Archive for INLA

Computational Bayesian Statistics [book review]

Posted in Books, Statistics with tags , , , , , , , , , , , , , , , , , , , , , , , , , , , , on February 1, 2019 by xi'an

This Cambridge University Press book by M. Antónia Amaral Turkman, Carlos Daniel Paulino, and Peter Müller is an enlarged translation of a set of lecture notes in Portuguese. (Warning: I have known Peter Müller from his PhD years in Purdue University and cannot pretend to perfect objectivity. For one thing, Peter once brought me frozen-solid beer: revenge can also be served cold!) Which reminds me of my 1994 French edition of Méthodes de Monte Carlo par chaînes de Markov, considerably upgraded into Monte Carlo Statistical Methods (1998) thanks to the input of George Casella. (Re-warning: As an author of books on the same topic(s), I can even less pretend to objectivity.)

“The “great idea” behind the development of computational Bayesian statistics is the recognition that Bayesian inference can be implemented by way of simulation from the posterior distribution.”

The book is written from a strong, almost militant, subjective Bayesian perspective (as, e.g., when half-Bayesians are mentioned!). Subjective (and militant) as in Dennis Lindley‘s writings, eminently quoted therein. As well as in Tony O’Hagan‘s. Arguing that the sole notion of a Bayesian estimator is the entire posterior distribution. Unless one brings in a loss function. The book also discusses the Bayes factor in a critical manner, which is fine from my perspective.  (Although the ban on improper priors makes its appearance in a very indirect way at the end of the last exercise of the first chapter.)

Somewhat at odds with the subjectivist stance of the previous chapter, the chapter on prior construction only considers non-informative and conjugate priors. Which, while understandable in an introductory book, is a wee bit disappointing. (When mentioning Jeffreys’ prior in multidimensional settings, the authors allude to using univariate Jeffreys’ rules for the marginal prior distributions, which is not a well-defined concept or else Bernardo’s and Berger’s reference priors would not have been considered.) The chapter also mentions the likelihood principle at the end of the last exercise, without a mention of the debate about its derivation by Birnbaum. Or Deborah Mayo’s recent reassessment of the strong likelihood principle. The following chapter is a sequence of illustrations in classical exponential family models, classical in that it is found in many Bayesian textbooks. (Except for the Poison model found in Exercise 3.3!)

Nothing to complain (!) about the introduction of Monte Carlo methods in the next chapter, especially about the notion of inference by Monte Carlo methods. And the illustration by Bayesian design. The chapter also introduces Rao-Blackwellisation [prior to introducing Gibbs sampling!]. And the simplest form of bridge sampling. (Resuscitating the weighted bootstrap of Gelfand and Smith (1990) may not be particularly urgent for an introduction to the topic.) There is furthermore a section on sequential Monte Carlo, including the Kalman filter and particle filters, in the spirit of Pitt and Shephard (1999). This chapter is thus rather ambitious in the amount of material covered with a mere 25 pages. Consensus Monte Carlo is even mentioned in the exercise section.

“This and other aspects that could be criticized should not prevent one from using this [Bayes factor] method in some contexts, with due caution.”

Chapter 5 turns back to inference with model assessment. Using Bayesian p-values for model assessment. (With an harmonic mean spotted in Example 5.1!, with no warning about the risks, except later in 5.3.2.) And model comparison. Presenting the whole collection of xIC information criteria. from AIC to WAIC, including a criticism of DIC. The chapter feels somewhat inconclusive but methinks this is the right feeling on the current state of the methodology for running inference about the model itself.

“Hint: There is a very easy answer.”

Chapter 6 is also a mostly standard introduction to Metropolis-Hastings algorithms and the Gibbs sampler. (The argument given later of a Metropolis-Hastings algorithm with acceptance probability one does not work.) The Gibbs section also mentions demarginalization as a [latent or auxiliary variable] way to simulate from complex distributions [as we do], but without defining the notion. It also references the precursor paper of Tanner and Wong (1987). The chapter further covers slice sampling and Hamiltonian Monte Carlo, the later with sufficient details to lead to reproducible implementations. Followed by another standard section on convergence assessment, returning to the 1990’s feud of single versus multiple chain(s). The exercise section gets much larger than in earlier chapters with several pages dedicated to most problems. Including one on ABC, maybe not very helpful in this context!

