Archive for the University life Category

Computing the variance of a conditional expectation via non-nested Monte Carlo

Posted in Books, pictures, Statistics, University life with tags , , , , on May 26, 2016 by xi'an

Fushimi Inari-Taisha shrine, Kyoto, June 27, 2012The recent arXival by Takashi Goda of Computing the variance of a conditional expectation via non-nested Monte Carlo led me to read it as I could not be certain of the contents from only reading the title! The short paper considers the issue of estimating the variance of a conditional expectation when able to simulate the joint distribution behind the quantity of interest. The second moment E(E[f(X)|Y]²) can be written as a triple integral with two versions of x given y and one marginal y, which means that it can approximated in an unbiased manner by simulating a realisation of y then conditionally two realisations of x. The variance requires a third simulation of x, which the author seems to deem too costly and that he hence replaces with another unbiased version based on two conditional generations only. (He notes that a faster biased version is available with bias going down faster than the Monte Carlo error, which makes the alternative somewhat irrelevant, as it is also costly to derive.) An open question after reading the paper stands with the optimal version of the generic estimator (5), although finding the optimum may require more computing time than it is worth spending. Another one is whether or not this version of the expected conditional variance is more interesting (computation-wise) that the difference between the variance and the expected conditional variance as reproduced in (3) given that both quantities can equally be approximated by unbiased Monte Carlo…

the end of Series B!

Posted in Books, pictures, Statistics, University life with tags , , , , on May 25, 2016 by xi'an

I received this news from the RSS today that all the RSS journals are turning 100% electronic. No paper version any longer! I deeply regret this move on which, as an RSS member, I would have appreciated to be consulted as I find much easier to browse through the current issue when it arrives in my mailbox, rather than being t best reminded by an email that I will most likely ignore and erase. And as I consider the production of the journals the prime goal of the Royal Statistical Society. And as I read that only 25% of the members had opted so far for the electronic format, which does not sound to me like a majority. In addition, moving to electronic-only journals does not bring the perks one would expect from electronic journals:

  • no bonuses like supplementary material, code, open or edited comments
  • no reduction in the subscription rate of the journals and penalty fees if one still wants a paper version, which amounts to a massive increase in the subscription price
  • no disengagement from the commercial publisher, whose role become even less relevant
  • no access to the issues of the years one has paid for, once one stops subscribing.

“The benefits of electronic publishing include: faster publishing speeds; increased content; instant access from a range of electronic devices; additional functionality; and of course, environmental sustainability.”

The move is sold with typical marketing noise. But I do not buy it: publishing speeds will remain the same as driven by the reviewing part, I do not see where the contents are increased, and I cannot seriously read a journal article from my phone, so this range of electronic devices remains a gadget. Not happy!

an avalanche of new arXivals

Posted in Books, Statistics, University life with tags on May 25, 2016 by xi'an

In the past few days, I spotted the following papers being arXived, far too many for me to comment them all!


likelihood inflating sampling algorithm

Posted in Statistics, University life, Books with tags , , , , , , , , on May 24, 2016 by xi'an

My friends from Toronto Radu Craiu and Jeff Rosenthal have arXived a paper along with Reihaneh Entezari on MCMC scaling for large datasets, in the spirit of Scott et al.’s (2013) consensus Monte Carlo. They devised an likelihood inflated algorithm that brings a novel perspective to the problem of large datasets. This question relates to earlier approaches like consensus Monte Carlo, but also kernel and Weierstrass subsampling, already discussed on this blog, as well as current research I am conducting with my PhD student Changye Wu. The approach by Entezari et al. is somewhat similar to consensus Monte Carlo and the other solutions in that they consider an inflated (i.e., one taken to the right power) likelihood based on a subsample, with the full sample being recovered by importance sampling. Somewhat unsurprisingly this approach leads to a less dispersed estimator than consensus Monte Carlo (Theorem 1). And the paper only draws a comparison with that sub-sampling method, rather than covering other approaches to the problem, maybe because this is the most natural connection, one approach being the k-th power of the other approach.

“…we will show that [importance sampling] is unnecessary in many instances…” (p.6)

An obvious question that stems from the approach is the call for importance sampling, since the numerator of the importance sampler involves the full likelihood which is unavailable in most instances when sub-sampled MCMC is required. I may have missed the part of the paper where the above statement is discussed, but the only realistic example discussed therein is the Bayesian regression tree (BART) of Chipman et al. (1998). Which indeed constitutes a challenging if one-dimensional example, but also one that requires delicate tuning that leads to cancelling importance weights but which may prove delicate to extrapolate to other models.

snapshot from München

Posted in pictures, Travel, University life with tags , , , , on May 22, 2016 by xi'an

on a day trip to München, Neues Rathaus, May 20, 2016

ABC random forests for Bayesian parameter inference

Posted in Books, Kids, R, Statistics, Travel, University life, Wines with tags , , , , , , , , , , , , , , on May 20, 2016 by xi'an

Before leaving Helsinki, we arXived [from the Air France lounge!] the paper Jean-Michel presented on Monday at ABCruise in Helsinki. This paper summarises the experiments Louis conducted over the past months to assess the great performances of a random forest regression approach to ABC parameter inference. Thus validating in this experimental sense the use of this new approach to conducting ABC for Bayesian inference by random forests. (And not ABC model choice as in the Bioinformatics paper with Pierre Pudlo and others.)

