A New Preconditioning Approachfor an Interior Point–Proximal Method of Multipliers for Linear and Convex Quadratic Programming

In this paper, we address the efficient numerical solution of linear and quadratic programming problems, often of large scale. With this aim, we devise an infeasible interior point method, blended with the proximal method of multipliers, which in turn results in a primal-dual regularized interior point method. Application of this method gives rise to a sequence of increasingly ill-conditioned linear systems which cannot always be solved by factorization methods, due to memory and CPU time restrictions. We propose a novel preconditioning strategy which is based on a suitable sparsification of the normal equations matrix in the linear case, and also constitutes the foundation of a block-diagonal preconditioner to accelerate MINRES for linear systems arising from the solution of general quadratic programming problems. Numerical results for a range of test problems demonstrate the robustness of the proposed preconditioning strategy, together with its ability to solve linear systems of very large dimension

A generic algorithm for layout of biological networks

BackgroundBiological networks are widely used to represent processes in biological systems and to capture interactions and dependencies between biological entities. Their size and complexity is steadily increasing due to the ongoing growth of knowledge in the life sciences. To aid understanding of biological networks several algorithms for laying out and graphically representing networks and network analysis results have been developed. However, current algorithms are specialized to particular layout styles and therefore different algorithms are required for each kind of network and/or style of layout. This increases implementation effort and means that new algorithms must be developed for new layout styles. Furthermore, additional effort is necessary to compose different layout conventions in the same diagram. Also the user cannot usually customize the placement of nodes to tailor the layout to their particular need or task and there is little support for interactive network exploration.ResultsWe present a novel algorithm to visualize different biological networks and network analysis results in meaningful ways depending on network types and analysis outcome. Our method is based on constrained graph layout and we demonstrate how it can handle the drawing conventions used in biological networks.ConclusionThe presented algorithm offers the ability to produce many of the fundamental popular drawing styles while allowing the exibility of constraints to further tailor these layouts.publishe

Nonzero-sum Stochastic Games

This paper treats of stochastic games. We focus on nonzero-sum games and provide a detailed survey of selected recent results. In Section 1, we consider stochastic Markov games. A correlation of strategies of the players, involving ``public signals'', is described, and a correlated equilibrium theorem proved recently by Nowak and Raghavan for discounted stochastic games with general state space is presented. We also report an extension of this result to a class of undiscounted stochastic games, satisfying some uniform ergodicity condition. Stopping games are related to stochastic Markov games. In Section 2, we describe a version of Dynkin's game related to observation of a Markov process with random assignment mechanism of states to the players. Some recent contributions of the second author in this area are reported. The paper also contains a brief overview of the theory of nonzero-sum stochastic games and stopping games which is very far from being complete