Archive for integrated likelihood

are profile likelihoods likelihoods?!

Posted in Books, Kids, Statistics, University life with tags , , , , , on March 27, 2018 by xi'an

A recent arXived paper by Oliver J. Maclaren is asking this very question. And argue for a positive answer. One of the invoked sources is Murray Aitkin’s integrated likelihood book, which I criticised here and elsewhere. With the idea of the paper being that

“….there is an appropriate notion of integration over variables that takes likelihood functions to likelihood functions via maximization.”

Hmm…. The switch there is to replace addition with maximisation, probability with possibility, and… profile likelihood as marginal possibility under this new concept. I just do not see how adapting these concepts for the interpretation of the profile likelihood makes the latter more meaningful, since it still overwhelmingly does not result from a distribution density at an observed realisation of a random variable. This reminds me a paper I refereed quite a long while ago where the authors were using Schwarz’ theory of distributions to expand the notion of unbiasedness. With unclear consequences.

Measuring statistical evidence using relative belief [book review]

Posted in Books, Statistics, University life with tags , , , , , , , , , , , , , , , , , , on July 22, 2015 by xi'an

“It is necessary to be vigilant to ensure that attempts to be mathematically general do not lead us to introduce absurdities into discussions of inference.” (p.8)

This new book by Michael Evans (Toronto) summarises his views on statistical evidence (expanded in a large number of papers), which are a quite unique mix of Bayesian  principles and less-Bayesian methodologies. I am quite glad I could receive a version of the book before it was published by CRC Press, thanks to Rob Carver (and Keith O’Rourke for warning me about it). [Warning: this is a rather long review and post, so readers may chose to opt out now!]

“The Bayes factor does not behave appropriately as a measure of belief, but it does behave appropriately as a measure of evidence.” (p.87)

Continue reading

Approximate Bayesian model choice

Posted in Books, R, Statistics, Travel, University life with tags , , , , , , , , , on March 17, 2014 by xi'an

The above is the running head of the arXived paper with full title “Implications of  uniformly distributed, empirically informed priors for phylogeographical model selection: A reply to Hickerson et al.” by Oaks, Linkem and Sukuraman. That I (again) read in the plane to Montréal (third one in this series!, and last because I also watched the Japanese psycho-thriller Midsummer’s Equation featuring a physicist turned detective in one of many TV episodes. I just found some common features with The Devotion of Suspect X, only to discover now that the book has been turned into another episode in the series.)

“Here we demonstrate that the approach of Hickerson et al. (2014) is dangerous in the sense that the empirically-derived priors often exclude from consideration the true values of the models’ parameters. On a more fundamental level, we question the value of adopting an empirical Bayesian stance for this model-choice problem, because it can mislead model posterior probabilities, which are inherently measures of belief in the models after prior knowledge is updated by the data.”

This paper actually is a reply to Hickerson et al. (2014, Evolution), which is itself a reply to an earlier paper by Oaks et al. (2013, Evolution). [Warning: I did not check those earlier references!] The authors object to the use of “narrow, empirically informed uniform priors” for the reason reproduced in the above quote. In connection with the msBayes of Huang et al. (2011, BMC Bioinformatics). The discussion is less about ABC used for model choice and posterior probabilities of models and more about the impact of vague priors, Oaks et al. (2013) arguing that this leads to a bias towards models with less parameters, a “statistical issue” in their words, while Hickerson et al. (2014) think this is due to msBayes way of selecting models and their parameters at random.

“…it is difficult to choose a uniformly distributed prior on divergence times that is broad enough to confidently contain the true values of parameters while being narrow enough to avoid spurious support of models with less parameter space.”

So quite an interesting debate that takes us in fine far away from the usual worries about ABC model choice! We are more at the level empirical versus natural Bayes, seen in the literature of the 80’s. (The meaning of empirical Bayes is not that clear in the early pages as the authors seem to involve any method using the data “twice”.) I actually do not remember reading papers about the formal properties of model choice done through classical empirical Bayes techniques. Except the special case of Aitkin’s (1991,2009) integrated likelihood. Which is essentially the analysis performed on the coin toy example (p.7)

“…models with more divergence parameters will be forced to integrate over much greater parameter space, all with equal prior density, and much of it with low likelihood.”

