a hybrid indexing method for approximate string matching

1

A Hybrid Indexing Method for Approximate String Matching

Journal of Discrete Algorithms, No. 1, Vol. 1, 2000, pp. 205-239, Gonzalo Navarro and Ricardo Baeza-Yates

Advisor: Prof. R. C. T. Lee Speaker: Y. K. Shieh

2

The approximate string matching problem is:

Given a text T of length n, a pattern P of length m (n > m), and a threshold k to the number of "errors" in the matches, find all occurrences of a pattern in a text with k errors.

3

This paper uses an exhaustive searching mechanism. We open a window T’ in T with size m+k (Rule 2) and try to determine whether we are sure that every prefix T’’ of this window T’ has ed(T’’,P) > k.

If the answer is yes, we ignore this window; otherwise, we use dynamic programming to examine whether any prefix T’’ of the window T’ has ed(T’’,P) ≦k.

4

We use dynamic programming to compute the edit distance between two strings.

A matrix C0…|m|,0…|n| is filled, where Cj,i represents the minimum number of operations need to match T1…i to P1…j. This is computed as follows

Cj,0 and C0,i represent the edit distance between a string of length j or i and the empty string.

),,min(1

)(

,

1,11,,1

1,1,

,00,

ijijij

ijjiij

ij

CCCelse

CthenPTifC

iCjC

5

example:T = surgeryP = surveyk = 2

s u r g e r y

0 1 2 3 4 5 6 7

s 1 0 1 2 3 4 5 6

u 2 1 0 1 2 3 4 5

r 3 2 1 0 1 2 3 4

v 4 3 2 1 1 2 3 4

e 5 4 3 2 2 1 2 3

y 6 5 4 3 3 2 2 2

There are only three prefixes of T, namely surge, surger and surgery, whose edit distances with P=survey aresmaller than or equal to k=2.

6

Let us now see how we can be sure that for a window T’ with size m+k , for every prefix T’’ of T’, ed(T’’,P) > k.

We present Lemma 1 of this paper as follows.

7

Lemma 1Let T’ in T and P be two strings such that ed(T’,

P) ≦ k. Let P = P1x1P2x2… xj-1Pj, for strings Pi and xi and for any j ≧ 1. Then, at least one string Pi appears in T’ with at most errors.

Thus, we always divide the pattern into j pieces. We shall point out how to divide later.

jk /

8

To be more precise, we may say that if ed(T’,P) ≦ k, there exists a Pi in P and a T’’ in T’ such that

ed(Pi,T’’) .≦ jk /

9

Lemma 1 tells us that if for all Pi in P and every substring b in T’, ed(Pi,b) > , then ed(P,T’) > k.

Suppose that there is a window T’ with size m+k andfor all Pi in P and for every substring b in T’, ed(Pi,b) > .

Then, we can be sure that for every prefix T’’of T’ , for all Pi in P and every substring b in T’’, ed(Pi,b) > .

jk /

jk /

jk /

bT

T’T’’

PiP

10

Let us define the following condition.

Condition A: For all Pi in P and every substring b inT’, ed(Pi, b) >

Thus, if Condition A is satisfied, then for every prefix T’’ of T’, ed(T’’,P)>k.

In such a case, we ignore T’ and shift P one step to the right.

./ jk

11

Question, how can we be sure that the above condition is satisfied.

The approach:

For each Pi, we generate all possible modified strings Pi whose distances with Pi are smaller than or equal to k.

After generating all possible modified , we may use the suffix tree of T to find all occurrences of , for all i, in T with error less than .iP

sPi '

jk /

12

We still have the following questions:

• Question 1. How to divide P into j pieces?

• Question 2. How to generate all modified Pi’s?

• Question 3. How to find the occurrences of Pi’s in T with edit distance less than or equal to . jk /

13

Question 1: How to divide P into j pieces?

