Related papers: Parallel Query in the Suffix Tree
Suffix trees are one of the most versatile data structures in stringology, with many applications in bioinformatics. Their main drawback is their size, which can be tens of times larger than the input sequence. Much effort has been put into…
Due to the coarse granularity of data accesses and the heavy use of latches, indices in the B-tree family are not efficient for in-memory databases, especially in the context of today's multi-core architecture. In this paper, we present PI,…
We study the problem of scheduling a set of jobs with release dates, deadlines and processing requirements (or works), on parallel speed-scaled processors so as to minimize the total energy consumption. We consider that both preemption and…
The suffix array is a data structure that finds numerous applications in string processing problems for both linguistic texts and biological data. It has been introduced as a memory efficient alternative for suffix trees. The suffix array…
We compare different methods for sampling from discrete probability distributions and introduce a new algorithm which is especially efficient on massively parallel processors, such as GPUs. The scheme preserves the distribution properties…
Regular expression matching is essential for many applications, such as finding patterns in text, exploring substrings in large DNA sequences, or lexical analysis. However, sequential regular expression matching may be time-prohibitive for…
The longest common prefix (LCP) array is a versatile auxiliary data structure in indexed string matching. It can be used to speed up searching using the suffix array (SA) and provides an implicit representation of the topology of an…
Given two point sets $R$ and $B$ in the plane, with cardinalities $m$ and $n$, respectively, and each set stored in a separate R-tree, we present an algorithm to decide whether $R$ and $B$ are linearly separable. Our algorithm exploits the…
Given a pattern string $P$ of length $n$ consisting of $\delta$ distinct characters and a query string $T$ of length $m$, where the characters of $P$ and $T$ are drawn from an alphabet $\Sigma$ of size $\Delta$, the {\em exact string…
Based on the Breslauer-Italiano online suffix tree construction algorithm (2013) with double logarithmic worst-case guarantees on the update time per letter, we develop near-real-time algorithms for several classical problems on strings,…
Given a string on an integer alphabet, we present an algorithm that computes the set of all distinct squares belonging to this string in time linear to the string length. As an application, we show how to compute the tree topology of the…
Computing the connected components of a graph is a fundamental problem in algorithmic graph theory. A major question in this area is whether we can compute connected components in $o(\log n)$ parallel time. Recent works showed an…
Two recent lower bounds on the compressibility of repetitive sequences, $\delta \le \gamma$, have received much attention. It has been shown that a length-$n$ string $S$ over an alphabet of size $\sigma$ can be represented within the…
We present $O(\log^2 \log n)$ time 3-coloring, maximal independent set and maximal matching algorithms for trees in the Massively Parallel Computation (MPC) model. Our algorithms are deterministic, apply to arbitrary-degree trees and work…
In online makespan minimization a sequence of jobs $\sigma = J_1,..., J_n$ has to be scheduled on $m$ identical parallel machines so as to minimize the maximum completion time of any job. We investigate the problem with an essentially new…
Motivated by the imminent growth of massive, highly redundant genomic databases, we study the problem of compressing a string database while simultaneously supporting fast random access, substring extraction and pattern matching to the…
Let $S$ be a string of length $n$ over an alphabet $\Sigma$ and let $Q$ be a subset of $\Sigma$ of size $q \geq 2$. The 'co-occurrence problem' is to construct a compact data structure that supports the following query: given an integer $w$…
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…
In this paper we propose a variant of the induced suffix sorting algorithm by Nong (TOIS, 2013) that computes simultaneously the Lyndon array and the suffix array of a text in $O(n)$ time using $\sigma + O(1)$ words of working space, where…
The tango tree is the first proven $O(\lg \lg n)$-competitive binary search tree (BST). We present the first ever experimental implementation of tango trees and compare the running time of the tango tree with the multi-splay tree and the…