Pareto epsilon-dominance and identifiable solutions for BioCAD modeling

Authors:
Claudio Angione;Jole Costanza;Giovanni Carapezza;Pietro Lió;Giuseppe Nicosia
Affiliations:
University of Cambridge, UK;University of Catania, Italy;University of Catania, Italy;University of Cambridge, UK;University of Catania, Italy
Venue:
Proceedings of the 50th Annual Design Automation Conference
Year:
2013

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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.