Owen Thomas

Owen Thomas, Raquel Sá-Leão, Hermínia de Lencastre et al.

Likelihood-free inference for simulator-based statistical models has developed rapidly from its infancy to a useful tool for practitioners. However, models with more than a handful of parameters still generally remain a challenge for the Approximate Bayesian Computation (ABC) based inference. To advance the possibilities for performing likelihood-free inference in higher dimensional parameter spaces, we introduce an extension of the popular Bayesian optimisation based approach to approximate discrepancy functions in a probabilistic manner which lends itself to an efficient exploration of the parameter space. Our approach achieves computational scalability for higher dimensional parameter spaces by using separate acquisition functions and discrepancies for each parameter. The efficient additive acquisition structure is combined with exponentiated loss -likelihood to provide a misspecification-robust characterisation of the marginal posterior distribution for all model parameters. The method successfully performs computationally efficient inference in a 100-dimensional space on canonical examples and compares favourably to existing modularised ABC methods. We further illustrate the potential of this approach by fitting a bacterial transmission dynamics model to a real data set, which provides biologically coherent results on strain competition in a 30-dimensional parameter space.

Owen Thomas, Jukka Corander

Model misspecification is a long-standing enigma of the Bayesian inference framework as posteriors tend to get overly concentrated on ill-informed parameter values towards the large sample limit. Tempering of the likelihood has been established as a safer way to do updates from prior to posterior in the presence of model misspecification. At one extreme tempering can ignore the data altogether and at the other extreme it provides the standard Bayes' update when no misspecification is assumed to be present. However, it is an open issue how to best recognize misspecification and choose a suitable level of tempering without access to the true generating model. Here we show how probabilistic classifiers can be employed to resolve this issue. By training a probabilistic classifier to discriminate between simulated and observed data provides an estimate of the ratio between the model likelihood and the likelihood of the data under the unobserved true generative process, within the discriminatory abilities of the classifier. The expectation of the logarithm of a ratio with respect to the data generating process gives an estimation of the negative Kullback-Leibler divergence between the statistical generative model and the true generative distribution. Using a set of canonical examples we show that this divergence provides a useful misspecification diagnostic, a model comparison tool, and a method to inform a generalised Bayesian update in the presence of misspecification for likelihood-based models.

Owen Thomas, Ritabrata Dutta, Jukka Corander et al.

We consider the problem of parametric statistical inference when likelihood computations are prohibitively expensive but sampling from the model is possible. Several so-called likelihood-free methods have been developed to perform inference in the absence of a likelihood function. The popular synthetic likelihood approach infers the parameters by modelling summary statistics of the data by a Gaussian probability distribution. In another popular approach called approximate Bayesian computation, the inference is performed by identifying parameter values for which the summary statistics of the simulated data are close to those of the observed data. Synthetic likelihood is easier to use as no measure of `closeness' is required but the Gaussianity assumption is often limiting. Moreover, both approaches require judiciously chosen summary statistics. We here present an alternative inference approach that is as easy to use as synthetic likelihood but not as restricted in its assumptions, and that, in a natural way, enables automatic selection of relevant summary statistic from a large set of candidates. The basic idea is to frame the problem of estimating the posterior as a problem of estimating the ratio between the data generating distribution and the marginal distribution. This problem can be solved by logistic regression, and including regularising penalty terms enables automatic selection of the summary statistics relevant to the inference task. We illustrate the general theory on canonical examples and employ it to perform inference for challenging stochastic nonlinear dynamical systems and high-dimensional summary statistics.