Archive for latent variable

Particle Gibbs for conjugate mixture posteriors

Posted in Books, Statistics, University life with tags , , , , , on September 8, 2015 by xi'an

Alexandre Bouchard-Coté, Arnaud Doucet, and Andrew Roth have arXived a paper “Particle Gibbs Split-Merge Sampling for Bayesian Inference in Mixture Models” that proposes an efficient algorithm to explore the posterior distribution of a mixture, when interpreted as a clustering model. (To clarify the previous sentence, this is a regular plain vanilla mixture model for which they explore the latent variable representation.)

I like very much the paper because it relates to an earlier paper of mine with George Casella and Marty Wells, paper we wrote right after a memorable JSM in Baltimore (during what may have been my last visit to Cornell University as George left for Florida the following year). The starting point of this approach to mixture estimation is that the (true) parameters of a mixture can be (exactly) integrated out when using conjugate priors and a completion step. Namely, the marginal posterior distribution of the latent variables given the data is available in closed form. The latent variables being the component allocations for the observations. The joint posterior is then a product of the prior on the parameters times the prior on the latents times a product of simple (e.g., Gaussian) terms. This equivalently means the marginal likelihoods conditional on the allocations are available in closed form. Looking directly at those marginal likelihoods, a prior distribution on the allocations can be introduced (e.g., the Pitman-Yor process or the finite Dirichlet prior) and, together, they define a closed form target. Albeit complex. As often on a finite state space. In our paper with George and Marty, we proposed using importance sampling to explore the set, using for instance marginal distributions for the allocations, which are uniform in the case of exchangeable priors, but this is not very efficient, as exhibited by our experiments where very few partitions would get most of the weight.

Even a Gibbs sampler on subsets of those indicators restricted to two components cannot be managed directly. The paper thus examines a specially designed particle Gibbs solution that implements a split and merge move on two clusters at a time. Merging or splitting the subset. With intermediate target distributions, SMC style. While this is quite an involved mechanism, that could be deemed as excessive for the problem at hand, as well as inducing extra computing time, experiments in the paper demonstrate the mostly big improvement in efficiency brought by this algorithm.

JSM 2015 [day #4]

Posted in pictures, Running, Statistics, Travel, University life with tags , , , , , , , , , , , , , , , , , , on August 13, 2015 by xi'an

My first session today was Markov Chain Monte Carlo for Contemporary Statistical Applications with a heap of interesting directions in MCMC research! Now, without any possible bias (!), I would definitely nominate Murray Pollock (incidentally from Warwick) as the winner for best slides, funniest presentation, and most enjoyable accent! More seriously, the scalable Langevin algorithm he developed with Paul Fearnhead, Adam Johansen, and Gareth Roberts, is quite impressive in avoiding computing costly likelihoods. With of course caveats on which targets it applies to. Murali Haran showed a new proposal to handle high dimension random effect models by a projection trick that reduces the dimension. Natesh Pillai introduced us (or at least me!) to a spectral clustering that allowed for an automated partition of the target space, itself the starting point to his parallel MCMC algorithm. Quite exciting, even though I do not perceive partitions as an ideal solution to this problem. The final talk in the session was Galin Jones’ presentation of consistency results and conditions for multivariate quantities which is a surprisingly unexplored domain. MCMC is still alive and running!

The second MCMC session of the morning, Monte Carlo Methods Facing New Challenges in Statistics and Science, was equally diverse, with Lynn Kuo’s talk on the HAWK approach, where we discovered that harmonic mean estimators are still in use, e.g., in MrBayes software employed in phylogenetic inference. The proposal to replace this awful estimator that should never be seen again (!) was rather closely related to an earlier solution of us for marginal likelihood approximation, based there on a partition of the whole space rather than an HPD region in our case… Then, Michael Betancourt brilliantly acted as a proxy for Andrew to present the STAN language, with a flashy trailer he most recently designed. Featuring Andrew as the sole actor. And with great arguments for using it, including the potential to run expectation propagation (as a way of life). In fine, Faming Liang proposed a bootstrap subsampling version of the Metropolis-Hastings algorithm, where the likelihood acknowledging the resulting bias in the limiting distribution.

My first afternoon session was another entry on Statistical Phylogenetics, somewhat continued from yesterday’s session. Making me realised I had not seen a single talk on ABC for the entire meeting! The issues discussed in the session were linked with aligning sequences and comparing  many trees. Again in settings where likelihoods can be computed more or less explicitly. Without any expertise in the matter, I wondered at a construction that would turn all trees, like  into realizations of a continuous model. For instance by growing one branch at a time while removing the MRCA root… And maybe using a particle like method to grow trees. As an aside, Vladimir Minin told me yesterday night about genetic mutations that could switch on and off phenotypes repeatedly across generations… For instance  the ability to glow in the dark for species of deep sea fish.

When stating that I did not see a single talk about ABC, I omitted Steve Fienberg’s Fisher Lecture R.A. Fisher and the Statistical ABCs, keeping the morceau de choix for the end! Even though of course Steve did not mention the algorithm! A was for asymptotics, or ancilarity, B for Bayesian (or biducial??), C for causation (or cuffiency???)… Among other germs, I appreciated that Steve mentioned my great-grand father Darmois in connection with exponential families! And the connection with Jon Wellner’s LeCam Lecture from a few days ago. And reminding us that Savage was a Fisher lecturer himself. And that Fisher introduced fiducial distributions quite early. And for defending the Bayesian perspective. Steve also set some challenges like asymptotics for networks, Bayesian model assessment (I liked the notion of stepping out of the model), and randomization when experimenting with networks. And for big data issues. And for personalized medicine, building on his cancer treatment. No trace of the ABC algorithm, obviously, but a wonderful Fisher’s lecture, also most obviously!! Bravo, Steve, keep thriving!!!

