Browsing by Author "González-Domínguez, Jorge"
Now showing items 1-20 of 51
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A 2D algorithm with asymmetric workload for the UPC conjugate gradient method
González-Domínguez, Jorge; Marques, Osni A.; Martín, María J.; Touriño, Juan (Springer New York LLC, 2014)[Abstract] This paper examines four different strategies, each one with its own data distribution, for implementing the parallel conjugate gradient (CG) method and how they impact communication and overall performance. ... -
A SIMD Algorithm for the Detection of Epistatic Interactions of Any Order
Ponte-Fernández, Christian; González-Domínguez, Jorge; Martín, María J. (Elsevier, 2022)[Abstract] Epistasis is a phenomenon in which a phenotype outcome is determined by the interaction of genetic variation at two or more loci and it cannot be attributed to the additive combination of effects corresponding ... -
Accelerating binary biclustering on platforms with CUDA-enabled GPUs
González-Domínguez, Jorge; Expósito, Roberto R. (Elsevier Ltd, 2018)[Abstract]: Data mining is nowadays essential in many scientific fields to extract valuable information from large input datasets and transform it into an understandable structure. For instance, biclustering techniques are ... -
Acceleration of a Feature Selection Algorithm Using High Performance Computing
Beceiro, Bieito; González-Domínguez, Jorge; Touriño, Juan (MDPI AG, 2020-09-01)[Abstract] Feature selection is a subfield of data analysis that is on reducing the dimensionality of datasets, so that subsequent analyses over them can be performed in affordable execution times while keeping the same ... -
Analysis of I/O Performance on an Amazon EC2 Cluster Compute and High I/O Platform
Expósito, Roberto R.; Taboada, Guillermo L.; Ramos Garea, Sabela; González-Domínguez, Jorge; Touriño, Juan; Doallo, Ramón (Springer Netherlands, 2013-12)[Abstract] Cloud computing is currently being explored by the scientific community to assess its suitability for High Performance Computing (HPC) environments. In this novel paradigm, compute and storage resources, as well ... -
Applying dynamic balancing to improve the performance of MPI parallel genomics applications
Fernández Fraga, Alejandro; González-Domínguez, Jorge; Martín, María J. (Association for Computing Machinery (ACM), 2024-05-21)[Absctract]: Genomics applications are becoming more and more important in the field of bioinformatics, as they allow researchers to extract meaningful information from the huge amount of data generated by the new sequencing ... -
Automatic mapping of parallel applications on multicore architectures using the Servet benchmark suite
González-Domínguez, Jorge; Taboada, Guillermo L.; Fraguela, Basilio B.; Martín, María J.; Touriño, Juan (Pergamon Press, 2012-03)[Abstract] Servet is a suite of benchmarks focused on detecting a set of parameters with high influence on the overall performance of multicore systems. These parameters can be used for autotuning codes to increase their ... -
BetaGPU: Harnessing GPU power for parallelized beta distribution functions
Fernández Fraga, Alejandro; González-Domínguez, Jorge; Martín, María J. (Elsevier, 2025-02)[Abstract]: The efficient computation of Beta distribution functions, particularly the Probability Density Function (PDF) and Cumulative Distribution Function (CDF), is critical in various scientific fields, including ... -
BigDEC: A multi-algorithm Big Data tool based on the k-mer spectrum method for scalable short-read error correction
Expósito, Roberto R.; González-Domínguez, Jorge (Elsevier, 2024-05)[Abstract]: Despite the significant improvements in both throughput and cost provided by modern Next-Generation Sequencing (NGS) platforms, sequencing errors in NGS datasets can still degrade the quality of downstream ... -
bioScience: A new python science library for high-performance computing bioinformatics analytics
López-Fernández, Aurelio; Gómez-Vela, Francisco A.; González-Domínguez, Jorge; Bidare-Divakarachari, Parameshachari (Elsevier Ltd, 2024)[Abstract]: BioScience is an advanced Python library designed to satisfy the growing data analysis needs in the field of bioinformatics by leveraging High-Performance Computing (HPC). This library encompasses a vast multitude ... -
