Savage-Dickey Ratio Research Articles

Bayesian Learning of Graph Substructures

Graphical models provide a powerful methodology for learning the conditional independence structure in multivariate data. Inference is often focused on estimating individual edges in the latent graph. Nonetheless, there is increasing interest in inferring more complex structures, such as communities, for multiple reasons, including more effective information retrieval and better interpretability. Stochastic blockmodels offer a powerful tool to detect such structure in a network. We thus propose to exploit advances in random graph theory and embed them within the graphical models framework. A consequence of this approach is the propagation of the uncertainty in graph estimation to large-scale structure learning. We consider Bayesian nonparametric stochastic blockmodels as priors on the graph. We extend such models to consider clique-based blocks and to multiple graph settings introducing a novel prior process based on a Dependent Dirichlet process. Moreover, we devise a tailored computation strategy of Bayes factors for block structure based on the Savage-Dickey ratio to test for presence of larger structure in a graph. We demonstrate our approach in simulations as well as on real data applications in finance and transcriptomics.

TAU-REX I: A NEXT GENERATION RETRIEVAL CODE FOR EXOPLANETARY ATMOSPHERES

Spectroscopy of exoplanetary atmospheres has become a well established method for the characterisation of extrasolar planets. We here present a novel inverse retrieval code for exoplanetary atmospheres. TauRex (Tau Retrieval for Exoplanets) is a line-by-line radiative transfer fully Bayesian retrieval framework. TauRex includes the following features: 1) the optimised use of molecular line-lists from the Exomol project; 2) an unbiased atmospheric composition prior selection, through custom built pattern recognition software; 3) the use of two independent algorithms to fully sample the Bayesian likelihood space: nested sampling as well as a more classical Markov Chain Monte Carlo approach; 4) iterative Bayesian parameter and model selection using the full Bayesian Evidence as well as the Savage-Dickey Ratio for nested models, and 5) the ability to fully map very large parameter spaces through optimal code parallelisation and scalability to cluster computing. In this publication we outline the TauRex framework and demonstrate, using a theoretical hot-Jupiter transmission spectrum, the parameter retrieval and model selection. We investigate the impact of Signal-to-Noise and spectral resolution on the retrievability of individual model parameters, both in terms of error bars on the temperature and molecular mixing ratios as well as its effect on the model's global Bayesian evidence.

On resolving the Savage–Dickey paradox

When testing a null hypothesis H0: θ=θ0 in a Bayesian framework, the Savage–Dickey ratio (Dickey, 1971) is known as a specific representation of the Bayes factor (O’Hagan and Forster, 2004) that only uses the posterior distribution under the alternative hypothesis at θ0, thus allowing for a plug-in version of this quantity. We demonstrate here that the Savage–Dickey representation is in fact a generic representation of the Bayes factor and that it fundamentally relies on specific measure-theoretic versions of the densities involved in the ratio, instead of being a special identity imposing some mathematically void constraints on the prior distributions. We completely clarify the measure-theoretic foundations of the Savage–Dickey representation as well as of the later generalisation of Verdinelli and Wasserman (1995). We provide furthermore a general framework that produces a converging approximation of the Bayes factor that is unrelated with the approach of Verdinelli and Wasserman (1995) and propose a comparison of this new approximation with their version, as well as with bridge sampling and Chib’s approaches.

Testing a molecular clock without an outgroup: derivations of induced priors on branch-length restrictions in a Bayesian framework.

We propose a Bayesian method for testing molecular clock hypotheses for use with aligned sequence data from multiple taxa. Our method utilizes a nonreversible nucleotide substitution model to avoid the necessity of specifying either a known tree relating the taxa or an outgroup for rooting the tree. We employ reversible jump Markov chain Monte Carlo to sample from the posterior distribution of the phylogenetic model parameters and conduct hypothesis testing using Bayes factors, the ratio of the posterior to prior odds of competing models. Here, the Bayes factors reflect the relative support of the sequence data for equal rates of evolutionary change between taxa versus unequal rates, averaged over all possible phylogenetic parameters, including the tree and root position. As the molecular clock model is a restriction of the more general unequal rates model, we use the Savage-Dickey ratio to estimate the Bayes factors. The Savage-Dickey ratio provides a convenient approach to calculating Bayes factors in favor of sharp hypotheses. Critical to calculating the Savage-Dickey ratio is a determination of the prior induced on the modeling restrictions. We demonstrate our method on a well-studied mtDNA sequence data set consisting of nine primates. We find strong support against a global molecular clock, but do find support for a local clock among the anthropoids. We provide mathematical derivations of the induced priors on branch length restrictions assuming equally likely trees. These derivations also have more general applicability to the examination of prior assumptions in Bayesian phylogenetics.

A Method for Testing Nested Point Null Hypotheses Using Multiple Bayes Factor

As a flexible Bayesian test criterion for nested point null hypotheses, asymmetric and multiple Bayes factors are introduced in the form of a modified Savage-Dickey density ratio. This leads to a simple method for obtaining pairwise comparisons of hypotheses in a statistical experiment with a partition on the parameter space. The method is derived from the fact that in general, the asymmetric Bayes factor can be written as the product of the Savage-Dickey ratio and a correction factor where both terms are easily estimated by means of posterior simulation. Analyses of a censored data problem and a serial correlation problem are illustrated for the method. For these cases, the method is straightforward for specifying distributionally and to implement computationally, with output readily adapted for required tests.