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

Directed Network Laplacians and Random Graph Models

We consider spectral methods that uncover hidden structures in directed networks. We develop a general framework that allows us to associate methods based on optimization formulations with maximum likelihood problems on random graphs. We focus on two existing spectral approaches that build and analyse Laplacian-style matrices via the minimization of frustration and trophic incoherence. These algorithms aim to reveal directed periodic and linear hierarchies, respectively. We show that reordering nodes using the two algorithms, or mapping them onto a specified lattice, is associated with new classes of directed random graph models. Using this random graph setting, we are able to compare the two algorithms on a given network and quantify which structure is more likely to be present. We illustrate the approach on synthetic and real networks, and discuss practical implementation issues

The connections between Lyapunov functions for some optimization algorithms and differential equations

In this manuscript, we study the properties of a family of second-order differential equations with damping, its discretizations and their connections with accelerated optimization algorithms for $m$-strongly convex and $L$-smooth functions. In particular, using the Linear Matrix Inequality LMI framework developed by \emph{Fazlyab et. al. $(2018)$}, we derive analytically a (discrete) Lyapunov function for a two-parameter family of Nesterov optimization methods, which allows for the complete characterization of their convergence rate. In the appropriate limit, this family of methods may be seen as a discretization of a family of second-order ordinary differential equations for which we construct(continuous) Lyapunov functions by means of the LMI framework. The continuous Lyapunov functions may alternatively, be obtained by studying the limiting behaviour of their discrete counterparts. Finally, we show that the majority of typical discretizations of the family of ODEs, such as the Heavy ball method, do not possess Lyapunov functions with properties similar to those of the Lyapunov function constructed here for the Nesterov method.Comment: 21 pages, 1 figur

Wasserstein distance estimates for the distributions of numerical approximations to ergodic stochastic differential equations

We present a framework that allows for the non-asymptotic study of the 2 -Wasserstein distance between the invariant distribution of an ergodic stochastic differential equation and the distribution of its numerical approximation in the strongly log-concave case. This allows us to study in a unified way a number of different integrators proposed in the literature for the overdamped and underdamped Langevin dynamics. In addition, we analyze a novel splitting method for the underdamped Langevin dynamics which only requires one gradient evaluation per time step. Under an additional smoothness assumption on a d --dimensional strongly log-concave distribution with condition number κ , the algorithm is shown to produce with an O(κ5/4d1/4ϵ−1/2) complexity samples from a distribution that, in Wasserstein distance, is at most ϵ>0 away from the target distribution

Data Assimilation: A Mathematical Introduction

This book provides a systematic treatment of the mathematical underpinnings of work in data assimilation, covering both theoretical and computational approaches. Specifically the authors develop a unified mathematical framework in which a Bayesian formulation of the problem provides the bedrock for the derivation, development and analysis of algorithms; the many examples used in the text, together with the algorithms which are introduced and discussed, are all illustrated by the MATLAB software detailed in the book and made freely available online. The book is organized into nine chapters: the first contains a brief introduction to the mathematical tools around which the material is organized; the next four are concerned with discrete time dynamical systems and discrete time data; the last four are concerned with continuous time dynamical systems and continuous time data and are organized analogously to the corresponding discrete time chapters. This book is aimed at mathematical researchers interested in a systematic development of this interdisciplinary field, and at researchers from the geosciences, and a variety of other scientific fields, who use tools from data assimilation to combine data with time-dependent models. The numerous examples and illustrations make understanding of the theoretical underpinnings of data assimilation accessible. Furthermore, the examples, exercises and MATLAB software, make the book suitable for students in applied mathematics, either through a lecture course, or through self-study