“…dimension padding (…) is essentially all that is to be said about the reversible jump. The rest are details.”

The next chapter is (somewhat logically) the follow-up for trans-dimensional problems and marginal likelihood approximations. Including Chib’s (1995) method [with no warning about potential biases], the spike & slab approach of George and McCulloch (1993) that I remember reading in a café at the University of Wyoming!, the somewhat antiquated MC³ of Madigan and York (1995). And then the much more recent array of Bayesian lasso techniques. The trans-dimensional issues are covered by the pseudo-priors of Carlin and Chib (1995) and the reversible jump MCMC approach of Green (1995), the later being much more widely employed in the literature, albeit difficult to tune [and even to comprehensively describe, as shown by the algorithmic representation in the book] and only recommended for a large number of models under comparison. Once again the exercise section is most detailed, with recent entries like the EM-like variable selection algorithm of Ročková and George (2014).

The book also includes a chapter on analytical approximations, which is also the case in ours [with George Casella] despite my reluctance to bring them next to exact (simulation) methods. The central object is the INLA methodology of Rue et al. (2009) [absent from our book for obvious calendar reasons, although Laplace and saddlepoint approximations are found there as well]. With a reasonable amount of details, although stopping short of implementable reproducibility. Variational Bayes also makes an appearance, mostly following the very recent Blei et al. (2017).

The gem and originality of the book are primarily to be found in the final and ninth chapter where four software are described, all with interfaces to R: OpenBUGS, JAGS, BayesX, and Stan, plus R-INLA which is processed in the second half of the chapter (because this is not a simulation method). As in the remainder of the book, the illustrations are related to medical applications. Worth mentioning is the reminder that BUGS came in parallel with Gelfand and Smith (1990) Gibbs sampler rather than as a consequence. Even though the formalisation of the Markov chain Monte Carlo principle by the later helped in boosting the power of this software. (I also appreciated the mention made of Sylvia Richardson’s role in this story.) Since every software is illustrated in depth with relevant code and output, and even with the shortest possible description of its principle and modus vivendi, the chapter is 60 pages long [and missing a comparative conclusion]. Given my total ignorance of the very existence of the BayesX software, I am wondering at the relevance of its inclusion in this description rather than, say, other general R packages developed by authors of books such as Peter Rossi. The chapter also includes a description of CODA, with an R version developed by Martin Plummer [now a Warwick colleague].

In conclusion, this is a high-quality and all-inclusive introduction to Bayesian statistics and its computational aspects. By comparison, I find it much more ambitious and informative than Albert’s. If somehow less pedagogical than the thicker book of Richard McElreath. (The repeated references to Paulino et al.  (2018) in the text do not strike me as particularly useful given that this other book is written in Portuguese. Unless an English translation is in preparation.)

Disclaimer: this book was sent to me by CUP for endorsement and here is what I wrote in reply for a back-cover entry:

An introduction to computational Bayesian statistics cooked to perfection, with the right mix of ingredients, from the spirited defense of the Bayesian approach, to the description of the tools of the Bayesian trade, to a definitely broad and very much up-to-date presentation of Monte Carlo and Laplace approximation methods, to an helpful description of the most common software. And spiced up with critical perspectives on some common practices and an healthy focus on model assessment and model selection. Highly recommended on the menu of Bayesian textbooks!

And this review is likely to appear in CHANCE, in my book reviews column.

Bayes for good

Posted in Books, Mountains, pictures, Running, Statistics, Travel, University life with tags , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , on November 27, 2018 by xi'an

A very special weekend workshop on Bayesian techniques used for social good in many different sense (and talks) that we organised with Kerrie Mengersen and Pierre Pudlo at CiRM, Luminy, Marseilles. It started with Rebecca (Beka) Steorts (Duke) explaining [by video from Duke] how the Syrian war deaths were processed to eliminate duplicates, to be continued on Monday at the “Big” conference, Alex Volfonsky (Duke) on a Twitter experiment on the impact of being exposed to adverse opinions as depolarising (not!) or further polarising (yes), turning into network causal analysis. And then Kerrie Mengersen (QUT) on the use of Bayesian networks in ecology, through observational studies she conducted. And the role of neutral statisticians in case of adversarial experts!

