Archive for Rao-Blackwellisation

Combining Particle MCMC with Rao-Blackwellized Monte Carlo Data Association

Posted in Books, Statistics, University life with tags , , , , , , , , , , , , on October 10, 2014 by xi'an

This recently arXived paper by Juho Kokkala and Simo Särkkä mixes a whole lot of interesting topics, from particle MCMC and Rao-Blackwellisation to particle filters, Kalman filters, and even bear population estimation. The starting setup is the state-space hidden process models where particle filters are of use. And where Andrieu, Doucet and Hollenstein (2010) introduced their particle MCMC algorithms. Rao-Blackwellisation steps have been proposed in this setup in the original paper, as well as in the ensuing discussion, like recycling rejected parameters and associated particles. The beginning of the paper is a review of the literature in this area, in particular of the Rao-Blackwellized Monte Carlo Data Association algorithm developed by Särkkä et al. (2007), of which I was not aware previously. (I alas have not followed closely enough the filtering literature in the past years.) Targets evolve independently according to Gaussian dynamics.

In the description of the model (Section 3), I feel there are prerequisites on the model I did not have (and did not check in Särkkä et al., 2007), like the meaning of targets and measurements: it seems the model assumes each measurement corresponds to a given target. More details or an example would have helped. The extension against the existing appears to be the (major) step of including unknown parameters. Due to my lack of expertise in the domain, I have no notion of the existence of similar proposals in the literature, but handling unknown parameters is definitely of direct relevance for the statistical analysis of such problems!

The simulation experiment based on an Ornstein-Uhlenbeck model is somewhat anticlimactic in that the posterior on the mean reversion rate is essentially the prior, conveniently centred at the true value, while the others remain quite wide. It may be that the experiment was too ambitious in selecting 30 simultaneous targets with only a total of 150 observations. Without highly informative priors, my beotian reaction is to doubt the feasibility of the inference. In the case of the Finnish bear study, the huge discrepancy between priors and posteriors, as well as the significant difference between the forestry expert estimations and the model predictions should be discussed, if not addressed, possibly via a simulation using the posteriors as priors. Or maybe using a hierarchical Bayes model to gather a time-wise coherence in the number of bear families. (I wonder if this technique would apply to the type of data gathered by Mohan Delampady on the West Ghats tigers…)

Overall, I am slightly intrigued by the practice of running MCMC chains in parallel and merging the outcomes with no further processing. This assumes a lot in terms of convergence and mixing on all the chains. However, convergence is never directly addressed in the paper.

efficient exploration of multi-modal posterior distributions

Posted in Books, Statistics, University life with tags , , , , on September 1, 2014 by xi'an

The title of this recent arXival had potential appeal, however the proposal ends up being rather straightforward and hence  anti-climactic! The paper by Hu, Hendry and Heng proposes to run a mixture of proposals centred at the various modes of  the target for an efficient exploration. This is a correct MCMC algorithm, granted!, but the requirement to know beforehand all the modes to be explored is self-defeating, since the major issue with MCMC is about modes that are  omitted from the exploration and remain undetected throughout the simulation… As provided, this is a standard MCMC algorithm with no adaptive feature and I would rather suggest our population Monte Carlo version, given the available information. Another connection with population Monte Carlo is that I think the performances would improve by Rao-Blackwellising the acceptance rate, i.e. removing the conditioning on the (ancillary) component of the index. For PMC we proved that using the mixture proposal in the ratio led to an ideally minimal variance estimate and I do not see why randomising the acceptance ratio in the current case would bring any improvement.

recycling accept-reject rejections

Posted in Statistics, University life with tags , , , , , , , , , on July 1, 2014 by xi'an

Vinayak Rao, Lizhen Lin and David Dunson just arXived a paper which proposes anew technique to handle intractable normalising constants. And which exact title is Data augmentation for models based on rejection sampling. (Paper that I read in the morning plane to B’ham, since this is one of my weeks in Warwick.) The central idea therein is that, if the sample density (aka likelihood) satisfies

p(x|\theta) \propto f(x|\theta) \le q(x|\theta) M\,,

where all terms but p are known in closed form, then completion by the rejected values of an hypothetical accept-reject algorithm−hypothetical in the sense that the data does not have to be produced by an accept-reject scheme but simply the above domination condition to hold−allows for a data augmentation scheme. Without requiring the missing normalising constant. Since the completed likelihood is

\prod_{i=1}^n \dfrac{f(x_i|\theta)}{M} \prod_{j=1}^{m_i} \left\{q(y_{ij}|\theta) -\dfrac{f(y_{ij}|\theta)}{M}\right\}

A closed-form, if not necessarily congenial, function.

