Moment-Based Variational Inference for Markov Jump Processes

We propose moment-based variational inference as a flexible framework for approximate smoothing of latent Markov jump processes. The main ingredient of our approach is to partition the set of all transitions of the latent process into classes. This allows to express the Kullback-Leibler divergence between the approximate and the exact posterior process in terms of a set of moment functions that arise naturally from the chosen partition. To illustrate possible choices of the partition, we consider special classes of jump processes that frequently occur in applications. We then extend the results to parameter inference and demonstrate the method on several examples.Comment: Accepted by the 36th International Conference on Machine Learning (ICML 2019

Parameter estimation and model testing for Markov processes via conditional characteristic functions

Markov processes are used in a wide range of disciplines, including finance. The transition densities of these processes are often unknown. However, the conditional characteristic functions are more likely to be available, especially for L\'{e}vy-driven processes. We propose an empirical likelihood approach, for both parameter estimation and model specification testing, based on the conditional characteristic function for processes with either continuous or discontinuous sample paths. Theoretical properties of the empirical likelihood estimator for parameters and a smoothed empirical likelihood ratio test for a parametric specification of the process are provided. Simulations and empirical case studies are carried out to confirm the effectiveness of the proposed estimator and test.Comment: Published in at http://dx.doi.org/10.3150/11-BEJ400 the Bernoulli (http://isi.cbs.nl/bernoulli/) by the International Statistical Institute/Bernoulli Society (http://isi.cbs.nl/BS/bshome.htm

Copula Processes

We define a copula process which describes the dependencies between arbitrarily many random variables independently of their marginal distributions. As an example, we develop a stochastic volatility model, Gaussian Copula Process Volatility (GCPV), to predict the latent standard deviations of a sequence of random variables. To make predictions we use Bayesian inference, with the Laplace approximation, and with Markov chain Monte Carlo as an alternative. We find both methods comparable. We also find our model can outperform GARCH on simulated and financial data. And unlike GARCH, GCPV can easily handle missing data, incorporate covariates other than time, and model a rich class of covariance structures.Comment: 11 pages, 1 table, 1 figure. Submitted for publication. Since last version: minor edits and reformattin

Inference for reaction networks using the Linear Noise Approximation

We consider inference for the reaction rates in discretely observed networks such as those found in models for systems biology, population ecology and epidemics. Most such networks are neither slow enough nor small enough for inference via the true state-dependent Markov jump process to be feasible. Typically, inference is conducted by approximating the dynamics through an ordinary differential equation (ODE), or a stochastic differential equation (SDE). The former ignores the stochasticity in the true model, and can lead to inaccurate inferences. The latter is more accurate but is harder to implement as the transition density of the SDE model is generally unknown. The Linear Noise Approximation (LNA) is a first order Taylor expansion of the approximating SDE about a deterministic solution and can be viewed as a compromise between the ODE and SDE models. It is a stochastic model, but discrete time transition probabilities for the LNA are available through the solution of a series of ordinary differential equations. We describe how a restarting LNA can be efficiently used to perform inference for a general class of reaction networks; evaluate the accuracy of such an approach; and show how and when this approach is either statistically or computationally more efficient than ODE or SDE methods. We apply the LNA to analyse Google Flu Trends data from the North and South Islands of New Zealand, and are able to obtain more accurate short-term forecasts of new flu cases than another recently proposed method, although at a greater computational cost

The Hitchhiker's Guide to Nonlinear Filtering

Nonlinear filtering is the problem of online estimation of a dynamic hidden variable from incoming data and has vast applications in different fields, ranging from engineering, machine learning, economic science and natural sciences. We start our review of the theory on nonlinear filtering from the simplest `filtering' task we can think of, namely static Bayesian inference. From there we continue our journey through discrete-time models, which is usually encountered in machine learning, and generalize to and further emphasize continuous-time filtering theory. The idea of changing the probability measure connects and elucidates several aspects of the theory, such as the parallels between the discrete- and continuous-time problems and between different observation models. Furthermore, it gives insight into the construction of particle filtering algorithms. This tutorial is targeted at scientists and engineers and should serve as an introduction to the main ideas of nonlinear filtering, and as a segway to more advanced and specialized literature.Comment: 64 page