title: A combined model reduction algorithm for controlled biochemical systems.
abstract: Systems Biology continues to produce increasingly large models of complex biochemical reaction networks. In applications requiring, for example, parameter estimation, the use of agent-based modelling approaches, or real-time simulation, this growing model complexity can present a significant hurdle. Often, however, not all portions of a model are of equal interest in a given setting. In such situations methods of model reduction offer one possible approach for addressing the issue of complexity by seeking to eliminate those portions of a pathway that can be shown to have the least effect upon the properties of interest.
  
  
  
  In this paper a model reduction algorithm bringing together the complementary aspects of proper lumping and empirical balanced truncation is presented. Additional contributions include the development of a criterion for the selection of state-variable elimination via conservation analysis and use of an 'averaged' lumping inverse. This combined algorithm is highly automatable and of particular applicability in the context of 'controlled' biochemical networks.
  
  
  
  The algorithm is demonstrated here via application to two examples; an 11 dimensional model of bacterial chemotaxis in Escherichia coli and a 99 dimensional model of extracellular regulatory kinase activation (ERK) mediated via the epidermal growth factor (EGF) and nerve growth factor (NGF) receptor pathways. In the case of the chemotaxis model the algorithm was able to reduce the model to 2 state-variables producing a maximal relative error between the dynamics of the original and reduced models of only 2.8% whilst yielding a 26 fold speed up in simulation time. For the ERK activation model the algorithm was able to reduce the system to 7 state-variables, incurring a maximal relative error of 4.8%, and producing an approximately 10 fold speed up in the rate of simulation. Indices of controllability and observability are additionally developed and demonstrated throughout the paper. These provide insight into the relative importance of individual reactants in mediating a biochemical system's input-output response even for highly complex networks.
  
  
  
  Through application, this paper demonstrates that combined model reduction methods can produce a significant simplification of complex Systems Biology models whilst retaining a high degree of predictive accuracy. In particular, it is shown that by combining the methods of proper lumping and empirical balanced truncation it is often possible to produce more accurate reductions than can be obtained by the use of either method in isolation.
authors.affiliation: Department of Mathematics and Statistics, University of Reading, Reading, RG6 6AX, UK.|Certara QSP, University of Kent Innovation Centre, Canterbury, CT2 7FG, UK.
authors.forename: Thomas J
authors.identifier: 0000-0001-9541-4043
authors.initials: TJ
authors.lastname: Snowden
authors.affiliation: Certara QSP, University of Kent Innovation Centre, Canterbury, CT2 7FG, UK.|Leiden Academic Centre for Drug Research, Universiteit Leiden, Leiden, NL-2333 CC, Netherlands.
authors.forename: Piet H
authors.initials: PH
authors.lastname: van der Graaf
authors.affiliation: Department of Mathematics and Statistics, University of Reading, Reading, RG6 6AX, UK. m.tindall@reading.ac.uk.|The Institute for Cardiovascular and Metabolic Research (ICMR), University of Reading, Reading, RG6 6AX, UK. m.tindall@reading.ac.uk.
authors.forename: Marcus J
authors.initials: MJ
authors.lastname: Tindall
mesh_terms: D000465:Algorithms; D002633:Chemotaxis; D004789:Enzyme Activation; D004926:Escherichia coli / Q000166:cytology; D048049:Extracellular Signal-Regulated MAP Kinases / Q000378:metabolism; D008954:Models, Biological; D010766:Phosphorylation; D017475:Receptors, Nerve Growth Factor / Q000378:metabolism; D015398:Signal Transduction; D049490:Systems Biology / Q000379:methods*
chemical_list: D017475:Receptors, Nerve Growth Factor; D048049:Extracellular Signal-Regulated MAP Kinases
keywords: Controlled systems; Empirical balanced truncation; Lumping; Model reduction