Related papers: Parallel Query in the Suffix Tree
We show how to determine whether a given pattern p of length m occurs in a given text t of length n in ${\tilde O}(\sqrt{n}+\sqrt{m})$\footnote{${\tilde O}$ allows for logarithmic factors in m and $n/m$} time, with inverse polynomial…
Sparse suffix sorting is the problem of sorting $b=o(n)$ suffixes of a string of length $n$. Efficient sparse suffix sorting algorithms have existed for more than a decade. Despite the multitude of works and their justified claims for…
We find a succinct expression for computing the sequence $x_t = a_t x_{t-1} + b_t$ in parallel with two prefix sums, given $t = (1, 2, \dots, n)$, $a_t \in \mathbb{R}^n$, $b_t \in \mathbb{R}^n$, and initial value $x_0 \in \mathbb{R}$. On…
The order preserving pattern matching (OPPM) problem is, given a pattern string $p$ and a text string $t$, find all substrings of $t$ which have the same relative orders as $p$. In this paper, we consider two variants of the OPPM problem…
We present space-efficient parallel strategies for two fundamental combinatorial search problems, namely, backtrack search and branch-and-bound, both involving the visit of an $n$-node tree of height $h$ under the assumption that a node can…
In this paper, we present a new data structure called the packed compact trie (packed c-trie) which stores a set $S$ of $k$ strings of total length $n$ in $n \log\sigma + O(k \log n)$ bits of space and supports fast pattern matching queries…
We introduce the lazy search tree data structure. The lazy search tree is a comparison-based data structure on the pointer machine that supports order-based operations such as rank, select, membership, predecessor, successor, minimum, and…
The suffix trees are fundamental data structures for various kinds of string processing. The suffix tree of a text string $T$ of length $n$ has $O(n)$ nodes and edges, and the string label of each edge is encoded by a pair of positions in…
The notions of synchronizing and partitioning sets are recently introduced variants of locally consistent parsings with great potential in problem-solving. In this paper we propose a deterministic algorithm that constructs for a given…
A longest repeat query on a string, motivated by its applications in many subfields including computational biology, asks for the longest repetitive substring(s) covering a particular string position (point query). In this paper, we extend…
Given a text $T$ of length $n$ and a pattern $P$ of length $m$, the string matching problem is a task to find all occurrences of $P$ in $T$. In this study, we propose an algorithm that solves this problem in $O((n + m)q)$ time considering…
We show how to use parallelization to speed up sampling from an arbitrary distribution $\mu$ on a product space $[q]^n$, given oracle access to counting queries: $\mathbb{P}_{X\sim \mu}[X_S=\sigma_S]$ for any $S\subseteq [n]$ and $\sigma_S…
We present the first worst-case linear time algorithm that directly computes the parameterized suffix and LCP arrays for constant sized alphabets. Previous algorithms either required quadratic time or the parameterized suffix tree to be…
We consider the problem of indexing a string $t$ of length $n$ to report the occurrences of a query pattern $p$ containing $m$ characters and $j$ wildcards. Let $occ$ be the number of occurrences of $p$ in $t$, and $\sigma$ the size of the…
In this paper we present two versions of a parallel finger structure FS on p processors that supports searches, insertions and deletions, and has a finger at each end. This is to our knowledge the first implementation of a parallel search…
Data processing systems offer an ever increasing degree of parallelism on the levels of cores, CPUs, and processing nodes. Query optimization must exploit high degrees of parallelism in order not to gradually become the bottleneck of query…
We deal with the problem of maintaining the suffix tree indexing structure for a fully-online collection of multiple strings, where a new character can be prepended to any string in the collection at any time. The only previously known…
We introduce a new metric of match, called Cartesian tree matching, which means that two strings match if they have the same Cartesian trees. Based on Cartesian tree matching, we define single pattern matching for a text of length n and a…
The wavelet tree (Grossi et al. [SODA, 2003]) and wavelet matrix (Claude et al. [Inf. Syst., 47:15--32, 2015]) are compact indices for texts over an alphabet $[0,\sigma)$ that support rank, select and access queries in $O(\lg \sigma)$ time.…
Given a pattern string $P$ of length $n$ and a query string $T$ of length $m$, where the characters of $P$ and $T$ are drawn from an alphabet of size $\Delta$, the {\em exact string matching} problem consists of finding all occurrences of…