21,584 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
An Exponential Lower Bound on the Complexity of Regularization Paths
For a variety of regularized optimization problems in machine learning,
algorithms computing the entire solution path have been developed recently.
Most of these methods are quadratic programs that are parameterized by a single
parameter, as for example the Support Vector Machine (SVM). Solution path
algorithms do not only compute the solution for one particular value of the
regularization parameter but the entire path of solutions, making the selection
of an optimal parameter much easier.
It has been assumed that these piecewise linear solution paths have only
linear complexity, i.e. linearly many bends. We prove that for the support
vector machine this complexity can be exponential in the number of training
points in the worst case. More strongly, we construct a single instance of n
input points in d dimensions for an SVM such that at least \Theta(2^{n/2}) =
\Theta(2^d) many distinct subsets of support vectors occur as the
regularization parameter changes.Comment: Journal version, 28 Pages, 5 Figure
Adjoint-based predictor-corrector sequential convex programming for parametric nonlinear optimization
This paper proposes an algorithmic framework for solving parametric
optimization problems which we call adjoint-based predictor-corrector
sequential convex programming. After presenting the algorithm, we prove a
contraction estimate that guarantees the tracking performance of the algorithm.
Two variants of this algorithm are investigated. The first one can be used to
solve nonlinear programming problems while the second variant is aimed to treat
online parametric nonlinear programming problems. The local convergence of
these variants is proved. An application to a large-scale benchmark problem
that originates from nonlinear model predictive control of a hydro power plant
is implemented to examine the performance of the algorithms.Comment: This manuscript consists of 25 pages and 7 figure
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