An improved multi-parametric programming algorithm for flux balance analysis of metabolic networks

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.Comment: Accepted in J. Optim. Theory Appl. First draft was submitted on August 4th, 201

A task-based approach to parallel parametric linear programming solving, and application to polyhedral computations

Parametric linear programming is a central operation for polyhedral computations, as well as in certain control applications.Here we propose a task-based scheme for parallelizing it, with quasi-linear speedup over large problems.This type of parallel applications is challenging, because several tasks mightbe computing the same region. In this paper, we are presenting thealgorithm itself with a parallel redundancy elimination algorithm, andconducting a thorough performance analysis.Comment: arXiv admin note: text overlap with arXiv:1904.0607

Polyhedral Approximation of Multivariate Polynomials using Handelman's Theorem

International audienceConvex polyhedra are commonly used in the static analysis of programs to represent over-approximations of sets of reachable states of numerical program variables. When the analyzed programs contain nonlinear instructions, they do not directly map to standard polyhedral operations: some kind of linearization is needed. Convex polyhe-dra are also used in satisfiability modulo theory solvers which combine a propositional satisfiability solver with a fast emptiness check for polyhedra. Existing decision procedures become expensive when nonlinear constraints are involved: a fast procedure to ensure emptiness of systems of nonlinear constraints is needed. We present a new linearization algorithm based on Handelman's representation of positive polynomials. Given a polyhedron and a polynomial (in)equality, we compute a polyhedron enclosing their intersection as the solution of a parametric linear programming problem. To get a scalable algorithm, we provide several heuristics that guide the construction of the Handelman's representation. To ensure the correctness of our polyhedral approximation , our Ocaml implementation generates certificates verified by a checker certified in Coq

Reduced Memory Footprint in Multiparametric Quadratic Programming by Exploiting Low Rank Structure

In multiparametric programming an optimization problem which is dependent on a parameter vector is solved parametrically. In control, multiparametric quadratic programming (mp-QP) problems have become increasingly important since the optimization problem arising in Model Predictive Control (MPC) can be cast as an mp-QP problem, which is referred to as explicit MPC. One of the main limitations with mp-QP and explicit MPC is the amount of memory required to store the parametric solution and the critical regions. In this paper, a method for exploiting low rank structure in the parametric solution of an mp-QP problem in order to reduce the required memory is introduced. The method is based on ideas similar to what is done to exploit low rank modifications in generic QP solvers, but is here applied to mp-QP problems to save memory. The proposed method has been evaluated experimentally, and for some examples of relevant problems the relative memory reduction is an order of magnitude compared to storing the full parametric solution and critical regions

Experiments with a Convex Polyhedral Analysis Tool for Logic Programs

Convex polyhedral abstractions of logic programs have been found very useful in deriving numeric relationships between program arguments in order to prove program properties and in other areas such as termination and complexity analysis. We present a tool for constructing polyhedral analyses of (constraint) logic programs. The aim of the tool is to make available, with a convenient interface, state-of-the-art techniques for polyhedral analysis such as delayed widening, narrowing, "widening up-to", and enhanced automatic selection of widening points. The tool is accessible on the web, permits user programs to be uploaded and analysed, and is integrated with related program transformations such as size abstractions and query-answer transformation. We then report some experiments using the tool, showing how it can be conveniently used to analyse transition systems arising from models of embedded systems, and an emulator for a PIC microcontroller which is used for example in wearable computing systems. We discuss issues including scalability, tradeoffs of precision and computation time, and other program transformations that can enhance the results of analysis.Comment: Paper presented at the 17th Workshop on Logic-based Methods in Programming Environments (WLPE2007

Branch-and-lift algorithm for deterministic global optimization in nonlinear optimal control

This paper presents a branch-and-lift algorithm for solving optimal control problems with smooth nonlinear dynamics and potentially nonconvex objective and constraint functionals to guaranteed global optimality. This algorithm features a direct sequential method and builds upon a generic, spatial branch-and-bound algorithm. A new operation, called lifting, is introduced, which refines the control parameterization via a Gram-Schmidt orthogonalization process, while simultaneously eliminating control subregions that are either infeasible or that provably cannot contain any global optima. Conditions are given under which the image of the control parameterization error in the state space contracts exponentially as the parameterization order is increased, thereby making the lifting operation efficient. A computational technique based on ellipsoidal calculus is also developed that satisfies these conditions. The practical applicability of branch-and-lift is illustrated in a numerical example. © 2013 Springer Science+Business Media New York

OSQP: An Operator Splitting Solver for Quadratic Programs

We present a general-purpose solver for convex quadratic programs based on the alternating direction method of multipliers, employing a novel operator splitting technique that requires the solution of a quasi-definite linear system with the same coefficient matrix at almost every iteration. Our algorithm is very robust, placing no requirements on the problem data such as positive definiteness of the objective function or linear independence of the constraint functions. It can be configured to be division-free once an initial matrix factorization is carried out, making it suitable for real-time applications in embedded systems. In addition, our technique is the first operator splitting method for quadratic programs able to reliably detect primal and dual infeasible problems from the algorithm iterates. The method also supports factorization caching and warm starting, making it particularly efficient when solving parametrized problems arising in finance, control, and machine learning. Our open-source C implementation OSQP has a small footprint, is library-free, and has been extensively tested on many problem instances from a wide variety of application areas. It is typically ten times faster than competing interior-point methods, and sometimes much more when factorization caching or warm start is used. OSQP has already shown a large impact with tens of thousands of users both in academia and in large corporations

Regularized Optimal Transport and the Rot Mover's Distance

This paper presents a unified framework for smooth convex regularization of discrete optimal transport problems. In this context, the regularized optimal transport turns out to be equivalent to a matrix nearness problem with respect to Bregman divergences. Our framework thus naturally generalizes a previously proposed regularization based on the Boltzmann-Shannon entropy related to the Kullback-Leibler divergence, and solved with the Sinkhorn-Knopp algorithm. We call the regularized optimal transport distance the rot mover's distance in reference to the classical earth mover's distance. We develop two generic schemes that we respectively call the alternate scaling algorithm and the non-negative alternate scaling algorithm, to compute efficiently the regularized optimal plans depending on whether the domain of the regularizer lies within the non-negative orthant or not. These schemes are based on Dykstra's algorithm with alternate Bregman projections, and further exploit the Newton-Raphson method when applied to separable divergences. We enhance the separable case with a sparse extension to deal with high data dimensions. We also instantiate our proposed framework and discuss the inherent specificities for well-known regularizers and statistical divergences in the machine learning and information geometry communities. Finally, we demonstrate the merits of our methods with experiments using synthetic data to illustrate the effect of different regularizers and penalties on the solutions, as well as real-world data for a pattern recognition application to audio scene classification