Longest Common Subsequence (LCS)

Subsequence:
Subset of letters in order from left to right.

Remember:
“Subsequence” is different from “substring”. Substring
is continuous, no gap. But, subsequence can have gap.

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 Example : Subsequence
X= {A B C B D A B } Y= {B D C A B A}
 CBD is a substring of X. BBA is a subsequence of X,
but not a substring of X.
 DBBB is not a subsequence of X, because order violation.
 BDAB is both substring and subsequence of X,
but it is only a subsequence of Y

 Substrings are also subsequence,

but a subsequence may not be a substring.

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 Example : LCS
Common Subsequence:
Subsequence of both.
Longest Common Subsequence:
Same subsequence of maximum length.

X= {A B C B D A B } Y= {B D C A B A}
 X = A BCBD AB, Y = BD CA BA LCS: BCBA
(4)

 Other examples: BCAB (4), BDAB (4).

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 Maximum possible length = 4
Longest Common Subsequence Problem

Problem:
Given two sequences X = < x1, x2, ….., xm > and
Y = < y1, y2, ….., yn > find a
maximum-length common subsequence of X and Y.

Solution (Idea):
Notice that the LCS problem has optimal substructure:
solutions of subproblems are parts of the final solution.

Subproblems: “Find LCS of pairs of prefixes of X and Y”

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 Notations

• X = < x1, x2, ….., xm > and Y = < y1, y2, ..., yn > : Sequences

• Xi, Yj : Prefixes of X and Y of length i and j respectively

• c[i,j] : The length of LCS of Xi and Yj

• c[m,n] : The length of LCS of X and Y

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 Optimal Substructure of an LCS

• Let X x1 , x2 ,  , xm  and Y  y1 , y2 ,  , yn  be

sequences and let Z z1 , z 2 ,  , z k  be any LCS of
X and Y .
• If x  y , then z  x  y and Z is an LCS of X and Y
m n k m n k1 m 1 n 1

• If xm  y n , then z k  xm
implies that Z is an LCS of X m  1 and Y

• If xm  y n , then z k  y n
implies that Z is an LCS of X and Yn  1
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Optimal Substructure of an LCS (Book: Cormen; Page-392)

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 The Recurrence

 0 if i 0 or j 0

c[i, j ]  c[i  1, j  1]  1 if i, j  0 and xi  y j ,
max(c[i, j  1], c[i  1, j ]) if i, j  0 and x  y
 i j

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 LCS Recursive Solution
• We start with i = j = 0 (empty substrings of x
and y)
• Since X0 and Y0 are empty strings, their LCS is
always empty (i.e. c[0,0] = 0)
• LCS of empty string and any other string is
empty, so for every i and j: c[0, j] = c[i,0] = 0

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 LCS Recursive Solution
 When we calculate c[i,j], we consider two cases:
• First case: x[i]=y[j]: one more symbol matches, so the
length of LCS Xi and Yj equals to the length of LCS of
smaller strings Xi-1 and Yi-1 , plus 1
• Second case: x[i] != y[j]: As symbols do not match,
solution is not improved, and the length of LCS(Xi , Yj)
is the same as before (maximum of LCS (Xi, Yj-1) and
LCS (Xi-1,Yj) )
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 LCS Example

What is the Longest Common

Subsequence of X and Y?

X = ABCB
Y = BDCAB

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 LCS Example (0)
j 0 1 2 3 4 5
i Yj B D C A B
0 Xi
A
1
2 B

3 C

4 B

X = ABCB; m = |X| = 4
Y = BDCAB; n = |Y| = 5
Allocate array c[6,5]
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 LCS Example (1)
j 0 1 2 3 4 5
i Yj B D C A B
0 Xi
A
1 0
2 B
0
3 C 0
4 B 0

for i = 1 to m c[i,0] = 0
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 LCS Example (2)
j 0 1 2 3 4 5
i Yj B D C A B
0 Xi 0 0 0 0 0 0
A
1 0
2 B
0
3 C 0
4 B 0

for j = 0 to n c[0,j] = 0
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 LCS Example (3)
j 0 1 2 3 4 5
i Yj B D C A B
0 Xi 0 0 0 0 0 0
A
1 0 0
2 B
0
3 C 0
4 B 0

