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…
Mohammad Javad Khani, Mahmood Ahmadi
Cyclic Redundancy Check (CRC) remains one of the most widely used error-detection mechanisms in communication, storage, and embedded systems. However, conventional software CRC implementations suffer from inherent sequential dependencies that limit efficient utilization of modern multi-core processors. This paper…
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…
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…
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…
Donald S. Ene, V.I.E Anireh
- Evaluating how well a whole system or set of subsystems performs is one of the primary objectives of performance testing. We can tell via performance assessment if the architecture implementation meets the design objectives. Performance evaluations of several parallel algorithms are compared in this study. Both…
Henrik Valter, Axel Karlsson, Miquel Pericàs
OpenMP is the de facto API for parallel programming in HPC applications. These programs are often computed in data centers, where energy consumption is a major issue. Whereas previous work has focused almost entirely on performance, we here analyse aspects of OpenMP from an energy consumption perspective. This analysis…
Junichiro Makino, Toshikazu Ebisuzaki, Ryutaro Himeno, Yoshihide Hayashizaki
Rapidly increasing amount of short read data generated by NGSs (new-generation sequencers) calls for the development of fast and accurate read alignment programs. The programs based on hash table (BLAST) and Burrows-Wheeler transform (bwa-mem) are used, and the latter is known to give superior performance. We here…
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…
Krzysztof Stuglik, Piotr Listkiewicz, Mateusz Kulczyk, Marcin Pietroń
'Marcin Pietroń'] Manual translation of the algorithms from sequential version to its parallel counterpart is time consuming and can be done only with the specific knowledge of hardware accelerator architecture, parallel programming or programming environment. The automation of this process makes porting the code much…
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…
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…