/// <summary>
/// Executes Viterbi on give input as per the defined parameters, scores and returns result which includes
/// a)A state representation b)Viterbi log probability c)And Subsequences in positive model.
/// </summary>
public ViterbiResult FindViterbiProbabilityScoreAndPath()
{
for (int columnIndex = 1; columnIndex <= viterbiProbabilityMatrix.GetUpperBound(1); columnIndex++)
{
for (int rowIndex = 0; rowIndex <= viterbiProbabilityMatrix.GetUpperBound(0); rowIndex++)
{
var element = new ViterbiMatrixElement
{
ContributingPredecessor = null,
StateIdentifier = this.parameters.StateIndices[rowIndex],
EmissionValue = this.input[columnIndex],
EmissionValueIndex = columnIndex
};
double maxProbability = double.MinValue;
ViterbiMatrixElement contributingPredecessor = null;
// calculate emission probability
for (int innerRowIndex = 0; innerRowIndex <= viterbiProbabilityMatrix.GetUpperBound(0); innerRowIndex++)
{
double probability;
probability = viterbiProbabilityMatrix[innerRowIndex, columnIndex - 1].MaxLogProbability +
this.parameters.GetStateTransitionProbabilty(
viterbiProbabilityMatrix[innerRowIndex, columnIndex - 1].StateIdentifier,
this.parameters.StateIndices[rowIndex]);
if (probability > maxProbability)
{
maxProbability = probability;
contributingPredecessor = viterbiProbabilityMatrix[innerRowIndex, columnIndex - 1];
}
}
element.MaxLogProbability = this.parameters.GetEmissionProbability(
value: this.input[columnIndex], state: this.parameters.StateIndices[rowIndex]) + maxProbability;
// set the contributing predecessor so that we dont have to reacalculate in traceback.
element.ContributingPredecessor = contributingPredecessor;
viterbiProbabilityMatrix[rowIndex, columnIndex] = element;
}
}
// Find the maximum probability
ViterbiMatrixElement traceBackProbabilityElement = null;
var traceBackProbability = Double.MinValue;
for (int rowIndex = viterbiProbabilityMatrix.GetUpperBound(0); rowIndex >= 0; rowIndex--)
{
if (viterbiProbabilityMatrix[rowIndex, viterbiProbabilityMatrix.GetUpperBound(1)].MaxLogProbability
> traceBackProbability)
{
traceBackProbability = viterbiProbabilityMatrix[rowIndex, viterbiProbabilityMatrix.GetUpperBound(1)]
.MaxLogProbability;
traceBackProbabilityElement = viterbiProbabilityMatrix[rowIndex, viterbiProbabilityMatrix.GetUpperBound(1)];
}
}
// Viterbi Traceback.
return(ViterbiTraceback(traceBackProbabilityElement, traceBackProbability));
}
/// <summary>
/// First column is easy to calculate and can be seeded from Begin state and first input.
/// </summary>
void IntializeMatrix()
{
for (int rowIndex = 0; rowIndex <= viterbiProbabilityMatrix.GetUpperBound(0); rowIndex++)
{
var element = new ViterbiMatrixElement
{
ContributingPredecessor = null,
StateIdentifier = this.parameters.StateIndices[rowIndex],
MaxLogProbability =
this.parameters.GetEmissionProbability(
value: this.input[0], state: this.parameters.StateIndices[rowIndex]) +
this.parameters.GetStateTransitionProbabilty('B', this.parameters.StateIndices[rowIndex]),
EmissionValue = this.input[0],
EmissionValueIndex = 0
};
viterbiProbabilityMatrix[rowIndex, 0] = element;
}
}
/// <summary>
/// Takes Viterbi matrix element corresponding to maximum probability and maximum probability and computes
/// a)StateRepresentation( FFFLLLFFFL as in dice roll example )
/// b)All the sub sequences an starting indexes ending at all the states in the model.
/// c)Probability score.
/// </summary>
ViterbiResult ViterbiTraceback(ViterbiMatrixElement traceBackProbabilityElement, double traceBackProbability)
{
var stateSequences = new Dictionary <int, List <ViterbiStateSequence> >();
var statePath = new StringBuilder();
var subSequence = new StringBuilder[this.parameters.StateIndices.Count];
var startIndex = new int[this.parameters.StateIndices.Count];
// Loop till we reach end of traceback list.
while (traceBackProbabilityElement != null)
{
// Add to state identifiers , we will reverse it at the end.
statePath.Append(traceBackProbabilityElement.StateIdentifier);
foreach (KeyValuePair <int, char> item in this.parameters.StateIndices)
{
if (!stateSequences.ContainsKey(item.Key))
{
stateSequences[item.Key] = new List <ViterbiStateSequence>();
subSequence[item.Key] = new StringBuilder();
}
if (traceBackProbabilityElement.StateIdentifier == item.Value)
{
// Start constructing subsequences at a given state. Again , we will reverse it at the end to align with input.
// Genomic indexes are 1 based. Increment the zero based index to reflect this convention.
startIndex[item.Key] = traceBackProbabilityElement.EmissionValueIndex + 1;;
subSequence[item.Key].Append(traceBackProbabilityElement.EmissionValue);
}
else
{
// Add to subsequence list per state once we are at the end of subsequence ( when state corresponding to matrix element is different )
if (subSequence[item.Key].Length > 0)
{
stateSequences[item.Key].Add(
new ViterbiStateSequence
{
Index = startIndex[item.Key],
StateSequence = new string(subSequence[item.Key].ToString().ToCharArray().Reverse().ToArray())
});
//Reset the index and sequence variable
startIndex[item.Key] = 0;
subSequence[item.Key].Clear();
}
}
// If we are going to reach end of traceback then add the current calculated subsequence.
if (traceBackProbabilityElement.ContributingPredecessor == null &&
subSequence[item.Key].Length > 0)
{
stateSequences[item.Key].Add(
new ViterbiStateSequence
{
Index = startIndex[item.Key],
StateSequence = new string(subSequence[item.Key].ToString().ToCharArray().Reverse().ToArray())
});
}
}
traceBackProbabilityElement = traceBackProbabilityElement.ContributingPredecessor;
}
// Construct the result.
var result = new ViterbiResult()
{
ProbabilityScore = traceBackProbability,
StateTransitionRepresentaton = new string(statePath.ToString().ToCharArray().Reverse().ToArray()),
ParametersUsed = this.parameters.Clone()
};
// Add all the state subsequences.
result.StateSequences = stateSequences;
return(result);
}