It can be proved that an optimal method is to partition P into j pieces with

, where σ is the alphabet size. We can get j pieces of P, and the size of every piece is around logσn.

nkmj log/)(

14

Question 2. How to generate all modified Pi’s?

The generation of all modified strings whose distanceswith P can be done trivially. One method can be found in [HHLS2006] which was reported by C. W. Lu.

Another method can be found in [HM2007] reportedBy L. C. Chen.

In this paper, the authors used the second method mentioned in [HM2007].

15

We can use non-deterministic finite automatons (NFA).A NFA is a five-tuple M=(Q, Σ, δ, q0 , F), where Q is a finite set of states, Σ is a finite input alphabet, δ is a mapping from Q×(Σ {ε}) into the set ∪of subsets of Q, q0 Q is an initial state, and F Q is a set of final states.

16

P = abac, k = 2.

The finite automaton M accepts Lk(P).

Lk(P)={aa, ab, ac, ba, bc, aaa, aab, aac, aba, abb, abc, acc, baa, bab, bac, bbc, bcc, aaaa, aaab, aaac, aaba, aabc, aaca, aacb, aacc, abaa, abab, abac, abba, abbb, abbc, abca, abcb, abcc, baac, babc, bbac, bbbc, bcac}.

}),(,|{)( kYPDYYPL Lk

2,0 3,0 4,01,00,0

2,1 3,1 4,11,1

2,2 3,2 4,2

a b a c

ca

ca

ε ε ε

ε ε ε

One matched, no error.

One matched, one error.

Two matched, two errors.

Four matched, no error.

ε

a

a a

a

a

c

b

b

bc

c

cb

one error

two errors

17

P = abac, k = 2.

The finite automaton M accepts Lk(P).

Lk(P)={aa, ab, ac, ba, bc, aaa, aab, aac, aba, abb, abc, acc, baa, bab, bac, bbc, bcc, aaaa, aaab, aaac, aaba, aabc, aaca, aacb, aacc, abaa, abab, abac, abba, abbb, abbc, abca, abcb, abcc, baac, babc, bbac, bbbc, bcac}.

2,0 3,0 4,01,00,0

2,1 3,1 4,11,1

2,2 3,2 4,2

a b a c

ca

ca

ε ε ε

ε ε ε

ε

a

a a

a

a

c

b

b

bc

c

cb

Recognize aa

18

Full example: T = GACACAGACCAAAGCAG n = 17 P = CAAG m = 4 k = 1

19

P = CAAG j = (m + k) / logσn = (4 + 1) / log317 = 1.9388 Therefore, we partition P into two pieces.

P1 = CAP2 = AG

According to Lemma 1, at least one piece appears in substrings of T with at most = 0 error. This means that we want to find exact matching of P1 and P2.

2/1

20

NFA with k = 1 of P1 = CA:

0,0 1,0 2,0

1,1 2,1

C A

A

ε εC A A

zero error

one error

NFA with k = 1 of P2 = AG:

0,0 1,0 2,0

1,1 2,1

A G

G

ε εA GG

zero error

one error

21

T = GACACGGACCAAAGCAG We construct the suffix tree of T.

A

CG

C G

CA

AA

GC

AG

$

GGACCAAAGCAG$

AC

GG

AC

CA

AA

GC

AG

$

A

AAGCAG$

CGGACCAAAGCAG$

G$

CA

AA

GC

AG

$

GG

AC

CA

AA

GC

AG

$

AC

AC

GG

AC

CA

AA

GC

AG

$

CA

AA

GC

AG

$

CA

G$

GA

CC

AA

AG

CA

G$

A

GC

AG

$

AG

CA

G$ $

CAG$11

12

13

14

15

16

$

17

10

9

8

7

6

5

4

3

2

1

22

We only need to consider the tree level from root to = 3 .

