Speeding up dynamic programming code

3 views (last 30 days)
Paolo Binetti
Paolo Binetti on 13 Jun 2017
Is there a way to speed up this piece of code implementing a dynamic programming algorithm?
% sample input
v = repmat('CGACAGCTACTCACTCAGTAGCCGCAGCGAGTGTCTTGACAATTCGGAGGGG', 1, 20);
w = repmat('TATACACATTCATGAATGAAAATTGACCTCCTACAGTTGTAGTGGTAGT', 1, 20);
n = numel(v);
m = numel(w);
s = zeros(n+1, m+1);
back = zeros(n, m);
for i = 1:n
temp = s(i, 1:end-1)+(v(i)==w);
for j = 1:m
[s(i+1, j+1), back(i, j)] = max([s(i, j+1) s(i+1, j) temp(j)]);
end
end
(Memory is also an issue when scaling up, due to the size of arrays "s" and "back", but I have found a way to reduce "s" to just two lines, and "back" could be expressed as uint8)

Answers (0)

Categories

Find more on Simulink in Help Center and File Exchange

Community Treasure Hunt

Find the treasures in MATLAB Central and discover how the community can help you!

Start Hunting!