case i=1 and j=1

A != B
but, c[0,1]>=c[1,0]
so c[1,1] = c[0,1], and b[1,1] =
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 LCS Example (4)
j 0 1 2 3 4 5
i Yj B D C A B
0 Xi 0 0 0 0 0 0
A
1 0 0 0
2 B
0
3 C 0
4 B 0

case i=1 and j=2

A != D
but, c[0,2]>=c[1,1]
so c[1,2] = c[0,2], and b[1,2] =
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 LCS Example (5)
j 0 1 2 3 4 5
i Yj B D C A B
0 Xi 0 0 0 0 0 0
A
1 0 0 0 0
2 B
0
3 C 0
4 B 0

case i=1 and j=3

A != C
but, c[0,3]>=c[1,2]
so c[1,3] = c[0,3], and b[1,3] =
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 LCS Example (6)
j 0 1 2 3 4 5
i Yj B D C A B
0 Xi 0 0 0 0 0 0
A
1 0 0 0 0 1
2 B
0
3 C 0
4 B 0

case i=1 and j=4

A=A
so c[1,4] = c[0,2]+1, and b[1,4] =

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 LCS Example (7)
j 0 1 2 3 4 5
i Yj B D C A B
0 Xi 0 0 0 0 0 0
A
1 0 0 0 0 1 1
2 B
0
3 C 0
4 B 0

case i=1 and j=5

A != B
this time c[0,5]<c[1,4]
so c[1,5] = c[1, 4], and b[1,5] =
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 LCS Example (8)
j 0 1 2 3 4 5
i Yj B D C A B
0 Xi 0 0 0 0 0 0
A
1 0 0 0 0 1 1
2 B
0 1
3 C 0
4 B 0

case i=2 and j=1

B=B
so c[2, 1] = c[1, 0]+1, and b[2, 1] =

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 LCS Example (9)
j 0 1 2 3 4 5
i Yj B D C A B
0 Xi 0 0 0 0 0 0
A
1 0 0 0 0 1 1
2 B
0 1 1
3 C 0
4 B 0

case i=2 and j=2

B != D
and c[1, 2] < c[2, 1]
so c[2, 2] = c[2, 1] and b[2, 2] =
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 LCS Example (10)
j 0 1 2 3 4 5
i Yj B D C A B
0 Xi 0 0 0 0 0 0
A
1 0 0 0 0 1 1
2 B
0 1 1 1
3 C 0
4 B 0

case i=2 and j=3

B != D
and c[1, 3] < c[2, 2]
so c[2, 3] = c[2, 2] and b[2, 3] =
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 LCS Example (11)
j 0 1 2 3 4 5
i Yj B D C A B
0 Xi 0 0 0 0 0 0
A
1 0 0 0 0 1 1
2 B
0 1 1 1 1
3 C 0
4 B 0

case i=2 and j=4

B != A
and c[1, 4] = c[2, 3]
so c[2, 4] = c[1, 4] and b[2, 2] =
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 LCS Example (12)
j 0 1 2 3 4 5
i Yj B D C A B
0 Xi 0 0 0 0 0 0
A
1 0 0 0 0 1 1
2 B
0 1 1 1 1 2
3 C 0
4 B 0

case i=2 and j=5

B=B
so c[2, 5] = c[1, 4]+1 and b[2, 5] =

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 LCS Example (13)
j 0 1 2 3 4 5
i Yj B D C A B
0 Xi 0 0 0 0 0 0
A
1 0 0 0 0 1 1
2 B
0 1 1 1 1 2
3 C 0 1
4 B 0

case i=3 and j=1

C != B
and c[2, 1] > c[3,0]
so c[3, 1] = c[2, 1] and b[3, 1] =
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 LCS Example (14)
j 0 1 2 3 4 5
i Yj B D C A B
0 Xi 0 0 0 0 0 0
A
1 0 0 0 0 1 1
2 B
0 1 1 1 1 2
3 C 0 1 1
4 B 0

case i=3 and j= 2

C != D
and c[2, 2] = c[3, 1]
so c[3, 2] = c[2, 2] and b[3, 2] =
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 LCS Example (15)
j 0 1 2 3 4 5
i Yj B D C A B
0 Xi 0 0 0 0 0 0
A
1 0 0 0 0 1 1
2 B
0 1 1 1 1 2
3 C 0 1 1 2
4 B 0

