Algoritmen & Datastructuren 2012 - 2013 Substring Search (Slides by Sedgewick)

Algoritmen & Datastructuren
2012 2013
Substring Search
(Slides by Sedgewick)
Philip Dutr & Benedict Brown
Dept. of Computer Science, K.U.Leuven
Goal: Find pattern of length M in a text of length N
Usually M << N
Copyright Ph.Dutr, Spring 2013
Applications
Parsers
Spam filters
Digital libraries
Word processors
Web search engines
Natural language processing
Computational molecular biology
Feature detection in digitized images
Application: spam filtering

Identify patterns indicative
of spam.
PROFITS
L0SE WE1GHT
herbal V1AGRA
There is no catch
L0W M0RTGAGE RATES
This is a one-time mailing.
This message is sent in
compliance with spam
regulations
Application: electronic surveillance

Look for certain phrases in email traffic
Detonate Bomb
Attack Belgians
Ik zal een taart in het gezicht van Leonard werpen
Huge amount of data, incoming streams, no backup
Application: page scraping

Goal. Extract relevant data from web page.
E.g. Find string delimited by <b> and </b> after first
occurrence of pattern Last Trade
Brute force
Check all possible starting positions,
check entire length of pattern
Brute force
Brute force: worst case
Brute-force algorithm can be slow if text and pattern

are repetitive
Worst case: ~ M.N character comparisons
M.(N-M+1) = M.N M.M + M ~ M.N if M << N

Challenges
In many applications, backup in data to be avoided
Solution 1: maintain buffer (memory!)

Solution 2: avoid backup
Challenge: we want linear time complexity!

10
Brute force: alternate implementation
Same sequence of character compares
11
i points to end of sequence of already-matched chars in text

j stores number of already-matched chars
(end of sequence in pattern)
Knuth-Morris-Pratt (KMP)
Intuition: Suppose we are searching in text for pattern

BAAAAAAAAA (alphabet = {A,B})
Suppose we match 5 chars, with mismatch on 6th char

We know previous 6 characters in text are BAAAAB
Don't need to back up text pointer!
12
Deterministic finite state automaton (DFA)
DFA is abstract string-searching machine.
13
Finite number of states (including start and halt)

Exactly one transition for each char in alphabet
Accept if sequence of transitions leads to halt state
Interpretation of Knuth-Morris-Pratt DFA
Interpretation of DFA state after reading in txt[i]?
State-number = number of characters in pattern that have

been matched.
length of longest prefix of pat[] that is at end of txt[0..i]
E.g. DFA is in state 3 after reading in character txt[6]
14
KMP trace
15
KMP Implementation
Differences from brute-force implementation:
Text pointer i never decrements (no backup needed)

Need to precompute dfa[][] from pattern (some work)
Running time
Simulate DFA on text: at most N character accesses
Build DFA: how to do efficiently?
16
How to build DFA from pattern?

Match transition
first j characters of pattern

have already been matched
next char matches
If in state j and next char c == pat.charAt(j),

then go to state j+1.
now first j+1 characters of

pattern have been matched
17
How to build DFA from pattern?
Mismatch transition
To compute dfa[c][j]:
If in state j and next char c != pat.charAt(j), then the last j characters

of input are pat[1..j-1], followed by c
Simulate pat[1..j-1] on DFA (so far ) and take transition c
Running time: Seems to require j steps

Simulation does not start from scratch: remember state X
18
19
20
KMP Analysis
KMP accesses no more than M + N chars
M for constructing DFA

N for actual search
KMP constructs dfa[][] in time and space

proportional to R.M
21
R = size of alphabet
The Art of Computer Programming
Donald
Knuth
"If you think you're a really good programmer . . . read

(Knuth's) Art of Computer Programming . . . You should
definitely send me a rsum if you can read the whole
thing. (Bill Gates)
22
Boyer-Moore
Intuition:
23
Scan characters in pattern from right to left

