An improved multi-parametric programming algorithm for flux balance analysis of metabolic networks
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Abstract: Flux balance analysis has proven an effective tool for analyzing metabolic networks. In flux balance analysis, reaction rates and optimal pathways are ascertained by solving a linear program, in which the growth rate is maximized subject to mass-balance constraints. A variety of cell functions in response to environmental stimuli can be quantified using flux balance analysis by parameterizing the linear program with respect to extracellular conditions. However, for most large, genome-scale metabolic networks of practical interest, the resulting parametric problem has multiple and highly degenerate optimal solutions, which are computationally challenging to handle. An improved multi-parametric programming algorithm based on active-set methods is introduced in this paper to overcome these computational difficulties. Degeneracy and multiplicity are handled, respectively, by introducing generalized inverses and auxiliary objective functions into the formulation of the optimality conditions. These improvements are especially effective for metabolic networks because their stoichiometry matrices are generally sparse; thus, fast and efficient algorithms from sparse linear algebra can be leveraged to compute generalized inverses and null-space bases. We illustrate the application of our algorithm to flux balance analysis of metabolic networks by studying a reduced metabolic model of Corynebacterium glutamicum and a genome-scale model of Escherichia coli. We then demonstrate how the critical regions resulting from these studies can be associated with optimal metabolic modes and discuss the physical relevance of optimal pathways arising from various auxiliary objective functions. Achieving more than five-fold improvement in computational speed over existing multi-parametric programming tools, the proposed algorithm proves promising in handling genome-scale metabolic models.
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Cites work
- scientific article; zbMATH DE number 1502618 (Why is no real title available?)
- scientific article; zbMATH DE number 2107836 (Why is no real title available?)
- scientific article; zbMATH DE number 5060482 (Why is no real title available?)
- Accelerated projection methods for computing pseudoinverse solutions of systems of linear equations
- Accurate Symmetric Indefinite Linear Equation Solvers
- An Explicit Solution of a Special Class of Linear Programming Problems
- An algorithm for multi-parametric quadratic programming and explicit MPC solutions
- An algorithm for the solution of multiparametric mixed integer linear programming problems
- Balinski-Tucker simplex tableaus: Dimensions, degeneracy degrees, and interior points of optimal faces
- Continuous selection and unique polyhedral representation of solutions to convex parametric quadratic programs
- Convex optimization theory.
- Convexity recognition of the union of polyhedra
- Efficient solution of ordinary differential equations with a parametric lexicographic linear program embedded
- Equivalent weights for lexicographic multi-objective programs: Characterizations and computations
- Generalized inverses. Theory and applications.
- Geometric algorithm for multiparametric linear programming
- LSQR: An Algorithm for Sparse Linear Equations and Sparse Least Squares
- Lexicographic perturbation for multiparametric linear programming with applications to control
- Linear and integer programming: Theory and practice.
- Lipschitz Continuity of Solutions of Linear Inequalities, Programs and Complementarity Problems
- Minimal representation of convex polyhedral sets
- Model predictive control based on linear programming - the explicit solution
- Multiparametric Linear Programming
- Nonlinear Perturbation of Linear Programs
- On the Computation of Null Spaces of Sparse Rectangular Matrices
- On the facet-to-facet property of solutions to convex parametric quadratic programs
- On the uniqueness of solutions to linear programs
- Preemptive and nonpreemptive multi-objective programming: Relationships and counterexamples
- The Existence of a Short Sequence of Admissible Pivots to an Optimal Basis in LP and LCP
- The explicit linear quadratic regulator for constrained systems
Cited in
(13)- Enumeration and Cartesian product decomposition of alternate optimal fluxes in cellular metabolism
- A space exploration algorithm for multiparametric programming via Delaunay triangulation
- Parameter estimation for metabolic networks with two stage Bregman regularization homotopy inversion algorithm
- The exact solution of multiparametric quadratically constrained quadratic programming problems
- Flux balance analysis: a geometric perspective
- A simplex approach to solving robust metabolic models with low-dimensional uncertainty
- Computational method for inferring objective function of glycerol metabolism in Klebsiella pneumoniae
- A novel parallel combinatorial algorithm for multiparametric programming
- Mixed-integer minimax dynamic optimization for structure identification of glycerol metabolic network
- Nonlinear multi-objective flux balance analysis of the Warburg Effect
- Parallelization of nullspace algorithm for the computation of metabolic pathways
- Capturing the essence of a metabolic network: a flux balance analysis approach
- On dynamically generating relevant elementary flux modes in a metabolic network using optimization
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