Pareto epsilon-dominance and identifiable solutions for BioCAD modeling

Claudio Angione; Jole Costanza; Giovanni Carapezza; Pietro Lió; Giuseppe Nicosia

doi:10.1145/2463209.2488787

Pareto epsilon-dominance and identifiable solutions for BioCAD modeling

Claudio Angione, Jole Costanza, Giovanni Carapezza, Pietro Lió, Giuseppe Nicosia

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

2 Citations (Scopus)

Abstract

We propose a framework to design metabolic pathways in which many objectives are optimized simultaneously. This allows to characterize the energy signature in models of algal and mitochondrial metabolism. The optimal design and assessment of the model is achieved through a multi-objective optimization technique driven by epsilon-dominance and identifiability analysis. A faster convergence process with robust candidate solutions is permitted by a relaxed Pareto dominance, regulating the granularity of the approximation of the Pareto front. Our framework is also suitable for black-box analysis, enabling to investigate and optimize any biological pathway modeled with ODEs, DAEs, FBA and GPR.

Original language	English
Title of host publication	Proceedings of the 50th Annual Design Automation Conference, DAC 2013
DOIs	https://doi.org/10.1145/2463209.2488787
Publication status	Published - 12 Jul 2013
Event	50th Annual Design Automation Conference - Austin, TX, United States Duration: 29 May 2013 → 7 Jun 2013

Conference

Conference	50th Annual Design Automation Conference
Abbreviated title	DAC 2013
Country/Territory	United States
City	Austin, TX
Period	29/05/13 → 7/06/13

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10.1145/2463209.2488787

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title = "Pareto epsilon-dominance and identifiable solutions for BioCAD modeling",

abstract = "We propose a framework to design metabolic pathways in which many objectives are optimized simultaneously. This allows to characterize the energy signature in models of algal and mitochondrial metabolism. The optimal design and assessment of the model is achieved through a multi-objective optimization technique driven by epsilon-dominance and identifiability analysis. A faster convergence process with robust candidate solutions is permitted by a relaxed Pareto dominance, regulating the granularity of the approximation of the Pareto front. Our framework is also suitable for black-box analysis, enabling to investigate and optimize any biological pathway modeled with ODEs, DAEs, FBA and GPR.",

author = "Claudio Angione and Jole Costanza and Giovanni Carapezza and Pietro Li{\'o} and Giuseppe Nicosia",

year = "2013",

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doi = "10.1145/2463209.2488787",

language = "English",

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T1 - Pareto epsilon-dominance and identifiable solutions for BioCAD modeling

AU - Angione, Claudio

AU - Costanza, Jole

AU - Carapezza, Giovanni

AU - Lió, Pietro

AU - Nicosia, Giuseppe

PY - 2013/7/12

Y1 - 2013/7/12

N2 - We propose a framework to design metabolic pathways in which many objectives are optimized simultaneously. This allows to characterize the energy signature in models of algal and mitochondrial metabolism. The optimal design and assessment of the model is achieved through a multi-objective optimization technique driven by epsilon-dominance and identifiability analysis. A faster convergence process with robust candidate solutions is permitted by a relaxed Pareto dominance, regulating the granularity of the approximation of the Pareto front. Our framework is also suitable for black-box analysis, enabling to investigate and optimize any biological pathway modeled with ODEs, DAEs, FBA and GPR.

AB - We propose a framework to design metabolic pathways in which many objectives are optimized simultaneously. This allows to characterize the energy signature in models of algal and mitochondrial metabolism. The optimal design and assessment of the model is achieved through a multi-objective optimization technique driven by epsilon-dominance and identifiability analysis. A faster convergence process with robust candidate solutions is permitted by a relaxed Pareto dominance, regulating the granularity of the approximation of the Pareto front. Our framework is also suitable for black-box analysis, enabling to investigate and optimize any biological pathway modeled with ODEs, DAEs, FBA and GPR.

UR - http://www.scopus.com/inward/record.url?scp=84879876869&partnerID=8YFLogxK

U2 - 10.1145/2463209.2488787

DO - 10.1145/2463209.2488787

M3 - Conference contribution

AN - SCOPUS:84879876869

SN - 9781450320719

BT - Proceedings of the 50th Annual Design Automation Conference, DAC 2013

T2 - 50th Annual Design Automation Conference

Y2 - 29 May 2013 through 7 June 2013

ER -

Pareto epsilon-dominance and identifiable solutions for BioCAD modeling

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