Listar GI-GAC - Artigos por título
Mostrando ítems 108-127 de 181
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MarDRe: efficient MapReduce-based removal of duplicate DNA reads in the cloud
(Oxford University Press, 2017)[Abstract] This article presents MarDRe, a de novo cloud-ready duplicate and near-duplicate removal tool that can process single- and paired-end reads from FASTQ/FASTA datasets. MarDRe takes advantage of the widely adopted ... -
Mobile Robot Positioning with 433-MHz Wireless Motes with Varying Transmission Powers and a Particle Filter
(Multidisciplinary Digital Publishing Institute, 2015)In wireless positioning systems, the transmitter’s power is usually fixed. In this paper, we explore the use of varying transmission powers to increase the performance of a wireless localization system. To this extent, we ... -
ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models
(Oxford University Press, 2019-08-21)[Abstract] ModelTest-NG is a reimplementation from scratch of jModelTest and ProtTest, two popular tools for selecting the best-fit nucleotide and amino acid substitution models, respectively. ModelTest-NG is one to two ... -
MPI and UPC broadcast, scatter and gather algorithms in Xeon Phi
(John Wiley & Sons Ltd., 2016-05-06)[Abstract] Accelerators have revolutionised the high performance computing (HPC) community. Despite their advantages, their very specific programming models and limited communication capabilities have kept them in a ... -
MPI-dot2dot: A Parallel Tool to Find DNA Tandem Repeats on Multicore Clusters
(Springer, 2022)[Abstract] Tandem Repeats (TRs) are segments that occur several times in a DNA sequence, and each copy is adjacent to other. In the last few years, TRs have gained significant attention as they are thought to be related ... -
MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems
(Oxford University Press, 2016)[Abstracts] MSAProbs is a state-of-the-art protein multiple sequence alignment tool based on hidden Markov models. It can achieve high alignment accuracy at the expense of relatively long runtimes for large-scale input ... -
Multimethod optimization in the cloud: A case‐study in systems biology modelling
(Wiley, 2018-06-25)[Abstract] Optimization problems appear in many different applications in science and engineering. A large number of different algorithms have been proposed for solving them; however, there is no unique general optimization ... -
Multithreaded and Spark parallelization of feature selection filters
(2016)[Abstract]: Vast amounts of data are generated every day, constituting a volume that is challenging to analyze. Techniques such as feature selection are advisable when tackling large datasets. Among the tools that provide ... -
Non-IID data and Continual Learning processes in Federated Learning: A long road ahead
(Elsevier, 2022)[Abstract] Federated Learning is a novel framework that allows multiple devices or institutions to train a machine learning model collaboratively while preserving their data private. This decentralized approach is prone ... -
Nonblocking collectives for scalable Java communications
(John Wiley & Sons Ltd., 2015-04-22)[Abstract] This paper presents a Java implementation of the recently published MPI 3.0 nonblocking message passing collectives in order to analyze and assess the feasibility of taking advantage of these operations in shared ... -
Novel parallelization of simulated annealing and Hooke & Jeeves search algorithms for multicore systems with application to complex fisheries stock assessment models
(Elsevier Ltd, 2016-11)[Abstract] Estimating parameters of a statistical fisheries assessment model typically involves a comparison of disparate datasets to a forward simulation model through a likelihood function. In all but trivial cases the ... -
Numerical Simulation of Pollutant Transport in a Shallow-Water System on the Cell Heterogeneous Processor
(Springer, 2013)[Abstract] This paper presents an implementation, optimized for the Cell processor, of a finite volume numerical scheme for 2D shallow-water systems with pollutant transport. A description of the special architecture and ... -
On processing extreme data
(Universitatea de Vest din Timisoara,West University of Timisoara, 2016)[Abstract] Extreme Data is an incarnation of Big Data concept distinguished by the massive amounts of data that must be queried, communicated and analyzed in near real-time by using a very large number of memory or storage ... -
OpenCNN: A Winograd Minimal Filtering Algorithm Implementation in CUDA
(MDPI, 2021)[Abstract] Improving the performance of the convolution operation has become a key target for High Performance Computing (HPC) developers due to its prevalence in deep learning applied mainly to video processing. The ... -
Optimization of Real-World MapReduce Applications With Flame-MR: Practical Use Cases
(Institute of Electrical and Electronics Engineers, 2018-11-12)[Abstract] Apache Hadoop is a widely used MapReduce framework for storing and processing large amounts of data. However, it presents some performance issues that hinder its utilization in many practical use cases. Although ... -
Optimizing Coherence Traffic in Manycore Processors Using Closed-Form Caching/Home Agent Mappings
(Institute of Electrical and Electronics Engineers, 2021-02-09)[Abstract] Manycore processors feature a high number of general-purpose cores designed to work in a multithreaded fashion. Recent manycore processors are kept coherent using scalable distributed directories. A paramount ... -
Optimizing parcel exchange among landowners: A soft alternative to land consolidation
(Elsevier, 2020-01)[Abstract]: For decades, public policy has favored the use of land consolidation to reduce the fragmentation of land ownership. Private actors, on the other hand, have focused on the purchase, rental and exchange of land ... -
Parallel and Scalable Short-Read Alignment on Multi-Core Clusters Using UPC++
(Johannes Gutenberg University Mainz, 2016)[Abstract]: The growth of next-generation sequencing (NGS) datasets poses a challenge to the alignment of reads to reference genomes in terms of alignment quality and execution speed. Some available aligners have been shown ... -
Parallel ant colony optimization for the training of cell signaling networks
(Elsevier, 2022)[Abstract]: Acquiring a functional comprehension of the deregulation of cell signaling networks in disease allows progress in the development of new therapies and drugs. Computational models are becoming increasingly popular ... -
Parallel Brownian dynamics simulations with the message-passing and PGAS programming models
(Elsevier BV, 2013-04)[Abstract] The simulation of particle dynamics is among the most important mechanisms to study the behavior of molecules in a medium under specific conditions of temperature and density. Several models can be used to compute ...
