14 papers · ranked by Valyu relevance
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…
János Végh
With both knowing more and more details about how neurons and complex neural networks work and having serious demand for making performable huge artificial networks, more and more efforts are devoted to build both hardware and/or software simulators and supercomputers targeting artificial intelligence applications…
SPT Krishnan, Sim Sze Liang, Bharadwaj Veeravalli
Background RNA structure prediction problem is a computationally complex task, especially with pseudo-knots. The problem is well-studied in existing literature and predominantly uses highly coupled Dynamic Programming (DP) solutions. The problem scale and complexity become embarrassingly humungous to handle as sequence…
Gonzalo Vera, Ritsert C Jansen, Remo L Suppi
Background R is the preferred tool for statistical analysis of many bioinformaticians due in part to the increasing number of freely available analytical methods. Such methods can be quickly reused and adapted to each particular experiment. However, in experiments where large amounts of data are generated, for example…
James S. Sims, William L. George, Steven G. Satterfield, Howard K. Hung + 21 more
'Howard K. Hung' 'John G. Hagedorn' 'Peter M. Ketcham' 'Terence J. Griffin' 'Stanley A. Hagstrom' 'Julien C. Franiatte' 'Garnett W. Bryant' 'W. Jaskólski' 'Nicos S. Martys' 'Charles E. Bouldin' 'Vernon Simmons' 'Oliver P. Nicolas' 'James A. Warren' 'Barbara A. am Ende' 'John E. Koontz' 'B. James Filla' 'Vital G.…
Zeyu Xia, Canqun Yang, Chenchen Peng, Yifei Guo + 3 more
'Tao Tang' 'Yingbo Cui'] Background The advent of Single Molecule Real-Time (SMRT) sequencing has overcome many limitations of second-generation sequencing, such as limited read lengths, PCR amplification biases. However, longer reads increase data volume exponentially and high error rates make many existing alignment…
Tao Liu, Yi Liu, Chen Qian, Depei Qian + 1 more
With the development of multi-/many-core processors, applications need to be written as parallel programs to improve execution efficiency. For data-intensive applications that use multiple threads to read/write files simultaneously, an I/O sub-system can easily become a bottleneck when too many of these types of…
Hassan Mushtaq, Sajid Gul Khawaja, Muhammad Usman Akram, Amanullah Yasin + 3 more
Clustering is the most common method for organizing unlabeled data into its natural groups (called clusters), based on similarity (in some sense or another) among data objects. The Partitioning Around Medoids (PAM) algorithm belongs to the partitioning-based methods of clustering widely used for objects categorization…
Xiandong Meng, Yanqing Ji
This paper focuses on the latest research and critical reviews on modern computing architectures, software and hardware accelerated algorithms for bioinformatics data analysis with an emphasis on one of the most important sequence analysis applications-hidden Markov models (HMM). We show the detailed performance…
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…
Ashish Chapagain, Dima Abuoliem, In Ho Cho, Tongbiao Wang
Multifunctional nanosurfaces receive growing attention due to their versatile properties. Capillary force lithography (CFL) has emerged as a simple and economical method for fabricating these surfaces. In recent works, the authors proposed to leverage the evolution strategies (ES) to modify nanosurface characteristics…
Vladislav Skorpil, Vaclav Oujezsky, Arcangelo Castiglione, Gianni D’Angelo
'Gianni D’Angelo'] This paper presents an implementation of the parallelization of genetic algorithms. Three models of parallelized genetic algorithms are presented, namely the Master-Slave genetic algorithm, the Coarse-Grained genetic algorithm, and the Fine-Grained genetic algorithm. Furthermore, these models are…
Kent Milfeld, Bronis R. de Supinski, Lars Koesterke, Jannis Klinkenberg + 2 more
'Jannis Klinkenberg' 'Fabian Orland' 'Christian Terboven'] Load balance is an important factor that fundamentally impacts the scalability of any parallel application. In this paper we present a case study to address a complex load imbalance related to the convergence behavior of the parallel SPMD implementation of a…