Now this is quite a different use of the “rejected values” from the accept reject algorithm when compared with our 1996 Biometrika paper on the Rao-Blackwellisation of accept-reject schemes (which, still, could have been mentioned there… Or Section 4.2 of Monte Carlo Statistical Methods. Rather than re-deriving the joint density of the augmented sample, “accepted+rejected”.)

It is a neat idea in that it completely bypasses the approximation of the normalising constant. And avoids the somewhat delicate tuning of the auxiliary solution of Moller et al. (2006)  The difficulty with this algorithm is however in finding an upper bound M on the unnormalised density f that is

  1. in closed form;
  2. with a manageable and tight enough “constant” M;
  3. compatible with running a posterior simulation conditional on the added rejections.

The paper seems to assume further that the bound M is independent from the current parameter value θ, at least as suggested by the notation (and Theorem 2), but this is not in the least necessary for the validation of the formal algorithm. Such a constraint would pull M higher, hence reducing the efficiency of the method. Actually the matrix Langevin distribution considered in the first example involves a bound that depends on the parameter κ.

The paper includes a result (Theorem 2) on the uniform ergodicity that relies on heavy assumptions on the proposal distribution. And a rather surprising one, namely that the probability of rejection is bounded from below, i.e. calling for a less efficient proposal. Now it seems to me that a uniform ergodicity result holds as well when the probability of acceptance is bounded from below since, then, the event when no rejection occurs constitutes an atom from the augmented Markov chain viewpoint. There therefore occurs a renewal each time the rejected variable set ϒ is empty, and ergodicity ensues (Robert, 1995, Statistical Science).

Note also that, despite the opposition raised by the authors, the method per se does constitute a pseudo-marginal technique à la Andrieu-Roberts (2009) since the independent completion by the (pseudo) rejected variables produces an unbiased estimator of the likelihood. It would thus be of interest to see how the recent evaluation tools of Andrieu and Vihola can assess the loss in efficiency induced by this estimation of the likelihood.

Maybe some further experimental evidence tomorrow…

[more] parallel MCMC

Posted in Books, Mountains with tags , , , , , , , , , , on April 3, 2014 by xi'an

Scott Schmidler and his Ph.D. student Douglas VanDerwerken have arXived a paper on parallel MCMC the very day I left for Chamonix, prior to MCMSki IV, so it is no wonder I missed it at the time. This work is somewhat in the spirit of the parallel papers Scott et al.’s consensus Bayes,  Neiswanger et al.’s embarrassingly parallel MCMC, Wang and Dunson’s Weierstrassed MCMC (and even White et al.’s parallel ABC), namely that the computation of the likelihood can be broken into batches and MCMC run over those batches independently. In their short survey of previous works on parallelization, VanDerwerken and Schmidler overlooked our neat (!) JCGS Rao-Blackwellisation with Pierre Jacob and Murray Smith, maybe because it sounds more like post-processing than genuine parallelization (in that it does not speed up the convergence of the chain but rather improves the Monte Carlo usages one can make of this chain), maybe because they did not know of it.

“This approach has two shortcomings: first, it requires a number of independent simulations, and thus processors, equal to the size of the partition; this may grow exponentially in dim(Θ). Second, the rejection often needed for the restriction doesn’t permit easy evaluation of transition kernel densities, required below. In addition, estimating the relative weights wi with which they should be combined requires care.” (p.3)

The idea of the authors is to replace an exploration of the whole space operated via a single Markov chain (or by parallel chains acting independently which all have to “converge”) with parallel and independent explorations of parts of the space by separate Markov chains. “Small is beautiful”: it takes a shorter while to explore each set of the partition, hence to converge, and, more importantly, each chain can work in parallel to the others. More specifically, given a partition of the space, into sets Ai with posterior weights wi, parallel chains are associated with targets equal to the original target restricted to those Ai‘s. This is therefore an MCMC version of partitioned sampling. With regard to the shortcomings listed in the quote above, the authors consider that there does not need to be a bijection between the partition sets and the chains, in that a chain can move across partitions and thus contribute to several integral evaluations simultaneously. I am a bit worried about this argument since it amounts to getting a random number of simulations within each partition set Ai. In my (maybe biased) perception of partitioned sampling, this sounds somewhat counter-productive, as it increases the variance of the overall estimator. (Of course, not restricting a chain to a given partition set Ai has the incentive of avoiding a possibly massive amount of rejection steps. It is however unclear (a) whether or not it impacts ergodicity (it all depends on the way the chain is constructed, i.e. against which target(s)…) as it could lead to an over-representation of some boundaries and (b) whether or not it improves the overall convergence properties of the chain(s).)