The above argument is an interesting rephrasing of Lindley’s paradox, which I cannot dispute, but of course it does not solve the fundamental issue of how to choose the prior away from vague uniform priors… I also like the quote “the estimated posterior probability of a model is a single value (rather than a distribution) lacking a measure of posterior uncertainty” as this is an issue on which we are currently working. I fully agree with the statement and we think an alternative assessment to posterior probabilities could be more appropriate for model selection in ABC settings (paper soon to come, hopefully!).

my DICussion

Posted in Books, Kids, pictures, Statistics, University life with tags , , , , , , , on September 25, 2013 by xi'an

IMG_1648Following the Re-Reading of Spiegelhalter et al. (2002) by David at the RSS Annual Conference a few weeks ago, and my invited discussion there, I was asked to contribute a written discussion to Series B, a request obviously impossible to refuse!

The main issue with DIC is the question of its worth for Bayesian decision analysis (since I doubt there are many proponents of DIC outside the Bayesian community). The appeal of DIC is, I presume, to deliver a single summary per model under comparison and to allow therefore for a complete ranking of those models. I however object at the worth of simplicity for simplicity’s sake: models are complex (albeit less than reality) and their usages are complex as well. To consider that model A is to be preferred upon model B just because DIC(A)=1228 < DiC(B)=1237 is a mimicry of the complex mechanisms at play behind model choice, especially given the wealth of information provided by a Bayesian framework. (Non-Bayesian paradigms are more familiar with procedures based on a single estimator value.) And to abstain from accounting for the significance of the difference between DIC(A) and DIC(B) clearly makes matters worse.

This is not even discussing the stylised setting where one model is considered as “true” and where procedures are compared by their ability to recover the “truth”. David Spiegelhalter repeatedly mentioned during his talk that he was not interested in this. This stance brings another objection, though, namely that models can only be compared against their predictive abilities, which DIC seems unable to capture. Once again, what is needed is a multi-factor and all-encompassing criterion that evaluates the predictive models in terms of their recovery of some features of the phenomenon under study. Or of the process being conducted. (Even stooping down to a one-dimensional loss function that is supposed to summarise the purpose of the model comparison does not produce anything close to the DIC function.)

ruins of the abbey at Tynemouth, Sept. 03, 2013Obviously, considering that asymptotic consistency is of no importance whatsoever (as repeated by David in Newcastle) avoids some embarrassing questions, except the one about the true purpose of statistical models and procedures. How can they be compared if no model is true and if accumulating data from a given model is not meaningful? How can simulation be conducted in such a barren landscape?  I find it the more difficult to accept this minimalist attitude that models are truly used as if they were or could be true, at several stages in the process. It also prevents the study of the criterion under model misspecification, which would clearly be of interest.

Another point, already exposed in our 2006 Bayesian Analysis paper with Gilles Celeux, Florence Forbes, and Mike Titterington, is that there is no unique driving principle for constructing DICs. In that paper, we examined eight different and natural versions of DIC for mixture models, resulting in highly diverging values for DIC and the effective dimension of the parameter, I believe that such a lack of focus is bound to reappear in any multimodal setting and fear that the answer about (eight) different focus on what matters in the model is too cursory and lacks direction for the hapless practitioner.

My final remark about DIC is that it shares very much the same perspective as Murray Aitkin’s integrated likelihood, Both Aitkin (1991, 2009) and Spiegelhalter et al. (2002) consider a posterior distribution on the likelihood function, taken as a function of the parameter but omitting the delicate fact that it also depends on the observable and hence does not exist a priori. We wrote a detailed review of Aitkin’s (2009) book, where most of the criticisms equally apply to DIC, and I will not repeat them here, except for pointing out that it escapes the Bayesian framework (and thus requires even more its own justifications).

re-read paper

Posted in Books, Statistics, Travel, University life with tags , , , , , , , on September 3, 2013 by xi'an

Today, I attended the RSS Annual Conference in Newcastle-upon-Tyne. For one thing, I ran a Memorial session in memory of George Casella, with my (and his) friends Jim Hobert and Elias Moreno as speakers. (The session was well-attended if not overwhelmingly so.) For another thing, the RSS decided to have the DIC Read Paper by David Spiegelhalter, Nicky Best, Brad Carlin and Angelika van der Linde Bayesian measures of model complexity and fit re-Read, and I was asked to re-discuss the 2002 paper. Here are the slides of my discussion, borrowing from the 2006 Bayesian Analysis paper with Gilles Celeux, Florence Forbes, and Mike Titterington where we examined eight different versions of DIC for mixture models. (I refrained from using the title “snow white and the seven DICs” for a slide…) I also borrowed from our recent discussion of Murray Aitkin’s (2009) book. The other discussant was Elias Moreno, who focussed on consistency issues. (More on this and David Spiegelhalter’s defence in a few posts!) This was the first time I was giving a talk on a basketball court (I once gave an exam there!)