Strain design as multiobjective network interdiction problem: A preliminary approach

Marina Torres; Shouyong Jiang; David Pelta; Marcus Kaiser; Natalio Krasnogor

doi:10.1007/978-3-030-00374-6_26

Strain design as multiobjective network interdiction problem: A preliminary approach

Marina Torres^*, Shouyong Jiang, David Pelta, Marcus Kaiser, Natalio Krasnogor

^*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceeding › Published conference contribution

1 Citation (Scopus)

Abstract

Computer-aided techniques have been widely applied to analyse the biological circuits of microorganisms and facilitate rational modification of metabolic networks for strain design in order to maximise the production of desired biochemicals for metabolic engineering. Most existing computational methods for strain design formulate the network redesign as a bilevel optimisation problem. While such methods have shown great promise for strain design, this paper employs the idea of network interdiction to fulfil the task. Strain design as a Multiobjective Network Interdiction Problem (MO-NIP) is proposed for which two objectives are optimised (biomass and bioengineering product) simultaneously in addition to the minimisation of the costs of genetic perturbations (design costs). An initial approach to solve the MO-NIP consists on a Nondominated Sorting Genetic Algorithm (NSGA-II). The shown examples demonstrate the usefulness of the proposed formulation for the MO-NIP and the feasibility of the NSGA-II as a problem solver.

Original language	English
Title of host publication	Advances in Artificial Intelligence - 18th Conference of the Spanish Association for Artificial Intelligence, CAEPIA 2018, Proceedings
Editors	Antonio Gonzalez, Alicia Troncoso, Francisco Herrera, Sergio Damas, Rosana Montes, Sergio Alonso, Oscar Cordon
Publisher	Springer Verlag
Pages	273-282
Number of pages	10
ISBN (Print)	9783030003739
DOIs	https://doi.org/10.1007/978-3-030-00374-6_26
Publication status	Published - 2018
Event	18th Conference of the Spanish Association for Artificial Intelligence, CAEPIA 2018 - Granada, Spain Duration: 23 Oct 2018 → 26 Oct 2018

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	11160 LNAI
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	18th Conference of the Spanish Association for Artificial Intelligence, CAEPIA 2018
Country/Territory	Spain
City	Granada
Period	23/10/18 → 26/10/18

Bibliographical note

Funding Information:
and TIN2017-86647-P from the Spanish Ministry of Economy and Competitiveness (including European Regional Development Funds). MT enjoys a Ph.D. research training staff grant associated with the project TIN2014-55024-P and co-funded by the European Social Fund.

Acknowledgements:
SJ, MK, and NK acknowledge the EPSRC for funding project “Synthetic Portabolomics: Leading the way at the crossroads of the Digital and the Bio Economies (EP/N031962/1)”.

Publisher Copyright:
© Springer Nature Switzerland AG 2018.

Keywords

Metabolic networks
Multiobjective bilevel optimisation
Network interdiction
Strain design

Access to Document

10.1007/978-3-030-00374-6_26

Cite this

Torres, M., Jiang, S., Pelta, D., Kaiser, M., & Krasnogor, N. (2018). Strain design as multiobjective network interdiction problem: A preliminary approach. In A. Gonzalez, A. Troncoso, F. Herrera, S. Damas, R. Montes, S. Alonso, & O. Cordon (Eds.), Advances in Artificial Intelligence - 18th Conference of the Spanish Association for Artificial Intelligence, CAEPIA 2018, Proceedings (pp. 273-282). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 11160 LNAI). Springer Verlag. https://doi.org/10.1007/978-3-030-00374-6_26

Strain design as multiobjective network interdiction problem: A preliminary approach. / Torres, Marina; Jiang, Shouyong; Pelta, David et al.
Advances in Artificial Intelligence - 18th Conference of the Spanish Association for Artificial Intelligence, CAEPIA 2018, Proceedings. ed. / Antonio Gonzalez; Alicia Troncoso; Francisco Herrera; Sergio Damas; Rosana Montes; Sergio Alonso; Oscar Cordon. Springer Verlag, 2018. p. 273-282 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 11160 LNAI).

Research output: Chapter in Book/Report/Conference proceeding › Published conference contribution

Torres, M, Jiang, S, Pelta, D, Kaiser, M & Krasnogor, N 2018, Strain design as multiobjective network interdiction problem: A preliminary approach. in A Gonzalez, A Troncoso, F Herrera, S Damas, R Montes, S Alonso & O Cordon (eds), Advances in Artificial Intelligence - 18th Conference of the Spanish Association for Artificial Intelligence, CAEPIA 2018, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 11160 LNAI, Springer Verlag, pp. 273-282, 18th Conference of the Spanish Association for Artificial Intelligence, CAEPIA 2018, Granada, Spain, 23/10/18. https://doi.org/10.1007/978-3-030-00374-6_26

Torres M, Jiang S, Pelta D, Kaiser M, Krasnogor N. Strain design as multiobjective network interdiction problem: A preliminary approach. In Gonzalez A, Troncoso A, Herrera F, Damas S, Montes R, Alonso S, Cordon O, editors, Advances in Artificial Intelligence - 18th Conference of the Spanish Association for Artificial Intelligence, CAEPIA 2018, Proceedings. Springer Verlag. 2018. p. 273-282. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). Epub 2018 Sept 27. doi: 10.1007/978-3-030-00374-6_26

Torres, Marina ; Jiang, Shouyong ; Pelta, David et al. / Strain design as multiobjective network interdiction problem : A preliminary approach. Advances in Artificial Intelligence - 18th Conference of the Spanish Association for Artificial Intelligence, CAEPIA 2018, Proceedings. editor / Antonio Gonzalez ; Alicia Troncoso ; Francisco Herrera ; Sergio Damas ; Rosana Montes ; Sergio Alonso ; Oscar Cordon. Springer Verlag, 2018. pp. 273-282 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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Strain design as multiobjective network interdiction problem: A preliminary approach

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