A

CG

C G

C G

A

A

AC

G

CA G

G

AC C

AG

A

A

G

A

$C11

12

13

14

15

16

$

17

10 98

6

543

2

17log3

1,7

T = GACACGGACCAAAGCAG

23

A

CG

C G

C G

A

A

AC

G

CA G

G

AC C

AG

A

A

G

A

$C11

12

13

14

15

16

$

17

10 98

6

543

2

1,7

0,0 1,0 2,0

1,1 2,1

C A

A

ε εC A A

A

0,0 1,0 2,0

1,1 2,1

A G

G

ε εA GG

A

NFA of P1:

NFA of P2

T = GACACGGACCAAAGCAG

k = 1

24

A

CG

C G

C G

A

A

AC

G

CA G

G

AC C

AG

A

A

G

A

$C11

12

13

14

15

16

$

17

10 98

6

543

2

1,7

0,0 1,0 2,0

1,1 2,1

C A

A

ε εC A A

A

0,0 1,0 2,0

1,1 2,1

A G

G

ε εA GGA

(not exact match)

(not exact match)

T = GACACGGACCAAAGCAG

k = 1

25

A

CG

C G

C G

A

A

AC

G

CA G

G

AC C

AG

A

A

G

A

$C11

12

13

14

15

16

$

17

10 98

6

543

2

1,7

0,0 1,0 2,0

1,1 2,1

C A

A

ε εC A A

0,0 1,0 2,0

1,1 2,1

A G

G

ε εA GGA

Out of active states.

(not exact match)

T = GACACGGACCAAAGCAG

k = 1

26

A

CG

C G

C G

A

A

AC

G

CA G

G

AC C

AG

A

A

G

A

$C11

12

13

14

15

16

$

17

10 98

6

543

2

1,7

0,0 1,0 2,0

1,1 2,1

C A

A

ε εC A A

0,0 1,0 2,0

1,1 2,1

A G

G

ε εA GG

G

(exact match)

Out of active states.

We record positions 13 and 16 where AG occurs.

T = GACACGGACCAAAGCAG 13 16

k = 1

27

A

CG

C G

C G

A

A

AC

G

CA G

G

AC C

AG

A

A

G

A

$C11

12

13

14

15

16

$

17

10 98

6

543

2

1,7

0,0 1,0 2,0

1,1 2,1

C A

A

ε εC A A

C

0,0 1,0 2,0

1,1 2,1

A G

G

ε εA GGC

T = GACACGGACCAAAGCAG

k = 1

28

A

CG

C G

C G

A

A

AC

G

CA G

G

AC C

AG

A

A

G

A

$C11

12

13

14

15

16

$

17

10 98

6

543

2

1,7

0,0 1,0 2,0

1,1 2,1

C A

A

ε εC A A

A

0,0 1,0 2,0

1,1 2,1

A G

G

ε εA GG

Out of active states.

(exact match)

We record positions 3, 10 and 15 where CA occurs.

T = GACACGGACCAAAGCAG

k = 1

29

A

CG

C G

C G

A

A

AC

G

CA G

G

AC C

AG

A

A

G

A

$C11

12

13

14

15

16

$

17

10 98

6

543

2

1,7

0,0 1,0 2,0

1,1 2,1

C A

A

ε εC A A C

0,0 1,0 2,0

1,1 2,1

A G

G

ε εA GG

Out of active states.

(not exact match)

T = GACACGGACCAAAGCAG

k = 1

30

A

CG

C G

C G

A

A

AC

G

CA G

G

AC C

AG

A

A

G

A

$C11

12

13

14

15

16

$

17

10 98

6

543

2

1,7

0,0 1,0 2,0

1,1 2,1

C A

A

ε εC A A

G

0,0 1,0 2,0

1,1 2,1

A G

G

ε εA GG

G

(not exact match)

(not exact match)

