Computational methods adopted in the field of Systems Biology require the complete knowledge of reaction kinetic constants to perform simulations of the dynamics and understand the emergent behavior of biochemical systems. However, kinetic parameters of biochemical reactions are often difficult or impossible to measure, thus they are generally inferred from experimental data, in a process known as Parameter Estimation (PE). We consider here a PE methodology that exploits Particle Swarm Optimization (PSO) to estimate an appropriate kinetic parameterization, by comparing experimental time-series target data with in silica dynamics, simulated by using the parameterization encoded by each particle. In this work we present three different reboot strategies for PSO, whose aim is to reinitialize particle positions to avoid particles to get trapped in local optima, and we compare the performance of PSO coupled with the reboot strategies with respect to standard PSO in the case of the PE of two biochemical systems. Since the PE requires a huge number of simulations at each iteration, in this work we exploit a GPU-powered deterministic simulator, cupSODA, which performs in a parallel fashion all simulations and fitness evaluations. Finally, we show that the performances of our implementation scale sublinearly with respect to the swarm size, even on outdated GPUs.

(2017). Reboot strategies in particle swarm optimization and their impact on parameter estimation of biochemical systems . Retrieved from http://hdl.handle.net/10446/112317

Reboot strategies in particle swarm optimization and their impact on parameter estimation of biochemical systems

Tangherloni, Andrea;Cazzaniga, Paolo
2017-01-01

Abstract

Computational methods adopted in the field of Systems Biology require the complete knowledge of reaction kinetic constants to perform simulations of the dynamics and understand the emergent behavior of biochemical systems. However, kinetic parameters of biochemical reactions are often difficult or impossible to measure, thus they are generally inferred from experimental data, in a process known as Parameter Estimation (PE). We consider here a PE methodology that exploits Particle Swarm Optimization (PSO) to estimate an appropriate kinetic parameterization, by comparing experimental time-series target data with in silica dynamics, simulated by using the parameterization encoded by each particle. In this work we present three different reboot strategies for PSO, whose aim is to reinitialize particle positions to avoid particles to get trapped in local optima, and we compare the performance of PSO coupled with the reboot strategies with respect to standard PSO in the case of the PE of two biochemical systems. Since the PE requires a huge number of simulations at each iteration, in this work we exploit a GPU-powered deterministic simulator, cupSODA, which performs in a parallel fashion all simulations and fitness evaluations. Finally, we show that the performances of our implementation scale sublinearly with respect to the swarm size, even on outdated GPUs.
2017
Spolaor, Simone; Tangherloni, Andrea; Rundo, Leonardo; Nobile, Marco S.; Cazzaniga, Paolo
File allegato/i alla scheda:
File Dimensione del file Formato  
2017-CIBCB.pdf

Solo gestori di archivio

Versione: publisher's version - versione editoriale
Licenza: Licenza default Aisberg
Dimensione del file 324.36 kB
Formato Adobe PDF
324.36 kB Adobe PDF   Visualizza/Apri
Pubblicazioni consigliate

Aisberg ©2008 Servizi bibliotecari, Università degli studi di Bergamo | Terms of use/Condizioni di utilizzo

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10446/112317
Citazioni
  • Scopus 14
  • ???jsp.display-item.citation.isi??? 5
social impact