Archive for random partition trees

miXtures on arXiv

Posted in Books, Statistics, University life with tags , , , , , , , , , , , , , , , , , , , , on February 5, 2025 by xi'an

A paper about Bayesian inference on mixtures was posted on arXiv last week, as of 13 Jan 2025.  Fast sampling and model selection for Bayesian mixture models, by M. E. J. Newman is based on the notion that (genuine) parameters of a mixture model can be marginalized out when using conjugate priors. This is something that we pointed out quite a while ago, in a 1999 paper with George and Marty, which was devised in a long ride from Baltimore to Cornell after JSM 1999, and again in the 2002 Series B perfect sampling paper with George, Kerrie and Mike. (Also written in 1999.) And marginal likelihood can furthermore be approximated along this way as discussed in the more recent papers Bayesian Inference on Mixtures of Distributions with Kate, Kerrie & Jean-Michel, as well as Approximating the marginal likelihood in mixture models with Jean-Michel.

“Standard mixture models, as commonly formulated, also suffer from a technical, but important, difficulty: the existence of empty components. In many models (…) the number of observations in a component can be zero. Arguably this is acceptable for a model with a fixed number of components, but when the number of components is a free random variable it causes ambiguity, because a given division of observations into components can be represented in more than one way in the model. For instance, we could divide observations into two components, or we could divide them into three components, one of which is empty. This in turn creates difficulties when estimating the number of components—do we have two components or three?”

A very puzzling perspective, imho, since potentially empty components are inherent to (both finite and infinite) mixture models with connected issues of prohibiting some improper priors (if not all) and non-identifiability, including non-identifiability of the number of empty components (which remains random conditional on the data!), but different numbers of components lead to different models and their comparison is handled straightforwardly by a Bayesian analysis.

The author then proceeds to “prohibit empty components” [as a prior choice ?] as we did in the original (!) Gibbs sampler for mixtures in 1990 (published in 1994 in Series B!), seeking posterior properness, a trick later validated by Larry Wasserman (in again 1999, the year of mixtures!). Who called the construct the combination of a fixed prior and of a pseudo-likelihood, correctly imho (as the data dependent part is not properly normalised by a function of the parameters), rather than a prior choice. (The very one who stated that “mixtures, like tequila, are evil and should be avoided“.)

From there, the modelling is rather standard, with an arbitrary prior on k, number of components, a random partition model that prohibits empty components, even though the constraint could be more stringent depending on the number of parameters of a given component and the degree of improperness of the prior, as in our 1990 Series B paper. (Impropriety is not discussed in the paper.) Bayesian inference on k is based on the simulated (pseudo-)posterior. The choice therein as the estimated clustering is the most frequent partition (consensus clustering), connected to our proposal of (again!) 1999 with Merrilee and Gilles. While the estimated mixture is not explicited. The approach is assessed as running at an O(k) cost, with no parallel in terms of the data size n, even though the examples include a 59,946 dataset. One notable algorithmic trick when moving k is in selecting a component at random first rather than an observation index.

Some minor issues: detailed balance indicated as required for convergence (p14), label switching is called component switching (p5), higher acceptance rate indicated as meaning improved performances (p7)

ordered allocation sampler

Posted in Books, Statistics with tags , , , , , , , , , , , on November 29, 2021 by xi'an

Recently, Pierpaolo De Blasi and María Gil-Leyva arXived a proposal for a novel Gibbs sampler for mixture models. In both finite and infinite mixture models. In connection with Pitman (1996) theory of species sampling and with interesting features in terms of removing the vexing label switching features.

“The key idea is to work with the mixture components in the random order of appearance in an exchangeable sequence from the mixing distribution (…) In accordance with the order of appearance, we derive a new Gibbs sampling algorithm that we name the ordered allocation sampler. “

This central idea is thus a reinterpretation of the mixture model as the marginal of the component model when its parameter is distributed as a species sampling variate. An ensuing marginal algorithm is to integrate out the weights and the allocation variables to only consider the non-empty component parameters and the partition function, which are label invariant. Which reminded me of the proposal we made in our 2000 JASA paper with Gilles Celeux and Merrilee Hurn (one of my favourite papers!). And of the [first paper in Statistical Methodology] 2004 partitioned importance sampling version with George Casella and Marty Wells. As in the later, the solution seems to require the prior on the component parameters to be conjugate (as I do not see a way to produce an unbiased estimator of the partition allocation probabilities).

The ordered allocation sample considers the posterior distribution of the different object made of the parameters and of the sequence of allocations to the components for the sample written in a given order, ie y¹,y², &tc. Hence y¹ always gets associated with component 1, y² with either component 1 or component 2, and so on. For this distribution, the full conditionals are available, incl. the full posterior on the number m of components, only depending on the data through the partition sizes and the number m⁺ of non-empty components. (Which relates to the debate as to whether or not m is estimable…) This sequential allocation reminded me as well of an earlier 2007 JRSS paper by Nicolas Chopin. Albeit using particles rather than Gibbs and applied to a hidden Markov model. Funny enough, their synthetic dataset univ4 almost resembles the Galaxy dataset (as in the above picture of mine)!

parallelizing MCMC with random partition trees

Posted in Books, pictures, Statistics, University life with tags , , , , , , , on July 7, 2015 by xi'an

Another arXived paper in the recent series about big or tall data and how to deal with it by MCMC. Which pertains to the embarrassingly parallel category. As in the previously discussed paper, the authors (Xiangyu Wang, Fangjian Guo, Katherine Heller, and David Dunson) chose to break the prior itself into m bits… (An additional point from last week criticism is that, were an unbiased estimator of each term in the product available in an independent manner, the product of the estimators would be the estimator of the product.) In this approach, the kernel estimator of Neiswanger et al. is replaced with a random partition tree histogram. Which uses the same block partition across all terms in the product representation of the posterior. And hence ends up with a smaller number of terms in the approximation, since it does not explode with m. (They could have used Mondrian forests as well! However I think their quantification of the regular kernel method cost as an O(Tm) approach does not account for Neiswanger et al.’s trick in exploiting the product of kernels…) The so-called tree estimate can be turned into a random forest by repeating the procedure several times and averaging. The simulation comparison runs in favour of the current method when compared with other consensus or non-parametric methods. Except in the final graph (Figure 5) which shows several methods achieving the same prediction accuracy against running time.