Archive for Bayesian lasso

O-Bayes15 [day #1]

Posted in Books, pictures, Running, Statistics, Travel, University life, Wines with tags , , , , , , on June 3, 2015 by xi'an

vale3So here we are back together to talk about objective Bayes methods, and in the City of Valencià as well.! A move back to a city where the 1998 O’Bayes took place. In contrast with my introductory tutorial, the morning tutorials by Luis Pericchi and Judith Rousseau were investigating fairly technical and advanced, Judith looking at the tools used in the frequentist (Bernstein-von Mises) analysis of priors, with forays in empirical Bayes, giving insights into a wide range of recent papers in the field. And Luis covering works on Bayesian robustness in the sense of resisting to over-influential observations. Following works of him and of Tony O’Hagan and coauthors. Which means characterising tails of prior versus sampling distribution to allow for the posterior reverting to the prior in case of over-influential datapoints. Funny enough, after a great opening by Carmen and Ed remembering Susie, Chris Holmes also covered Bayesian robust analysis. More in the sense of incompletely or mis-  specified models. (On the side, rekindling one comment by Susie and the need to embed robust Bayesian analysis within decision theory.) Which was also much Chris’ point, in line with the recent Watson and Holmes’ paper. Dan Simpson in his usual kick-the-anthill-real-hard-and-set-fire-to-it discussion pointed out the possible discrepancy between objective and robust Bayesian analysis. (With lines like “modern statistics has proven disruptive to objective Bayes”.) Which is not that obvious because the robust approach simply reincorporates the decision theory within the objective framework. (Dan also concluded with the comic strip below, whose message can be interpreted in many ways…! Or not.)

The second talk of the afternoon was given by Veronika Ročková on a novel type of spike-and-slab prior to handle sparse regression, bringing an alternative to the standard Lasso. The prior is a mixture of two Laplace priors whose scales are constrained in connection with the actual number of non-zero coefficients. I had not heard of this approach before (although Veronika and Ed have an earlier paper on a spike-and-slab prior to handle multicolinearity that Veronika presented in Boston last year) and I was quite impressed by the combination of minimax properties and practical determination of the scales. As well as by the performances of this spike-and-slab Lasso. I am looking forward the incoming paper!

The day ended most nicely in the botanical gardens of the University of Valencià, with an outdoor reception surrounded by palm trees and parakeet cries…

projective covariate selection

Posted in Mountains, pictures, Statistics, Travel, University life with tags , , , , , , , , , , , , , , on October 28, 2014 by xi'an

While I was in Warwick, Dan Simpson [newly arrived from Norway on a postdoc position] mentioned to me he had attended a talk by Aki Vehtari in Norway where my early work with Jérôme Dupuis on projective priors was used. He gave me the link to this paper by Peltola, Havulinna, Salomaa and Vehtari that indeed refers to the idea that a prior on a given Euclidean space defines priors by projections on all subspaces, despite the zero measure of all those subspaces. (This notion first appeared in a joint paper with my friend Costas Goutis, who alas died in a diving accident a few months later.) The projection further allowed for a simple expression of the Kullback-Leibler deviance between the corresponding models and for a Pythagorean theorem on the additivity of the deviances between embedded models. The weakest spot of this approach of ours was, in my opinion and unsurprisingly, about deciding when a submodel was too far from the full model. The lack of explanatory power introduced therein had no absolute scale and later discussions led me to think that the bound should depend on the sample size to ensure consistency. (The recent paper by Nott and Leng that was expanding on this projection has now appeared in CSDA.)

“Specifically, the models with subsets of covariates are found by maximizing the similarity of their predictions to this reference as proposed by Dupuis and Robert [12]. Notably, this approach does not require specifying priors for the submodels and one can instead focus on building a good reference model. Dupuis and Robert (2003) suggest choosing the size of the covariate subset based on an acceptable loss of explanatory power compared to the reference model. We examine using cross-validation based estimates of predictive performance as an alternative.” T. Peltola et al.

The paper also connects with the Bayesian Lasso literature, concluding on the horseshoe prior being more informative than the Laplace prior. It applies the selection approach to identify biomarkers with predictive performances in a study of diabetic patients. The authors rank model according to their (log) predictive density at the observed data, using cross-validation to avoid exploiting the data twice. On the MCMC front, the paper implements the NUTS version of HMC with STAN.

this issue of Series B

Posted in Books, Statistics, Travel, University life with tags , , , , , , , , , , on September 5, 2014 by xi'an

The September issue of [JRSS] Series B I received a few days ago is of particular interest to me. (And not as an ex-co-editor since I was never involved in any of those papers!) To wit: a paper by Hani Doss and Aixin Tan on evaluating normalising constants based on MCMC output, a preliminary version I had seen at a previous JSM meeting, a paper by Nick Polson, James Scott and Jesse Windle on the Bayesian bridge, connected with Nick’s talk in Boston earlier this month, yet another paper by Ariel Kleiner, Ameet Talwalkar, Purnamrita Sarkar and Michael Jordan on the bag of little bootstraps, which presentation I heard Michael deliver a few times when he was in Paris. (Obviously, this does not imply any negative judgement on the other papers of this issue!)

