An almost cyclic 2-coordinate descent method for singly linearly constrained problems

A block decomposition method is proposed for minimizing a (possibly non-convex) continuously differentiable function subject to one linear equality constraint and simple bounds on the variables. The proposed method iteratively selects a pair of coordinates according to an almost cyclic strategy that does not use first-order information, allowing us not to compute the whole gradient of the objective function during the algorithm. Using first-order search directions to update each pair of coordinates, global convergence to stationary points is established for different choices of the stepsize under an appropriate assumption on the level set. In particular, both inexact and exact line search strategies are analyzed. Further, linear convergence rate is proved under standard additional assumptions. Numerical results are finally provided to show the effectiveness of the proposed method.Comment: Computational Optimization and Application

Variable-step finite difference schemes for the solution of Sturm-Liouville problems

We discuss the solution of regular and singular Sturm-Liouville problems by means of High Order Finite Difference Schemes. We describe a code to define a discrete problem and its numerical solution by means of linear algebra techniques. Different test problems are proposed to emphasize the behaviour of the proposed algorithm

Efficient simulation of stochastic chemical kinetics with the Stochastic Bulirsch-Stoer extrapolation method

BackgroundBiochemical systems with relatively low numbers of components must be simulated stochastically in order to capture their inherent noise. Although there has recently been considerable work on discrete stochastic solvers, there is still a need for numerical methods that are both fast and accurate. The Bulirsch-Stoer method is an established method for solving ordinary differential equations that possesses both of these qualities.ResultsIn this paper, we present the Stochastic Bulirsch-Stoer method, a new numerical method for simulating discrete chemical reaction systems, inspired by its deterministic counterpart. It is able to achieve an excellent efficiency due to the fact that it is based on an approach with high deterministic order, allowing for larger stepsizes and leading to fast simulations. We compare it to the Euler ?-leap, as well as two more recent ?-leap methods, on a number of example problems, and find that as well as being very accurate, our method is the most robust, in terms of efficiency, of all the methods considered in this paper. The problems it is most suited for are those with increased populations that would be too slow to simulate using Gillespie’s stochastic simulation algorithm. For such problems, it is likely to achieve higher weak order in the moments.ConclusionsThe Stochastic Bulirsch-Stoer method is a novel stochastic solver that can be used for fast and accurate simulations. Crucially, compared to other similar methods, it better retains its high accuracy when the timesteps are increased. Thus the Stochastic Bulirsch-Stoer method is both computationally efficient and robust. These are key properties for any stochastic numerical method, as they must typically run many thousands of simulations