String Matching

Algorithms

Advanced Algorithms and

Data Structure

Sirwe Saeedi
Spring 2019

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Applications 1

• BioInformatics
• DNA sequencing
 Applications 2

• Web pages search engine

 Formalize String

Matching Problem

• A text as an array of characters T[1..n]

• A pattern as an array of characters P[1..m]
• m<=n
• The characters
Formalize String

Matching Problem

T[1..15] L O L O E L L O H E L L O

P[1..5] H E L L O
Formalize String

Matching Problem

T[1..15] L O L O E L L O H E L L O

P[1..5] H E L L O
Formalize String

Matching Problem

T[1..15] L O L O E L L O H E L L O

P[1..5] H E L L O
 String Matching 

Problem

T[1..15] L O L O E L L O H E L L O

P[1..5] H E L L O

T[12] = P[2]

T[14] = P[4]
T[15] = P[5]
T[13] = P[3]
T[11] = P[1]
s = 10
First occurrence of pattern
 Naive String 

MatchingAlgorithm

Check P with each substring of T for all possible shifts

T[1..15] L O L O E L L O H E L L O

P[1..5] H E L L O

for s=0 test T[1..5] = P[1..5]

 Naive String 

MatchingAlgorithm

check P with each substring of T for all possible shifts

T[1..15] L O L O E L L O H E L L O

P[1..5] H E L L O

for s=1 test T[2..5+1] = P[1..5]

 Naive String 

MatchingAlgorithm

check P with each substring of T for all possible shifts

T[1..15] L O L O E L L O H E L L O

P[1..5] H E L L O

for s=0 test T[3..5+2] = P[1..5]

 Naive String 

MatchingAlgorithm

check P with each substring of T for all possible shifts

T[1..15] L O L O E L L O H E L L O

P[1..5] H E L L O

for s=0 test T[11..5+10] = P[1..5]

 Naive String 

MatchingAlgorithm

https://labs.xjtudlc.com/labs/wldmt/reading%20list/books/Algorithms%20and%20optimization/Introduction%20to%20Algorithms.pdf
 Naive String 

Matching Algorithm
Time Complexity

Matching time in the worst case: O(m(n-m+1)) ~ O(n^2)

Text = a^n a a a a a a a a a . . . a a a

Pattern = a^m a a a a a
 Naive String 

Matching Algorithm
Time Complexity

Matching time in the worst case: O(m(n-m+1)) ~ O(n^2)

Text = a^n a a a a a a a a a . . . a a a

Pattern = a^m a a a a a
 Naive String 

Matching Algorithm
Time Complexity

Matching time in the worst case: O(m(n-m+1)) ~ O(n^2)

Text = a^n a a a a a a a a a . . . a a a

Pattern = a^m a a a a a
 Naive String 

Matching Algorithm
Time Complexity

Matching time in the worst case: O(m(n-m+1)) ~ O(n^2)

Text = a^n a a a a a a a a a . . . a a a

Pattern = a^m a a a a a
Rabin-Karp String 

Matching Algorithm

• The Rabin-Karp algorithm calculates a hash value for the pattern, 


and for each M-character subsequence of text to be compared.

• If the hash values are unequal, the algorithm will calculate the hash 

value for next M-character sequence.

• If the hash values are equal, the algorithm will compare the pattern

and the M-character sequence.

• In this way, there is only one comparison per text subsequence, and

character matching is only needed when hash values match.
Some mathematics

• Consider an M-character sequence as an M-digit number in base b, 


where b is the number of letters in the alphabet. The subsequent

t[i..i+M-1] is mapped to the number:

x(i) = t[i]*b^(M-1) + t[i+1]*b^(M-2) + … + t[i+M-1]

• Furthermore, given x(i) we can compute x(i+1) for the next subsequent 

t[i+1..i+M] in constant time, as follows:

x(i+1) = t[i+1]*b^(M-1) + t[i+2]*b^(M-2) + … + t[i+M]

Some mathematics

• x(i+1) = x(i)*b ———> Shift left one digit

-t[i]*b^M ———> Subtract leftmost digit
+t[i+M] ———> Add new rightmost digit

• We adjust the existing value when we move over one character

• Constant time to compute M-digit numbers of each M-characters 

subsequence
Some mathematics

• We hash the value by taking it mod a prime number q


The mod function is useful in this case:
1. [(x mod q) + (y mod q)] mod q = (x+y) mod q
2. (x mod q) mod q = x mod q

• For these reasons:

hash(x(i)) = ((t[i]*b^(M-1) mod q) + (t[i+1]* b^(M-2) mod q) +

… + (t[i+M-1] mod q)) mod q
• So:
h(x(i+1)) = ( h(x(i)*b mod q -t[i]*b^M mod q +t[i+M] mod q) mod q