For instance, Doss and Tan consider the multiple mixture estimator [my wording, the authors do not give the method a name, referring to Vardi (1985) but missing the connection with Owen and Zhou (2000)] of k ratios of normalising constants, namely

\sum_{l=1}^k \frac{1}{n_l} \sum_{t=1}^{n_l} \dfrac{n_l g_j(x_t^l)}{\sum_{s=1}^k n_s g_s(x_t^l) z_1/z_s } \longrightarrow \dfrac{z_j}{z_1}

where the z’s are the normalising constants and with possible different numbers of iterations of each Markov chain. An interesting starting point (that Hans Künsch had mentioned to me a while ago but that I had since then forgotten) is that the problem was reformulated by Charlie Geyer (1994) as a quasi-likelihood estimation where the ratios of all z’s relative to one reference density are the unknowns. This is doubling interesting, actually, because it restates the constant estimation problem into a statistical light and thus somewhat relates to the infamous “paradox” raised by Larry Wasserman a while ago. The novelty in the paper is (a) to derive an optimal estimator of the ratios of normalising constants in the Markov case, essentially accounting for possibly different lengths of the Markov chains, and (b) to estimate the variance matrix of the ratio estimate by regeneration arguments. A favourite tool of mine, at least theoretically as practically useful minorising conditions are hard to come by, if at all available.

reading classics (#2)

Posted in Statistics, University life with tags , , , , , , , , , , , on November 8, 2012 by xi'an

Following last week read of Hartigan and Wong’s 1979 K-Means Clustering Algorithm, my Master students in the Reading Classics Seminar course, listened today to Agnė Ulčinaitė covering Rob Tibshirani‘s original LASSO paper Regression shrinkage and selection via the lasso in JRSS Series B. Here are her (Beamer) slides

Again not the easiest paper in the list, again mostly algorithmic and requiring some background on how it impacted the field. Even though Agnė also went through the Elements of Statistical Learning by Hastie, Friedman and Tibshirani, it was hard to get away from the paper to analyse more widely the importance of the paper, the connection with the Bayesian (linear) literature of the 70’s, its algorithmic and inferential aspects, like the computational cost, and the recent extensions like Bayesian LASSO. Or the issue of handling n<p models. Remember that one of the S in LASSO stands for shrinkage: it was quite pleasant to hear again about ridge estimators and Stein’s unbiased estimator of the risk, as those were themes of my Ph.D. thesis… (I hope the students do not get discouraged by the complexity of those papers: there were fewer questions and fewer students this time. Next week, the compass will move to the Bayesian pole with a talk on Lindley and Smith’s 1973 linear Bayes paper by one of my PhD students.)

Monte Carlo Statistical Methods third edition

Posted in Books, R, Statistics, University life with tags , , , , , , , , , , , , , on September 23, 2010 by xi'an

Last week, George Casella and I worked around the clock on starting the third edition of Monte Carlo Statistical Methods by detailing the changes to make and designing the new table of contents. The new edition will not see a revolution in the presentation of the material but rather a more mature perspective on what matters most in statistical simulation:

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The day I invented Bayesian Lasso…

Posted in Books, Statistics with tags , , , on August 16, 2010 by xi'an

George Casella remarked to me last month in Padova that, once he and Trevor Park published The Bayesian Lasso in JASA, they received many claims for prior discovery of “Bayesian Lasso”! So, as a joke, let me add my claim as well! Indeed, in the first (1994) edition of The Bayesian Choice, I included an example in Chapter 4 (Example 4.2) about the fact that using a double exponential prior along a Cauchy likelihood was producing a zero MAP (maximum a posteriori) estimate. Isn’t that the essence of the Bayesian lasso?! Of course, as you can still check in the current edition, the example was intended as a counter-example to the use of MAP estimates, not as an argument about the parsimony induced by double exponential priors. (Exercice 4.6 in both editions builds upon this example to notice that, with a small enough scale parameter, the absolute shrinkage to zero vanishes.) I thus lost the opportunity of “inventing” the Bayesian Lasso! To my shame, I must add that in the even earlier 1992 French edition of the book, I made a mistake in the derivation of the MAP and hence completely missed the point!!!


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