Next day, the first talk of David Corlis (Peace-Work), who writes the Stats for Good column in CHANCE and here gave a recruiting spiel for volunteering in good initiatives. Quoting Florence Nightingale as the “first” volunteer. And presenting a broad collection of projects as supports to his recommendations for “doing good”. We then heard [by video] Julien Cornebise from Element AI in London telling of his move out of DeepMind towards investing in social impacting projects through this new startup. Including working with Amnesty International on Darfour village destructions, building evidence from satellite imaging. And crowdsourcing. With an incoming report on the year activities (still under embargo). A most exciting and enthusiastic talk!

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Masterclass in Bayesian Statistics in Marseilles next Fall

Posted in Books, Kids, Mountains, pictures, R, Running, Statistics, Travel, University life with tags , , , , , , , , , , , , , , , , on April 9, 2018 by xi'an

This post is to announce a second occurrence of the exciting “masterclass in Bayesian Statistics” that we organised in 2016, near Marseilles. It will take place on 22-26 October 2018 once more at CIRM (Centre International de Recherches Mathématiques, Luminy, Marseilles, France). The targeted audience includes all scientists interested in learning how Bayesian inference may be used to tackle the practical problems they face in their own research. In particular PhD students and post-docs should benefit most directly from this masterclass. Among the invited speakers, Kerrie Mengersen from QUT, Brisbane, visiting Marseilles this Fall, will deliver a series of lectures on the interface between Bayesian statistics and applied modelling, Havard Rue from KAUST will talk on computing with INLA, and Aki Vehtari from Aalto U, Helsinki, will give a course on Bayesian model assessment and model choice. There will be two tutorials on R and on Stan.

All interested participants in this masterclass should pre-register as early as possible, given that the total attendance is limited to roughly 90 participants. Some specific funding for local expenses (i.e., food + accommodation on-siteat CIRM) is available (thanks to CIRM, and potentially to Fondation Jacques Hadamard, to be confirmed); this funding will be attributed by the scientific committee, with high priority to PhD students and post-docs.

European statistics in Finland [EMS17]

Posted in Books, pictures, Running, Statistics, Travel, University life with tags , , , , , , , , , , , , , , on August 2, 2017 by xi'an

While this European meeting of statisticians had a wide range of talks and topics, I found it to be more low key than the previous one I attended in Budapest, maybe because there was hardly any talk there in applied probability. (But there were some sessions in mathematical statistics and Mark Girolami gave a great entry to differential geometry and MCMC, in the spirit of his 2010 discussion paper. Using our recent trip to Montréal as an example of geodesic!) In the Bayesian software session [organised by Aki Vetahri], Javier Gonzáles gave a very neat introduction to Bayesian optimisation: he showed how optimisation can be turned into Bayesian inference or more specifically as a Bayesian decision problem using a loss function related to the problem of interest. The point in following a Bayesian path [or probabilist numerics] is to reduce uncertainty by the medium of prior measures on functions, although resorting [as usual] to Gaussian processes whose arbitrariness I somehow dislike within the infinity of priors (aka stochastic processes) on functions! One of his strong arguments was that the approach includes the possibility for design in picking the next observation point (as done in some ABC papers of Michael Guttman and co-authors, incl. the following talk at EMS 2017) but again the devil may be in the implementation when looking at minimising an objective function… The notion of the myopia of optimisation techniques was another good point: only looking one step ahead in the future diminishes the returns of the optimisation and an alternative presented at AISTATS 2016 [that I do not remember seeing in Càdiz] goes against this myopia.

Umberto Piccini also gave a talk on exploiting synthetic likelihoods in a Bayesian fashion (in connection with the talk he gave last year at MCqMC 2016). I wondered at the use of INLA for this Gaussian representation, as well as at the impact of the parameterisation of the summary statistics. And the session organised by Jean-Michel involved Jimmy Olson, Murray Pollock (Warwick) and myself, with great talks from both other speakers, on PaRIS and PaRISian algorithms by Jimmy, and on a wide range of exact simulation methods of continuous time processes by Murray, both managing to convey the intuition behind their results and avoiding the massive mathematics at work there. By comparison, I must have been quite unclear during my talk since someone interrupted me about how Owen & Zhou (2000) justified their deterministic mixture importance sampling representation. And then left when I could not make sense of his questions [or because it was lunchtime already].

