Prague Stringology Conference 2016

Diptarama, Ryo Yoshinaka and Ayumi Shinohara

Fast Full Permuted Pattern Matching Algorithms on Multi-track Strings

Abstract:
A multi-track string is a tuple of strings of the same length. The full permuted pattern matching problem is, given two multi-track strings = (t1, t2, . . ., tN) and = (p1, p2, . . ., pN) such that |p1|= ⸳ ⸳ ⸳ =|pN| ≤ |t1|= ⸳ ⸳ ⸳ =|tN|, to find all positions i such that = (tr1[i:i+m-1], ⸳ ⸳ ⸳, trN[i:i+m-1]) for some permutation (r1, ⸳ ⸳ ⸳, rN) of (1, ⸳ ⸳ ⸳, N), where m=|p1| and $t[i:j] denotes the substring of t from position i to j. We propose new algorithms that perform full permuted pattern matching practically fast. The first and second algorithms are based on the Boyer-Moore algorithm and the Horspool algorithm, respectively. The third algorithm is based on the Aho-Corasick algorithm where we use a multi-track character instead of a single character in the so-called goto function. The fourth algorithm is an improvement of the multi-track Knuth-Morris-Pratt algorithm that uses an automaton instead of the failure function of the original algorithm. Our experiment results demonstrate that those algorithms perform permuted pattern matching faster than existing algorithms.

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