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Posted 8 Nov 2010

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# Approximate String Matching - Row-wise Bit-parallelism Algorithm (BPR)

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One of the best methods for solving approximate string matching problem

## Introduction

Approximate `string `matching, also called "`string `matching allowing errors", is the problem of finding a pattern p in a text T when a limited number k of differences is permitted between the pattern and its occurrences in the text.

## Solutions

The oldest solution to the problem relies on dynamic programming. For example, see Levenstein distance implementation on Code Project (www.codeproject.com/KB/recipes/fuzzysearch.aspx) or in Wikipedia(http://en.wikipedia.org/wiki/Fuzzy_string_searching).

An alternative and very useful way to consider the approximate search problem is to model the search with a nondeterministic finite automaton (NFA). Consider the NFA for k = 2 errors. Every row denotes the number of errors seen. Every column represents matching a pattern prefix. Horizontal arrows represent matching a character (i.e., if the pattern and text characters match, we advance in the pattern and in the text). All the others increment the number of errors by moving to the next row: Vertical arrows insert a character in the pattern (we advance in the text but not in the pattern), short diagonal arrows substitute a character (we advance in the text and pattern), and long diagonal arrows delete a character of the pattern (they are e-transitions, since we advance in the pattern without advancing in the text). The initial self-loop allows an occurrence to start anywhere in the text. The automaton signals (the end of) an occurrence whenever a rightmost state is active.

## BPR Algorithm

Bit-parallel algorithms are a simple and fast way to encode NFA states thanks to their higher locality of reference. Here is the pseudo-code for this algorithm that is described in the book "Flexible Pattern Matching in Strings" (see References for more information).

```BPR (p = p1p2...pm, T = t1t2...tn, k)
1.    Preprocessing
2.        For c e S Do B[c] <- 0m
3.        For j e 1 ... m Do B[pj] <- B[pj] | 0m-j10j-1
4.    Searching
5.       For i e 0 ... k Do Ri <- 0m-i1i
6.       For pos e 1 ... n Do
7.            oldR <- R0
8.            newR <- ((oldR << 1) | 1) & B[tpos]
9.            R0 <- newR
10.           For i e 1 ... k Do
11.              newR <- ((Ri << 1) & B[tpos]) | oldR | ((oldR | newR) << 1)
12.              oldR <- Ri, Ri <- newR
13.           End of for
14.           If newR & 10m-1 <> 0 Then report an occurrence at pos
15.      End of for```

For example, let's search for pattern "`rain`" in "`brain`" text with 2 errors. We start with B=

 r 0001 a 0010 i 0100 n 1000 * 0000

and { R0=0000 R1=0001 R2=0011 }. And here is step by step run:

b - 0000

R0- 0000

R1- 0000

R2- 0011

r - 0001

R0- 0001

R1- 0010

R2- 0100

a - 0010

R0- 0010

R1- 0111

R2- 1110

Occurrence at position 3

i - 0100

R0- 0100

R1- 1110

R2- 11111

Occurrence at position 4

n - 1000

R0- 1000

R1- 1100

R2- 1110

Occurrence at position 5

## C# Implementation

C#
```public static void BPR(string pattern, string text, int errors)
{
int[] B = new int[ushort.MaxValue];
for (int i = 0; i < ushort.MaxValue; i++) B[i] = 0;
// Initialize all characters positions
for (int i = 0; i < pattern.Length; i++)
{
B[(ushort)pattern[i]] |= 1 << i;
}
// Initialize NFA states
int[] states = new int[errors+1];
for(int i= 0; i <= errors; i++)
{
states[i] = (i == 0) ? 0 : (1 << (i - 1) | states[i-1]);
}
//
int oldR, newR;
int exitCriteria = 1 << pattern.Length -1;

for (int i = 0; i < text.Length; i++)
{
oldR = states[0];
newR = ((oldR << 1) | 1) & B[text[i]];
states[0] = newR;

for (int j = 1; j <= errors; j++)
{
newR = ((states[j] << 1) & B[text[i]]) | oldR | ((oldR | newR) << 1);

oldR = states[j];
states[j] = newR;
}

if ((newR & exitCriteria) != 0)
Console.WriteLine("Occurrence at position {0}", i+1);

}
} ```

## Share

 Retired Israel
Name: Statz Dima
Fields of interest: software

 First Prev Next
 My vote of 4 Đỗ Hồng Ngọc23-Nov-10 5:50 Đỗ Hồng Ngọc 23-Nov-10 5:50
 Re: My vote of 4 Dima Statz23-Nov-10 23:13 Dima Statz 23-Nov-10 23:13
 Hey WhiteRose1611, 1. Q: "When we work with char, it should be considered as int but not ushort" A: Why do you propose to use 32bit integer to store 16bit char? Does it make sense to you? 2. Q: "And, using a full array (ushort.MaxValue) is not a good idea. Why don't we use a Hastable or Dictionary? It won't take time too much because pattern.Length is just small normally." A: Pay attention, if you are going to re-implement it for your personal purposes, it seems that you did not understand what is going on here. The array length is not function of pattern length, it depends on char values range which is Pow(2,16). Your another idea of using Dictionary does not make sense also, because it will add some penalty to execution time. Good luck, and do not hesitate to contact me if you need any help. Dima S
 Re: My vote of 4 codeprojectqas24-Nov-10 0:15 codeprojectqas 24-Nov-10 0:15
 Re: My vote of 4 Dima Statz24-Nov-10 0:27 Dima Statz 24-Nov-10 0:27
 Re: My vote of 4 Richard Deeming24-Nov-10 9:18 Richard Deeming 24-Nov-10 9:18
 Re: My vote of 4 Dima Statz15-Dec-10 2:59 Dima Statz 15-Dec-10 2:59
 My vote of 5 Mark Jerde9-Nov-10 2:28 Mark Jerde 9-Nov-10 2:28
 how to find the start point of the approximate string [modified] zxj1987061613-Jun-11 21:42 zxj19870616 13-Jun-11 21:42
 Short and sweet, but.. `leppie`8-Nov-10 23:02 `leppie` 8-Nov-10 23:02
 Re: Short and sweet, but.. Dima Statz23-Nov-10 23:17 Dima Statz 23-Nov-10 23:17
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