Fast Searching in Packed Strings

Given strings $P$ and $Q$ the (exact) string matching problem is to find all positions of substrings in $Q$ matching $P$. The classical Knuth-Morris-Pratt algorithm [SIAM J. Comput., 1977] solves the string matching problem in linear time which is optimal if we can only read one character at the time. However, most strings are stored in a computer in a packed representation with several characters in a single word, giving us the opportunity to read multiple characters simultaneously. In this paper we study the worst-case complexity of string matching on strings given in packed representation. Let $m \leq n$ be the lengths $P$ and $Q$, respectively, and let $\sigma$ denote the size of the alphabet. On a standard unit-cost word-RAM with logarithmic word size we present an algorithm using time O\left(\frac{n}{\log_\sigma n} + m + \occ\right). Here \occ is the number of occurrences of $P$ in $Q$. For $m = o(n)$ this improves the $O(n)$ bound of the Knuth-Morris-Pratt algorithm. Furthermore, if $m = O(n/\log_\sigma n)$ our algorithm is optimal since any algorithm must spend at least \Omega(\frac{(n+m)\log \sigma}{\log n} + \occ) = \Omega(\frac{n}{\log_\sigma n} + \occ) time to read the input and report all occurrences. The result is obtained by a novel automaton construction based on the Knuth-Morris-Pratt algorithm combined with a new compact representation of subautomata allowing an optimal tabulation-based simulation.Comment: To appear in Journal of Discrete Algorithms. Special Issue on CPM 200

Synchronization Strings: Explicit Constructions, Local Decoding, and Applications

This paper gives new results for synchronization strings, a powerful combinatorial object that allows to efficiently deal with insertions and deletions in various communication settings: $\bullet$ We give a deterministic, linear time synchronization string construction, improving over an $O(n^5)$ time randomized construction. Independently of this work, a deterministic $O(n\log^2\log n)$ time construction was just put on arXiv by Cheng, Li, and Wu. We also give a deterministic linear time construction of an infinite synchronization string, which was not known to be computable before. Both constructions are highly explicit, i.e., the $i^{th}$ symbol can be computed in $O(\log i)$ time. $\bullet$ This paper also introduces a generalized notion we call long-distance synchronization strings that allow for local and very fast decoding. In particular, only $O(\log^3 n)$ time and access to logarithmically many symbols is required to decode any index. We give several applications for these results: $\bullet$ For any $\delta0$ we provide an insdel correcting code with rate $1-\delta-\epsilon$ which can correct any $O(\delta)$ fraction of insdel errors in $O(n\log^3n)$ time. This near linear computational efficiency is surprising given that we do not even know how to compute the (edit) distance between the decoding input and output in sub-quadratic time. We show that such codes can not only efficiently recover from $\delta$ fraction of insdel errors but, similar to [Schulman, Zuckerman; TransInf'99], also from any $O(\delta/\log n)$ fraction of block transpositions and replications. $\bullet$ We show that highly explicitness and local decoding allow for infinite channel simulations with exponentially smaller memory and decoding time requirements. These simulations can be used to give the first near linear time interactive coding scheme for insdel errors

Improved Parallel Rabin-Karp Algorithm Using Compute Unified Device Architecture

String matching algorithms are among one of the most widely used algorithms in computer science. Traditional string matching algorithms efficiency of underlaying string matching algorithm will greatly increase the efficiency of any application. In recent years, Graphics processing units are emerged as highly parallel processor. They out perform best of the central processing units in scientific computation power. By combining recent advancement in graphics processing units with string matching algorithms will allows to speed up process of string matching. In this paper we proposed modified parallel version of Rabin-Karp algorithm using graphics processing unit. Based on that, result of CPU as well as parallel GPU implementations are compared for evaluating effect of varying number of threads, cores, file size as well as pattern size.Comment: Information and Communication Technology for Intelligent Systems (ICTIS 2017

Fast and Compact Regular Expression Matching

We study 4 problems in string matching, namely, regular expression matching, approximate regular expression matching, string edit distance, and subsequence indexing, on a standard word RAM model of computation that allows logarithmic-sized words to be manipulated in constant time. We show how to improve the space and/or remove a dependency on the alphabet size for each problem using either an improved tabulation technique of an existing algorithm or by combining known algorithms in a new way

Quantum pattern matching fast on average

The $d$-dimensional pattern matching problem is to find an occurrence of a pattern of length $m \times \dots \times m$ within a text of length $n \times \dots \times n$, with $n \ge m$. This task models various problems in text and image processing, among other application areas. This work describes a quantum algorithm which solves the pattern matching problem for random patterns and texts in time $\widetilde{O}((n/m)^{d/2} 2^{O(d^{3/2}\sqrt{\log m})})$. For large $m$ this is super-polynomially faster than the best possible classical algorithm, which requires time $\widetilde{\Omega}( (n/m)^d + n^{d/2} )$. The algorithm is based on the use of a quantum subroutine for finding hidden shifts in $d$ dimensions, which is a variant of algorithms proposed by Kuperberg.Comment: 22 pages, 2 figures; v3: further minor changes, essentially published versio

Duel and sweep algorithm for order-preserving pattern matching

Given a text $T$ and a pattern $P$ over alphabet $\Sigma$, the classic exact matching problem searches for all occurrences of pattern $P$ in text $T$. Unlike exact matching problem, order-preserving pattern matching (OPPM) considers the relative order of elements, rather than their real values. In this paper, we propose an efficient algorithm for OPPM problem using the "duel-and-sweep" paradigm. Our algorithm runs in $O(n + m\log m)$ time in general and $O(n + m)$ time under an assumption that the characters in a string can be sorted in linear time with respect to the string size. We also perform experiments and show that our algorithm is faster that KMP-based algorithm. Last, we introduce the two-dimensional order preserved pattern matching and give a duel and sweep algorithm that runs in $O(n^2)$ time for duel stage and $O(n^2 m)$ time for sweeping time with $O(m^3)$ preprocessing time.Comment: 13 pages, 5 figure

Faster Approximate String Matching for Short Patterns

We study the classical approximate string matching problem, that is, given strings $P$ and $Q$ and an error threshold $k$, find all ending positions of substrings of $Q$ whose edit distance to $P$ is at most $k$. Let $P$ and $Q$ have lengths $m$ and $n$, respectively. On a standard unit-cost word RAM with word size $w \geq \log n$ we present an algorithm using time $$O(nk \cdot \min(\frac{\log^2 m}{\log n},\frac{\log^2 m\log w}{w}) + n)$$ When $P$ is short, namely, $m = 2^{o(\sqrt{\log n})}$ or $m = 2^{o(\sqrt{w/\log w})}$ this improves the previously best known time bounds for the problem. The result is achieved using a novel implementation of the Landau-Vishkin algorithm based on tabulation and word-level parallelism.Comment: To appear in Theory of Computing System