Archive for Pima Indians

new estimators of evidence

Posted in Books, Statistics with tags , , , , , , , , , , , , on June 19, 2018 by xi'an

In an incredible accumulation of coincidences, I came across yet another paper about evidence and the harmonic mean challenge, by Yu-Bo Wang, Ming-Hui Chen [same as in Chen, Shao, Ibrahim], Lynn Kuo, and Paul O. Lewis this time, published in Bayesian Analysis. (Disclaimer: I was not involved in the reviews of any of these papers!)  Authors who arelocated in Storrs, Connecticut, in geographic and thematic connection with the original Gelfand and Dey (1994) paper! (Private joke about the Old Man of Storr in above picture!)

“The working parameter space is essentially the constrained support considered by Robert and Wraith (2009) and Marin and Robert (2010).”

The central idea is to use a more general function than our HPD restricted prior but still with a known integral. Not in the sense of control variates, though. The function of choice is a weighted sum of indicators of terms of a finite partition, which implies a compact parameter set Ω. Or a form of HPD region, although it is unclear when the volume can be derived. While the consistency of the estimator of the inverse normalising constant [based on an MCMC sample] is unsurprising, the more advanced part of the paper is about finding the optimal sequence of weights, as in control variates. But it is also unsurprising in that the weights are proportional to the inverses of the inverse posteriors over the sets in the partition. Since these are hard to derive in practice, the authors come up with a fairly interesting alternative, which is to take the value of the posterior at an arbitrary point of the relevant set.

The paper also contains an extension replacing the weights with functions that are integrable and with known integrals. Which is hard for most choices, even though it contains the regular harmonic mean estimator as a special case. And should also suffer from the curse of dimension when the constraint to keep the target almost constant is implemented (as in Figure 1).

The method, when properly calibrated, does much better than harmonic mean (not a surprise) and than Petris and Tardella (2007) alternative, but no other technique, on toy problems like Normal, Normal mixture, and probit regression with three covariates (no Pima Indians this time!). As an aside I find it hard to understand how the regular harmonic mean estimator takes longer than this more advanced version, which should require more calibration. But I find it hard to see a general application of the principle, because the partition needs to be chosen in terms of the target. Embedded balls cannot work for every possible problem, even with ex-post standardisation.


Metropolis-Hastings importance sampling

Posted in Books, Statistics, University life with tags , , , , , , , , , on June 6, 2018 by xi'an

[Warning: As I first got the paper from the authors and sent them my comments, this paper read contains their reply as well.]

In a sort of crazy coincidence, Daniel Rudolf and Björn Sprungk arXived a paper on a Metropolis-Hastings importance sampling estimator that offers similarities with  the one by Ingmar Schuster and Ilja Klebanov posted on arXiv the same day. The major difference in the construction of the importance sampler is that Rudolf and Sprungk use the conditional distribution of the proposal in the denominator of their importance weight, while Schuster and Klebanov go for the marginal (or a Rao-Blackwell representation of the marginal), mostly in an independent Metropolis-Hastings setting (for convergence) and for a discretised Langevin version in the applications. The former use a very functional L² approach to convergence (which reminded me of the early Schervish and Carlin, 1990, paper on the convergence of MCMC algorithms), not all of it necessary in my opinion. As for instance the extension of convergence properties to the augmented chain, namely (current, proposed), is rather straightforward since the proposed chain is a random transform of the current chain. An interesting remark at the end of the proof of the CLT is that the asymptotic variance of the importance sampling estimator is the same as with iid realisations from the target. This is a point we also noticed when constructing population Monte Carlo techniques (more than ten years ago), namely that dependence on the past in sequential Monte Carlo does not impact the validation and the moments of the resulting estimators, simply because “everything cancels” in importance ratios. The mean square error bound on the Monte Carlo error (Theorem 20) is not very surprising as the term ρ(y)²/P(x,y) appears naturally in the variance of importance samplers.

The first illustration where the importance sampler does worse than the initial MCMC estimator for a wide range of acceptance probabilities (Figures 2 and 3, which is which?) and I do not understand the opposite conclusion from the authors.

[Here is an answer from Daniel and Björn about this point:]

Indeed the formulation in our paper is unfortunate. The point we want to stress is that we observed in the numerical experiments certain ranges of step-sizes for which MH importance sampling shows a better performance than the classical MH algorithm with optimal scaling. Meaning that the MH importance sampling with optimal step-size can outperform MH sampling, without using additional computational resources. Surprisingly, the optimal step-size for the MH importance sampling estimator seems to remain constant for an increasing dimension in contrast to the well-known optimal scaling of the MH algorithm (given by a constant optimal acceptance rate).

The second uses the Pima Indian diabetes benchmark, amusingly (?) referring to Chopin and Ridgway (2017) who warn against the recourse to this dataset and to this model! The loss in mean square error due to the importance sampling may again be massive (Figure 5) and setting for an optimisation of the scaling factor in Metropolis-Hastings algorithms sounds unrealistic.

[And another answer from Daniel and Björn about this point:]

Indeed, Chopin and Ridgway suggest more complex problems with a larger number of covariates as benchmarks. However, the well-studied PIMA data set is a sufficient example in order to illustrate the possible benefits but also the limitations of the MH importance sampling approach. The latter are clearly (a) the required knowledge about the optimal step-size—otherwise the performance can indeed be dramatically worse than for the MH algorithm—and (b) the restriction to a small or at most moderate number of covariates. As you are indicating, optimizing the scaling factor is a challenging task. However, the hope is to derive some simple rule of thumb for the MH importance sampler similar to the well-known acceptance rate tuning for the standard MCMC estimator.

