MOTIVATION: Several applications in constraint-based modelling can be mathematically formulated as cardinality optimization problems involving the minimization or maximization of the number of nonzeros in a vector. These problems include testing for stoichiometric consistency, testing for flux consistency, testing for thermodynamic flux consistency, computing sparse solutions to flux balance analysis problems and computing the minimum number of constraints to relax to render an infeasible flux balance analysis problem feasible. Such cardinality optimization problems are computationally complex, with no known polynomial time algorithms capable of returning an exact and globally optimal solution. RESULTS: By approximating the zero-norm with nonconvex continuous functions, we reformulate a set of cardinality optimization problems in constraint-based modelling into a difference of convex functions. We implemented and numerically tested novel algorithms that approximately solve the reformulated problems using a sequence of convex programs. We applied these algorithms to various biochemical networks and demonstrate that our algorithms match or outperform existing related approaches. In particular, we illustrate the efficiency and practical utility of our algorithms for cardinality optimization problems that arise when extracting a model ready for thermodynamic flux balance analysis given a human metabolic reconstruction. AVAILABILITY AND IMPLEMENTATION: Open source scripts to reproduce the results are here https://github.com/opencobra/COBRA.papers/2023_cardOpt with general purpose functions integrated within the COnstraint-Based Reconstruction and Analysis toolbox: https://github.com/opencobra/cobratoolbox.

We introduce a relaxed inertial forward-backward-forward (RIFBF) splitting algorithm for approaching the set of zeros of the sum of a maximally monotone operator and a single-valued monotone and Lipschitz continuous operator. This work aims to extend Tseng's forward-backward-forward method by both using inertial effects as well as relaxation parameters. We formulate first a second order dynamical system that approaches the solution set of the monotone inclusion problem to be solved and provide an asymptotic analysis for its trajectories. We provide for RIFBF, which follows by explicit time discretization, a convergence analysis in the general monotone case as well as when applied to the solving of pseudo-monotone variational inequalities. We illustrate the proposed method by applications to a bilinear saddle point problem, in the context of which we also emphasize the interplay between the inertial and the relaxation parameters, and to the training of Generative Adversarial Networks (GANs).