1,091 research outputs found
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
Airline crew scheduling
An airline must cover each flight leg with a full complement of cabin crew in a manner consistent with safety regulations and award requirements. Methods are investigated for solving the set partitioning and covering problem. A test example illustrates the problem and the use of heuristics. The Study Group achieved an understanding of the problem and a plan for further work
Conservation Prioritization Problems and their Shadow Prices
Systematic conservation planning is an essential part of biodiversity preservation
A Primal-Dual Augmented Lagrangian
Nonlinearly constrained optimization problems can be solved by minimizing a sequence of simpler unconstrained or linearly constrained subproblems. In this paper, we discuss the formulation of subproblems in which the objective is a primal-dual generalization of the Hestenes-Powell augmented Lagrangian function. This generalization has the crucial feature that it is minimized with respect to both the primal and the dual variables simultaneously. A benefit of this approach is that the quality of the dual variables is monitored explicitly during the solution of the subproblem. Moreover, each subproblem may be regularized by imposing explicit bounds on the dual variables. Two primal-dual variants of conventional primal methods are proposed: a primal-dual bound constrained Lagrangian (pdBCL) method and a primal-dual 1 linearly constrained Lagrangian (pd1-LCL) method
- …