marginal likelihoods from MCMC

Posted in Books, pictures, Statistics, University life with tags , , , , , , , , , , , on April 26, 2017 by xi'an

A new arXiv entry on ways to approximate marginal likelihoods based on MCMC output, by astronomers (apparently). With an application to the 2015 Planck satellite analysis of cosmic microwave background radiation data, which reminded me of our joint work with the cosmologists of the Paris Institut d’Astrophysique ten years ago. In the literature review, the authors miss several surveys on the approximation of those marginals, including our San Antonio chapter, on Bayes factors approximations, but mention our ABC survey somewhat inappropriately since it is not advocating the use of ABC for such a purpose. (They mention as well variational Bayes approximations, INLA, powered likelihoods, if not nested sampling.)

The proposal of this paper is to identify the marginal m [actually denoted a there] as the normalising constant of an unnormalised posterior density. And to do so the authors estimate the posterior by a non-parametric approach, namely a k-nearest-neighbour estimate. With the additional twist of producing a sort of Bayesian posterior on the constant m. [And the unusual notion of number density, used for the unnormalised posterior.] The Bayesian estimation of m relies on a Poisson sampling assumption on the k-nearest neighbour distribution. (Sort of, since k is actually fixed, not random.)

If the above sounds confusing and imprecise it is because I am myself rather mystified by the whole approach and find it difficult to see the point in this alternative. The Bayesian numerics does not seem to have other purposes than producing a MAP estimate. And using a non-parametric density estimate opens a Pandora box of difficulties, the most obvious one being the curse of dimension(ality). This reminded me of the commented paper of Delyon and Portier where they achieve super-efficient convergence when using a kernel estimator, but with a considerable cost and a similar sensitivity to dimension.

reflections on the probability space induced by moment conditions with implications for Bayesian Inference [refleXions]

Posted in Statistics, University life with tags , , , , , , , , , , on November 26, 2014 by xi'an

“The main finding is that if the moment functions have one of the properties of a pivotal, then the assertion of a distribution on moment functions coupled with a proper prior does permit Bayesian inference. Without the semi-pivotal condition, the assertion of a distribution for moment functions either partially or completely specifies the prior.” (p.1)

Ron Gallant will present this paper at the Conference in honour of Christian Gouréroux held next week at Dauphine and I have been asked to discuss it. What follows is a collection of notes I made while reading the paper , rather than a coherent discussion, to come later. Hopefully prior to the conference.

The difficulty I have with the approach presented therein stands as much with the presentation as with the contents. I find it difficult to grasp the assumptions behind the model(s) and the motivations for only considering a moment and its distribution. Does it all come down to linking fiducial distributions with Bayesian approaches? In which case I am as usual sceptical about the ability to impose an arbitrary distribution on an arbitrary transform of the pair (x,θ), where x denotes the data. Rather than a genuine prior x likelihood construct. But I bet this is mostly linked with my lack of understanding of the notion of structural models.

“We are concerned with situations where the structural model does not imply exogeneity of θ, or one prefers not to rely on an assumption of exogeneity, or one cannot construct a likelihood at all due to the complexity of the model, or one does not trust the numerical approximations needed to construct a likelihood.” (p.4)

As often with econometrics papers, this notion of structural model sets me astray: does this mean any latent variable model or an incompletely defined model, and if so why is it incompletely defined? From a frequentist perspective anything random is not a parameter. The term exogeneity also hints at this notion of the parameter being not truly a parameter, but including latent variables and maybe random effects. Reading further (p.7) drives me to understand the structural model as defined by a moment condition, in the sense that

\mathbb{E}[m(\mathbf{x},\theta)]=0

has a unique solution in θ under the true model. However the focus then seems to make a major switch as Gallant considers the distribution of a pivotal quantity like

Z=\sqrt{n} W(\mathbf{x},\theta)^{-\frac{1}{2}} m(\mathbf{x},\theta)

as induced by the joint distribution on (x,θ), hence conversely inducing constraints on this joint, as well as an associated conditional. Which is something I have trouble understanding, First, where does this assumed distribution on Z stem from? And, second, exchanging randomness of terms in a random variable as if it was a linear equation is a pretty sure way to produce paradoxes and measure theoretic difficulties.

