26 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…
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…
H.K. Al-Mahdawi, A. I Sidikova, Hussein Alkattan, Mostafa Abotaleb + 2 more
'Ammar Kadi' 'El-Sayed M El-kenawy'] We considered in this work the linear operator equation and used the Landweber iterative method as an iterative solver. After that, we used the multigrid method as an optimization method for obtaining an approximation solution with a highly accurate and fast process. A new parallel…
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
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…
Authors not listed
Protein conformational landscapes contain the functionally relevant information useful for understanding biological processes. Mapping out conformational landscapes provides valuable insights into protein behaviors and biological phenomena, and has relevance to therapeutic design. While experimental structural biology…
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…
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…
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…
Authors not listed
Cyclic peptides become attractive therapeutic candidates due to their diverse biological activities. However, existing deep learning-based sequence design models, such as ProteinMPNN, are primarily optimized using cross-entropy loss and often overlook the unique topological constraints of cyclic peptides. This limits…
Authors not listed
A significant advancement in Merrifield’s classic solid-phase peptide synthesis (SPPS) that greatly expands the scope of accessible peptide structures is reported here. Building upon the one-bead, one-compound concept, this approach enables the simultaneous synthesis of multiple peptides on a single bead, followed by a…
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…
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…
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…
Riley Hickman, Malcolm Sim, Sergio Pablo-García, Ivan Woolhouse + 6 more
Self-driving laboratories (SDLs) are next-generation research and development platforms for closed-loop, autonomous experimentation that combine ideas from artificial intelligence, robotics, and high-performance computing. A critical component of SDLs is the decision-making algorithm used to prioritize experiments to…
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…
David Herrmann, Patrick Hodapp, Martin Starman, Pei-Chi Huang + 16 more
Analytical data in chemistry and other disciplines is usually generated in different formats and lacks common data and metadata standards that are necessary for a FAIR handling of research data. In the work presented herein, we describe a workflow that uses non-standardized, in some cases proprietary data formats from…
Sirilak Ketchaya, Apisit Rattanatranurak
Quicksort is an important algorithm that uses the divide and conquer concept, and it can be run to solve any problem. The performance of the algorithm can be improved by implementing this algorithm in parallel. In this paper, the parallel sorting algorithm named the Multi-Deque Partition Dual-Deque Merge Sorting…
Frances Smith, Rhys Griffiths, Declan Meehan, Harriet Knowles + 4 more
Synthetic methods that enable the macrocyclisation of peptides facilitate the development of more effective therapeutic and diagnostic tools. Herein we report a peptide cyclisation strategy based on intramolecular interception of visible-light-mediated cysteine desulfurisation. This method allows cyclisation 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…
Authors not listed
Automated chemistry platforms hold the potential to enable large-scale organic synthesis campaigns, such as producing a library of compounds for biological evaluation. The efficiency of such platforms will depend on the schedule according to which the synthesis operations are executed. In this work, we study the…