T = GACACGGACCAAAGCAG

k = 1

31

A

CG

C G

C G

A

A

AC

G

CA G

G

AC C

AG

A

A

G

A

$C11

12

13

14

15

16

$

17

10 98

6

543

2

1,7

0,0 1,0 2,0

1,1 2,1

C A

A

ε εC A A

G

0,0 1,0 2,0

1,1 2,1

A G

G

ε εA GGG

T = GACACGGACCAAAGCAG

k = 1

32

A

CG

C G

C G

A

A

AC

G

CA G

G

AC C

AG

A

A

G

A

$C11

12

13

14

15

16

$

17

10 98

6

543

2

1,7

0,0 1,0 2,0

1,1 2,1

C A

A

ε εC A A

0,0 1,0 2,0

1,1 2,1

A G

G

ε εA GG

Out of active states.

Out of active states.

T = GACACGGACCAAAGCAG

k = 1

33

A

CG

C G

C G

A

A

AC

G

CA G

G

AC C

AG

A

A

G

A

$C11

12

13

14

15

16

$

17

10 98

6

543

2

1,7

0,0 1,0 2,0

1,1 2,1

C A

A

ε εC A A

A

0,0 1,0 2,0

1,1 2,1

A G

G

ε εA GG

Out of active states.

(not exact match)

T = GACACGGACCAAAGCAG

k = 1

34

A

CG

C G

C G

A

A

AC

G

CA G

G

AC C

AG

A

A

G

A

$C11

12

13

14

15

16

$

17

10 98

6

543

2

1,7

0,0 1,0 2,0

1,1 2,1

C A

A

ε εC A A

0,0 1,0 2,0

1,1 2,1

A G

G

ε εA GG

Out of active states.

Out of active states.

T = GACACGGACCAAAGCAG

k = 1

35

A

CG

C G

C G

A

A

AC

G

CA G

G

AC C

AG

A

A

G

A

$C11

12

13

14

15

16

$

17

10 98

6

543

2

1,7

0,0 1,0 2,0

1,1 2,1

C A

A

ε εC A A

0,0 1,0 2,0

1,1 2,1

A G

G

ε εA GG

G

Out of active states.

(not exact match)

T = GACACGGACCAAAGCAG

k = 1

36

After we find all probable positions in T, we verify every substring of those positions.

The probable positions of T are: 3, 10, 13, 15, 16

We use the dynamic program to verify whether any approximate string matching occurs between T and P at the above locations .

37

The probable positions of T are 3, 10, 13, 15, 16

C A A G

G A C A C G G A C C A A A G C A G1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17

m+k

G A C A C

0 1 2 3 4 5

C 1 1 2 2 3 4

A 2 2 1 2 2 3

A 3 3 2 2 2 3

G 4 3 3 3 3 3

k = 1

No approximatematching with k=1found.

38

C A A G

G A C A C G G A C C A A A G C A G1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17

m+k

A C A C G

0 1 2 3 4 5

C 1 1 1 2 3 4

A 2 1 2 1 2 3

A 3 2 2 2 2 3

G 4 3 3 3 3 2

The probable positions of T are: 3, 10, 13, 15, 16 k = 1

No approximatematching with k=1found.

39

C A A G

G A C A C G G A C C A A A G C A G1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17

m+k

C A C G G

0 1 2 3 4 5

C 1 0 1 2 3 4

A 2 1 0 1 2 3

A 3 2 1 1 2 3

G 4 3 2 2 1 2

The probable positions of T are: 3, 10, 13, 15, 16

CACG is found.

k = 1

40

C A A G

G A C A C G G A C C A A A G C A G1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17

m+k

The probable positions of T are: 3, 10, 13, 15, 16

This window does not include any probable position.Therefore we can ignore this window.

41

C A A G

G A C A C G G A C C A A A G C A G1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17

m+k

The probable positions of T are: 3, 10, 13, 15, 16

The window does not include any probable position.Therefore we can shift the window directly.

