Optimality conditions for linear copositive programming problems with isolated immobile indices

In the present paper, we apply our recent results on optimality for convex semi-infinite programming to a problem of linear copositive programming (LCP). We prove explicit optimality conditions that use concepts of immobile indices and their immobility orders and do not require the Slater constraint qualification to be satisfied. The only assumption that we impose here is that the set of immobile indices consists of isolated points and hence is finite. This assumption is weaker than the Slater condition; therefore, the optimality conditions obtained in the paper are more general when compared with those usually used in LCP. We present an example of a problem in which the new optimality conditions allow one to test the optimality of a given feasible solution while the known optimality conditions fail to do this. Further, we use the immobile indices to construct a pair of regularized dual copositive problems and show that regardless of whether the Slater condition is satisfied or not, the duality gap between the optimal values of these problems is zero. An example of a problem is presented for which the standard strict duality fails, but the duality gap obtained by using the regularized dual problem vanishes.publishe

Six topics on inscribable polytopes

Inscribability of polytopes is a classic subject but also a lively research area nowadays. We illustrate this with a selection of well-known results and recent developments on six particular topics related to inscribable polytopes. Along the way we collect a list of (new and old) open questions.Comment: 11 page

Finding the Maximal Independent Sets of a Graph Including the Maximum Using a Multivariable Continuous Polynomial Objective Optimization Formulation

We propose a multivariable continuous polynomial optimization formulation to find arbitrary maximal independent sets of any size for any graph. A local optima of the optimization problem yields a maximal independent set, while the global optima yields a maximum independent set. The solution is two phases. The first phase is listing all the maximal cliques of the graph and the second phase is solving the optimization problem. We believe that our algorithm is efficient for sparse graphs, for which there exist fast algorithms to list their maximal cliques. Our algorithm was tested on some of the DIMACS maximum clique benchmarks and produced results efficiently. In some cases our algorithm outperforms other algorithms, such as cliquer

Computing the vertices of tropical polyhedra using directed hypergraphs

We establish a characterization of the vertices of a tropical polyhedron defined as the intersection of finitely many half-spaces. We show that a point is a vertex if, and only if, a directed hypergraph, constructed from the subdifferentials of the active constraints at this point, admits a unique strongly connected component that is maximal with respect to the reachability relation (all the other strongly connected components have access to it). This property can be checked in almost linear-time. This allows us to develop a tropical analogue of the classical double description method, which computes a minimal internal representation (in terms of vertices) of a polyhedron defined externally (by half-spaces or hyperplanes). We provide theoretical worst case complexity bounds and report extensive experimental tests performed using the library TPLib, showing that this method outperforms the other existing approaches.Comment: 29 pages (A4), 10 figures, 1 table; v2: Improved algorithm in section 5 (using directed hypergraphs), detailed appendix; v3: major revision of the article (adding tropical hyperplanes, alternative method by arrangements, etc); v4: minor revisio

Identically self-blocking clutters

A clutter is identically self-blocking if it is equal to its blocker. We prove that every identically self-blocking clutter different from is nonideal. Our proofs borrow tools from Gauge Duality and Quadratic Programming. Along the way we provide a new lower bound for the packing number of an arbitrary clutter

From counting to construction of BPS states in N=4 SYM

We describe a universal element in the group algebra of symmetric groups, whose characters provides the counting of quarter and eighth BPS states at weak coupling in N=4 SYM, refined according to representations of the global symmetry group. A related projector acting on the Hilbert space of the free theory is used to construct the matrix of two-point functions of the states annihilated by the one-loop dilatation operator, at finite N or in the large N limit. The matrix is given simply in terms of Clebsch-Gordan coefficients of symmetric groups and dimensions of U(N) representations. It is expected, by non-renormalization theorems, to contain observables at strong coupling. Using the stringy exclusion principle, we interpret a class of its eigenvalues and eigenvectors in terms of giant gravitons. We also give a formula for the action of the one-loop dilatation operator on the orthogonal basis of the free theory, which is manifestly covariant under the global symmetry.Comment: 41 pages + Appendices, 4 figures; v2 - refs and acknowledgments adde

Exhaustive identification of steady state cycles in large stoichiometric networks

BACKGROUND: Identifying cyclic pathways in chemical reaction networks is important, because such cycles may indicate in silico violation of energy conservation, or the existence of feedback in vivo. Unfortunately, our ability to identify cycles in stoichiometric networks, such as signal transduction and genome-scale metabolic networks, has been hampered by the computational complexity of the methods currently used. RESULTS: We describe a new algorithm for the identification of cycles in stoichiometric networks, and we compare its performance to two others by exhaustively identifying the cycles contained in the genome-scale metabolic networks of H. pylori, M. barkeri, E. coli, and S. cerevisiae. Our algorithm can substantially decrease both the execution time and maximum memory usage in comparison to the two previous algorithms. CONCLUSION: The algorithm we describe improves our ability to study large, real-world, biochemical reaction networks, although additional methodological improvements are desirable

Immobile indices and CQ-free optimality criteria for linear copositive programming problems

We consider problems of linear copositive programming where feasible sets consist of vectors for which the quadratic forms induced by the corresponding linear matrix combinations are nonnegative over the nonnegative orthant. Given a linear copositive problem, we define immobile indices of its constraints and a normalized immobile index set. We prove that the normalized immobile index set is either empty or can be represented as a union of a finite number of convex closed bounded polyhedra. We show that the study of the structure of this set and the connected properties of the feasible set permits to obtain new optimality criteria for copositive problems. These criteria do not require the fulfillment of any additional conditions (constraint qualifications or other). An illustrative example shows that the optimality conditions formulated in the paper permit to detect the optimality of feasible solutions for which the known sufficient optimality conditions are not able to do this. We apply the approach based on the notion of immobile indices to obtain new formulations of regularized primal and dual problems which are explicit and guarantee strong duality.publishe

A scalable algorithm to explore the Gibbs energy landscape of genome-scale metabolic networks

The integration of various types of genomic data into predictive models of biological networks is one of the main challenges currently faced by computational biology. Constraint-based models in particular play a key role in the attempt to obtain a quantitative understanding of cellular metabolism at genome scale. In essence, their goal is to frame the metabolic capabilities of an organism based on minimal assumptions that describe the steady states of the underlying reaction network via suitable stoichiometric constraints, specifically mass balance and energy balance (i.e. thermodynamic feasibility). The implementation of these requirements to generate viable configurations of reaction fluxes and/or to test given flux profiles for thermodynamic feasibility can however prove to be computationally intensive. We propose here a fast and scalable stoichiometry-based method to explore the Gibbs energy landscape of a biochemical network at steady state. The method is applied to the problem of reconstructing the Gibbs energy landscape underlying metabolic activity in the human red blood cell, and to that of identifying and removing thermodynamically infeasible reaction cycles in the Escherichia coli metabolic network (iAF1260). In the former case, we produce consistent predictions for chemical potentials (or log-concentrations) of intracellular metabolites; in the latter, we identify a restricted set of loops (23 in total) in the periplasmic and cytoplasmic core as the origin of thermodynamic infeasibility in a large sample ($10^6$) of flux configurations generated randomly and compatibly with the prior information available on reaction reversibility.Comment: 11 pages, 6 figures, 1 table; for associated supporting material see http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.100256