Estimating reaction constants in stochastic biological systems with a multi-swarm PSO running on GPUs

Marco S. Nobile; Daniela Besozzi; Paolo Cazzaniga; Giancarlo Mauri; Dario Pescini

doi:10.1145/2330784.2330964

Estimating reaction constants in stochastic biological systems with a multi-swarm PSO running on GPUs

Marco S. Nobile
, Daniela Besozzi
, Paolo Cazzaniga
, Giancarlo Mauri
, Dario Pescini

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Academic › peer-review

21 Citations (Scopus)

Abstract

We present a parameter estimation method, based on particle swarm optimization (PSO) and embedding the tauleaping algorithm, for the efficient estimation of reaction constants in stochastic models of biological systems, using as target a set of discrete-time measurements of molecular amounts sampled in different experimental conditions. To account for the multiplicity of data, we consider a multiswarm formulation of PSO. The whole method is developed for GPGPU architecture to reduce the computational costs. Copyright is held by the author/owner(s).

Original language	English
Title of host publication	GECCO'12 - Proceedings of the 14th International Conference on Genetic and Evolutionary Computation Companion
Place of Publication	New York
Publisher	Association for Computing Machinery, Inc.
Pages	1421-1422
Number of pages	2
ISBN (Electronic)	978-1-4503-1178-6
DOIs	https://doi.org/10.1145/2330784.2330964
Publication status	Published - 20 Aug 2012
Externally published	Yes
Event	2012 Genetic and Evolutionary Computation Conference, GECCO 2012 - Philadelphia, PA, United States Duration: 7 Jul 2012 → 11 Jul 2012 Conference number: 14

Conference

Conference	2012 Genetic and Evolutionary Computation Conference, GECCO 2012
Country/Territory	United States
City	Philadelphia, PA
Period	7/07/12 → 11/07/12

Keywords

GPU computing
Parameter estimation
Particle swarm optimization
Systems biology
Tau leaping

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10.1145/2330784.2330964

Cite this

Nobile, M. S., Besozzi, D., Cazzaniga, P., Mauri, G., & Pescini, D. (2012). Estimating reaction constants in stochastic biological systems with a multi-swarm PSO running on GPUs. In GECCO'12 - Proceedings of the 14th International Conference on Genetic and Evolutionary Computation Companion (pp. 1421-1422). Association for Computing Machinery, Inc.. https://doi.org/10.1145/2330784.2330964

@inproceedings{1beaf98bfa8a4f5d90028834b8a28be9,

title = "Estimating reaction constants in stochastic biological systems with a multi-swarm PSO running on GPUs",

abstract = "We present a parameter estimation method, based on particle swarm optimization (PSO) and embedding the tauleaping algorithm, for the efficient estimation of reaction constants in stochastic models of biological systems, using as target a set of discrete-time measurements of molecular amounts sampled in different experimental conditions. To account for the multiplicity of data, we consider a multiswarm formulation of PSO. The whole method is developed for GPGPU architecture to reduce the computational costs. Copyright is held by the author/owner(s).",

keywords = "GPU computing, Parameter estimation, Particle swarm optimization, Systems biology, Tau leaping",

author = "Nobile, \{Marco S.\} and Daniela Besozzi and Paolo Cazzaniga and Giancarlo Mauri and Dario Pescini",

year = "2012",

month = aug,

day = "20",

doi = "10.1145/2330784.2330964",

language = "English",

pages = "1421--1422",

booktitle = "GECCO'12 - Proceedings of the 14th International Conference on Genetic and Evolutionary Computation Companion",

publisher = "Association for Computing Machinery, Inc.",

address = "United States",

note = "2012 Genetic and Evolutionary Computation Conference, GECCO 2012 ; Conference date: 07-07-2012 Through 11-07-2012",

}

Nobile, MS, Besozzi, D, Cazzaniga, P, Mauri, G & Pescini, D 2012, Estimating reaction constants in stochastic biological systems with a multi-swarm PSO running on GPUs. in GECCO'12 - Proceedings of the 14th International Conference on Genetic and Evolutionary Computation Companion. Association for Computing Machinery, Inc., New York, pp. 1421-1422, 2012 Genetic and Evolutionary Computation Conference, GECCO 2012, Philadelphia, PA, United States, 7/07/12. https://doi.org/10.1145/2330784.2330964

Estimating reaction constants in stochastic biological systems with a multi-swarm PSO running on GPUs. / Nobile, Marco S.; Besozzi, Daniela; Cazzaniga, Paolo et al.
GECCO'12 - Proceedings of the 14th International Conference on Genetic and Evolutionary Computation Companion. New York: Association for Computing Machinery, Inc., 2012. p. 1421-1422.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Academic › peer-review

TY - GEN

T1 - Estimating reaction constants in stochastic biological systems with a multi-swarm PSO running on GPUs

AU - Nobile, Marco S.

AU - Besozzi, Daniela

AU - Cazzaniga, Paolo

AU - Mauri, Giancarlo

AU - Pescini, Dario

N1 - Conference code: 14

PY - 2012/8/20

Y1 - 2012/8/20

N2 - We present a parameter estimation method, based on particle swarm optimization (PSO) and embedding the tauleaping algorithm, for the efficient estimation of reaction constants in stochastic models of biological systems, using as target a set of discrete-time measurements of molecular amounts sampled in different experimental conditions. To account for the multiplicity of data, we consider a multiswarm formulation of PSO. The whole method is developed for GPGPU architecture to reduce the computational costs. Copyright is held by the author/owner(s).

AB - We present a parameter estimation method, based on particle swarm optimization (PSO) and embedding the tauleaping algorithm, for the efficient estimation of reaction constants in stochastic models of biological systems, using as target a set of discrete-time measurements of molecular amounts sampled in different experimental conditions. To account for the multiplicity of data, we consider a multiswarm formulation of PSO. The whole method is developed for GPGPU architecture to reduce the computational costs. Copyright is held by the author/owner(s).

KW - GPU computing

KW - Parameter estimation

KW - Particle swarm optimization

KW - Systems biology

KW - Tau leaping

UR - https://www.scopus.com/pages/publications/84864989985

U2 - 10.1145/2330784.2330964

DO - 10.1145/2330784.2330964

M3 - Conference contribution

AN - SCOPUS:84864989985

SP - 1421

EP - 1422

BT - GECCO'12 - Proceedings of the 14th International Conference on Genetic and Evolutionary Computation Companion

PB - Association for Computing Machinery, Inc.

CY - New York

T2 - 2012 Genetic and Evolutionary Computation Conference, GECCO 2012

Y2 - 7 July 2012 through 11 July 2012

ER -

Nobile MS, Besozzi D, Cazzaniga P, Mauri G, Pescini D. Estimating reaction constants in stochastic biological systems with a multi-swarm PSO running on GPUs. In GECCO'12 - Proceedings of the 14th International Conference on Genetic and Evolutionary Computation Companion. New York: Association for Computing Machinery, Inc. 2012. p. 1421-1422 doi: 10.1145/2330784.2330964

Estimating reaction constants in stochastic biological systems with a multi-swarm PSO running on GPUs

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