Estimation of kinetic reaction constants: exploiting reboot strategies to improve PSO’s performance

Simone Spolaor, Andrea Tangherloni, Leonardo Rundo, Paolo Cazzaniga, Marco S. Nobile

Research output: Chapter in Book/Report/Conference proceedingConference contributionAcademicpeer-review

Abstract

The simulation and analysis of mathematical models of biological systems require a complete knowledge of the reaction kinetic constants. Unfortunately, these values are often difficult to measure, but they can be inferred from experimental data in a process known as Parameter Estimation (PE). In this work, we tackle the PE problem using Particle Swarm Optimization (PSO) coupled with three different reboot strategies, which aim to reinitialize particle positions to avoid local optima. In particular, we highlight the better performance of PSO coupled with the reboot strategies with respect to standard PSO. Finally, since the PE requires a huge number of simulations at each iteration of PSO, we exploit cupSODA, a GPU-powered deterministic simulator, which performs all simulations and fitness evaluations in parallel.

Original languageEnglish
Title of host publicationComputational Intelligence Methods for Bioinformatics and Biostatistics - 14th International Meeting, CIBB 2017, Revised Selected Papers
EditorsAlberto Policriti, Gunnar W. Klau, Andrea Bracciali, Massimo Bartoletti, Roberto Tagliaferri, Annalisa Barla, Leif Peterson
Place of PublicationCham
PublisherSpringer
Pages92-102
Number of pages11
ISBN (Electronic)978-3-030-14160-8
ISBN (Print)978-3-030-14159-2
DOIs
Publication statusPublished - 14 Feb 2019
Event14th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, CIBB 2017 - Cagliari, Italy
Duration: 7 Sep 20179 Sep 2017

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume10834 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference14th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, CIBB 2017
CountryItaly
CityCagliari
Period7/09/179/09/17

Keywords

  • cupSODA
  • GPGPU computing
  • Parameter estimation
  • Particle swarm optimization
  • Systems biology

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