## Archive for Bayesian Analysis

## SADA’16

Posted in pictures, Statistics, Travel, University life with tags Africa, applied statistics, Bayesian Analysis, Bénin, big data, biostatistics, conference, Cotonou, data analysis, econometrics, Pau, SADA'16, surveys on April 28, 2016 by xi'an## comments on Watson and Holmes

Posted in Statistics, Books, Travel, pictures with tags Statistical Science, decision theory, Bayesian Analysis, University of Oxford, Dirichlet process, Sherlock Holmes, Kullback-Leibler divergence, Conan Doyle, Bayesian robustness, Saint Giles cemetery on April 1, 2016 by xi'an

“The world is full of obvious things which nobody by any chance ever observes.” The Hound of the Baskervilles

**I**n connection with the incoming publication of James Watson’s and Chris Holmes’ Approximating models and robust decisions in Statistical Science, Judith Rousseau and I wrote a discussion on the paper that has been arXived yesterday.

“Overall, we consider that the calibration of the Kullback-Leibler divergence remains an open problem.” (p.18)

While the paper connects with earlier ones by Chris and coauthors, and possibly *despite* the overall critical tone of the comments!, I really appreciate the renewed interest in robustness advocated in this paper. I was going to write *Bayesian robustness* but to differ from the perspective adopted in the 90’s where robustness was mostly about the prior, I would say this is rather a Bayesian approach to model robustness from a decisional perspective. With definitive innovations like considering the impact of posterior uncertainty over the decision space, uncertainty being defined e.g. in terms of Kullback-Leibler neighbourhoods. Or with a Dirichlet process distribution on the posterior. This may step out of the standard Bayesian approach but it remains of definite interest! (And note that this discussion of ours [reluctantly!] refrained from capitalising on the names of the authors to build easy puns linked with the most Bayesian of all detectives!)

## approximate Bayesian inference

Posted in Books, pictures, Statistics, Travel, University life with tags ABC in London, alive particle filter, Bayesian Analysis, Dirichlet prior, empirical likelihood, expectation-propagation, integer time-series, pMCMC, pseudo-marginal MCMC on March 23, 2016 by xi'an**M**aybe it is just a coincidence, but both most recent issues of Bayesian Analysis have an article featuring approximate Bayesian inference. One is by Daniel Add Contact Form Graham and co-authors on Approximate Bayesian Inference for Doubly Robust Estimation, while the other one is by Chris Drovandi and co-authors from QUT on Exact and Approximate Bayesian Inference for Low Integer-Valued Time Series Models with Intractable Likelihoods. The first paper has little connection with ABC. Even though it (a) uses a lot of three letter acronyms [which does not help with speed reading] and (b) relies on moment based and propensity score models. Instead, it relies on Bayesian bootstrap, which suddenly seems to me to be rather connected with empirical likelihood! Except the weights are estimated via a Dirichlet prior instead of being optimised. The approximation lies in using the bootstrap to derive a posterior predictive. I did not spot any assessment or control of the approximation effect in the paper.

“Note that we are always using the full data so avoiding the need to choose a summary statistic” (p.326)

The second paper connects pMCMC with ABC. Plus pseudo-marginals on the side! And even simplified reversible jump MCMC!!! I am far from certain I got every point of the paper, though, especially the notion of dimension reduction associated with *this* version of reversible jump MCMC. It may mean that latent variables are integrated out in approximate (marginalised) likelihoods [as explicated in Andrieu and Roberts (2009)].

“The difference with the common ABC approach is that we match on observations one-at-a-time” (p.328)

The model that the authors study is an integer value time-series, like the INAR(p) model. Which integer support allows for a non-zero probability of exact matching between simulated and observed data. One-at-a-time as indicated in the above quote. And integer valued tolerances like ε=1 otherwise. In the case auxiliary variables are necessary, the authors resort to the alive particle filter of Jasra et al. (2013), which main point is to produce an unbiased estimate of the (possibly approximate) likelihood, to be exploited by pseudo-marginal techniques. However, unbiasedness sounds less compelling when moving to approximate methods, as illustrated by the subsequent suggestion to use a more stable estimate of the log-likelihood. In fact, when the tolerance ε is positive, the pMCMC acceptance probability looks quite close to an ABC-MCMC probability when relying on several pseudo-data simulations. Which is unbiased for the “right” approximate target. A fact that may actually holds for *all* ABC algorithms. One quite interesting aspect of the paper is its reflection about the advantage of pseudo-marginal techniques for RJMCMC algorithms since they allow for trans-dimension moves to be simplified, as they consider marginals on the space of interest. Up to this day, I had not realised Andrieu and Roberts (2009) had a section on this aspect… I am still unclear about the derivation of the posterior probabilities of the models under comparison, unless it is a byproduct of the RJMCMC algorithm. A last point is that, for some of the Markov models used in the paper, the pseudo observations can be produced as a random one-time move away from the current true observation, which makes life much easier for ABC and explain why exact simulations can sometimes be produced. (*A side note:* the authors mention on p.326 that EP is only applicable when the posterior is from an exponential family, while my understanding is that it uses an exponential family to approximate the true posterior.)