Can skip M text chars when finding one not in the pattern
Boyer-Moore
How much to skip?
right[c] = rightmost occurrence of character c in pattern
-1 for characters not in pattern
24
Boyer-Moore
25
Boyer-Moore
26
Boyer-Moore Analysis
~ N/M character compares
(characters in pattern < characters in alphabet)
Worst-case: ~ M.N
27
KMP-like rules to avoid repetition linear ~ N
Rabin-Karp
Basic idea = modular hashing
28
Compute a hash of pattern characters 0 to M-1

For each i, compute a hash of text characters i to M+i-1
If pattern hash = text substring hash, check for a match
Rabin-Karp
Intuition: M-digit, base-R integer, modulo Q
ti = txt.charAt(i)
Horner's method
29
Linear-time method to evaluate degree-M polynomial
Rabin-Karp
Can update hash function in constant time!
30
Rabin-Karp
31
Rabin-Karp
Las Vegas variant
If hash is equal, then check pattern

100% correct
Extremely likely to run in linear time (but worst case

M.N)
Monte Carlo variant
If hash is equal, we assume pattern is equal as well

Always runs in linear time
Extremely likely to return correct answer
32
Probability 1/Q choose large Q


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Algoritmen & Datastructuren

Goal: Find pattern of length M in a text of length N

Copyright Ph.Dutr, Spring 2013

Copyright Ph.Dutr, Spring 2013

Application: spam filtering

Copyright Ph.Dutr, Spring 2013

Application: electronic surveillance

Huge amount of data, incoming streams, no backup

Copyright Ph.Dutr, Spring 2013

Application: page scraping

Copyright Ph.Dutr, Spring 2013

Copyright Ph.Dutr, Spring 2013

Copyright Ph.Dutr, Spring 2013

Brute force: worst case

Brute-force algorithm can be slow if text and pattern

Worst case: ~ M.N character comparisons

M.(N-M+1) = M.N M.M + M ~ M.N if M << N

In many applications, backup in data to be avoided

Solution 1: maintain buffer (memory!)

Challenge: we want linear time complexity!

Copyright Ph.Dutr, Spring 2013

Brute force: alternate implementation

Same sequence of character compares

i points to end of sequence of already-matched chars in text

Copyright Ph.Dutr, Spring 2013

Intuition: Suppose we are searching in text for pattern

Suppose we match 5 chars, with mismatch on 6th char

Copyright Ph.Dutr, Spring 2013

Deterministic finite state automaton (DFA)

DFA is abstract string-searching machine.

Finite number of states (including start and halt)

Copyright Ph.Dutr, Spring 2013

Interpretation of Knuth-Morris-Pratt DFA

Interpretation of DFA state after reading in txt[i]?

State-number = number of characters in pattern that have

E.g. DFA is in state 3 after reading in character txt[6]

Copyright Ph.Dutr, Spring 2013

Copyright Ph.Dutr, Spring 2013

Differences from brute-force implementation:

Text pointer i never decrements (no backup needed)

Simulate DFA on text: at most N character accesses

Build DFA: how to do efficiently?

Copyright Ph.Dutr, Spring 2013

How to build DFA from pattern?

first j characters of pattern

next char matches

If in state j and next char c == pat.charAt(j),

now first j+1 characters of

Copyright Ph.Dutr, Spring 2013

How to build DFA from pattern?

If in state j and next char c != pat.charAt(j), then the last j characters

Running time: Seems to require j steps

Copyright Ph.Dutr, Spring 2013

Copyright Ph.Dutr, Spring 2013

Copyright Ph.Dutr, Spring 2013

KMP accesses no more than M + N chars

M for constructing DFA

KMP constructs dfa[][] in time and space

Copyright Ph.Dutr, Spring 2013

The Art of Computer Programming

"If you think you're a really good programmer . . . read

Copyright Ph.Dutr, Spring 2013

Scan characters in pattern from right to left