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Register a new userInformed Sub-Sampling MCMC: Approximate Bayesian Inference for Large Datasets
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Florian Maire
Publication date
2017
fields
Mathematical Statistics
and research's language is
English
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This paper introduces a framework for speeding up Bayesian inference conducted in presence of large datasets. We design a Markov chain whose transition kernel uses an (unknown) fraction of (fixed size) of the available data that is randomly refreshed throughout the algorithm. Inspired by the Approximate Bayesian Computation (ABC) literature, the subsampling process is guided by the fidelity to the observed data, as measured by summary statistics. The resulting algorithm, Informed Sub-Sampling MCMC (ISS-MCMC), is a generic and flexible approach which, contrary to existing scalable methodologies, preserves the simplicity of the Metropolis-Hastings algorithm. Even though exactness is lost, i.e. the chain distribution approximates the posterior, we study and quantify theoretically this bias and show on a diverse set of examples that it yields excellent performances when the computational budget is limited. If available and cheap to compute, we show that setting the summary statistics as the maximum likelihood estimator is supported by theoretical arguments.
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Light and Widely Applicable (LWA-) MCMC is a novel approximation of the Metropolis-Hastings kernel targeting a posterior distribution defined on a large number of observations. Inspired by Approximate Bayesian Computation, we design a Markov chain whose transition makes use of an unknown but fixed, fraction of the available data, where the random choice of sub-sample is guided by the fidelity of this sub-sample to the observed data, as measured by summary (or sufficient) statistics. LWA-MCMC is a generic and flexible approach, as illustrated by the diverse set of examples which we explore. In each case LWA-MCMC yields excellent performance and in some cases a dramatic improvement compared to existing methodologies.
We use the theory of normal variance-mean mixtures to derive a data augmentation scheme for models that include gamma functions. Our methodology applies to many situations in statistics and machine learning, including Multinomial-Dirichlet distributions, Negative binomial regression, Poisson-Gamma hierarchical models, Extreme value models, to name but a few. All of those models include a gamma function which does not admit a natural conjugate prior distribution providing a significant challenge to inference and prediction. To provide a data augmentation strategy, we construct and develop the theory of the class of Exponential Reciprocal Gamma distributions. This allows scalable EM and MCMC algorithms to be developed. We illustrate our methodology on a number of examples, including gamma shape inference, negative binomial regression and Dirichlet allocation. Finally, we conclude with directions for future research.
In forecasting problems it is important to know whether or not recent events represent a regime change (low long-term predictive potential), or rather a local manifestation of longer term effects (potentially higher predictive potential). Mathematically, a key question is about whether the underlying stochastic process exhibits memory, and if so whether the memory is long in a precise sense. Being able to detect or rule out such effects can have a profound impact on speculative investment (e.g., in financial markets) and inform public policy (e.g., characterising the size and timescales of the earth systems response to the anthropogenic CO2 perturbation). Most previous work on inference of long memory effects is frequentist in nature. Here we provide a systematic treatment of Bayesian inference for long memory processes via the Autoregressive Fractional Integrated Moving Average (ARFIMA) model. In particular, we provide a new approximate likelihood for efficient parameter inference, and show how nuisance parameters (e.g., short memory effects) can be integrated over in order to focus on long memory parameters and hypothesis testing more directly than ever before. We illustrate our new methodology on both synthetic and observational data, with favorable comparison to the standard estimators.
This preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100036). Approximate Bayesian computation (ABC) has grown into a standard methodology that manages Bayesian inference for models associated with intractable likelihood functions. Most ABC implementations require the preliminary selection of a vector of informative statistics summarizing raw data. Furthermore, in almost all existing implementations, the tolerance level that separates acceptance from rejection of simulated parameter values needs to be calibrated. We propose to conduct likelihood-free Bayesian inferences about parameters with no prior selection of the relevant components of the summary statistics and bypassing the derivation of the associated tolerance level. The approach relies on the random forest methodology of Breiman (2001) applied in a (non parametric) regression setting. We advocate the derivation of a new random forest for each component of the parameter vector of interest. When compared with earlier ABC solutions, this method offers significant gains in terms of robustness to the choice of the summary statistics, does not depend on any type of tolerance level, and is a good trade-off in term of quality of point estimator precision and credible interval estimations for a given computing time. We illustrate the performance of our methodological proposal and compare it with earlier ABC methods on a Normal toy example and a population genetics example dealing with human population evolution. All methods designed here have been incorporated in the R package abcrf (version 1.7) available on CRAN.
This report is a collection of comments on the Read Paper of Fearnhead and Prangle (2011), to appear in the Journal of the Royal Statistical Society Series B, along with a reply from the authors.
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