The purely mathematical problem itself is puzzling: if one knows the distribution of the transform Z=Z(X,Λ), what does that imply on the joint distribution of (X,Λ)? It seems unlikely this will induce a single prior and/or a single likelihood… It is actually more probable that the distribution one arbitrarily selects on m(x,θ) is incompatible with a joint on (x,θ), isn’t it?

“The usual computational method is MCMC (Markov chain Monte Carlo) for which the best known reference in econometrics is Chernozhukov and Hong (2003).” (p.6)

While I never heard of this reference before, it looks like a 50 page survey and may be sufficient for an introduction to MCMC methods for econometricians. What I do not get though is the connection between this reference to MCMC and the overall discussion of constructing priors (or not) out of fiducial distributions. The author also suggests using MCMC to produce the MAP estimate but this always stroke me as inefficient (unless one uses our SAME algorithm of course).

“One can also compute the marginal likelihood from the chain (Newton and Raftery (1994)), which is used for Bayesian model comparison.” (p.22)

Not the best solution to rely on harmonic means for marginal likelihoods…. Definitely not. While the author actually uses the stabilised version (15) of Newton and Raftery (1994) estimator, which in retrospect looks much like a bridge sampling estimator of sorts, it remains dangerously close to the original [harmonic mean solution] especially for a vague prior. And it only works when the likelihood is available in closed form.

“The MCMC chains were comprised of 100,000 draws well past the point where transients died off.” (p.22)

I wonder if the second statement (with a very nice image of those dying transients!) is intended as a consequence of the first one or independently.

“A common situation that requires consideration of the notions that follow is that deriving the likelihood from a structural model is analytically intractable and one cannot verify that the numerical approximations one would have to make to circumvent the intractability are sufficiently accurate.” (p.7)

This then is a completely different business, namely that defining a joint distribution by mean of moment equations prevents regular Bayesian inference because the likelihood is not available. This is more exciting because (i) there are alternative available! From ABC to INLA (maybe) to EP to variational Bayes (maybe). And beyond. In particular, the moment equations are strongly and even insistently suggesting that empirical likelihood techniques could be well-suited to this setting. And (ii) it is no longer a mathematical worry: there exist a joint distribution on m(x,θ), induced by a (or many) joint distribution on (x,θ). So the question of finding whether or not it induces a single proper prior on θ becomes relevant. But, if I want to use ABC, being given the distribution of m(x,θ) seems to mean I can only generate new values of this transform while missing a natural distance between observations and pseudo-observations. Still, I entertain lingering doubts that this is the meaning of the study. Where does the joint distribution come from..?!

“Typically C is coarse in the sense that it does not contain all the Borel sets (…)  The probability space cannot be used for Bayesian inference”

My understanding of that part is that defining a joint on m(x,θ) is not always enough to deduce a (unique) posterior on θ, which is fine and correct, but rather anticlimactic. This sounds to be what Gallant calls a “partial specification of the prior” (p.9).

Overall, after this linear read, I remain very much puzzled by the statistical (or Bayesian) implications of the paper . The fact that the moment conditions are central to the approach would once again induce me to check the properties of an alternative approach like empirical likelihood.

Bayes 250th versus Bayes 2.5.0.

Posted in Books, Statistics, Travel, University life with tags , , , , , , , , , , , , , , , , , on July 20, 2013 by xi'an

More than a year ago Michael Sørensen (2013 EMS Chair) and Fabrizzio Ruggeri (then ISBA President) kindly offered me to deliver the memorial lecture on Thomas Bayes at the 2013 European Meeting of Statisticians, which takes place in Budapest today and the following week. I gladly accepted, although with some worries at having to cover a much wider range of the field rather than my own research topic. And then set to work on the slides in the past week, borrowing from my most “historical” lectures on Jeffreys and Keynes, my reply to Spanos, as well as getting a little help from my nonparametric friends (yes, I do have nonparametric friends!). Here is the result, providing a partial (meaning both incomplete and biased) vision of the field.

Since my talk is on Thursday, and because the talk is sponsored by ISBA, hence representing its members, please feel free to comment and suggest changes or additions as I can still incorporate them into the slides… (Warning, I purposefully kept some slides out to preserve the most surprising entry for the talk on Thursday!)