## Bayesian composite likelihood

Posted in Books, Statistics, University life with tags ABC, approximate likelihood, Bayesian Analysis, composite likelihood, Kullback-Leibler divergence, machine learning, mixture of experts on February 11, 2016 by xi'an

“…the pre-determined weights assigned to the different associations between observed and unobserved values represent strong a priori knowledge regarding the informativeness of clues. A poor choice of weights will inevitably result in a poor approximation to the “true” Bayesian posterior…”

**L**ast Xmas, Alexis Roche arXived a paper on Bayesian inference via composite likelihood. I find the paper quite interesting in that [and only in that] it defends the innovative notion of writing a composite likelihood as a pool of opinions about some features of the data. Recall that each term in the composite likelihood is a marginal likelihood for some projection z=f(y) of the data y. As in ABC settings, although it is rare to derive closed-form expressions for those marginals. The composite likelihood is parameterised by powers of those components. Each component is associated with an expert, whose weight reflects the importance. The sum of the powers is constrained to be equal to one, even though I do not understand why the dimensions of the projections play no role in this constraint. Simplicity is advanced as an argument, which sounds rather weak… Even though this may be infeasible in any realistic problem, it would be more coherent to see the weights as producing the best Kullback approximation to the true posterior. Or to use a prior on the weights and estimate them along the parameter θ. The former could be incorporated into the later following the approach of Holmes & Walker (2013). While the ensuing discussion is most interesting, it remains missing in connecting the different components in terms of the (joint) information brought about the parameters. Especially because the weights are assumed to be given rather than inferred. Especially when they depend on θ. I also wonder why the variational Bayes interpretation is not exploited any further. And see no clear way to exploit this perspective in an ABC environment.

## R typos

Posted in Books, Kids, R, Statistics, Travel, University life with tags Amsterdam, Bayesian Analysis, MCMskv, Metropolis-Hastings algorithm, mixtures, Monte Carlo Statistical Methods, R, random walk, testing as mixture estimation on January 27, 2016 by xi'an**A**t MCMskv, Alexander Ly (from Amsterdam) pointed out to me some R programming mistakes I made in the introduction to Metropolis-Hastings algorithms I wrote a few months ago for the Wiley on-line encyclopedia! While the outcome (Monte Carlo posterior) of the corrected version is moderately changed this is nonetheless embarrassing! The example (if not the R code) was a mixture of a Poisson and a Geometric distributions borrowed from our testing as mixture paper. Among other things, I used a flat prior on the mixture weights instead of a Beta(1/2,1/2) prior *and* a simple log-normal random walk on the mean parameter instead of a more elaborate second order expansion discussed in the text. And I also inverted the probabilities of success and failure for the Geometric density. The new version is now available on arXiv, and hopefully soon on the Wiley site, but one (the?) fact worth mentioning here is that the (right) corrections in the R code first led to overflows, because I was using the Beta random walk Be(εp,ε(1-p)) which major drawback I discussed here a few months ago. With the drag that nearly zero or one values of the weight parameter produced infinite values of the density… Adding 1 (or 1/2) to each parameter of the Beta proposal solved the problem. And led to a posterior on the weight still concentrating on the correct corner of the unit interval. In any case, a big thank you to Alexander for testing the R code and spotting out the several mistakes…

## done! [#1]

Posted in Kids, pictures, University life with tags Bayesian Analysis, final exam, grading, mathematical statistics, multiple answer test, statistics exam, undergraduates on January 16, 2016 by xi'an**A**fter spending a few hours grading my 127 exams for most nights of this week, I am finally done with it! One of the exam questions was the simulation of XY when (X,Y) is a bivariate normal vector with correlation ρ, following the trick described in a X validated question asked a few months ago, namely that

XY≡R{cos(πU)+ρ}

but no one managed to establish this representation. And, as usual, some students got confused between parameters θ and observations x when writing a posterior density, since the density of the prior was defined in the exam with the *dummy* x, thereby recovering the prior as the posterior. Nothing terrible and nothing exceptional with this cohort of undergraduates. And now I still have to go through my second pile of exams for the graduate course I taught on Bayesian computational tools…

