], out likelihood);
Assert.AreEqual(expected, actual);
}
HiddenMarkovModel threshold = classifier.Threshold;
Assert.AreEqual(6, threshold.States);
Assert.AreEqual(classifier.Models[0].Transitions[0, 0], threshold.Transitions[0, 0], 1e-10);
Assert.AreEqual(classifier.Models[0].Transitions[1, 1], threshold.Transitions[1, 1], 1e-10);
Assert.AreEqual(classifier.Models[0].Transitions[2, 2], threshold.Transitions[2, 2], 1e-10);
Assert.AreEqual(classifier.Models[1].Transitions[0, 0], threshold.Transitions[3, 3], 1e-10);
Assert.AreEqual(classifier.Models[1].Transitions[1, 1], threshold.Transitions[4, 4], 1e-10);
Assert.AreEqual(classifier.Models[1].Transitions[2, 2], threshold.Transitions[5, 5], 1e-10);
Assert.IsFalse(Matrix.HasNaN(threshold.Transitions));
int[] r0 = new int[] { 1, 1, 0, 0, 2 };
double logRejection;
int c = classifier.Compute(r0, out logRejection);
Assert.AreEqual(-1, c);
Assert.AreEqual(0.99569011079012049, logRejection);
Assert.IsFalse(double.IsNaN(logRejection));
logRejection = threshold.Evaluate(r0);
Assert.AreEqual(-6.7949285513628528, logRejection, 1e-10);
Assert.IsFalse(double.IsNaN(logRejection));
threshold.Decode(r0, out logRejection);
Assert.AreEqual(-8.902077561009957, logRejection, 1e-10);
Assert.IsFalse(double.IsNaN(logRejection));
}
public void LearnTest6()
{
// We will try to create a Hidden Markov Model which
// can detect if a given sequence starts with a zero
// and has any number of ones after that.
int[][] sequences = new int[][]
{
new int[] { 0, 1, 1, 1, 1, 0, 1, 1, 1, 1 },
new int[] { 0, 1, 1, 1, 0, 1, 1, 1, 1, 1 },
new int[] { 0, 1, 1, 1, 1, 1, 1, 1, 1, 1 },
new int[] { 0, 1, 1, 1, 1, 1 },
new int[] { 0, 1, 1, 1, 1, 1, 1 },
new int[] { 0, 1, 1, 1, 1, 1, 1, 1, 1, 1 },
new int[] { 0, 1, 1, 1, 1, 1, 1, 1, 1, 1 },
};
// Creates a new Hidden Markov Model with 3 states for
// an output alphabet of two characters (zero and one)
HiddenMarkovModel hmm = new HiddenMarkovModel(3, 2);
// Try to fit the model to the data until the difference in
// the average log-likelihood changes only by as little as 0.0001
var teacher = new BaumWelchLearning(hmm)
{
Tolerance = 0.0001, Iterations = 0
};
double ll = teacher.Run(sequences);
// Calculate the probability that the given
// sequences originated from the model
double l1 = hmm.Evaluate(new int[] { 0, 1 }); // 0.999
double l2 = hmm.Evaluate(new int[] { 0, 1, 1, 1 }); // 0.916
// Sequences which do not start with zero have much lesser probability.
double l3 = hmm.Evaluate(new int[] { 1, 1 }); // 0.000
double l4 = hmm.Evaluate(new int[] { 1, 0, 0, 0 }); // 0.000
// Sequences which contains few errors have higher probability
// than the ones which do not start with zero. This shows some
// of the temporal elasticity and error tolerance of the HMMs.
double l5 = hmm.Evaluate(new int[] { 0, 1, 0, 1, 1, 1, 1, 1, 1 }); // 0.034
double l6 = hmm.Evaluate(new int[] { 0, 1, 1, 1, 1, 1, 1, 0, 1 }); // 0.034
double pl = System.Math.Exp(ll);
double p1 = System.Math.Exp(l1);
double p2 = System.Math.Exp(l2);
double p3 = System.Math.Exp(l3);
double p4 = System.Math.Exp(l4);
double p5 = System.Math.Exp(l5);
double p6 = System.Math.Exp(l6);
Assert.AreEqual(0.95151126952069587, pl, 1e-6);
Assert.AreEqual(0.99996863060890995, p1, 1e-6);
Assert.AreEqual(0.91667240076011669, p2, 1e-6);
Assert.AreEqual(0.00002335133758386, p3, 1e-6);
Assert.AreEqual(0.00000000000000012, p4, 1e-6);
Assert.AreEqual(0.034237231443226858, p5, 1e-6);
Assert.AreEqual(0.034237195920532461, p6, 1e-6);
Assert.IsTrue(l1 > l3 && l1 > l4);
Assert.IsTrue(l2 > l3 && l2 > l4);
}
/*
* this method passes all the possible directions
* that can create a square to the HMM library
* as observations. A and B are the state and
* observation probabilities for the model
* pi is the intial state of the model
* the function returns true if the input matches any
* of the observations used to train the model
*/
bool squareEvalution(int [] input)
{
if(input.Length != 4){
return false;
}
int[][] sequences = new int[][]
{
new int[]{ NORTH, EAST, SOUTH, WEST},
new int[] { EAST, SOUTH, WEST, NORTH},
new int[] { SOUTH, WEST, NORTH, EAST},
new int[] { WEST, NORTH, EAST, SOUTH}
