A primal-dual splitting algorithm for composite monotone inclusions with minimal lifting.

In this work, we study resolvent splitting algorithms for solving composite monotone inclusion problems. The objective of these general problems is finding a zero in the sum of maximally monotone operators composed with linear operators. Our main contribution is establishing the first primal-dual splitting algorithm for composite monotone inclusions with minimal lifting. Specifically, the proposed scheme reduces the dimension of the product space where the underlying fixed point operator is defined, in comparison to other algorithms, without requiring additional evaluations of the resolvent operators. We prove the convergence of this new algorithm and analyze its performance in a problem arising in image deblurring and denoising. This work also contributes to the theory of resolvent splitting algorithms by extending the minimal lifting theorem recently proved by Malitsky and Tam to schemes with resolvent parameters.

APPROACHES TO ITERATIVE ALGORITHMS FOR SOLVING NONLINEAR EQUATIONS WITH AN APPLICATION IN TOMOGRAPHIC ABSORPTION SPECTROSCOPY.

In this paper we propose an approach for solving systems of nonlinear equations without computing function derivatives. Motivated by the application area of tomographic absorption spectroscopy, which is a highly-nonlinear problem with variables coupling, we consider a situation where straightforward translation to a fixed point problem is not possible because the operators that represent the relevant systems of nonlinear equations are not self-mappings, i.e., they operate between spaces of different dimensions. To overcome this difficulty we suggest an "alternating common fixed points algorithm" that acts alternatingly on the different vector variables. This approach translates the original problem to a common fixed point problem for which iterative algorithms are abound and exhibits a viable alternative to translation to an optimization problem, which usually requires derivatives information. However, to apply any of these iterative algorithms requires to ascertain the conditions that appear in their convergence theorems. To circumvent the need to verify conditions for convergence, we propose and motivate a derivative-free algorithm that better suits the tomographic absorption spectroscopy problem at hand and is even further improved by applying to it the superiorization approach. This is presented along with experimental results that demonstrate our approach.

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0.

Constraint-based reconstruction and analysis (COBRA) provides a molecular mechanistic framework for integrative analysis of experimental molecular systems biology data and quantitative prediction of physicochemically and biochemically feasible phenotypic states. The COBRA Toolbox is a comprehensive desktop software suite of interoperable COBRA methods. It has found widespread application in biology, biomedicine, and biotechnology because its functions can be flexibly combined to implement tailored COBRA protocols for any biochemical network. This protocol is an update to the COBRA Toolbox v.1.0 and v.2.0. Version 3.0 includes new methods for quality-controlled reconstruction, modeling, topological analysis, strain and experimental design, and network visualization, as well as network integration of chemoinformatic, metabolomic, transcriptomic, proteomic, and thermochemical data. New multi-lingual code integration also enables an expansion in COBRA application scope via high-precision, high-performance, and nonlinear numerical optimization solvers for multi-scale, multi-cellular, and reaction kinetic modeling, respectively. This protocol provides an overview of all these new features and can be adapted to generate and analyze constraint-based models in a wide variety of scenarios. The COBRA Toolbox v.3.0 provides an unparalleled depth of COBRA methods.