Longest Common Substring

Computing Longest Common Substrings Using Sufx Arrays
Maxim A. Babenko, Tatiana A. Starikovskaya

Moscow State University
Computer Science in Russia, 2008
Maxim A. Babenko, Tatiana A. Starikovskaya (MSU) Computing LCS Using Sufx Arrays
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Outline
Problem Denition
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Outline
1 2
Problem Denition Sufx Arrays
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Outline
1 2 3
Problem Denition Sufx Arrays The Algorithm
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Outline
1 2 3 4
Problem Denition Sufx Arrays The Algorithm Conclusions
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Part 1 Problem Denition
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LCS
Problem (LCS, Longest Common Substring): Given a collection of N strings A = {1 , . . . , N } and an integer K (2 K N) nd the longest string that is a substring of at least K strings in A.
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LCS
Problem (LCS, Longest Common Substring): Given a collection of N strings A = {1 , . . . , N } and an integer K (2 K N) nd the longest string that is a substring of at least K strings in A. Tools: Sufx Arrays Time and Space: Linear and alphabet-independent Model of Computation: RAM
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Part 2 Sufx Arrays
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Useful Denitions
Denition (Sufx): Let = 1 2 . . . n be an arbitrary string of length n. For each i (1 i n) [i..] = i i+1 . . . n is a sufx of . Denition (Lexicographic order): Suppose we have some order on letters of the alphabet . This order can be extended in a standard way to strings over : < iff either is proper prex of or [1] = [1], . . . , [i] = [i], [i + 1] < [i + 1].
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Sufx Arrays
Denition (Sufx Array): Let be an arbitrary string of length n. Consider its non-empty sufxes [1..], [2..], . . . , [n..]. and order them lexicographically. Let SA(i) denote the starting position of the sufx appearing on the i-th place (1 i n): [SA(1)..] < [SA(2)..] < . . . < [SA(n)..].
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An Example of Sufx Array

sufxes mississippi ississippi ssissippi sissippi issippi ssippi sippi ippi ppi pi i SA 11 8 5 2 1 10 9 7 4 6 3 sorted sufxes i ippi issippi ississippi mississippi pi ppi sippi sissippi ssippi ssissippi
1 2 3 4 5 6 7 8 9 10 11
Figure: String mississippi, its sufxes, and the corresponding sufx array.
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Why Sufx Arrays?
A simple data structure containing all the necessary information.
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Why Sufx Arrays?
A simple data structure containing all the necessary information. Many nice and simple efcient construction algoritms (e.g. Krkinen, Sanders [2003]) with alphabet-independent time and space complexity.
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Part 3 The Algorithm
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Our Main Result
Theorem Let the total length of strings 1 , . . . , N be equal to L. Then the answer to the LCS problem can be computed in O(L) time and in O(L) space.
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LCS Example
Consider the following example with N = 3, K = 2: 1 = abb 2 = cb 3 = abc Clearly, the answer is ab.
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Observation
The longest common substring for K strings of our set is the longest common prex of some sufxes of these strings.
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Observation
The longest common substring for K strings of our set is the longest common prex of some sufxes of these strings. We calculate the longest common prex of every K sufxes of different strings and take the longest one; the latter is the answer to the LCS problem.
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Preprocessing: Step 1
Combine the strings in A as follows: = 1 $1 2 $2 . . . N $N . Here $i are special symbols (sentinels) that are different and lexicographically less than other symbols of the initial alphabet
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Combine the strings in A as follows: = 1 $1 2 $2 . . . N $N . Here $i are special symbols (sentinels) that are different and lexicographically less than other symbols of the initial alphabet Example: = abb$1 cb$2 abc$3
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Denition (Longest Common Prexes (LCP) array): The array containing lengths of the longest common prexes for every pair of consecutive sufxes (w.r.t. lexicographical order). LCP array can be easily constructed in linear time and space.
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Denition (Longest Common Prexes (LCP) array): The array containing lengths of the longest common prexes for every pair of consecutive sufxes (w.r.t. lexicographical order). LCP array can be easily constructed in linear time and space. We construct the sufx array and the LCP array for .
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Step 2. Example of SA and LCP

String: abb$1 cb$2 abc$3 4 7 11 1 8 SA: LCP: 0 0 0 2 0 3 1 6 1 SA 4 7 11 1 8 3 6 2 9 10 5 2 1 9 0 10 1 LCP 0 0 0 2 0 1 1 1 0 1
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1 2 3 4 5 6 7 8 9 10 11
sufxes abb$1 cb$2 abc$3 bb$1 cb$2 abc$3 b$1 cb$2 abc$3 $1 cb$2 abc$3 cb$2 abc$3 b$2 abc$3 $2 abc$3 abc$3 bc$3 c$3 $3
sorted sufxes $1 cb$2 abc$3 $2 abc$3 $3 abb$1 cb$2 abc$3 abc$3 b$1 cb$2 abc$3 b$2 abc$3 bb$1 cb$2 abc$3 bc$3 c$3 cb$2 abc$3
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Further Ideas
The longest prex of sufxes of K different strings in A is the longest common prex of sufxes of K different colors in .
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Further Ideas
The longest prex of sufxes of K different strings in A is the longest common prex of sufxes of K different colors in . Consider K sufxes at positions i1 , . . . , iK and assume that SA[i1 ] < SA[i2 ] < . . . < SA[iK ]. The length of the longest common prex of these K sufxes is equal to the minimum of LCP[i1 ], . . . , LCP[iK 1].
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Further Ideas
The longest prex of sufxes of K different strings in A is the longest common prex of sufxes of K different colors in . Consider K sufxes at positions i1 , . . . , iK and assume that SA[i1 ] < SA[i2 ] < . . . < SA[iK ]. The length of the longest common prex of these K sufxes is equal to the minimum of LCP[i1 ], . . . , LCP[iK 1]. Example: SA: LCP: Sufxes: 4 0 7 0 11 0 1 2 8 0 3 1 6 1 2 1 9 0 10 1 5
abb$1 cb$2 abc$3 abc$3
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Extensions
Theorem Problem: Given a collection of N strings A = {1 , . . . , N }, for each K (2 K N) nd the longest string that is a substring of at least K strings in A.
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Extensions
Theorem Problem: Given a collection of N strings A = {1 , . . . , N }, for each K (2 K N) nd the longest string that is a substring of at least K strings in A. Let the total length of strings 1 , . . . , N be equal to L. Then the answer to the above problem can be computed in O(L log L) time and in O(L) space.
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Part 4 Conclusions
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Open Problem
How to compute an inexact longest common substring?
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Acknowledgements
The authors are thankful to the students of Department of Mathematical Logic and Theory of Algorithms and to Maxim Ushakov and Victor Khimenko (Google Moscow) for many helpful discussions.
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The End :-)
Thank you for your attention. Questions are welcome!
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Computing Longest Common Substrings Using Sufx Arrays

Maxim A. Babenko, Tatiana A. Starikovskaya

Computer Science in Russia, 2008

Problem Denition Sufx Arrays

Problem Denition Sufx Arrays The Algorithm

Problem Denition Sufx Arrays The Algorithm Conclusions

Part 1 Problem Denition

Part 2 Sufx Arrays

An Example of Sufx Array

Why Sufx Arrays?

A simple data structure containing all the necessary information.

Why Sufx Arrays?

Part 3 The Algorithm

Our Main Result

Step 2. Example of SA and LCP

abb$1 cb$2 abc$3 abc$3

How to compute an inexact longest common substring?

The End :-)

Thank you for your attention. Questions are welcome!

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