Related papers: String Matching with Multicore CPUs: Performing Be…
This article presents an automatic approach to quickly derive a good solution for hardware resource partition and task granularity for task-based parallel applications on heterogeneous many-core architectures. Our approach employs a…
String matching is a fundamental problem in computer science, with critical applications in text retrieval, bioinformatics, and data analysis. Among the numerous solutions that have emerged for this problem in recent decades,…
Sorting is one of the most fundamental problems in the field of computer science. With the rapid development of manycore processors, it shows great importance to design efficient parallel sort algorithm on manycore architecture. This paper…
Motif discovery in DNA sequences is a challenging task in molecular biology. In computational motif discovery, Planted (l, d) motif finding is a widely studied problem and numerous algorithms are available to solve it. Both hardware and…
Multicore architectures dominate today's processor market. Even though the number of cores and threads are pretty high and continues to grow, inherently serial algorithms do not benefit from the abundance of cores and threads. In this…
This work proposes a novel approach to evaluate and analyze the behavior of multi-population parallel genetic algorithms (PGAs) when running on a cluster of multi-core processors. In particular, we deeply study their numerical and…
Integer sorting on multicores and GPUs can be realized by a variety of approaches that include variants of distribution-based methods such as radix-sort, comparison-oriented algorithms such as deterministic regular sampling and random…
The approximate string matching is a fundamental and recurrent problem that arises in most computer science fields. This problem can be defined as follows: Let $D=\{x_1,x_2,\ldots x_d\}$ be a set of $d$ words defined on an alphabet…
Heterogeneous many-cores are now an integral part of modern computing systems ranging from embedding systems to supercomputers. While heterogeneous many-core design offers the potential for energy-efficient high-performance, such potential…
Many modern sequence alignment tools implement fast string matching using the space efficient data structure called FM-index. The succinct nature of this data structure presents unique challenges for the algorithm designers. In this paper,…
String sorting is an important part of tasks such as building index data structures. Unfortunately, current string sorting algorithms do not scale to massively parallel distributed-memory machines since they either have latency (at least)…
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…
This paper investigates co-scheduling algorithms for processing a set of parallel applications. Instead of executing each application one by one, using a maximum degree of parallelism for each of them, we aim at scheduling several…
Searching for all occurrences of a pattern in a text is a fundamental problem in computer science with applications in many other fields, like natural language processing, information retrieval and computational biology. In the last two…
This paper presents a new, parallel implementation of clustering and demonstrates its utility in greatly speeding up the process of identifying homologous proteins. Clustering is a technique to reduce the number of comparison needed to find…
Dynamically adaptive multi-core architectures have been proposed as an effective solution to optimize performance for peak power constrained processors. In processors, the micro-architectural parameters or voltage/frequency of each core to…
Evolutionary modeling applications are the best way to provide full information to support in-depth understanding of evaluation of organisms. These applications mainly depend on identifying the evolutionary history of existing organisms and…
This article introduces a highly parallel algorithm for molecular dynamics simulations with short-range forces on single node multi- and many-core systems. The algorithm is designed to achieve high parallel speedups for strongly…
The abelian pattern matching problem consists in finding all substrings of a text which are permutations of a given pattern. This problem finds application in many areas and can be solved in linear time by a naive sliding window approach.…
A new generation of manycore processors is on the rise that offers dozens and more cores on a chip and, in a sense, fuses host processor and accelerator. In this paper we target the efficient training of generalized linear models on these…