Communication avoiding and overlapping for numerical linear algebra
Georganas, Evangelos; González-Domínguez, Jorge; Solomonik, Edgar; Zheng, Yili; Touriño, Juan; Yelick, Katherine (IEEE Computer Society, 2013-02-25)[Abstract] To efficiently scale dense linear algebra problems to future exascale systems, communication cost must be avoided or overlapped. Communication-avoiding 2.5D algorithms improve scalability by reducing inter-processor ... -
CUDA acceleration of MI-based feature selection methods
Beceiro, Bieito; González-Domínguez, Jorge; Morán-Fernández, Laura; Bolón-Canedo, Verónica; Touriño, Juan (Elsevier, 2024-08)[Abstract]: Feature selection algorithms are necessary nowadays for machine learning as they are capable of removing irrelevant and redundant information to reduce the dimensionality of the data and improve the quality of ... -
CUDA-JMI: Acceleration of feature selection on heterogeneous systems
González-Domínguez, Jorge; Expósito, Roberto R.; Bolón-Canedo, Verónica (Elsevier, 2020-01)[Abstract]: Feature selection is a crucial step nowadays in machine learning and data analytics to remove irrelevant and redundant characteristics and thus to provide fast and reliable analyses. Many research works have ... -
Evaluation of Existing Methods for High-Order Epistasis Detection
Ponte-Fernández, Christian; González-Domínguez, Jorge; Carvajal-Rodriguez, Antonio; Martín, María J. (Institute of Electrical and Electronics Engineers, 2020-10-15)[Abstract] Finding epistatic interactions among loci when expressing a phenotype is a widely employed strategy to understand the genetic architecture of complex traits in GWAS. The abundance of methods dedicated to the ... -
Fast search of third-order epistatic interactions on CPU and GPU clusters
Ponte-Fernández, Christian; González-Domínguez, Jorge; Martín, María J. (Sage Publications Ltd., 2019-05-27)[Abstract] Genome-Wide Association Studies (GWASs), analyses that try to find a link between a given phenotype (such as a disease) and genetic markers, have been growing in popularity in the recent years. Relations between ... -
Fiuncho: a program for any-order epistasis detection in CPU clusters
Ponte-Fernández, Christian; González-Domínguez, Jorge; Martín, María J. (Springer, 2022)[Abstract]: Epistasis can be defined as the statistical interaction of genes during the expression of a phenotype. It is believed that it plays a fundamental role in gene expression, as individual genetic variants have ... -
GPU-accelerated exhaustive search for third-order epistatic interactions in case–control studies
González-Domínguez, Jorge; Schmidt, Bertil (Elsevier Ltd, 2015)[Abstract] Interest in discovering combinations of genetic markers from case–control studies, such as Genome Wide Association Studies (GWAS), that are strongly associated to diseases has increased in recent years. Detecting ... -
High-speed exhaustive 3-locus interaction epistasis analysis on FPGAs
Kässens, Jan Christian; Wienbrandt, Lars; González-Domínguez, Jorge; Schmidt, Bertil; Schimmler, Manfred (Elsevier B.V., 2015-07)[Abstract]: Epistasis, the interaction between genes, has become a major topic in molecular and quantitative genetics. It is believed that these interactions play a significant role in genetic variations causing complex ... -
HSRA: Hadoop-based spliced read aligner for RNA sequencing data
Expósito, Roberto R.; González-Domínguez, Jorge; Touriño, Juan (Public Library of Science, 2018-07-31)[Abstract] Nowadays, the analysis of transcriptome sequencing (RNA-seq) data has become the standard method for quantifying the levels of gene expression. In RNA-seq experiments, the mapping of short reads to a reference ... -
Hybrid CPU/GPU Acceleration of Detection of 2-SNP Epistatic Interactions in GWAS
González-Domínguez, Jorge; Schmidt, Bertil; Kässens, Jan Christian; Wienbrandt, Lars (Springer, 2014-08)[Abstract] High-throughput genotyping technologies allow the collection of up to a few million genetic markers (such as SNPs) of an individual within a few minutes of time. Detecting epistasis, such as 2-SNP interactions, ...