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Dennis Prangle

Publications and source records attributed to Dennis Prangle.

27 records · Page 2Linked to original sources
arXiv2017

gk: An R Package for the g-and-k and generalised g-and-h Distributions

The g-and-k and (generalised) g-and-h distributions are flexible univariate distributions which can model highly skewed or heavy tailed data through only four parameters: location and scale, and two shape parameters influencing the skewness and kurtosis. These distributions have the unusual property that they are defined through their quantile function (inverse cumulative distribution function) and their density is unavailable in closed form, which makes parameter inference complicated. This paper presents the gk R package to work with these distributions. It provides the usual distribution functions and several algorithms for inference of independent identically distributed data, including the finite difference stochastic approximation method, which has not been used before for this problem.

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arXiv2017

A rare event approach to high dimensional Approximate Bayesian computation

Approximate Bayesian computation (ABC) methods permit approximate inference for intractable likelihoods when it is possible to simulate from the model. However they perform poorly for high dimensional data, and in practice must usually be used in conjunction with dimension reduction methods, resulting in a loss of accuracy which is hard to quantify or control. We propose a new ABC method for high dimensional data based on rare event methods which we refer to as RE-ABC. This uses a latent variable representation of the model. For a given parameter value, we estimate the probability of the rare event that the latent variables correspond to data roughly consistent with the observations. This is performed using sequential Monte Carlo and slice sampling to systematically search the space of latent variables. In contrast standard ABC can be viewed as using a more naive Monte Carlo estimate. We use our rare event probability estimator as a likelihood estimate within the pseudo-marginal Metropolis-Hastings algorithm for parameter inference. We provide asymptotics showing that RE-ABC has a lower computational cost for high dimensional data than standard ABC methods. We also illustrate our approach empirically, on a Gaussian distribution and an application in infectious disease modelling.

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arXiv2015

Summary Statistics in Approximate Bayesian Computation

This document is due to appear as a chapter of the forthcoming Handbook of Approximate Bayesian Computation (ABC) edited by S. Sisson, Y. Fan, and M. Beaumont. Since the earliest work on ABC, it has been recognised that using summary statistics is essential to produce useful inference results. This is because ABC suffers from a curse of dimensionality effect, whereby using high dimensional inputs causes large approximation errors in the output. It is therefore crucial to find low dimensional summaries which are informative about the parameter inference or model choice task at hand. This chapter reviews the methods which have been proposed to select such summaries, extending the previous review paper of Blum et al. (2013) with recent developments. Related theoretical results on the ABC curse of dimensionality and sufficiency are also discussed.

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arXiv2015

Adapting the ABC distance function

Approximate Bayesian computation performs approximate inference for models where likelihood computations are expensive or impossible. Instead simulations from the model are performed for various parameter values and accepted if they are close enough to the observations. There has been much progress on deciding which summary statistics of the data should be used to judge closeness, but less work on how to weight them. Typically weights are chosen at the start of the algorithm which normalise the summary statistics to vary on similar scales. However these may not be appropriate in iterative ABC algorithms, where the distribution from which the parameters are proposed is updated. This can substantially alter the resulting distribution of summary statistics, so that different weights are needed for normalisation. This paper presents two iterative ABC algorithms which adaptively update their weights and demonstrates improved results on test applications.

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arXiv2015

Lazier ABC

ABC algorithms involve a large number of simulations from the model of interest, which can be very computationally costly. This paper summarises the lazy ABC algorithm of Prangle (2015), which reduces the computational demand by abandoning many unpromising simulations before completion. By using a random stopping decision and reweighting the output sample appropriately, the target distribution is the same as for standard ABC. Lazy ABC is also extended here to the case of non-uniform ABC kernels, which is shown to simplify the process of tuning the algorithm effectively.

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arXiv2014

Lazy ABC

Approximate Bayesian computation (ABC) performs statistical inference for otherwise intractable probability models by accepting parameter proposals when corresponding simulated datasets are sufficiently close to the observations. Producing the large quantity of simulations needed requires considerable computing time. However, it is often clear before a simulation ends that it is unpromising: it is likely to produce a poor match or require excessive time. This paper proposes lazy ABC, an ABC importance sampling algorithm which saves time by sometimes abandoning such simulations. This makes ABC more scalable to applications where simulation is expensive. By using a random stopping rule and appropriate reweighting step, the target distribution is unchanged from that of standard ABC. Theory and practical methods to tune lazy ABC are presented and illustrated on a simple epidemic model example. They are also demonstrated on the computationally demanding spatial extremes application of Erhardt and Smith (2012), producing efficiency gains, in terms of effective sample size per unit CPU time, of roughly 3 times for a 20 location dataset, and 8 times for 35 locations.

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arXiv2013

Semi-automatic selection of summary statistics for ABC model choice

A central statistical goal is to choose between alternative explanatory models of data. In many modern applications, such as population genetics, it is not possible to apply standard methods based on evaluating the likelihood functions of the models, as these are numerically intractable. Approximate Bayesian computation (ABC) is a commonly used alternative for such situations. ABC simulates data x for many parameter values under each model, which is compared to the observed data xobs. More weight is placed on models under which S(x) is close to S(xobs), where S maps data to a vector of summary statistics. Previous work has shown the choice of S is crucial to the efficiency and accuracy of ABC. This paper provides a method to select good summary statistics for model choice. It uses a preliminary step, simulating many x values from all models and fitting regressions to this with the model as response. The resulting model weight estimators are used as S in an ABC analysis. Theoretical results are given to justify this as approximating low dimensional sufficient statistics. A substantive application is presented: choosing between competing coalescent models of demographic growth for Campylobacter jejuni in New Zealand using multi-locus sequence typing data.

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arXiv2011

Constructing Summary Statistics for Approximate Bayesian Computation: Semi-automatic ABC

Many modern statistical applications involve inference for complex stochastic models, where it is easy to simulate from the models, but impossible to calculate likelihoods. Approximate Bayesian computation (ABC) is a method of inference for such models. It replaces calculation of the likelihood by a step which involves simulating artificial data for different parameter values, and comparing summary statistics of the simulated data to summary statistics of the observed data. Here we show how to construct appropriate summary statistics for ABC in a semi-automatic manner. We aim for summary statistics which will enable inference about certain parameters of interest to be as accurate as possible. Theoretical results show that optimal summary statistics are the posterior means of the parameters. While these cannot be calculated analytically, we use an extra stage of simulation to estimate how the posterior means vary as a function of the data; and then use these estimates of our summary statistics within ABC. Empirical results show that our approach is a robust method for choosing summary statistics, that can result in substantially more accurate ABC analyses than the ad-hoc choices of summary statistics proposed in the literature. We also demonstrate advantages over two alternative methods of simulation-based inference.

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