Browsing by Author "Banga, Julio R."
Now showing items 1-20 of 22
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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 ... -
An approach to support generic topologies in distributed PSO algorithms in Spark
Pardo, Xoán C.; González, Patricia; Banga, Julio R.; Doallo, Ramón (Armando De Giusti, Marcelo Naiouf, Franco Chichizola, Enzo Rucci, Laura De Giusti. Universidad Nacional de La Plata. Facultad de Informática., 2023)[Abstract] Particle Swarm Optimization (PSO) is a popular population-based search algorithm that has been applied to all kinds of complex optimization problems. Although the performance of the algorithm strongly depends ... -
An Efficient Ant Colony Optimization Framework for HPC Environments
González, Patricia; Osorio, Roberto; Pardo, Xoán C.; Banga, Julio R.; Doallo, Ramón (Elsevier, 2022)[Abstract] Combinatorial optimization problems arise in many disciplines, both in the basic sciences and in applied fields such as engineering and economics. One of the most popular combinatorial optimization methods is ... -
Análisis de observabilidad e identificabilidad estructural de modelos no lineales: aplicación a la vía de señalización JAK/STAT
Villaverde, Alejandro; Banga, Julio R. (Universidade da Coruña, Servizo de Publicacións, 2019)[Resumen] La observabilidad e identificabilidad estructural son propiedades que se corresponden con la posibilidad teórica de determinar los vectores de estado y de parámetros de un modelo a partir de su salida. Recientemente ... -
Automated design of synthetic biocircuits in the stochastic regime
Sequeiros Ferreiro, Carlos Xosé; Vázquez, Carlos; Banga, Julio R.; Otero-Muras, Irene (IFAC Secretariat / Elsevier, 2022)[Abstract]: In this work, we present an optimization-based design strategy for gene regulatory networks (GRNs) in the stochastic regime (i.e., in the presence of molecular noise). The approach exploits a recently developed ... -
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 ... -
IDESS: a toolbox for identification and automated design of stochastic gene circuits
Sequeiros Ferreiro, Carlos Xosé; Pájaro Diéguez, Manuel; Vázquez, Carlos; Banga, Julio R.; Otero-Muras, Irene (Oxford University Press, 2023-11)[Abstract]: Motivation One of the main causes hampering predictability during the model identification and automated design of gene circuits in synthetic biology is the effect of molecular noise. Stochasticity may ... -
Implementing cloud-based parallel metaheuristics: an overview
González, Patricia; Pardo, Xoán C.; Doallo, Ramón; Banga, Julio R. (Universidad Nacional de la Plata - Facultad de Informatica, 2018-12-12)[Abstract] Metaheuristics are among the most popular methods for solving hard global optimization problems in many areas of science and engineering. Their parallel im- plementation applying HPC techniques is a common ... -
Implementing Parallel Differential Evolution on Spark
Teijeiro, Diego; Pardo, Xoán C.; González, Patricia; Banga, Julio R.; Doallo, Ramón (Springer, 2016-04-02)[Abstract] Metaheuristics are gaining increased attention as an efficient way of solving hard global optimization problems. Differential Evolution (DE) is one of the most popular algorithms in that class. However, its ... -
Improved cooperative Ant Colony Optimization for the solution of binary combinatorial optimization applications
Prado-Rodríguez, Roberto; González, Patricia; Banga, Julio R.; Doallo, Ramón (John Wiley & Sons, 2024)[Abstract]: Binary combinatorial optimization plays a crucial role in various scientific and engineering fields. While deterministic approaches have traditionally been used to solve these problems, stochastic methods, ... -
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 ... -
Parallel ant colony optimization for the training of cell signaling networks
González, Patricia; Prado-Rodriguez, Roberto; Gábor, Attila; Saez-Rodriguez, Julio; Banga, Julio R.; Doallo, Ramón (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 ... -
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 ... -
Population based metaheuristics in Spark: Towards a general framework using PSO as a case study
Pardo, Xoán C.; González, Patricia; Banga, Julio R.; Doallo, Ramón (Elsevier, 2024-03)[Abstract]: Over the years metaheuristics have been successfully applied to optimization problems in many real-world applications. The increasing complexity and scale of the problems addressed has posed new challenges to ... -
Self-adaptive Cooperation Scheme in a Parallel ACO Algorithm for Binary Combinatorial Problems
Prado-Rodríguez, Roberto; González, Patricia; Banga, Julio R.; Doallo, Ramón (Universidade da Coruña, Servizo de Publicacións, 2023)[Abstract] The ant colony optimization (ACO) is widely used for combinatorial optimization problems, although it can suffer from fast convergence to local minima. In order to provide a versatile implementation of ACO, ... -
Spark Implementation of the Enhanced Scatter Search Metaheuristic: Methodology and Assessment
Pardo, Xoán C.; Argüeso-Alejandro, Pablo; González, Patricia; Banga, Julio R.; Doallo, Ramón (Elsevier BV, 2020-12)[Abstract] Optimization problems arise nowadays in all disciplines, not only in the scientific area but also in the field of engineering or economics, and in many others. Currently, challenging optimization problems require ...