13 papers · ranked by Valyu relevance
Bahman Arasteh, Seyed Salar Sefati, Huseyin Kusetogullari, Farzad Kiani + 3 more
Efficient task scheduling remains a key challenge in High-Performance Computing and Internet of Things (IoT) systems, where the sequential execution of nested loops often limits parallelism. This paper proposes a hybrid approach that dynamically parallelizes nested loops in heterogeneous IoT environments. The suggested…
Peiyu Zong, Wenpeng Deng, Jian Liu, Jue Ruan
Farrar recommends employing a stripe method to enhance the implementation of in-sequence parallelism, resulting in significant improvements in parallel performance through the utilization of the SIMD instruction set. This method involves reorganizing the originally sequential computation. The length of each stripe…
Peiyu Zong, Wenpeng Deng, Jian Liu, Jue Ruan
The rapid advancements in sequencing length necessitate the adoption of increasingly efficient sequence alignment algorithms. The Needleman-Wunsch method introduces the foundational dynamic programming (DP) matrix calculation for global alignment, which evaluates the overall alignment of sequences. However, this method…
Wilfried Agbeto, Camille Coti, Vladimir Reinharz
Advances in graph algorithmics have allowed in-depth study of many natural objects from molecular biology or chemistry to social networks. Particularly in molecular biology and cheminformatics, understanding complex structures by identifying conserved sub-structures is a key milestone towards the artificial design of…
Kecong Tang, Ahsan Sanaullah, Degui Zhi, Shaojie Zhang
Durbin’s positional Burrows-Wheeler transform (PBWT) enables algorithms with the optimal time complexity of O(MN) for reporting all vs all haplotype matches in a population panel with M haplotypes and N variant sites. However, even this efficiency may still be too slow when the number of haplotypes reaches millions. To…
Stuart Byma, Akash Dhasade, Adrian Altenhoff, Christophe Dessimoz + 1 more
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 similar pairs in a set of n elements such as protein sequences. Precise…
Francois Besnier, Kevin A. Glover, Maria Anisimova
This software package provides an R-based framework to make use of multi-core computers when running analyses in the population genetics program STRUCTURE. It is especially addressed to those users of STRUCTURE dealing with numerous and repeated data analyses, and who could take advantage of an efficient script to…
Patrizio Dazzi
Embarrassingly parallel problems are characterised by a very small amount of information to be exchanged among the parts they are split in, during their parallel execution. As a consequence they do not require sophisticated, low-latency, high-bandwidth interconnection networks but can be efficiently computed in…
Mohammed Abutaha, Islam Amar, Salman AlQahtani, Xiaowei Li + 2 more
Encrypting pictures quickly and securely is required to secure image transmission over the internet and local networks. This may be accomplished by employing a chaotic scheme with ideal properties such as unpredictability and non-periodicity. However, practically every modern-day system is a real-time system, for which…
Bérenger Bramas, Gang Mei
Task-based programming models have demonstrated their efficiency in the development of scientific applications on modern high-performance platforms. They allow delegation of the management of parallelization to the runtime system (RS), which is in charge of the data coherency, the scheduling, and the assignment of the…
Alvaro Estebanez, Diego R. Llanos, David Orden, Belen Palop + 1 more
'Rafael Sachetto Oliveira'] Loops are a rich source of parallelism. Unfortunately, many loops cannot be safely parallelized at compile time because the compiler is not able to guarantee that there will be no dependence violations. Thread-Level Speculation (TLS) techniques, either hardware or software-based, allow the…
Yuma Osako, Aineias Arango, Toshitake Asabuki
Animals flexibly combine learned behaviors into novel actions without practicing their combinations, yet the computational mechanisms that enable independently acquired computations to be expressed in parallel remain unclear. Here we show that feedback geometry during learning determines whether recurrent dynamics can…
Max Doblas, Oscar Lostes-Cazorla, Quim Aguado-Puig, Cristian Iñiguez + 2 more
Pairwise sequence alignment is a core component of multiple sequencing-data analysis tools. Recent advancements in sequencing technologies have enabled the generation of longer sequences at a much lower price. Thus, long-read sequencing technologies have become increasingly popular in sequencing-based studies. However…