Archive for Gaussian mixture

scale matters [maths as well]

Posted in pictures, R, Statistics with tags , , , , , , , , on June 2, 2021 by xi'an

A question from X validated on why an independent Metropolis sampler of a three component Normal mixture based on a single Normal proposal was failing to recover the said mixture…

When looking at the OP’s R code, I did not notice anything amiss at first glance (I was about to drive back from Annecy, hence did not look too closely) and reran the attached code with a larger variance in the proposal, which returned the above picture for the MCMC sample, close enough (?) to the target. Later, from home, I checked the code further and noticed that the Metropolis ratio was only using the ratio of the targets. Dividing by the ratio of the proposals made a significant (?) to the representation of the target.

More interestingly, the OP was fundamentally confused between independent and random-walk Rosenbluth algorithms, from using the wrong ratio to aiming at the wrong scale factor and average acceptance ratio, and furthermore challenged by the very notion of Hessian matrix, which is often suggested as a default scale.

parallel tempering on optimised paths

Posted in Statistics with tags , , , , , , , , , , , , , , , on May 20, 2021 by xi'an


Saifuddin Syed, Vittorio Romaniello, Trevor Campbell, and Alexandre Bouchard-Côté, whom I met and discussed with on my “last” trip to UBC, on December 2019, just arXived a paper on parallel tempering (PT), making the choice of tempering path an optimisation problem. They address the touchy issue of designing a sequence of tempered targets when the starting distribution π⁰, eg the prior, and the final distribution π¹, eg the posterior, are hugely different, eg almost singular.

“…theoretical analysis of reversible variants of PT has shown that adding too many intermediate chains can actually deteriorate performance (…) [while] on non reversible regime adding more chains is guaranteed to improve performances.”

The above applies to geometric combinations of π⁰ and π¹. Which “suffers from an arbitrarily suboptimal global communication barrier“, according to the authors (although the counterexample is not completely convincing since π⁰ and π¹ share the same variance). They propose a more non-linear form of tempering with constraints on the dependence of the powers on the temperature t∈(0,1).  Defining the global communication barrier as an average over temperatures of the rejection rate, the path characteristics (e.g., the coefficients of a spline function) can then be optimised in terms of this objective. And the temperature schedule is derived from the fact that the non-asymptotic round trip rate is maximized when the rejection rates are all equal. (As a side item, the technique exposed in the earlier tempering paper by Syed et al. was recently exploited for a night high resolution imaging of a black hole from the M87 galaxy.)

likelihood-free and summary-free?

Posted in Books, Mountains, pictures, Statistics, Travel with tags , , , , , , , , , , , , , on March 30, 2021 by xi'an

My friends and coauthors Chris Drovandi and David Frazier have recently arXived a paper entitled A comparison of likelihood-free methods with and without summary statistics. In which they indeed compare these two perspectives on approximate Bayesian methods like ABC and Bayesian synthetic likelihoods.

“A criticism of summary statistic based approaches is that their choice is often ad hoc and there will generally be an  inherent loss of information.”

In ABC methods, the recourse to a summary statistic is often advocated as a “necessary evil” against the greater evil of the curse of dimension, paradoxically providing a faster convergence of the ABC approximation (Fearnhead & Liu, 2018). The authors propose a somewhat generic selection of summary statistics based on [my undergrad mentors!] Gouriéroux’s and Monfort’s indirect inference, using a mixture of Gaussians as their auxiliary model. Summary-free solutions, as in our Wasserstein papers, rely on distances between distributions, hence are functional distances, that can be seen as dimension-free as well (or criticised as infinite dimensional). Chris and David consider energy distances (which sound very much like standard distances, except for averaging over all permutations), maximum mean discrepancy as in Gretton et al. (2012), Cramèr-von Mises distances, and Kullback-Leibler divergences estimated via one-nearest-neighbour formulas, for a univariate sample. I am not aware of any degree of theoretical exploration of these functional approaches towards the precise speed of convergence of the ABC approximation…

“We found that at least one of the full data approaches was competitive with or outperforms ABC with summary statistics across all examples.”

