EvoPER-An R package for applying evolutionary computation methods in the parameter estimation of individual-based models implemented in Repast

Prestes García, Antonio and Rodríguez-Patón Aradas, Alfonso (2016). EvoPER-An R package for applying evolutionary computation methods in the parameter estimation of individual-based models implemented in Repast. "PeerJ Preprint", v. 1 (n. 2279); pp. 1-10. ISSN 2167-9843. https://doi.org/doi.org/10.7287/peerj.preprints.2279v1.

Description

Title: EvoPER-An R package for applying evolutionary computation methods in the parameter estimation of individual-based models implemented in Repast
Author/s:
  • Prestes García, Antonio
  • Rodríguez-Patón Aradas, Alfonso
Item Type: Article
Título de Revista/Publicación: PeerJ Preprint
Date: 2016
Volume: 1
Subjects:
Freetext Keywords: Individual-Based Modeling; Parameter Estimation; Evolutionary Computation; Systems Biology
Faculty: E.T.S. de Ingenieros Informáticos (UPM)
Department: Inteligencia Artificial
Creative Commons Licenses: Recognition - No derivative works - Non commercial

Full text

[img]
Preview
PDF - Requires a PDF viewer, such as GSview, Xpdf or Adobe Acrobat Reader
Download (206kB) | Preview

Abstract

Individual-based models are complex and they normally have an elevated number of input parameters which must be tuned in order to reproduce the experimental or observed data as accurately as possible. Hence one of the weakest points of such kind of models is the fact that rarely the modeler has the enough information about the correct values or even the acceptable range for the input parameters. Therefore, several parameter combinations must be checked to find an acceptable set of input factors minimizing the deviations of simulated and observed data. In practice, most of the times, is computationally unfeasible to traverse the complete search space to check all parameter combination in order to find the best of them. That is precisely the kind of combinatorial problem suitable for evolutionary computation techniques. In this work we present the EvoPER, an R package for simplifying the parameter estimation using evolutionary computation techniques. The current version of EvoPER includes implementations of PSO, SA and ACO algorithms for parameter estimation of models generated with the open source agent-based modeling toolkit Repast.

Funding Projects

TypeCodeAcronymLeaderTitle
FP7612146PLASWIRESUniversidad Politécnica de MadridEngineering multicellular biocircuits: programming cell-cell communication using plasmids as wires
Government of SpainTIN2012-36992UnspecifiedUnspecifiedProgramación e ingeniería de biocircuitos: diseño y modelado in silico

More information

Item ID: 45442
DC Identifier: http://oa.upm.es/45442/
OAI Identifier: oai:oa.upm.es:45442
DOI: doi.org/10.7287/peerj.preprints.2279v1
Official URL: https://peerj.com/preprints/2279/
Deposited by: Memoria Investigacion
Deposited on: 30 Oct 2017 17:19
Last Modified: 19 Mar 2019 14:20
  • Logo InvestigaM (UPM)
  • Logo GEOUP4
  • Logo Open Access
  • Open Access
  • Logo Sherpa/Romeo
    Check whether the anglo-saxon journal in which you have published an article allows you to also publish it under open access.
  • Logo Dulcinea
    Check whether the spanish journal in which you have published an article allows you to also publish it under open access.
  • Logo de Recolecta
  • Logo del Observatorio I+D+i UPM
  • Logo de OpenCourseWare UPM