public ForwardBackward(List<HMM> HmmList, List<InputLine> Sequence)
{
m_HmmList = HmmList;
m_Sequence = Sequence;
m_WorkingStates = new List<HMM>();
m_WorkingStatesQty = 0;
foreach (HMM Hmm in HmmList)
if (!(Hmm.IsFirst || Hmm.IsFinal))
{
m_WorkingStatesQty++;
m_WorkingStates.Add(Hmm);
}
m_BeginingState = HmmList.Find(x => x.IsFirst == true);
m_EndingState = HmmList.Find(x => x.IsFinal == true);
m_FullSequenceCount = Sequence.Count + 2; // + 2 = for ending and beg
BackwardValues = new double[m_FullSequenceCount,m_WorkingStatesQty];
ForwardValues = new double[m_FullSequenceCount,m_WorkingStatesQty];
for(int I = 0; I < m_FullSequenceCount; I++)
for(int J = 0; J < m_WorkingStatesQty; J++)
{
BackwardValues[I,J] = 0;
ForwardValues[I,J] = 0;
}
// backward L + 1;
for (int I = 0; I < m_WorkingStatesQty; I++)
BackwardValues[m_FullSequenceCount - 1, I] = 1;
// Forward 0
for (int I = 0; I < m_WorkingStatesQty; I++)
ForwardValues[0, I] = 1;
}
public Viterbi(List<HMM> HmmList, List<InputLine> Sequence)
{
m_WorkingStates = new List<HMM>();
m_Sequence = Sequence;
foreach (HMM Hmm in HmmList)
if (!(Hmm.IsFirst || Hmm.IsFinal))
m_WorkingStates.Add(Hmm);
m_BeginingState = HmmList.Find(x => x.IsFirst == true);
m_EndingState = HmmList.Find(x => x.IsFinal == true);
//+2 for fist and last state
Results = new ViterbiResult[Sequence.Count + 2, m_WorkingStates.Count];
}
public ViterbiResult GetResult(int Position, HMM State)
{
int StateIndex = -1;
for (int I = 0; I < m_WorkingStates.Count; I++)
if (m_WorkingStates [I].Name == State.Name)
{
StateIndex = I;
break;
}
//cheat
if (StateIndex == -1)
StateIndex = 0;
return Results[Position, StateIndex];
}
private void MakeStep(int Pos, HMM State, int ArrayStateIndex)
{
double PrevMaxStateValue = 0;
string PrevStateName = "";
for (int I = 0; I < m_WorkingStates.Count; I++)
{
HMM PrevState = (Pos == 1) ? m_BeginingState : m_WorkingStates[I];
double PrevStateValue = Results[Pos - 1, I].Possibility *
PrevState.GetTransitionStrength(State.Name);
if (PrevStateValue > PrevMaxStateValue)
{
PrevMaxStateValue = PrevStateValue;
PrevStateName = PrevState.Name;
}
}
double Emission =
(Pos == m_Sequence.Count + 1) ?
