Longest Common Subsequence

Question

Consider 2 sequences X[1..m] and Y[1..n]. The memoization algorithm would compute the LCS in time O(m*n). Is there any better algorithm to find out LCS wrt time? I guess memoization done diagonally can give us O(min(m,n)) time complexity.

Oestrone

Perhaps you mean Longest Common Substring? en.wikipedia.org/wiki/Longest_common_substring_problem – Elfish

Nope. en.wikipedia.org/wiki/Longest_common_subsequence_problem – Cutch

Nope its subsequence allright. – Oestrone

Answer 1

Gene Myers in 1986 came up with a very nice algorithm for this, described here: An O(ND) Difference Algorithm and Its Variations.

This algorithm takes time proportional to the edit distance between sequences, so it is much faster when the difference is small. It works by looping over all possible edit distances, starting from 0, until it finds a distance for which an edit script (in some ways the dual of an LCS) can be constructed. This means that you can "bail out early" if the difference grows above some threshold, which is sometimes convenient.

I believe this algorithm is still used in many diff implementations.

Radioisotope

Answer 2

If you know a priori an upper bound on the maximum size k you care about, you can force the LCS algorithm to exit early by adding an extra check in the inner loop. This means then when k << min(m,n) you can get small running times in spite of the fact you are doing LCS.

Concubinage

Answer 3

yes we could create a better algorithm than Order O(m*n)--- i.e O(min(m,n)). to find a length..... just compare the diagonal elements.and whenever the increment is done suppose it occured in c[2,2] then increment all the value from c[2,2++] and c[2++,2] by 1.. and proceed till c[m,m]..(suppose m

Limiter