The main part of the paper, besides a survey of the existing solutions, is to compare the performances of these over a few chosen (univariate) examples, with the exact posterior as the golden standard. In the g & k model, the Pima Indian benchmark of ABC studies!, Cramèr does somewhat better. While it does much worse in an M/G/1 example (where Wasserstein does better, and similarly for a stereological extremes example of Bortot et al., 2007). An ordering inversed again for a toad movement model I had not seen before. While the usual provision applies, namely that this is a simulation study on unidimensional data and a small number of parameters, the design of the four comparison experiments is very careful, eliminating versions that are either too costly or too divergence, although this could be potentially criticised for being unrealistic (i.e., when the true posterior is unknown). The computing time is roughly the same across methods, which essentially remove the call to kernel based approximations of the likelihood. Another point of interest is that the distance methods are significantly impacted by transforms on the data, which should not be so for intrinsic distances! Demonstrating the distances are not intrinsic…

Jeffreys priors for hypothesis testing [Bayesian reads #2]

Posted in Books, Statistics, University life with tags , , , , , , , , , , , , , , , , on February 9, 2019 by xi'an

A second (re)visit to a reference paper I gave to my OxWaSP students for the last round of this CDT joint program. Indeed, this may be my first complete read of Susie Bayarri and Gonzalo Garcia-Donato 2008 Series B paper, inspired by Jeffreys’, Zellner’s and Siow’s proposals in the Normal case. (Disclaimer: I was not the JRSS B editor for this paper.) Which I saw as a talk at the O’Bayes 2009 meeting in Phillie.

The paper aims at constructing formal rules for objective proper priors in testing embedded hypotheses, in the spirit of Jeffreys’ Theory of Probability “hidden gem” (Chapter 3). The proposal is based on symmetrised versions of the Kullback-Leibler divergence κ between null and alternative used in a transform like an inverse power of 1+κ. With a power large enough to make the prior proper. Eventually multiplied by a reference measure (i.e., the arbitrary choice of a dominating measure.) Can be generalised to any intrinsic loss (not to be confused with an intrinsic prior à la Berger and Pericchi!). Approximately Cauchy or Student’s t by a Taylor expansion. To be compared with Jeffreys’ original prior equal to the derivative of the atan transform of the root divergence (!). A delicate calibration by an effective sample size, lacking a general definition.

At the start the authors rightly insist on having the nuisance parameter v to differ for each model but… as we all often do they relapse back to having the “same ν” in both models for integrability reasons. Nuisance parameters make the definition of the divergence prior somewhat harder. Or somewhat arbitrary. Indeed, as in reference prior settings, the authors work first conditional on the nuisance then use a prior on ν that may be improper by the “same” argument. (Although conditioning is not the proper term if the marginal prior on ν is improper.)

The paper also contains an interesting case of the translated Exponential, where the prior is L¹ Student’s t with 2 degrees of freedom. And another one of mixture models albeit in the simple case of a location parameter on one component only.

weakly informative reparameterisations

Posted in Books, pictures, R, Statistics, University life with tags , , , , , , , , , on February 14, 2018 by xi'an

Our paper, weakly informative reparameterisations of location-scale mixtures, with Kaniav Kamary and Kate Lee, got accepted by JCGS! Great news, which comes in perfect timing for Kaniav as she is currently applying for positions. The paper proposes a unidimensional mixture Bayesian modelling based on the first and second moment constraints, since these turn the remainder of the parameter space into a compact. While we had already developed an associated R package, Ultimixt, the current editorial policy of JCGS imposes the R code used to produce all results to be attached to the submission and it took us a few more weeks than it should have to produce a directly executable code, due to internal library incompatibilities. (For this entry, I was looking for a link to our special JCGS issue with my picture of Edinburgh but realised I did not have this picture.)