1 : State.GetEmmisionStrength(m_Sequence[Pos - 1].Sequence);
Results[Pos, ArrayStateIndex] = new ViterbiResult(
Pos, State.Name, PrevStateName, Emission * PrevMaxStateValue);
}
public static void ReadFile(string FileName)
{
HmmList = new List<HMM>();
Sequence = new List<InputLine>();
using (StreamReader SR = new StreamReader(FileName))
{
string FileLine;
LastState = null;
Regex StatesReg = new Regex(StatesRegex);
Regex StatesEm = new Regex(StatesEmissions);
Regex SeqReg = new Regex(SequenceRegex);
while((FileLine = SR.ReadLine()) != null)
{
Match M = StatesReg.Match(FileLine);
if (M.Success)
AddModifyState(M);
M = StatesEm.Match(FileLine);
if (M.Success)
AddEmission(M, LastState);
M = SeqReg.Match(FileLine);
if (M.Success)
AddToSequence(FileLine);
}
foreach(HMM H in HmmList)
{
Console.WriteLine(H.Name);
foreach(HmmLink L in H.Links)
Console.WriteLine("\t" + L.Hmm.Name + " = " + L.Strength.ToString());
foreach(Emission E in H.Emissions)
Console.WriteLine("" +
"Emmision for " + E.EmissionSequence +
" is " + E.EmissionStrength.ToString());
}
foreach(InputLine I in Sequence)
Console.WriteLine(I.SequenceNo.ToString() + " " +
I.StateName + " " +
I.Sequence);
}
}
private static HMM FindOrCreate(List<HMM> HList, string Name)
{
HMM Hmm = HList.Find (x => x.Name == Name);
if (Hmm == null)
{
Hmm = new HMM (Name);
HList.Add (Hmm);
}
return Hmm;
}
private static void AddModifyState(Match M)
{
//State St1 Transitions: B = 0.000 St1 = 0.960 St2 = 0.039 E = 0.001
LastState = FindOrCreate(HmmList, M.Groups [1].Value);
foreach (Capture C in M.Groups[3].Captures)
AddLink(LastState, C.Value);
}
private static void AddLink(HMM Hmm, string Link)
{
//State = str
string[] Expr = Link.Split(' ');
HmmLink NewLink = new HmmLink();
NewLink.Hmm = FindOrCreate(HmmList, Expr[0]);
NewLink.Strength = double.Parse(Expr[2]);
if (Hmm.Links.Exists(x => x.Hmm.Name == NewLink.Hmm.Name))
throw (new Exception("Redefining value found for: " + Hmm.Name +
"at " + NewLink.Hmm.Name));
Hmm.Links.Add(NewLink);
}
private static void AddEmission(Match M, HMM StateToEdit)
{
// Emissions a = 0.139 b = 0.639 c = 0.222
foreach(Capture C in M.Groups[2].Captures)
{
string[] Expr = C.Value.Split(' ');
StateToEdit.Emissions.Add(
new Emission(Expr[0], double.Parse(Expr[2])));
}
}
private double CalcForwardState(HMM Hmm, int SeqPos)
{
double Result = 0;
int State = 0;
double[] LogSums = new double[m_WorkingStatesQty];
double EmmisionStr = 1; // for endingState
if (SeqPos < m_Sequence.Count)
EmmisionStr = Hmm.GetEmmisionStrength(m_Sequence[SeqPos].Sequence);
foreach(HMM HmmKm1 in m_WorkingStates)
{
// explog trick
LogSums[State] = Math.Log(EmmisionStr) +
Math.Log(HmmKm1.GetTransitionStrength(Hmm.Name)) +
Math.Log(ForwardValues[SeqPos,State]); // seqpos - 1 + 1 to shift for begining state
State++;
}
double MaxVal = LogSums[0];
for(int I = 1; I < m_WorkingStatesQty; I++)
MaxVal = Math.Max(MaxVal,LogSums[I]);
for(int I = 0; I < m_WorkingStatesQty; I++)
Result += Math.Exp(MaxVal + Math.Log(Math.Exp(LogSums[I] - MaxVal)));
return Result;
}
private double CalcBackwardState(HMM Hmm, int SeqPos)
{
double Result = 0;
int State = 0;
double[] LogSums = new double[m_WorkingStatesQty];
foreach (HMM HmmKp1 in m_WorkingStates)
{
LogSums[State] = Math.Log(Hmm.GetTransitionStrength(HmmKp1.Name)) +
Math.Log(HmmKp1.GetEmmisionStrength(m_Sequence[SeqPos + 1].Sequence)) +
Math.Log(BackwardValues[SeqPos + 2,State]); // + 2 to shift from ending result
State++;
}
double MaxVal = LogSums[0];
for (int I = 1; I < m_WorkingStatesQty; I++)
MaxVal = Math.Max(MaxVal,LogSums[I]);
for(int I = 0; I < m_WorkingStatesQty; I++)
Result += Math.Exp(MaxVal + Math.Log(Math.Exp(LogSums[I] - MaxVal)));
return Result;
}