Hybrid deterministic/stochastic algorithm for large sets of rate equations

We propose a hybrid algorithm for the time integration of large sets of rate equations coupled by a relatively small number of degrees of freedom. A subset containing fast degrees of freedom evolves deterministically, while the rest of the variables evolves stochastically. The emphasis is put on the coupling between the two subsets, in order to achieve both accuracy and efficiency. The algorithm is tested on the problem of nucleation, growth and coarsening of clusters of defects in iron, treated by the formalism of cluster dynamics. We show that it is possible to obtain results indistinguishable from fully deterministic and fully stochastic calculations, while speeding up significantly the computations with respect to these two cases.Comment: 9 pages, 7 figure

A Primer on Causality in Data Science

Many questions in Data Science are fundamentally causal in that our objective is to learn the effect of some exposure, randomized or not, on an outcome interest. Even studies that are seemingly non-causal, such as those with the goal of prediction or prevalence estimation, have causal elements, including differential censoring or measurement. As a result, we, as Data Scientists, need to consider the underlying causal mechanisms that gave rise to the data, rather than simply the pattern or association observed in those data. In this work, we review the 'Causal Roadmap' of Petersen and van der Laan (2014) to provide an introduction to some key concepts in causal inference. Similar to other causal frameworks, the steps of the Roadmap include clearly stating the scientific question, defining of the causal model, translating the scientific question into a causal parameter, assessing the assumptions needed to express the causal parameter as a statistical estimand, implementation of statistical estimators including parametric and semi-parametric methods, and interpretation of our findings. We believe that using such a framework in Data Science will help to ensure that our statistical analyses are guided by the scientific question driving our research, while avoiding over-interpreting our results. We focus on the effect of an exposure occurring at a single time point and highlight the use of targeted maximum likelihood estimation (TMLE) with Super Learner.Comment: 26 pages (with references); 4 figure

Asymptotics of work distributions in a stochastically driven system

We determine the asymptotic forms of work distributions at arbitrary times $T$, in a class of driven stochastic systems using a theory developed by Engel and Nickelsen (EN theory) (arXiv:1102.4505v1 [cond-mat.stat-mech]), which is based on the contraction principle of large deviation theory. In this paper, we extend the theory, previously applied in the context of deterministically driven systems, to a model in which the driving is stochastic. The models we study are described by overdamped Langevin equations and the work distributions in the path integral form, are characterised by having quadratic actions. We first illustrate EN theory, for a deterministically driven system - the breathing parabola model, and show that within its framework, the Crooks flucutation theorem manifests itself as a reflection symmetry property of a certain characteristic polynomial function. We then extend our analysis to a stochastically driven system, studied in ( arXiv:1212.0704v2 [cond-mat.stat-mech], arXiv:1402.5777v1 [cond-mat.stat-mech]) using a moment-generating-function method, for both equilibrium and non - equilibrium steady state initial distributions. In both cases we obtain new analytic solutions for the asymptotic forms of (dissipated) work distributions at arbitrary $T$. For dissipated work in the steady state, we compare the large $T$ asymptotic behaviour of our solution to that already obtained in ( arXiv:1402.5777v1 [cond-mat.stat-mech]). In all cases, special emphasis is placed on the computation of the pre-exponential factor and the results show excellent agreement with the numerical simulations. Our solutions are exact in the low noise limit.Comment: 26 pages, 8 figures. Changes from version 1: Several typos and equations corrected, references added, pictures modified. Version to appear in EPJ

Unscented Orientation Estimation Based on the Bingham Distribution

Orientation estimation for 3D objects is a common problem that is usually tackled with traditional nonlinear filtering techniques such as the extended Kalman filter (EKF) or the unscented Kalman filter (UKF). Most of these techniques assume Gaussian distributions to account for system noise and uncertain measurements. This distributional assumption does not consider the periodic nature of pose and orientation uncertainty. We propose a filter that considers the periodicity of the orientation estimation problem in its distributional assumption. This is achieved by making use of the Bingham distribution, which is defined on the hypersphere and thus inherently more suitable to periodic problems. Furthermore, handling of non-trivial system functions is done using deterministic sampling in an efficient way. A deterministic sampling scheme reminiscent of the UKF is proposed for the nonlinear manifold of orientations. It is the first deterministic sampling scheme that truly reflects the nonlinear manifold of the orientation