Archive for the Books Category

label switching in Bayesian mixture models

Posted in Books, Statistics, University life with tags , , , , , , , , , , , on October 31, 2014 by xi'an

cover of Mixture Estimation and ApplicationsA referee of our paper on approximating evidence for mixture model with Jeong Eun Lee pointed out the recent paper by Carlos Rodríguez and Stephen Walker on label switching in Bayesian mixture models: deterministic relabelling strategies. Which appeared this year in JCGS and went beyond, below or above my radar.

Label switching is an issue with mixture estimation (and other latent variable models) because mixture models are ill-posed models where part of the parameter is not identifiable. Indeed, the density of a mixture being a sum of terms

\sum_{j=1}^k \omega_j f(y|\theta_i)

the parameter (vector) of the ω’s and of the θ’s is at best identifiable up to an arbitrary permutation of the components of the above sum. In other words, “component #1 of the mixture” is not a meaningful concept. And hence cannot be estimated.

This problem has been known for quite a while, much prior to EM and MCMC algorithms for mixtures, but it is only since mixtures have become truly estimable by Bayesian approaches that the debate has grown on this issue. In the very early days, Jean Diebolt and I proposed ordering the components in a unique way to give them a meaning. For instant, “component #1″ would then be the component with the smallest mean or the smallest weight and so on… Later, in one of my favourite X papers, with Gilles Celeux and Merrilee Hurn, we exposed the convergence issues related with the non-identifiability of mixture models, namely that the posterior distributions were almost always multimodal, with a multiple of k! symmetric modes in the case of exchangeable priors, and therefore that Markov chains would have trouble to visit all those modes in a symmetric manner, despite the symmetry being guaranteed from the shape of the posterior. And we conclude with the slightly provocative statement that hardly any Markov chain inferring about mixture models had ever converged! In parallel, time-wise, Matthew Stephens had completed a thesis at Oxford on the same topic and proposed solutions for relabelling MCMC simulations in order to identify a single mode and hence produce meaningful estimators. Giving another meaning to the notion of “component #1″.

And then the topic began to attract more and more researchers, being both simple to describe and frustrating in its lack of definitive answer, both from simulation and inference perspectives. Rodriguez’s and Walker’s paper provides a survey on the label switching strategies in the Bayesian processing of mixtures, but its innovative part is in deriving a relabelling strategy. Which consists of finding the optimal permutation (at each iteration of the Markov chain) by minimising a loss function inspired from k-means clustering. Which is connected with both Stephens’ and our [JASA, 2000] loss functions. The performances of this new version are shown to be roughly comparable with those of other relabelling strategies, in the case of Gaussian mixtures. (Making me wonder if the choice of the loss function is not favourable to Gaussian mixtures.) And somehow faster than Stephens’ Kullback-Leibler loss approach.

“Hence, in an MCMC algorithm, the indices of the parameters can permute multiple times between iterations. As a result, we cannot identify the hidden groups that make [all] ergodic averages to estimate characteristics of the components useless.”

One section of the paper puzzles me, albeit it does not impact the methodology and the conclusions. In Section 2.1 (p.27), the authors consider the quantity

p(z_i=j|{\mathbf y})

which is the marginal probability of allocating observation i to cluster or component j. Under an exchangeable prior, this quantity is uniformly equal to 1/k for all observations i and all components j, by virtue of the invariance under permutation of the indices… So at best this can serve as a control variate. Later in Section 2.2 (p.28), the above sentence does signal a problem with those averages but it seem to attribute it to MCMC behaviour rather than to the invariance of the posterior (or to the non-identifiability of the components per se). At last, the paper mentions that “given the allocations, the likelihood is invariant under permutations of the parameters and the allocations” (p.28), which is not correct, since eqn. (8)

f(y_i|\theta_{\sigma(z_i)}) =f(y_i|\theta_{\tau(z_i)})

does not hold when the two permutations σ and τ give different images of zi

Relevant statistics for Bayesian model choice [hot off the press!]

Posted in Books, Statistics, University life with tags , , , , , , on October 30, 2014 by xi'an

jrssbabcOur paper about evaluating statistics used for ABC model choice has just appeared in Series B! It somewhat paradoxical that it comes out just a few days after we submitted our paper on using random forests for Bayesian model choice, thus bypassing the need for selecting those summary statistics by incorporating all statistics available and letting the trees automatically rank those statistics in term of their discriminating power. Nonetheless, this paper remains an exciting piece of work (!) as it addresses the more general and pressing question of the validity of running a Bayesian analysis with only part of the information contained in the data. Quite usefull in my (biased) opinion when considering the emergence of approximate inference already discussed on this ‘Og…

[As a trivial aside, I had first used fresh from the press(es) as the bracketted comment, before I realised the meaning was not necessarily the same in English and in French.]