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


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.

ABC for bivariate betas

Posted in Statistics, University life with tags , , , , , , , on February 19, 2014 by xi'an

Crakel and Flegal just arXived a short paper running ABC for doing inference on the parameters of two families of bivariate betas. And I could not but read it thru. And wonder why ABC was that necessary to handle the model. The said bivariate betas are defined from




U_i\sim \text{Ga}(\delta_i,1)


X_1=V_1/(1+V_1)\,,\ X_2=V_2/(1+V_2)

This makes each term in the pair Beta and the two components dependent. This construct was proposed by Arnold and Ng (2011). (The five-parameter version cancels the gammas for i=3,4,5.)

Since the pdf of the joint distribution is not available in closed form, Crakel and Flegal zoom on ABC-MCMC as the method of choice and discuss simulation experiments. (The choice of the tolerance ε as an absolute rather than relative value, ε=0.2,0.0.6,0.8, puzzles me, esp. since the distance between the summary statistics is not scaled.) I however wonder why other approaches are impossible. (Or why it is necessary to use this distribution to model correlated betas. Unless I am confused copulas were invented to this effect.) First, this is a latent variable model, so latent variables could be introduced inside an MCMC scheme. A wee bit costly but feasible. Second, several moments of those distributions are known so a empirical likelihood approach could be considered.

On the use of marginal posteriors in marginal likelihood estimation via importance-sampling

Posted in R, Statistics, University life with tags , , , , , , , , , , , , , on November 20, 2013 by xi'an

Perrakis, Ntzoufras, and Tsionas just arXived a paper on marginal likelihood (evidence) approximation (with the above title). The idea behind the paper is to base importance sampling for the evidence on simulations from the product of the (block) marginal posterior distributions. Those simulations can be directly derived from an MCMC output by randomly permuting the components. The only critical issue is to find good approximations to the marginal posterior densities. This is handled in the paper either by normal approximations or by Rao-Blackwell estimates. the latter being rather costly since one importance weight involves B.L computations, where B is the number of blocks and L the number of samples used in the Rao-Blackwell estimates. The time factor does not seem to be included in the comparison studies run by the authors, although it would seem necessary when comparing scenarii.

After a standard regression example (that did not include Chib’s solution in the comparison), the paper considers  2- and 3-component mixtures. The discussion centres around label switching (of course) and the deficiencies of Chib’s solution against the current method and Neal’s reference. The study does not include averaging Chib’s solution over permutations as in Berkoff et al. (2003) and Marin et al. (2005), an approach that does eliminate the bias. Especially for a small number of components. Instead, the authors stick to the log(k!) correction, despite it being known for being quite unreliable (depending on the amount of overlap between modes). The final example is Diggle et al. (1995) longitudinal Poisson regression with random effects on epileptic patients. The appeal of this model is the unavailability of the integrated likelihood which implies either estimating it by Rao-Blackwellisation or including the 58 latent variables in the analysis.  (There is no comparison with other methods.)

As a side note, among the many references provided by this paper, I did not find trace of Skilling’s nested sampling or of safe harmonic means (as exposed in our own survey on the topic).

Correlated Poissons

Posted in Statistics with tags , , on March 2, 2011 by xi'an

A graduate student came to see me the other day with a bivariate Poisson distribution and a question about using EM in this framework. The problem boils down to adding one correlation parameter and an extra term in the likelihood

(1-\rho)^{n_1}(1+\lambda\rho)^{n_2}(1+\mu\rho)^{n_3}(1-\lambda\mu\rho)^{n_4}\quad 0\le\rho\le\min(1,\frac{1}{\lambda\mu})

Both terms involving sums are easy to deal with, using latent variables as in mixture models. The subtractions are trickier, as the negative parts cannot appear in a conditional distribution. Even though the problem can be handled by a direct numerical maximisation or by an almost standard Metropolis-within-Gibbs sampler, my suggestion regarding EM per se was to proceed by conditional EM, one parameter at a time. For instance, when considering \rho conditional on both Poisson parameters, depending on whether \lambda\mu>1 or not, one can consider either


and turn

(1-\theta/\lambda\mu) \text{ into } (1-\theta+\theta\{1-\frac{1}{\lambda\mu}\})

thus producing a Beta-like target function in \theta after completion, or turn

(1-\lambda\mu\rho) \text{ into } (1-\rho+\{1-\lambda\mu\}\rho)

to produce a Beta-like target function in \rho after completion. In the end, this is a rather pedestrian exercise and I am still frustrated at missing the trick to handle the subtractions directly, however it was nonetheless a nice question!

Computing evidence

Posted in Books, R, Statistics with tags , , , , , , , , , , on November 29, 2010 by xi'an

The book Random effects and latent variable model selection, edited by David Dunson in 2008 as a Springer Lecture Note. contains several chapters dealing with evidence approximation in mixed effect models. (Incidentally, I would be interested in the story behind the  Lecture Note as I found no explanation in the backcover or in the preface. Some chapters but not all refer to a SAMSI workshop on model uncertainty…) The final chapter written by Joyee Ghosh and David Dunson (similar to a corresponding paper in JCGS) contains in particular the interesting identity that the Bayes factor opposing model h to model h-1 can be unbiasedly approximated by (the average of the terms)



  • \mathfrak{M} is the model index,
  • the \theta_{i,h}‘s are simulated from the posterior under model h,
  • the model \mathfrak{M}=h-1 only considers the h-1 first components of \theta_{i,h},
  • the prior under model h-1 is the projection of the prior under model h. (Note that this marginalisation is not the projection used in Bayesian Core.)

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