Archive for nested sampling

Split Sampling: expectations, normalisation and rare events

Posted in Books, Statistics, University life with tags , , , , , , on January 27, 2014 by xi'an

Just before Christmas (a year ago), John Birge, Changgee Chang, and Nick Polson arXived a paper with the above title. Split sampling is presented a a tool conceived to handle rare event probabilities, written in this paper as


where π is the prior and L the likelihood, m being a large enough bound to make the probability small. However, given John Skilling’s representation of the marginal likelihood as the integral of the Z(m)’s, this simulation technique also applies to the approximation of the evidence. The paper refers from the start to nested sampling as a motivation for this method, presumably not as a way to run nested sampling, which was created as a tool for evidence evaluation, but as a competitor. Nested sampling may indeed face difficulties in handling the coverage of the higher likelihood regions under the prior and it is an approximative method, as we detailed in our earlier paper with Nicolas Chopin. The difference between nested and split sampling is that split sampling adds a distribution ω(m) on the likelihood levels m. If pairs (x,m) can be efficiently generated by MCMC for the target


the marginal density of m can then be approximated by Rao-Blackwellisation. From which the authors derive an estimate of Z(m), since the marginal is actually proportional to ω(m)Z(m). (Because of the Rao-Blackwell argument, I wonder how much this differs from Chib’s 1995 method, i.e. if the split sampling estimator could be expressed as a special case of Chib’s estimator.) The resulting estimator of the marginal also requires a choice of ω(m) such that the associated cdf can be computed analytically. More generally, the choice of ω(m) impacts the quality of the approximation since it determines how often and easily high likelihood regions will be hit. Note also that the conditional π(x|m) is the same as in nested sampling, hence may run into difficulties for complex likelihoods or large datasets.

When reading the beginning of the paper, the remark that “the chain will visit each level roughly uniformly” (p.13) made me wonder at a possible correspondence with the Wang-Landau estimator. Until I read the reference to Jacob and Ryder (2012) on page 16. Once again, I wonder at a stronger link between both papers since the Wang-Landau approach aims at optimising the exploration of the simulation space towards a flat histogram. See for instance Figure 2.

The following part of the paper draws a comparison with both nested sampling and the product estimator of Fishman (1994). I do not fully understand the consequences of the equivalence between those estimators and the split sampling estimator for specific choices of the weight function ω(m). Indeed, it seemed to me that the main point was to draw from a joint density on (x,m) to avoid the difficulties of exploring separately each level set. And also avoiding the approximation issues of nested sampling. As a side remark, the fact that the harmonic mean estimator occurs at several points of the paper makes me worried. The qualification of “poor Monte Carlo error variances properties” is an understatement for the harmonic mean estimator, as it generally has infinite variance and it hence should not be used at all, even as a starting point. The paper does not elaborate much about the cross-entropy method, despite using an example from Rubinstein and Kroese (2004).

In conclusion, an interesting paper that made me think anew about the nested sampling approach, which keeps its fascination over the years! I will most likely use it to build an MSc thesis project this summer in Warwick.

MCMSki [day 2]

Posted in Mountains, pictures, Statistics, University life with tags , , , , , , , , , on January 8, 2014 by xi'an

ridge3I was still feeling poorly this morning with my brain in a kind of flu-induced haze so could not concentrate for a whole talk, which is a shame as I missed most of the contents of the astrostatistics session put together by David van Dyk… Especially the talk by Roberto Trotta I was definitely looking for. And the defence of nested sampling strategies for marginal likelihood approximations. Even though I spotted posterior distributions for WMAP and Plank data on the ΛCDM that reminded me of our own work in this area… Apologies thus to all speakers for dozing in and out, it was certainly not due to a lack of interest!

Sebastian Seehars mentioned emcee (for ensemble Monte Carlo), with a corresponding software nicknamed “the MCMC hammer”, and their own CosmoHammer software. I read the paper by Goodman and Ware (2010) this afternoon during the ski break (if not on a ski lift!). Actually, I do not understand why an MCMC should be affine invariant: a good adaptive MCMC sampler should anyway catch up the right scale of the target distribution. Other than that, the ensemble sampler reminds me very much of the pinball sampler we developed with Kerrie Mengersen (1995 Valencia meeting), where the target is the product of L targets,


and a Gibbs-like sampler can be constructed, moving one component (with index k, say) of the L-sample at a time. (Just as in the pinball sampler.) Rather than avoiding all other components (as in the pinball sampler), Goodman and Ware draw a single other component at random  (with index j, say) and make a proposal away from it:

\eta=x_j(t) + \zeta \{x_k(t)-x_j(t)\}

where ζ is a scale random variable with (log-) symmetry around 1. The authors claim improvement over a single track Metropolis algorithm, but it of course depends on the type of Metropolis algorithms that is chosen… Overall, I think the criticism of the pinball sampler also applies here: using a product of targets can only slow down the convergence. Further, the affine structure of the target support is not a given. Highly constrained settings should not cope well with linear transforms and non-linear reparameterisations would be more efficient….