“The approach presented here represents a solution to this problem which can completely remove the waiting times for crossing between modes, leaving only the relatively short within-mode equilibration times.” (p.4)

A more delicate issue with the partitioned MCMC approach (in my opinion!) stands with the partitioning. Indeed, in a complex and high-dimension model, the construction of the appropriate partition is a challenge in itself as we often have no prior idea where the modal areas are. Waiting for a correct exploration of the modes is indeed faster than waiting for crossing between modes, provided all modes are represented and the chain for each partition set Ai has enough energy to explore this set. It actually sounds (slightly?) unlikely that a target with huge gaps between modes will see a considerable improvement from the partioned version when the partition sets Ai are selected on the go, because some of the boundaries between the partition sets may be hard to reach with a off-the-shelf proposal. (Obviously, the second part of the method on the adaptive construction of partitions is yet in the writing and I am looking forward its aXival!)

Furthermore, as noted by Pierre Jacob (of Statisfaction fame!), the adaptive construction of the partition has a lot in common with Wang-Landau schemes. Which goal is to produce a flat histogram proposal from the current exploration of the state space. Connections with Atchadé’s and Liu’s (2010, Statistical Sinica) extension of the original Wang-Landau algorithm could have been spelled out. Esp. as the Voronoï tessellation construct seems quite innovative in this respect.

Bayesian multimodel inference by RJMCMC: A Gibbs sampling approach

Posted in Books, pictures, Statistics, Travel, University life with tags , , , , , , on December 27, 2013 by xi'an

img_5288Barker (from the lovely city of Dunedin) and Link published a paper in the American Statistician last September that I missed, as I missed their earlier email about the paper since it arrived The Day After… The paper is about a new specification of RJMCMC, almost twenty years after Peter Green’s (1995) introduction of the method. The authors use the notion of a palette, “from which all model specific parameters can be calculated” (in a deterministic way). One can see the palette ψ as an intermediary step in the move between two models. This reduces the number of bijections, if not the construction of the dreaded Jacobians!, but forces the construction of pseudo-priors on the unessential parts of ψ for every model. Because the dimension of ψ is fixed, a Gibbs sampling interleaving model index and palette value is then implementable. The conditional of the model index given the palette is available provided there are not too many models under competitions, with the probabilities recyclable towards a Rao-Blackwell approximation of the model probability. I wonder at whether or not another Rao-Blackwellisation is possible, namely to draw from all the simulated palettes a sample for the parameter of an arbitrarily chosen model.

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).

another vanilla Rao-Blackwellisation

Posted in Statistics, University life with tags , , , , , on September 16, 2013 by xi'an

In the latest issue of Statistics and Computing (2013, Issue 23, pages 577-587), Iliopoulos and Malefaki published a paper that relates to our vanilla Rao-Blackwellisation paper with Randal Douc. The idea is to derive another approximation to the ideal importance sampling weight using the “accepted” Markov chain. (With Randal, we had a Bernoulli factory representation.) The density g(x) of the accepted chain being unknown; it is represented as the expectation under π of the function

\min\left\{q(z|x)/\pi(z),q(x|z)/\pi(x)\right\}

and hence estimated by a self-normalised average based on the whole Markov chain. This means the resulting importance estimate uses twice the output of the algorithm and that it is biased and of order O(n²), thus the same order as our original Rao-Blackwellised estimator (Robert & Casella, 1996)… This also means convergence and CLT are very hard to establish: the main convergence theorem of the paper holds only for finite state spaces, with a surprising smaller asymptotic variance for this self-normalised average than for the ideal importance sampling estimator in the independent Metropolis-Hastings case. (Both are biased by being self-normalised and the paper does not consider the magnitude of those biases.)

Interestingly, the authors also ran a comparison with our parallelised Rao-Blackwellised version (with Pierre Jacob and Murray Smith), but conclude (P.58) at a larger CPU (should be GPU!!) required by the parallelisation, which does not really make sense: when compared with the plain Metropolis-Hastings implementation, run on a single processor, the parallel version only requires an extra random permutation per thread or per processor. I thus suspect a faulty implementation that induces this CPU being linear in the size of the blocks, like maybe only saving one output per block… Also interestingly, the paper re-analyses the Pima Indian probit model Jean-Michel Marin and I (and many others) used as benchmark in several of our papers. As in the most standard examples, the outcome shows a mild reduction in variance when using this estimated importance sampling version. Maybe a comparison with the ideal importance sampler (i.e. the one that does not divide by the sum of the weights since using normalised versions of the target and importance densities) would have helped in the comparison.

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