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Dynamic Programming Longest Common Subsequence

The longest common subsequence (LCS) problem finds the longest subsequence common to two given sequences. It has applications in biology. The LCS problem exhibits optimal substructure and can be solved using dynamic programming by building a table where each entry represents the LCS length of the prefixes. The algorithm runs in O(mn) time where m and n are the lengths of the input sequences.

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138 views

Dynamic Programming Longest Common Subsequence

The longest common subsequence (LCS) problem finds the longest subsequence common to two given sequences. It has applications in biology. The LCS problem exhibits optimal substructure and can be solved using dynamic programming by building a table where each entry represents the LCS length of the prefixes. The algorithm runs in O(mn) time where m and n are the lengths of the input sequences.

Uploaded by

Ankit
Copyright
© © All Rights Reserved
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Download as PDF, TXT or read online on Scribd
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Longest Common Subsequence

A subsequence of a given sequence is the given sequence with just some elements left out
(order should be from left-to-right, not necessarily consecutive).. A common sequence of two
sequences X and Y, is a subsequence of both X and Y.A longest common subsequence is the one
with maximum length. For example, if X = {A,B,C,B,D,A,B} and Y = { B,D,C,A,B,A} then the
longest common subsequence is of length 4 and they are {B,C,B,A} and {B,D,A,B}.
Finding the longest common subsequence has applications in areas like biology. The longest
subsequence (LCS) problem has an optimal substructure property. Thus, dynamic programming
method can be used to solve this problem.
Theorem used - Let X =< x1, x2, . . . , xm > and Y =< y1, y2, . . . , yn > be sequences, and let Z
=< z1, z2, . . . , zk > be any LCS of X and Y .
1. If xm = yn, then zk = xm = yn and Zk1 is an LCS of Xm1 and Yn1.
2. If xm = yn, then zk = xm implies that Z is an LCS of Xm1 and Y.
3. If xm = yn, then zk = yn implies that Z is an LCS of X and Yn1.
Algorithm:
S,T are two strings for which we have to find the longest common sub sequence. Input the two
sequences. Now print the longest common subsequence using LongestCommonSubsequence function.
LongestCommonSubsequence function : This function takes the two sequences (S, T) as arguments and
returns the longest common subsequence found.
Store the length of both the subsequences. Slength = strlen(S), Tlength = strlen(T).
We will Start with the index from 1 for our convenience (avoids handling special cases for
negative indices).

Declare common[Slength][Tlength]. Where, common[i][j] represents length of the


longest common sequence in S[1..i], T[1..j].
If there are no characters from string S, common[0][i]=0 for all i or if there are no
characters from string T, common[i][0]=0 for all i.
Recurrence: for i=1 to Slength
for j=1 to Tlength
common[i][j] = common[i-1][j-1] + 1, if S[i]=T[j]. Else, common[i][j] =
max(common[i-1][j],common[i][j-1]). Where max is a function which takes the two
variables as arguments and returns the maximum of them.
Return, common[Slength][Tlength].
Property:
Time complexity is O(mn), where m and n are the length of two strings.

Example:

S = {A, B, C, B}, T = {B, D, C, A}


SLength = 4 and TLength = 4, common[0][04] = 0 and common[04][0] = 0
Recurrence
i=1
j=1
A B, common[1][1] = max(common[1][0] , common[0][1]) = 0
j=2
A D, common[1][2] = max(common[1][1] , common[0][2]) = 0
j=3
A C, common[1][3] = max(common[1][2] , common[0][3]) = 0
j=4
A = A, common[1][4] = common[0][2] + 1 = 1
i=2
j=1
B = B, common[2][1] = common[1][0] + 1 = 1
j=2
B D, common[2][2] = max(common[2][1] , common[1][2]) = 1
j=3
B C, common[2][3] = max(common[2][2] , common[1][3]) = 1
j=4
B A, common[2][4] = max(common[2][3] , common[1][4]) = 1
i=3
j=1
C B, common[3][1] = max(common[3][0] , common[2][1]) = 1
j=2
C D, common[3][2] = max(common[3][1] , common[2][2]) = 1
j=3
C = C, common[3][3] = common[2][2] + 1 = 2
j=4
C A, common[3][4] = max(common[3][3] , common[2][4]) = 2
i=4
j=1
B B, common[4][1] = max(common[4][0] , common[3][1]) = 1
j=2
B D, common[4][2] = max(common[4][1] , common[3][2]) = 1
j=3
B C, common[4][3] = max(common[4][2] , common[3][3]) = 2

j=4
B A, common[4][4] = max(common[4][3] , common[3][4]) = 2
common[4][4] = 2
Output: Longest common susequence is of length 2
An example: Xi = A B C B D A B and Yi = B D C A B A
i/j

Yj

0
0

Xi

2 B

3 C

4 B

5 D

6 A

To reconstruct the elements of an LCS, follow the matrix arrows from the lower right-hand
corner; the path is shaded. Each
on the path corresponds to an entry (highlighted) for
which Xi = Yi, is a member of LCS. The length of the common subsequence is 4.

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