I am cold all over…

Posted in Books, Kids, Statistics, University life with tags , , , , , , , on October 29, 2014 by xi'an

unusual snowfall on Bois de Boulogne, March 12, 2013An email from one of my Master students who sent his problem sheet (taken from Monte Carlo Statistical Methods) late:

Bonsoir Professeur
Je « suis » votre cours du mercredi dont le formalisme mathématique me fait froid partout
Avec beaucoup de difficulté je vous envoie mes exercices du premier chapitre de votre livre.

which translates as

Good evening Professor,
I “follow” your Wednesday class which mathematical formalism makes me cold all over. With much hardship, I send you the first batch of problems from your book.

I know that winter is coming, but, still, making students shudder from mathematical cold is not my primary goal when teaching Monte Carlo methods!

marauders of the lost sciences

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

The editors of a new blog entitled Marauders of the Lost Sciences (Learn from the giants) sent me an email to signal the start of this blog with a short excerpt from a giant in maths or stats posted every day:

There is  a new blog I wanted to tell you 
about which  excerpts one  interesting or 
classic  paper  or  book  a day  from the 
mathematical  sciences.  We plan on daily
posting across the  range of mathematical 
fields and at any level, but about 20-30% 
of the posts in queue are from statistics.

The goal is to entice people to read the great 
works of old.

The first post today was from an old paper by 
Fisher applying Group Theory to the design of 

Interesting concept, which will hopefully generate comments to put the quoted passage into context. Somewhat connected to my Reading Statistical Classics posts. Which incidentally if sadly will not take place this year since only two students registered. should take place in the end since more students registered! (I am unsure about the references behind the title of that blog, besides Spielberg’s Raiders of the Lost Ark and Norman’s Marauders of Gor… I just hope Statistics does not qualify as a lost science!)

Rivers of London [book review]

Posted in Books, Kids, Travel with tags , , , , , , , , , , , on October 25, 2014 by xi'an

London by Delta, Dec. 14, 2011Yet another book I grabbed on impulse while in Birmingham last month. And which had been waiting for me on a shelf of my office in Warwick. Another buy I do not regret! Rivers of London is delightful, as much for taking place in all corners of London as for the story itself. Not mentioning the highly enjoyable writing style!

“I though you were a sceptic, said Lesley. I though you were scientific”

The first volume in this detective+magic series, Rivers of London, sets the universe of this mix of traditional Metropolitan Police work and of urban magic, the title being about the deities of the rivers of London, including a Mother and a Father Thames… I usually dislike any story mixing modern life and fantasy but this is a definitive exception! What I enjoy in this book setting is primarily the language used in the book that is so uniquely English (to the point of having the U.S. edition edited!, if the author’s blog is to be believed). And the fact that it is so much about London, its history and inhabitants. But mostly about London, as an entity on its own. Even though my experience of London is limited to a few boroughs, there are many passages where I can relate to the location and this obviously makes the story much more appealing. The style is witty, ironic and full of understatements, a true pleasure.

“The tube is a good place for this sort of conceptual breakthrough because, unless you’ve got something to read, there’s bugger all else to do.”

The story itself is rather fun, with at least three levels of plots and two types of magic. It centres around two freshly hired London constables, one of them discovering magical abilities and been drafted to the supernatural section of the Metropolitan Police. And making all the monologues in the book. The supernatural section is made of a single Inspector, plus a few side characters, but with enough fancy details to give it life. In particular, Isaac Newton is credited with having started the section, called The Folly. Which is also the name of Ben Aaronovitch’s webpage.

“There was a poster (…) that said: `Keep Calm and Carry On’, which I thought was good advice.”

This quote is unvoluntarily funny in that it takes place in a cellar holding material from World War II. Except that the now invasive red and white poster was never distributed during the war… On the opposite it was pulped to save paper and the fact that a few copies survived is a sort of (minor) miracle. Hence a double anachronism in that it did not belong to a WWII room and that Peter Grant should have seen its modern avatars all over London.

“Have you ever been to London? Don’t worry, it’s basically  just like the country. Only with more people.”