## the philosophical importance of Stein’s paradox [a reply from the authors]

Posted in Books, pictures, Statistics, University life with tags Bayesian Analysis, Bayesian Choice, Charles Stein, decision theory, frequentist inference, James-Stein estimator, loss functions, philosophy of sciences, Stein effect, Stein's phenomenon, Stephen Stigler on January 15, 2016 by xi'an*[In the wake of my comment on this paper written by three philosophers of Science, I received this reply from Olav Vassend.]*

Thank you for reading our paper and discussing it on your blog! Our purpose with the paper was to give an introduction to Stein’s phenomenon for a philosophical audience; it was not meant to — and probably will not — offer a new and interesting perspective for a statistician who is already very familiar with Stein’s phenomenon and its extensive literature.

I have a few more specific comments:

1. We don’t rechristen Stein’s phenomenon as “holistic pragmatism.” Rather, holistic pragmatism is the attitude to frequentist estimation that we think is underwritten by Stein’s phenomenon. Since MLE is sometimes admissible and sometimes not, depending on the number of parameters estimated, the researcher has to take into account his or her goals (whether total accuracy or individual-parameter accuracy is more important) when picking an estimator. To a statistician, this might sound obvious, but to philosophers it’s a pretty radical idea.

2.* “The part connecting Stein with Bayes again starts on the wrong foot, since it is untrue that any shrinkage estimator can be expressed as a Bayes posterior mean. This is not even true for the original James-Stein estimator, i.e., it is not a Bayes estimator and cannot be a Bayes posterior mean.”*

That seems to depend on what you mean by a “Bayes estimator.” It is possible to have an empirical Bayes prior (constructed from the sample) whose posterior mean is identical to the original James-Stein estimator. But if you don’t count empirical Bayes priors as Bayesian, then you are right.

3. *“And to state that improper priors “integrate to a number larger than 1” and that “it’s not possible to be more than 100% confident in anything”… And to confuse the Likelihood Principle with the prohibition of data dependent priors. And to consider that the MLE and any shrinkage estimator have the same expected utility under a flat prior (since, if they had, there would be no Bayes estimator!).”*

I’m not sure I completely understand your criticisms here. First, as for the relation between the LP and data-dependent priors — it does seem to me that the LP precludes the use of data-dependent priors. If you use data from an experiment to construct your prior, then — contrary to the LP — it will not be true that all the information provided by the experiment regarding which parameter is true is contained in the likelihood function, since some of the information provided by the experiment will also be in your prior.

Second, as to our claim that the ML estimator has the same expected utility (under the flat prior) as a shrinkage prior that it is dominated by—we incorporated this claim into our paper because it was an objection made by a statistician who read and commented on our paper. Are you saying the claim is false? If so, we would certainly like to know so that we can revise the paper to make it more accurate.

4. I was aware of Rubin’s idea that priors and utility functions (supposedly) are non-separable, but I didn’t (and don’t) quite see the relevance of that idea to Stein estimation.

5. *“Similarly, very little of substance can be found about empirical Bayes estimation and its philosophical foundations.”*

What we say about empirical Bayes priors is that they cannot be interpreted as degrees of belief; they are just tools. It will be surprising to many philosophers that priors are sometimes used in such an instrumentalist fashion in statistics.

6. The reason why we made a comparison between Stein estimation and AIC was two-fold: (a) for sociological reasons, philosophers are much more familiar with model selection than they are with, say, the LASSO or other regularized regression methods. (b) To us, it’s precisely because model selection and estimation are such different enterprises that it’s interesting that they have such a deep connection: despite being very different, AIC and shrinkage both rely on a bias-variance trade-off.

7. *“I also object to the envisioned possibility of a shrinkage estimator that would improve every component of the MLE (in a uniform sense) as it contradicts the admissibility of the single component MLE!”*

I don’t think our suggestion here contradicts the admissibility of single component MLE. The idea is just that if we have data D and D’ about parameters φ and φ’, then the estimates of both φ and φ’ can sometimes be improved if the estimation problems are lumped together and a shrinkage estimator is used. This doesn’t contradict the admissibility of MLE, because MLE is still admissible on each of the data sets for each of the parameters.

Again, thanks for reading the paper and for the feedback—we really do want to make sure our paper is accurate, so your feedback is much appreciated. Lastly, I apologize for the length of this comment.

Olav Vassend