Viterbi算法

clc;
clear all;
close all;

Start_Pi = [-1,-1];
State_k = ['H','L'];
% 转移矩阵
Transition_matrix = [-1,-1.322;-1.322,-0.737];
% 0 H L
% H -1 -1
% L -1.322,-0.373
% 序列中包含字母ACTG
sequence = ['A','C','G','T'];
Emission_matrix = [-2.322,-1.737,-1.737,-2.322;
-1.737,-2.322,-2.322,-1.737];
Observation_sequence = ['G','G','C','A','C','T','G','A','A'];
k = length(State_k);
l = length(Observation_sequence);
Result_matrix = zeros(k + 1,l + 1);
Result_matrix(1,2:l+1) = Observation_sequence;
Result_matrix(2:k+1,1) = State_k ;
%% Viterbi algorithm(这里是用权值代替概率计算的)
Result_matrix(2,2) = Start_Pi(1) + Emission_matrix(1,find(sequence ...
== Observation_sequence(1),1));
Result_matrix(3,2) = Start_Pi(2) + Emission_matrix(2,find(sequence ...
== Observation_sequence(1),1));
for i = 3 : l + 1
for j = 2: k+1
if j ~= k + 1
Result_matrix(j,i) = Emission_matrix(j - 1,find(sequence == Observation_sequence(i - 1),1)) +...
max(Result_matrix(j,i - 1) + Transition_matrix(j - 1,1),Result_matrix(j + 1,i - 1) + Transition_matrix(j,1) );
else
Result_matrix(j,i) = Emission_matrix(j - 1,find(sequence == Observation_sequence(i - 1),1)) +...
max(Result_matrix(j -1,i - 1) + Transition_matrix(j - 2,2),Result_matrix(j ,i - 1) + Transition_matrix(j - 1,2) );
end
end
end
%% back tracing
Result = max(Result_matrix(2:k+1,l+1));
[row,~ ]= find(Result_matrix == Result);
State_sequence = [];
State_sequence= strcat(State_k(row-1));
for i = l : -1: 3
if row == k+ 1
if Result == Result_matrix(row,i ) + Transition_matrix(row - 1,2) +...
Emission_matrix(row - 1,find(sequence == Observation_sequence(i),1))
State_sequence = strcat(State_k(2),State_sequence);
Result = Result_matrix(row,i );
else
State_sequence =strcat(State_k(1),State_sequence);
row = row -1;
Result = Result_matrix(row,i );
end
elseif row == 2
if Result == Result_matrix(row,i ) + Transition_matrix(row - 1,1) + ...
Emission_matrix(row - 1,find(sequence == Observation_sequence(i),1));
State_sequence=strcat(State_k(1),State_sequence);
Result = Result_matrix(row,i );
else
State_sequence=strcat(State_k(2),State_sequence);
row = row + 1;
Result = Result_matrix(row,i );
end
else
break;% 因为例子只有两个状态，其他就没有写
end
end
%% 输出序列头部处理
tem = max(Result_matrix(2:3,2));
[r,~] = find(Result_matrix == tem);
State_sequence= strcat(State_k(r-1),State_sequence);
disp(State_sequence)