Listar por autor "Penas, David R."
Mostrando ítems 1-11 de 11
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A cloud-based enhanced differential evolution algorithm for parameter estimation problems in computational systems biology
Teijeiro, Diego; Pardo, Xoán C.; Penas, David R.; González, Patricia; Banga, Julio R.; Doallo, Ramón (Springer New York LLC, 2017)[Abstract] Metaheuristics are gaining increasing recognition in many research areas, computational systems biology among them. Recent advances in metaheuristics can be helpful in locating the vicinity of the global solution ... -
A parallel metaheuristic for large mixed-integer dynamic optimization problems, with applications in computational biology
Penas, David R.; Henriques, David; González, Patricia; Doallo, Ramón; Saez-Rodriguez, Julio; Banga, Julio R. (Public Library of Science, 2017)[Abstract] Background: We consider a general class of global optimization problems dealing with nonlinear dynamic models. Although this class is relevant to many areas of science and engineering, here we are interested ... -
Computational advances in polynomial optimization: RAPOSa, a freely available global solver
González Rodríguez, Brais; Ossorio-Castillo, Joaquin; González-Díaz, Julio; González Rueda, Ángel Manuel; Penas, David R.; Rodríguez-Martínez, Diego (Springer Netherlands, 2022-09)[Abstract]: In this paper we introduce RAPOSa, a global optimization solver specifically designed for (continuous) polynomial programming problems with box-constrained variables. Written entirely in C++, RAPOSa is based ... -
Enhanced global optimization methods applied to complex fisheries stock assessment models
Penas, David R.; Gómez, Andrés; Fraguela, Basilio B.; Martín, María J.; Cerviño, Santiago (Elsevier BV, 2019-04)[Abstract] Statistical fisheries models are frequently used by researchers and agencies to understand the behavior of marine ecosystems or to estimate the maximum acceptable catch of different species of commercial interest. ... -
Enhanced parallel Differential Evolution algorithm for problems in computational systems biology
Penas, David R.; Banga, Julio R.; González, Patricia; Doallo, Ramón (Elsevier BV, 2015)[Abstract] Many key problems in computational systems biology and bioinformatics can be formulated and solved using a global optimization framework. The complexity of the underlying mathematical models require the use of ... -
Evaluation of Parallel Differential Evolution Implementations on MapReduce and Spark
Teijeiro, Diego; Pardo, Xoán C.; Penas, David R.; González, Patricia; Banga, Julio R.; Doallo, Ramón (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 ... -
Hybrid parallel multimethod hyperheuristic for mixed-integer dynamic optimization problems in computational systems biology
González, Patricia; Argüeso-Alejandro, Pablo; Penas, David R.; Pardo, Xoán C.; Sáez-Rodríguez, Julio; Banga, Julio R.; Doallo, Ramón (Springer New York LLC, 2019-05-08)[Abstract] This paper describes and assesses a parallel multimethod hyperheuristic for the solution of complex global optimization problems. In a multimethod hyperheuristic, different metaheuristics cooperate to outperform ... -
Multimethod Optimization for Reverse Engineering of Complex Biological Networks
González, Patricia; Penas, David R.; Pardo, Xoán C.; Banga, Julio R.; Doallo, Ramón (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 ... -
Multimethod optimization in the cloud: A case‐study in systems biology modelling
González, Patricia; Penas, David R.; Pardo, Xoán C.; Banga, Julio R.; Doallo, Ramón (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 ... -
Parameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy
Penas, David R.; González, Patricia; Egea, Jose A.; Doallo, Ramón; Banga, Julio R. (BioMed Central Ltd., 2017)[Abstract] Background The development of large-scale kinetic models is one of the current key issues in computational systems biology and bioinformatics. Here we consider the problem of parameter estimation in nonlinear ... -
Using the Cloud for Parameter Estimation Problems: Comparing Spark vs MPI with a Case-Study
González, Patricia; Pardo, Xoán C.; Penas, David R.; Teijeiro, Diego; Banga, Julio R.; Doallo, Ramón (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 ...