case i=3 and j= 3

C=C
so c[3, 3] = c[2, 2]+1 and b[3, 3] =

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 LCS Example (16)
j 0 1 2 3 4 5
i Yj B D C A B
0 Xi 0 0 0 0 0 0
A
1 0 0 0 0 1 1
2 B
0 1 1 1 1 2
3 C 0 1 1 2 2
4 B 0

case i=3 and j= 4

C != A
c[2, 4] < c[3, 3]
so c[3, 4] = c[3, 3] and b[3, 3] =
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 LCS Example (17)
j 0 1 2 3 4 5
i Yj B D C A B
0 Xi 0 0 0 0 0 0
A
1 0 0 0 0 1 1
2 B
0 1 1 1 1 2
3 C 0 1 1 2 2 2
4 B 0

case i=3 and j= 5

C != B
c[2, 5] = c[3, 4]
so c[3, 5] = c[2, 5] and b[3, 5] =
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 LCS Example (18)
j 0 1 2 3 4 5
i Yj B D C A B
0 Xi 0 0 0 0 0 0
A
1 0 0 0 0 1 1
2 B
0 1 1 1 1 2
3 C 0 1 1 2 2 2
4 B 0 1

case i=4 and j=1

B=B
so c[4, 1] = c[3, 0]+1 and b[4, 1] =

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 LCS Example (19)
j 0 1 2 3 4 5
i Yj B D C A B
0 Xi 0 0 0 0 0 0
A
1 0 0 0 0 1 1
2 B
0 1 1 1 1 2
3 C 0 1 1 2 2 2
4 B 0 1 1

case i=4 and j=2

B != D
c[3, 2] = c[4, 1]
so c[4, 2] = c[3, 2] and b[4, 2] =
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 LCS Example (20)
j 0 1 2 3 4 5
i Yj B D C A B
0 Xi 0 0 0 0 0 0
A
1 0 0 0 0 1 1
2 B
0 1 1 1 1 2
3 C 0 1 1 2 2 2
4 B 0 1 1 2

case i=4 and j= 3

B != C
c[3, 3] > c[4, 2]
so c[4, 3] = c[3, 3] and b[4, 3] =
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 LCS Example (21)
j 0 1 2 3 4 5
i Yj B D C A B
0 Xi 0 0 0 0 0 0
A
1 0 0 0 0 1 1
2 B
0 1 1 1 1 2
3 C 0 1 1 2 2 2
4 B 0 1 1 2 2

case i=4 and j=4

B != A
c[3, 4] = c[4, 3]
so c[4, 4] = c[3, 4] and b[3, 5] =
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 LCS Example (22)
j 0 1 2 3 4 5
i Yj B D C A B
0 Xi 0 0 0 0 0 0
A
1 0 0 0 0 1 1
2 B
0 1 1 1 1 2
3 C 0 1 1 2 2 2
4 B 0 1 1 2 2 3

case i=4 and j=5

B= B
so c[4, 5] = c[3, 4]+1 and b[4, 5] =

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LCS-Length(X, Y)
m = length(X), n = length(Y)
Algorithm: LCS
for i = 1 to m
c[i, 0] = 0
for j = 0 to n
c[0, j] = 0
for i = 1 to m
for j = 1 to n
if ( xi = = yj )
c[i, j] = c[i - 1, j - 1] + 1
bi, j  " "
else if c[i - 1, j]>=c[i, j - 1]
c[i, j] = c[i - 1, j]
bi, j  "  "
else c[i, j] = c[i, j - 1]
bi, j  "  "
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return c and b
 Finding LCS
j 0 1 2 3 4 5
i Yj B D C A B
0 Xi 0 0 0 0 0 0
A
1 0 0 0 0 1 1
2 B
0 1 1 1 1 2
3 C 0 1 1 2 2 2
4 B 0 1 1 2 2 3

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 Finding LCS (2)
j 0 1 2 3 4 5
i Yj B D C A B
0 Xi 0 0 0 0 0 0
A
1 0 0 0 0 1 1
2 B
0 1 1 1 1 2
3 C 0 1 1 2 2 2
4 B 0 1 1 2 2 3
LCS (reversed order): B C B
LCS (straight order): B C B
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 Algorithm: Finding LCS

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Practice Example (Book: Cormen; Page-395)

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LCS : BCBA Length : 4 39
 Thank You

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 Stay Safe

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