I think the major incentives in exploiting the (still mysterious) tool of random forests [against more traditional ABC approaches like Fearnhead and Prangle (2012) on summary selection] are that (i) forests do not require a preliminary selection of the summary statistics, since an arbitrary number of summaries can be used as input for the random forest, even when including a large number of useless white noise variables; (b) there is no longer a tolerance level involved in the process, since the many trees in the random forest define a natural if rudimentary distance that corresponds to being or not being in the same leaf as the observed vector of summary statistics η(y); (c) the size of the reference table simulated from the prior (predictive) distribution does not need to be as large as for in usual ABC settings and hence this approach leads to significant gains in computing time since the production of the reference table usually is the costly part! To the point that deriving a different forest for each univariate transform of interest is truly a minor drag in the overall computing cost of the approach.

An intriguing point we uncovered through Louis’ experiments is that an unusual version of the variance estimator is preferable to the standard estimator: we indeed exposed better estimation performances when using a weighted version of the out-of-bag residuals (which are computed as the differences between the simulated value of the parameter transforms and their expectation obtained by removing the random trees involving this simulated value). Another intriguing feature [to me] is that the regression weights as proposed by Meinshausen (2006) are obtained as an average of the inverse of the number of terms in the leaf of interest. When estimating the posterior expectation of a transform h(θ) given the observed η(y), this summary statistic η(y) ends up in a given leaf for each tree in the forest and all that matters for computing the weight is the number of points from the reference table ending up in this very leaf. I do find this difficult to explain when confronting the case when many simulated points are in the leaf against the case when a single simulated point makes the leaf. This single point ends up being much more influential that all the points in the other situation… While being an outlier of sorts against the prior simulation. But now that I think more about it (after an expensive Lapin Kulta beer in the Helsinki airport while waiting for a change of tire on our airplane!), it somewhat makes sense that rare simulations that agree with the data should be weighted much more than values that stem from the prior simulations and hence do not translate much of an information brought by the observation. (If this sounds murky, blame the beer.) What I found great about this new approach is that it produces a non-parametric evaluation of the cdf of the quantity of interest h(θ) at no calibration cost or hardly any. (An R package is in the making, to be added to the existing R functions of abcrf we developed for the ABC model choice paper.)

Using MCMC output to efficiently estimate Bayes factors

Posted in Books, R, Statistics, University life with tags , , , , on May 19, 2016 by xi'an

As I was checking for software to answer a query on X validated about generic Bayes factor derivation, I came across an R software called BayesFactor, which only applies in regression settings and relies on the Savage-Dickey representation of the Bayes factor


when the null hypothesis writes as θ=θ⁰ (and possibly additional nuisance parameters with [roughly speaking] an independent prior). As we discussed in our paper with Jean-Michel Marin [which got ignored by large!], this representation of the Bayes factor is based on picking a very specific version of the prior, or more exactly of three prior densities. Assuming such versions are selected, I wonder at the performances of this approximation, given that it involves approximating the marginal posterior at θ⁰….

“To ensure that the Bayes factor we compute using the Savage–Dickey ratio is the the ratio of marginal densities that we intend, the condition (…) is easily met by models which specify priors in which the nuisance parameters are independent of the parameters of interest.” Morey et al. (2011)

First, when reading Morey at al. (2011), I realised (a wee bit late!) that Chib’s method is nothing but a version of the Savage-Dickey representation when the marginal posterior can be estimated in a parametric (Rao-Blackwellised) way. However, outside hierarchical models based on conjugate priors such parametric approximations are intractable and non-parametric versions must be invoked instead, which necessarily degrades the quality of the method. A degradation that escalates with the dimension of the parameter θ. In addition, I am somewhat perplexed by the use of a Rao-Blackwell argument in the setting of the Dickey-Savage representation. Indeed this representation assumes that

\pi_1(\psi|\theta_0)=\pi_0(\psi) \  \ \text{or}\quad \pi_1(\theta_0,\psi)=\pi_1(\theta_0)\pi_0(\psi)

which means that [the specific version of] the conditional density of θ⁰ given ψ should not depend on the nuisance parameter. But relying on a Rao-Blackwellisation leads to estimate the marginal posterior via full conditionals. Of course, θ given ψ and y may depend on ψ, but still… Morey at al. (2011) advocate the recourse to Chib’s formula as optimal but this obviously requires the full conditional to be available. They acknowledge this point as moot, since it is sufficient from their perspective to specify a conjugate prior. They consider this to be a slight modification of the model (p.377). However, I see the evaluation of an estimated density at a single (I repeat, single!) point as being the direst part of the method as it is clearly more sensitive to approximations that the evaluation of a whole integral, since the later incorporates an averaging effect by definition. Hence, even if this method was truly available for all models, I would be uncertain of its worth when compared with other methods, except the harmonic mean estimator of course!

On the side, Morey at al. (2011) study a simple one-sample t test where they use an improper prior on the nuisance parameter σ, under both models. While the Savage-Dickey representation is correct in this special case, I fail to see why the identity would apply in every case under an improper prior. In particular, independence does not make sense with improper priors. The authors also indicate the possible use of this Bayes factor approximation for encompassing models. At first, I thought this could be most useful in our testing by mixture framework where we define an encompassing model as a mixture. However, I quickly realised that using a Beta Be(a,a) prior on the weight α with a<1 leads to an infinite density value at both zero and one, hence cannot be compatible with a Savage-Dickey representation of the Bayes factor.


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