/// <summary>
/// Executes Viterbi in a loop , every loop begins with new updated parameters
/// </summary>
public List <ViterbiResult> ExecuteViterbiAndTrain(int executionCount)
{
var resultsCollection = new List <ViterbiResult>();
Stopwatch timer = new Stopwatch();
timer.Restart();
for (int i = 1; i <= executionCount; i++)
{
ViterbiResult result = FindViterbiProbabilityScoreAndPath();
resultsCollection.Add(result);
this.parameters.UpdateParameters(result);
}
timer.Stop();
Console.WriteLine("Timetaken: {0}", timer.ElapsedMilliseconds);
return(resultsCollection);
}
/// <summary> /// Updates parameters given the viterbi result. /// </summary> public abstract void UpdateParameters(ViterbiResult result);
/// <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);
}