};
double [,] A = new double[8,8]
{
{0, 0, 1, 0, 0, 0, 0, 0},
{0, 0, 0, 1, 0, 0, 0, 0},
{0, 1, 0, 0, 0, 0, 0, 0},
{1, 0, 0, 0, 0, 0, 0, 0},
{0, 0, 0, 0, 0, 0, 0, 0},
{0, 0, 0, 0, 0, 0, 0, 0},
{0, 0, 0, 0, 0, 0, 0, 0},
{0, 0, 0, 0, 0, 0, 0, 0}
};
double [,] B = new double[8,8]
{
{1, 0, 0, 0, 0, 0, 0, 0},
{0, 1, 0, 0, 0, 0, 0, 0},
{0, 0, 1, 0, 0, 0, 0, 0},
{0, 0, 0, 1, 0, 0, 0, 0},
{0, 0, 0, 0, 1, 0, 0, 0},
{0, 0, 0, 0, 0, 1, 0, 0},
{0, 0, 0, 0, 0, 0, 1, 0},
{0, 0, 0, 0, 0, 0, 0, 1}
};
double [] pi = new double [] {0.25,0.25,0.25,0.25, 0, 0, 0, 0};
HiddenMarkovModel model = new HiddenMarkovModel(A, B, pi);
model.Learn(sequences, 0.0001);
if(model.Evaluate(input) >= 0.25){
return true;
}else{
return false;
}
}
public void PosteriorTest1()
{
// Example from http://ai.stanford.edu/~serafim/CS262_2007/notes/lecture5.pdf
double[,] A =
{
{ 0.95, 0.05 }, // fair dice state
{ 0.05, 0.95 }, // loaded dice state
};
double[,] B =
{
{ 1 / 6.0, 1 / 6.0, 1 / 6.0, 1 / 6.0, 1 / 6.0, 1 / 6.0 }, // fair dice probabilities
{ 1 / 10.0, 1 / 10.0, 1 / 10.0, 1 / 10.0, 1 / 10.0, 1 / 2.0 }, // loaded probabilities
};
double[] pi = { 0.5, 0.5 };
HiddenMarkovModel hmm = new HiddenMarkovModel(A, B, pi);
int[] x = new int[] { 1, 2, 1, 5, 6, 2, 1, 5, 2, 4 }.Subtract(1);
int[] y = new int[] { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 };
double py = Math.Exp(hmm.Evaluate(x, y));
Assert.AreEqual(0.00000000521158647211, py, 1e-16);
x = new int[] { 1, 2, 1, 5, 6, 2, 1, 5, 2, 4 }.Subtract(1);
y = new int[] { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 };
py = Math.Exp(hmm.Evaluate(x, y));
Assert.AreEqual(0.00000000015756235243, py, 1e-16);
Accord.Math.Tools.SetupGenerator(0);
var u = new UniformDiscreteDistribution(0, 6);
int[] sequence = u.Generate(1000);
int start = 120;
int end = 150;
for (int i = start; i < end; i += 2)
{
sequence[i] = 5;
}
// Predict the next observation in sequence
int[] path;
double[][] p = hmm.Posterior(sequence, out path);
for (int i = 0; i < path.Length; i++)
{
Assert.AreEqual(1, p[i][0] + p[i][1], 1e-10);
}
int loaded = 0;
for (int i = 0; i < start; i++)
{
if (p[i][1] > 0.95)
{
loaded++;
}
}
Assert.AreEqual(0, loaded);
loaded = 0;
for (int i = start; i < end; i++)
{
if (p[i][1] > 0.95)
{
loaded++;
}
}
Assert.IsTrue(loaded > 15);
loaded = 0;
for (int i = end; i < p.Length; i++)
{
if (p[i][1] > 0.95)
{
loaded++;
}
}
Assert.AreEqual(0, loaded);
}
public double Run(int[][] observations_db, int[][] path_db)
{
int K = observations_db.Length;
DiagnosticsHelper.Assert(path_db.Length == K);
int N = mModel.StateCount;
int M = mModel.SymbolCount;
int[] initial = new int[N];
int[,] transition_matrix = new int[N, N];
int[,] emission_matrix = new int[N, M];
for (int k = 0; k < K; ++k)
{
initial[path_db[k][0]]++;
}
int T = 0;
for (int k = 0; k < K; ++k)
{
int[] path = path_db[k];
int[] observations = observations_db[k];
T = path.Length;
for (int t = 0; t < T - 1; ++t)
{
transition_matrix[path[t], path[t + 1]]++;
}
for (int t = 0; t < T; ++t)
{
emission_matrix[path[t], observations[t]]++;
}
}
if (mUseLaplaceRule)
{
for (int i = 0; i < N; ++i)
{
initial[i]++;
for (int j = 0; j < N; ++j)
{
transition_matrix[i, j]++;
}
for (int j = 0; j < M; ++j)
{
emission_matrix[i, j]++;
}
}
}
int initial_sum = initial.Sum();
int[] transition_sum_vec = Sum(transition_matrix, 1);
int[] emission_sum_vec = Sum(emission_matrix, 1);
for (int i = 0; i < N; ++i)
{
mModel.LogProbabilityVector[i] = System.Math.Log(initial[i] / (double)initial_sum);
}
for (int i = 0; i < N; ++i)
{
double transition_sum = (double)transition_sum_vec[i];
for (int j = 0; j < N; ++j)
{
mModel.LogTransitionMatrix[i, j] = System.Math.Log(transition_matrix[i, j] / transition_sum);
}
}
for (int i = 0; i < N; ++i)
{
double emission_sum = (double)emission_sum_vec[i];
for (int m = 0; m < M; ++m)
{
mModel.LogEmissionMatrix[i, m] = System.Math.Log(emission_matrix[i, m] / emission_sum);
}
}
double logLikelihood = double.NegativeInfinity;
for (int i = 0; i < observations_db.Length; i++)
{
logLikelihood = LogHelper.LogSum(logLikelihood, mModel.Evaluate(observations_db[i]));
}
return(logLikelihood);
}