42

C A A G

G A C A C G G A C C A A A G C A G1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17

m+k

G G A C C

0 1 2 3 4 5

C 1 1 2 3 3 4

A 2 2 2 2 3 4

A 3 3 3 2 3 4

G 4 3 3 3 3 4

The probable positions of T are: 3, 10, 13, 15, 16 k = 1

No approximatematching with k=1found.

43

C A A G

G A C A C G G A C C A A A G C A G1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17

m+k

G A C C A

0 1 2 3 4 5

C 1 1 2 2 3 4

A 2 2 1 2 3 3

A 3 3 2 2 3 3

G 4 3 3 3 3 4

The probable positions of T are: 3, 10, 13, 15, 16 k = 1

No approximatematching with k=1found.

44

C A A G

G A C A C G G A C C A A A G C A G1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17

m+k

A C C A A

0 1 2 3 4 5

C 1 1 1 2 3 4

A 2 1 2 2 2 3

A 3 2 2 3 2 2

G 4 3 3 4 3 3

The probable positions of T are: 3, 10, 13, 15, 16 k = 1

No approximatematching with k=1found.

45

C A A G

G A C A C G G A C C A A A G C A G1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17

m+k

C C A A A

0 1 2 3 4 5

C 1 0 1 2 3 4

A 2 1 1 1 2 3

A 3 2 2 1 1 2

G 4 3 3 2 2 2

The probable positions of T are: 3, 10, 13, 15, 16 k = 1

No approximatematching with k=1found.

46

C A A G

G A C A C G G A C C A A A G C A G1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17

m+k

C A A A G

0 1 2 3 4 5

C 1 0 1 2 3 4

A 2 1 0 1 2 3

A 3 2 1 0 1 2

G 4 3 2 1 1 1

The probable positions of T are: 3, 10, 13, 15, 16

CAA, CAAA and CAAAG are found.

k = 1

47

C A A G

G A C A C G G A C C A A A G C A G1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17

m+k

A A A G C

0 1 2 3 4 5

C 1 1 2 3 4 4

A 2 2 1 2 3 4

A 3 2 2 1 2 3

G 4 3 3 2 1 2

The probable positions of T are: 3, 10, 13, 15, 16 k = 1

AAAG is found.

48

C A A G

G A C A C G G A C C A A A G C A G1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17

m+k

A A G C A

0 1 2 3 4 5

C 1 1 2 3 3 4

A 2 1 1 2 3 3

A 3 2 1 2 3 3

G 4 3 2 1 2 3

The probable positions of T are: 3, 10, 13, 15, 16 k = 1

AAG is found.

49

C A A G

G A C A C G G A C C A A A G C A G1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17

m+k

A G C A G

0 1 2 3 4 5

C 1 1 2 2 3 4

A 2 1 2 3 2 3

A 3 2 2 4 3 3

G 4 3 2 5 4 3

The probable positions of T are: 3, 10, 13, 15, 16 k = 1

No approximatematching with k=1found.

50

C A A G

G A C A C G G A C C A A A G C A G1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17

m

G C A G

0 1 2 3 4

C 1 1 1 2 3

A 2 2 2 1 2

A 3 3 3 2 2

G 4 3 3 3 2

The probable positions of T are: 3, 10, 13, 15, 16 k = 1

No approximatematching with k=1found.

51

C A A G

G A C A C G G A C C A A A G C A G1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17

m-k

C A G

0 1 2 3

C 1 0 1 2

A 2 1 0 1

A 3 2 1 1

G 4 3 2 1

The probable positions of T are: 3, 10, 13, 15, 16 k = 1

CAG is found.

52

Time complexity

• The preprocessing time complexity of constructing automatons and a suffix tree of T is O(|N|*|m|) and O(n) respectively, |N| is the number of states in a NFA and |m| is the length of m.

• The search time obtained using the partitioning scheme is O(nλlogn), where λ < 1 when error tolerated α < 1-e/ , where e = 2.718… .

53

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