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).

arXiv recent postings

Posted in Statistics, University life with tags , , , , , , , on June 14, 2013 by xi'an

As I glanced thru the recent arXiv postings in statistics, I found an overload of potential goodies, many more than I could handle in a reasonable time (unless I give up the NYT altogether!)…

For instance, Paulo Marques—a regular ‘Og commenter—wrote about an extension of Chib’s formula when the posterior is approximated in a non-parametric manner. (This was an idea I had toyed with at a time without pursuing it anywhere…)   I wonder at the stability of the approximation for two reasons: (i) Chib’s or Bayes’ formula does not require an expectation as the ratio is constant in θ; averaging over realisations of θ could have negative effects on the stability of the approximation (or not); (ii) using a non-parametric estimate will see the performances of Chib’s approximation plummet as the dimension of θ increases, most likely.

Another post is by Nogales, Pérez, and Monfort and deals with a Monte Carlo formula for conditional expectations that leaves me quite puzzled… More than excited about a potential application in ABC. Indeed, the idea is to replace the conditioning on the (hard) equality with a soft ball around the equality with a tolerance level ε. Since the authors do not seem particularly interested in ABC, I do no see the point in this technique. The first example they present does not account for the increasing computational effort as ε decreases. The second part of the paper deals with the best invariant estimator of the position parameter of a general half-normal distribution, using two conditional expectations in Proposition 2. I wonder how the method compares with bridge sampling and MCMC methods. As the paper seems to have gone beyond the Monte Carlo issue at this stage. And focus on this best invariant estimation…

Then Feroz, Hobson,  Cameron and Pettitt posted a work on importance nested sampling, on which I need to spend more time given the connection to our nested sampling paper with Nicolas. The paper builds on the Multinest software developped by Feroz, Hobson and co-authors. (Whose above picture is borrowed from.)

A side post on the moments of the partial non-central chi-square distribution function by Gill, Segura and Temme, since I always liked the specifics of this distribution… No comments so far!

Initializing adaptive importance sampling with Markov chains

Posted in Statistics with tags , , , , , , , , , , , on May 6, 2013 by xi'an

Another paper recently arXived by Beaujean and Caldwell elaborated on our population Monte Carlo papers (Cappé et al., 2005, Douc et al., 2007, Wraith et al., 2010) to design a more thorough starting distribution. Interestingly, the authors mention the fact that PMC is an EM-type algorithm to emphasize the importance of the starting distribution, as with “poor proposal, PMC fails as proposal updates lead to a consecutively poorer approximation of the target” (p.2). I had not thought of this possible feature of PMC, which indeed proceeds along integrated EM steps, and thus could converge to a local optimum (if not poorer than the start as the Kullback-Leibler divergence decreases).

The solution proposed in this paper is similar to the one we developed in our AMIS paper. An important part of the simulation is dedicated to the construction of the starting distribution, which is a mixture deduced from multiple Metropolis-Hastings runs. I find the method spends an unnecessary long time on refining this mixture by culling the number of components: down-the-shelf clustering techniques should be sufficient, esp. if one considers that the value of the target is available at every simulated point. This has been my pet (if idle) theory for a long while: we do not take (enough) advantage of this informative feature in our simulation methods… I also find the Student’s t versus Gaussian kernel debate (p.6) somehow superfluous: as we shown in Douc et al., 2007, we can process Student’s t distributions so we can as well work with those. And rather worry about the homogeneity assumption this choice implies: working with any elliptically symmetric kernel assumes a local Euclidean structure on the parameter space, for all components, and does not model properly highly curved spaces. Another pet theory of mine’s. As for picking the necessary number of simulations at each PMC iteration, I would add to the ESS and the survival rate of the components a measure of the Kullback-Leibler divergence, as it should decrease at each iteration (with an infinite number of particles).

Another interesting feature is in the comparison with Multinest, the current version of nested sampling, developed by Farhan Feroz. This is the second time I read a paper involving nested sampling in the past two days. While this PMC implementation does better than nested sampling on the examples processed in the paper, the Multinest outcome remains relevant, particularly because it handles multi-modality fairly well. The authors seem to think parallelisation is an issue with nested sampling, while I do see why: at the most naïve stage, several nested samplers can be run in parallel and the outcomes pulled together.


Get every new post delivered to your Inbox.

Join 557 other followers