Rabin-Karp String 

Matching Algorithm

https://labs.xjtudlc.com/labs/wldmt/reading%20list/books/Algorithms%20and%20optimization/Introduction%20to%20Algorithms.pdf
Rabin-Karp Algorithm
Example

hash(‘aab’) = 3

Text = ‘aabbcaba’ a a b b c a b a

Pattern = ‘cab’ c a b
hash(‘cab’) = 0

hash(‘abb’) = 0

Text = ‘aabbcaba’ a a b b c a b a

Pattern = ‘cab’ c a b
hash(‘cab’) = 0
Rabin-Karp Algorithm
Example

hash(‘bbc’) = 3

Text = ‘aabbcaba’ a a b b c a b a

Pattern = ‘cab’ c a b
hash(‘cab’) = 0

hash(‘bca’) = 0

Text = ‘aabbcaba’ a a b b c a b a

Pattern = ‘cab’ c a b
hash(‘cab’) = 0
Rabin-Karp Algorithm
Example

hash(‘cba’) = 0

Text = ‘aabbcaba’ a a b b c a b a

Collision happened
Pattern = ‘cab’ c a b
in hashing 

hash(‘cab’) = 0 But the algorithm
handles it
hash(‘aba’) = 0

Text = ‘aabbcaba’ a a b b c a b a

Pattern = ‘cab’ c a b
hash(‘cab’) = 0
Time Complexity

Matching time in the worst case



O(m(n-m+1)) ~ O(n^2)

Performs better in average case


preprocessing time

O(m)
 KMP String 

Matching Algorithm

• Knuth-Morris-Pratt Algorithm
• Improves the worst case time complexity to O(n)
• Use degenerating property of the pattern
KMP Algorithm
Example

A A A A A B A A A B A

A A A A Initial Position
KMP Algorithm
Example

A A A A A B A A A B A

A A A A Pattern shifted one position

KMP Algorithm
Example

A A A A A B A A A B A

A A A A Pattern shifted one position

Need preprocessing of pattern

KMP Algorithm
Preprocessing

• text = T[1..n]
• pattern = P[1..m]
• LPS = [1..m]
 KMP Algorithm
Preprocessing

• pattern[] A B X A B

• LPS[]
0 1 2 3 4

LPS[i]
length of maximum matching
prefix(suffix) of pattern[0..i]
 KMP Algorithm
Preprocessing

• pattern[] A B X A B

• LPS[] 0

0 1 2 3 4

LPS[0] = 0
 KMP Algorithm
Preprocessing

• pattern[] A B X A B

• LPS[] 0 0

0 1 2 3 4

LPS[0] = 0
LPS[1] = 0
 KMP Algorithm
Preprocessing

• pattern[] A B X A B

• LPS[] 0 0 0

0 1 2 3 4

LPS[0] = 0
LPS[1] = 0
LPS[2] = 0
 KMP Algorithm
Preprocessing

• pattern[] A B X A B

• LPS[] 0 0 0

0 1 2 3 4

LPS[0] = 0
LPS[1] = 0
LPS[2] = 0
LPS[3] =
 KMP Algorithm
Preprocessing

• pattern[] A B X A B

• LPS[] 0 0 0 1

0 1 2 3 4

LPS[0] = 0
LPS[1] = 0
LPS[2] = 0
LPS[3] = 1
 KMP Algorithm
Preprocessing

• pattern[] A B X A B

• LPS[] 0 0 0 1 2

0 1 2 3 4
LPS[0] = 0
LPS[1] = 0
LPS[2] = 0
LPS[3] = 1
LPS[4] = 2
 KMP Algorithm
Searching the Pattern

• To search pattern in the main text use the LPS array

• For each value of LPS we can decide which next characters

should be matched

• The idea is not matching characters that we already know

match anyway
 KMP Algorithm
Searching the Pattern

• Text[] A B X A B A B X A B

A B X A B
• pattern[]
• LPS[] 0 0 0 1 2

0 1 2 3 4
 KMP Algorithm
Searching the Pattern

• Text[] A B X A B A B X A B

A B X A B
• pattern[]
• LPS[] 0 0 0 1 2

0 1 2 3 4
 KMP Algorithm
Searching the Pattern

• Text[] A B X A B A B X A B

A B X A B
• pattern[]
• LPS[] 0 0 0 1 2

0 1 2 3 4
 KMP Algorithm
Searching the Pattern

• Text[] A B X A B A B X A B

A B X A B
• pattern[]
• LPS[] 0 0 0 1 2

0 1 2 3 4
 KMP Algorithm
Searching the Pattern

• Text[] A B X A B A B X A B

A B X A B
• pattern[]
• LPS[] 0 0 0 1 2

0 1 2 3 4
 KMP Algorithm
Searching the Pattern

• Text[] A B X A B A B X A B

A B X A B
• pattern[]
• LPS[] 0 0 0 1 2 Current Character

0 1 2 3 4
 KMP Algorithm
Searching the Pattern

• Text[] A B X A B A B X A B

A B X A B
• pattern[]
• LPS[] 0 0 0 1 2
Substring behind the
0 1 2 3 4 current character
pattern[0..1] = ‘AB’
 KMP Algorithm
Searching the Pattern

• Text[] A B X A B A B X A B

A B X A B
• pattern[]
• LPS[] 0 0 0 1 2

0 1 2 3 4
 References

• Introduction to Algorithms Third Edition, Thomas H. Cormen 


Charles E. Leiserson Ronald L. Rivest Clifford Stein

• https://www.ics.uci.edu/~eppstein/161/960227.html
• https://www.nayuki.io/
 Thank you
any questions

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