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Using the Cloud for Parameter Estimation Problems: Comparing Spark vs MPI with a Case-Study
(Institute of Electrical and Electronics Engineers, 2017-07-13)
[Abstract]
Systems biology is an emerging approach focused in generating new knowledge about complex biological systems by combining experimental data with mathematical modeling and advanced computational techniques. Many ...
Multimethod Optimization for Reverse Engineering of Complex Biological Networks
(Association for Computing Machinery, 2018-09)
[Abstract] Optimization problems appears in different areas of science and engineering. This paper considers the general problem of reverse engineering in computational biology by means of mixed-integer nonlinear dynamic ...
Facilitating the development of stencil applications using the Heterogeneous Programming Library
(2017)
[Abstract] Stencil computations are very common in scientific codes. Heterogeneous systems achieve good results solving these problems, but their programming is complex because of the ghost regions required in multi-device ...
Parallel Sparse Modified Gram-Schmidt QR Decomposition
(Springer, 1996)
[Abstract] We present a parallel computational method for the QR decomposition with column pivoting of a sparse matrix by means of Modified Gram-Schmidt orthogonalization. Nonzero elements of the matrix M to be decomposed ...
Performance Optimization of a Parallel Error Correction Tool
(MDPI, 2021)
[Abstract] Due to the continuous development in the field of Next Generation Sequencing (NGS) technologies that have allowed researchers to take advantage of greater genetic samples in less time, it is a matter of relevance ...
Non-blocking Java Communications Support on Clusters
(Springer, 2006)
[Abstract] This paper presents communication strategies for supporting efficient non-blocking Java communication on clusters. The communication performance is critical for the overall cluster performance. It is possible ...
Sparse Householder QR factorization on a mesh
(IEEE Computer Society, 1996-01)
[Abstract] We analyze the parallelization of QR factorization by means of Householder transformations. This parallelization is carried out on a machine with a mesh topology (a 2-D torus to be more precise). We use a cyclic ...
Evaluation of Parallel Differential Evolution Implementations on MapReduce and Spark
(Springer, 2017-09)
[Abstract] Global optimization problems arise in many areas of science and engineering, computational and systems biology and bioinformatics among them. Many research efforts have focused on developing parallel metaheuristics ...
Design and Implementation of MapReduce using the PGAS Programming Model with UPC
(IEEE Computer Society, 2012-01-03)
[Abstract] MapReduce is a powerful tool for processing large data sets used by many applications running in distributed environments. However, despite the increasing number of computationally intensive problems that require ...
NPB-MPJ: NAS Parallel Benchmarks Implementation for Message-Passing in Java
(IEEE Computer Society, 2009-05-08)
[Abstract] Java is a valuable and emerging alternative for the development of parallel applications, thanks to the availability of several Java message-passing libraries and its full multithreading support. The combination ...
