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

Improved Primal Simplex: A More General Theoretical Framework and an Extended Experimental Analysis

International audienceIn this article, we propose a general framework for an algorithm derived from the primal simplex that guarantees a strict improvement in the objective after each iteration. Our approach relies on the identification of compatible variables that ensure a nondegenerate iteration if pivoted into the basis. The problem of finding a strict improvement in the objective function is proved to be equivalent to two smaller problems respectively focusing on compatible and incompatible variables. We then show that the improved primal simplex (IPS) of Elhallaoui et al. is a particular implementation of this generic theoretical framework. The resulting new description of IPS naturally emphasizes what should be considered as necessary adaptations of the framework versus specific implementation choices. This provides original insight into IPS that allows for the identification of weaknesses and potential alternative choices that would extend the efficiency of the method to a wider set of problems. We perform experimental tests on an extended collection of data sets including instances of Mittelmann's benchmark for linear programming. The results confirm the excellent potential of IPS and highlight some of its limits while showing a path toward an improved implementation of the generic algorithm

Least absolute deviation estimation of linear econometric models: A literature review

Econometricians generally take for granted that the error terms in the econometric models are generated by distributions having a finite variance. However, since the time of Pareto the existence of error distributions with infinite variance is known. Works of many econometricians, namely, Meyer & Glauber (1964), Fama (1965) and Mandlebroth (1967), on economic data series like prices in financial and commodity markets confirm that infinite variance distributions exist abundantly. The distribution of firms by size, behaviour of speculative prices and various other recent economic phenomena also display similar trends. Further, econometricians generally assume that the disturbance term, which is an influence of innumerably many factors not accounted for in the model, approaches normality according to the Central Limit Theorem. But Bartels (1977) is of the opinion that there are limit theorems, which are just likely to be relevant when considering the sum of number of components in a regression disturbance that leads to non-normal stable distribution characterized by infinite variance. Thus, the possibility of the error term following a non-normal distribution exists. The Least Squares method of estimation of parameters of linear (regression) models performs well provided that the residuals (disturbances or errors) are well behaved (preferably normally or near-normally distributed and not infested with large size outliers) and follow Gauss-Markov assumptions. However, models with the disturbances that are prominently non-normally distributed and contain sizeable outliers fail estimation by the Least Squares method. An intensive research has established that in such cases estimation by the Least Absolute Deviation (LAD) method performs well. This paper is an attempt to survey the literature on LAD estimation of single as well as multi-equation linear econometric models.Lad estimator; Least absolute deviation estimation; econometric model; LAD Estimator; Minimum Absolute Deviation; Robust; Outliers; L1 Estimator; Review of literature

On implicit-factorization constraint preconditioners

Recently Dollar and Wathen [14] proposed a class of incomplete factorizations for saddle-point problems, based upon earlier work by Schilders [40]. In this paper, we generalize this class of preconditioners, and examine the spectral implications of our approach. Numerical tests indicate the efficacy of our preconditioners

The positive edge pricing rule for the dual simplex

International audienceIn this article, we develop the two-dimensional positive edge criterion for the dual simplex. This work extends a similar pricing rule implemented by Towhidi et al. [24] to reduce the negative effects of degeneracy in the primal simplex. In the dual simplex, degeneracy occurs when nonbasic variables have a zero reduced cost, and it may lead to pivots that do not improve the objective value. We analyze dual degeneracy to characterize a particular set of dual compatible variables such that if any of them is selected to leave the basis the pivot will be nondegenerate. The dual positive edge rule can be used to modify any pivot selection rule so as to prioritize compatible variables. The expected effect is to reduce the number of pivots during the solution of degenerate problems with the dual simplex. For the experiments, we implement the positive edge rule within the dual simplex of the COIN-OR LP solver, and combine it with both the dual Dantzig and the dual steepest edge criteria. We test our implementation on 62 instances from four well-known benchmarks for linear programming. The results show that the dual positive edge rule significantly improves on the classical pricing rules

Network flow algorithms and applications

This paper looks at several methods for solving network flow problems. The first chapter gives a brief background for linear programming (LP) problems. It includes basic definitions and theorems. The second chapter gives an overview of graph theory including definitions, theorems, and examples. Chapters 3-5 are the heart of this thesis. Chapter 3 includes algorithms and applications for maximum flow problems. It includes a look at a very important theorem. Maximum Flow/Minimum Cut Theorem. There is also a section on the Augmenting Path Algorithm. Chapter 4 Deals with shortest path problem. It includes Dijsksta\u27s Algorithm and the All-Pairs Labeling Algorithm. Chapter 5 includes information on algorithms and applications for the minimum cost flow(MCF)problem. The algorithms covered include the Cycle Canceling,Successive ShortestPath,and Primal-Dual Algorithms. Each of these chapters 3-5 contain definitions,theorems,and algorithms to solve network flow problems. Throughout the paper the computer program LINDO is used. It serves a couple of functions. First it is a way of checking each solution. The second use is to expose the reader to a very valuable tool in linear programming

Experiments with Active-Set LP Algorithms Allowing Basis Deficiency

n interesting question for linear programming (LP) algorithms is how to deal with solutions in which the number of nonzero variables is less than the number of rows of the matrix in standard form. An approach is that of basis deficiency-allowing (BDA) simplex variations, which work with a subset of independent columns of the coefficient matrix in standard form, wherein the basis is not necessarily represented by a square matrix. We describe one such algorithm with several variants. The research question deals with studying the computational behaviour by using small, extreme cases. For these instances, we must wonder which parameter setting or variants are more appropriate. We compare the setting of two nonsimplex active-set methods with Holmström’s TomLab LpSimplex v3.0 commercial sparse primal simplex commercial implementation. All of them update a sparse QR factorization in Matlab. The first two implementations require fewer iterations and provide better solution quality and running time.This work has been funded by grant PID2021-123278OB-I00 from the Spanish Ministry of Science and Innovation. Partial funding for open access charge: Universidad de Málag