Archive for Dirichlet prior

hidden dangers of noninformative priors

Posted in Books, Statistics, University life with tags , , , , , on November 21, 2013 by xi'an

Last year, John Seaman (III), John Seaman (Jr.), and James Stamey published a paper in The American Statistician with the title Hidden dangers of specifying noninformative priors. (It does not seem to be freely available on-line.) I gave it to read to my PhD students, meaning to read towards the goal of writing a critical reply to the authors. In the meanwhile, here are my own two-cents on the paper.

“Applications typically employ Markov chain Monte Carlo (MCMC) methods to obtain posterior features, resulting in the need for proper priors, even when the modeler prefers that priors be relatively noninformative.” (p.77)

Apart from the above quote, which confuses proper priors with proper posteriors (maybe as the result of a contagious BUGS!), and which is used to focus solely and sort-of inappropriately on proper priors, there is no hard fact to bite in, but rather a collection of soft decisions and options that end up weakly supporting the authors’ thesis. (Obviously, following an earlier post, there is no such thing as a “noninformative” prior.) The paper is centred on four examples where a particular choice of (“noninformative”) prior leads to peaked or informative priors on some transform(s) of the parameters. Note that there is no definition provided for informative, non-informative, diffuse priors, except those found in BUGS with “extremely large variance” (p.77). (The quote below seems to settle on a uniform prior if one understands the “likely” as evaluated through the posterior density.) The argument of the authors is that “if parameters with diffuse proper priors are subsequently transformed, the resulting induced priors can, of course, be far from diffuse, possibly resulting in unintended influence on the posterior of the transformed parameters” (p.77).

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Estimating the number of species

Posted in Statistics with tags , , , , , on November 20, 2009 by xi'an

Bayesian Analysis just published on-line a paper by Hongmei Zhang and Hal Stern on a (new) Bayesian analysis of the problem of estimating the number of unseen species within a population. This problem has always fascinated me, as it seems at first sight to be an impossible problem, how can you estimate the number of species you do not know?! The approach relates to capture-recapture models, with an extra hierarchical layer for the species. The Bayesian analysis of the model obviously makes a lot of sense, with the prior modelling being quite influential. Zhang and Stern use a hierarchical Dirichlet prior on the capture probabilities, \theta_i, when the captures follow a multinomial model

y|\theta,S \sim \mathcal{M}(N, \theta_1,\ldots,\theta_S)

where N=\sum_i y_i the total number of observed individuals,

\mathbf{\theta}|S \sim \mathcal{D}(\alpha,\ldots,\alpha)

and

\pi(\alpha,S) = f(1-f)^{S-S_\text{min}} \alpha^{-3/2}

forcing the coefficients of the Dirichlet prior towards zero. The paper also covers predictive design, analysing the capture effort corresponding to a given recovery rate of species. The overall approach is not immensely innovative in its methodology, the MCMC part being rather straightforward, but the predictive abilities of the model are nonetheless interesting.

The previously accepted paper in Bayesian Analysis is a note by Ron Christensen about an inconsistent Bayes estimator that you may want to use in an advanced Bayesian class. For all practical purposes, it should not overly worry you, since the example involves a sampling distribution that is normal when its parameter is irrational and is Cauchy otherwise. (The prior is assumed to be absolutely continuous wrt the Lebesgue measure and it thus gives mass zero to the set of rational numbers \mathbb{Q}. The fact that \mathbb{Q} is dense in \mathbb{R} is irrelevant from a measure-theoretic viewpoint.)