The last part of the book is darker and feels less well-written, maybe simply because of the darker side and of the accumulation of events, while the central character gets rather too central and too much of an unexpected hero that saves the day. There is in particular a part where he seems to forget about his friend Lesley who is in deep trouble at the time and this does not seem to make much sense. But, except for this lapse (maybe due to my quick reading of the book over the week in Warwick), the flow and pace are great, with this constant undertone of satire and wit from the central character. I am definitely looking forward reading tomes 2 and 3 in the series (having already read tome 4 in Austria!, which was a mistake as there were spoilers about earlier volumes).

Feller’s shoes and Rasmus’ socks [well, Karl's actually...]

Posted in Books, Kids, R, Statistics, University life with tags , , , , on October 24, 2014 by xi'an

Yesterday, Rasmus Bååth [of puppies' fame!] posted a very nice blog using ABC to derive the posterior distribution of the total number of socks in the laundry when only pulling out orphan socks and no pair at all in the first eleven draws. Maybe not the most pressing issue for Bayesian inference in the era of Big data but still a challenge of sorts!

Rasmus set a prior on the total number m of socks, a negative Binomial Neg(15,1/3) distribution, and another prior of the proportion of socks that come by pairs, a Beta B(15,2) distribution, then simulated pseudo-data by picking eleven socks at random, and at last applied ABC (in Rubin’s 1984 sense) by waiting for the observed event, i.e. only orphans and no pair [of socks]. Brilliant!

The overall simplicity of the problem set me wondering about an alternative solution using the likelihood. Cannot be that hard, can it?! After a few computations rejected by opposing them to experimental frequencies, I put the problem on hold until I was back home and with access to my Feller volume 1, one of the few [math] books I keep at home… As I was convinced one of the exercises in Chapter II would cover this case. After checking, I found a partial solution, namely Exercice 26:

A closet contains n pairs of shoes. If 2r shoes are chosen at random (with 2r<n), what is the probability that there will be (a) no complete pair, (b) exactly one complete pair, (c) exactly two complete pairs among them?

This is not exactly a solution, but rather a problem, however it leads to the value


as the probability of obtaining j pairs among those 2r shoes. Which also works for an odd number t of shoes:


as I checked against my large simulations. socksSo I solved Exercise 26 in Feller volume 1 (!), but not Rasmus’ problem, since there are those orphan socks on top of the pairs. If one draws 11 socks out of m socks made of f orphans and g pairs, with f+2g=m, the number k of socks from the orphan group is an hypergeometric H(11,m,f) rv and the probability to observe 11 orphan socks total (either from the orphan or from the paired groups) is thus the marginal over all possible values of k:

\sum_{k=0}^{11} \dfrac{\binom{f}{k}\binom{2g}{11-k}}{\binom{m}{11}}\times\dfrac{2^{11-k}\binom{g}{11-k}}{\binom{2g}{11-k}}

so it could be argued that we are facing a closed-form likelihood problem. Even though it presumably took me longer to achieve this formula than for Rasmus to run his exact ABC code!

BibTool on the air

Posted in Books, Linux, Travel, University life with tags , , , , , , , , , , on October 23, 2014 by xi'an

Yesterday night, just before leaving for Coventry, I realised I had about 30 versions of my “mother of all .bib” bib file, spread over directories and with broken links with the original mother file… (I mean, I always create bib files in new directories by a hard link,

    ln ~/mother.bib

but they eventually and inexplicably end up with a life of their own!) So I decided a Spring clean-up was in order and installed BibTool on my Linux machine to gather all those versions into a new encompassing all-inclusive bib reference. I did not take advantage of the many possibilities of the program, written by Gerd Neugebauer, but it certainly solved my problem: once I realised I had to set the variates

check.double = on
check.double.delete = on
pass.comments = off

all I had to do was to call

bibtool -s -i ../*/*.bib -o mother.bib
bibtool -d -i mother.bib -o mother.bib
bibtool -s -i mother.bib -o mother.bib

to merge all bib file and then to get rid of the duplicated entries in mother.bib (the -d option commented out the duplicates and the second call with -s removed them). And to remove the duplicated definitions in the preamble of the file. This took me very little time in the RER train from Paris-Dauphine (where I taught this morning, having a hard time to make the students envision the empirical cdf as an average of Dirac masses!) to Roissy airport, in contrast with my pedestrian replacement of all stray siblings of the mother bib into new proper hard links, one by one. I am sure there is a bash command that could have done it in one line, but I spent instead my flight to Birmingham switching all existing bib files, one by one…


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