13 papers · ranked by Valyu relevance
Jovan Blanuša, Paolo Ienne, Kubilay Atasu
Enumerating simple cycles has important applications in computational biology, network science, and financial crime analysis. In this work, we focus on parallelising the state-of-the-art simple cycle enumeration algorithms by Johnson and Read-Tarjan along with their applications to temporal graphs. To our knowledge, we…
Meisam Razaviyayn, Mingyi Hong, Zhi‐Quan Luo, Jong‐Shi Pang
Consider the problem of minimizing the sum of a smooth (possibly non-convex) and a convex (possibly nonsmooth) function involving a large number of variables. A popular approach to solve this problem is the block coordinate descent (BCD) method whereby at each iteration only one variable block is updated while the…
Yang Yu
Sequence Authors: ['Yang Yu'] Recent advances in reasoning models have demonstrated significant improvements in accuracy, particularly for complex tasks such as mathematical reasoning, by employing detailed and comprehensive reasoning processes. However, generating these lengthy reasoning sequences is computationally…
Daniel Ruprecht
The paper introduces an OpenMP implementation of pipelined Parareal and compares it to a standard MPI-based implementation. Both versions yield essentially identical runtimes, but, depending on the compiler, the OpenMP variant consumes about 7% less energy. However, its key advantage is a significantly smaller memory…
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…
Adrian Jackson, Orestis Agathokleous
—Regions of nested loops are a common feature of High Performance Computing (HPC) codes. In shared memory programming models, such as OpenMP, these structure are the most common source of parallelism. Parallelising these structures requires the programmers to make a static decision on how parallelism should be applied.…
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…
Temitayo Adefemi
—Parallelization has become a cornerstone of modern computing, influencing everything from high-performance supercomputers to everyday mobile devices. This paper presents a comprehensive guide on the fundamentals of parallelization that every computer scientist should know, beginning with a historical perspective that…
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…
V. Schwambach, S. Cleyet-Merle, Alain Issard, Stéphane Mancini
—Computer vision applications constitute one of the key drivers for embedded multicore architectures. Although the number of available cores is increasing in new architectures, designing an application to maximize the utilization of the platform is still a challenge. In this sense, parallel performance prediction tools…
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…