WBIC, practically

Posted in Statistics with tags , , , , , , , , , on October 20, 2017 by xi'an

“Thus far, WBIC has received no more than a cursory mention by Gelman et al. (2013)”

I had missed this 2015  paper by Nial Friel and co-authors on a practical investigation of Watanabe’s WBIC. Where WBIC stands for widely applicable Bayesian information criterion. The thermodynamic integration approach explored by Nial and some co-authors for the approximation of the evidence, thermodynamic integration that produces the log-evidence as an integral between temperatures t=0 and t=1 of a powered evidence, is eminently suited for WBIC, as the widely applicable Bayesian information criterion is associated with the specific temperature t⁰ that makes the power posterior equidistant, Kullback-Leibler-wise, from the prior and posterior distributions. And the expectation of the log-likelihood under this very power posterior equal to the (genuine) evidence. In fact, WBIC is often associated with the sub-optimal temperature 1/log(n), where n is the (effective?) sample size. (By comparison, if my minimalist description is unclear!, thermodynamic integration requires a whole range of temperatures and associated MCMC runs.) In an ideal Gaussian setting, WBIC improves considerably over thermodynamic integration, the larger the sample the better. In more realistic settings, though, including a simple regression and a logistic [Pima Indians!] model comparison, thermodynamic integration may do better for a given computational cost although the paper is unclear about these costs. The paper also runs a comparison with harmonic mean and nested sampling approximations. Since the integral of interest involves a power of the likelihood, I wonder if a safe version of the harmonic mean resolution can be derived from simulations of the genuine posterior. Provided the exact temperature t⁰ is known…

X divergence for approximate inference

Posted in Statistics with tags , , , , , , , on March 14, 2017 by xi'an

Dieng et al. arXived this morning a new version of their paper on using the Χ divergence for variational inference. The Χ divergence essentially is the expectation of the squared ratio of the target distribution over the approximation, under the approximation. It is somewhat related to Expectation Propagation (EP), which aims at the Kullback-Leibler divergence between the target distribution and the approximation, under the target. And to variational Bayes, which is the same thing just the opposite way! The authors also point a link to our [adaptive] population Monte Carlo paper of 2008. (I wonder at a possible version through Wasserstein distance.)

Some of the arguments in favour of this new version of variational Bayes approximations is that (a) the support of the approximation over-estimates the posterior support; (b) it produces over-dispersed versions; (c) it relates to a well-defined and global objective function; (d) it allows for a sandwich inequality on the model evidence; (e) the function of the [approximation] parameter to be minimised is under the approximation, rather than under the target. The latest allows for a gradient-based optimisation. While one of the applications is on a Bayesian probit model applied to the Pima Indian women dataset [and will thus make James and Nicolas cringe!], the experimental assessment shows lower error rates for this and other benchmarks. Which in my opinion does not tell so much about the original Bayesian approach.

read paper [in Bristol]

Posted in Books, pictures, Statistics, Travel, University life with tags , , , , , , , , , , , , , , on January 29, 2016 by xi'an

Clifton & Durdham Downs, Bristol, Sept. 25, 2012I went to give a seminar in Bristol last Friday and I chose to present the testing with mixture paper. As we are busy working on the revision, I was eagerly looking for comments and criticisms that could strengthen this new version. As it happened, the (Bristol) Bayesian Cake (Reading) Club had chosen our paper for discussion, two weeks in a row!, hence the title!, and I got invited to join the group the morning prior to the seminar! This was, of course, most enjoyable and relaxed, including an home-made cake!, but also quite helpful in assessing our arguments in the paper. One point of contention or at least of discussion was the common parametrisation between the components of the mixture. Although all parametrisations are equivalent from a single component point of view, I can [almost] see why using a mixture with the same parameter value on all components may impose some unsuspected constraint on that parameter. Even when the parameter is the same moment for both components. This still sounds like a minor counterpoint in that the weight should converge to either zero or one and hence eventually favour the posterior on the parameter corresponding to the “true” model.

Another point that was raised during the discussion is the behaviour of the method under misspecification or for an M-open framework: when neither model is correct does the weight still converge to the boundary associated with the closest model (as I believe) or does a convexity argument produce a non-zero weight as it limit (as hinted by one example in the paper)? I had thought very little about this and hence had just as little to argue though as this does not sound to me like the primary reason for conducting tests. Especially in a Bayesian framework. If one is uncertain about both models to be compared, one should have an alternative at the ready! Or use a non-parametric version, which is a direction we need to explore deeper before deciding it is coherent and convergent!

A third point of discussion was my argument that mixtures allow us to rely on the same parameter and hence the same prior, whether proper or not, while Bayes factors are less clearly open to this interpretation. This was not uniformly accepted!

Thinking afresh about this approach also led me to broaden my perspective on the use of the posterior distribution of the weight(s) α: while previously I had taken those weights mostly as a proxy to the posterior probabilities, to be calibrated by pseudo-data experiments, as for instance in Figure 9, I now perceive them primarily as the portion of the data in agreement with the corresponding model [or hypothesis] and more importantly as a solution for staying away from a Neyman-Pearson-like decision. Or error evaluation. Usually, when asked about the interpretation of the output, my answer is to compare the behaviour of the posterior on the weight(s) with a posterior associated with a sample from each model. Which does sound somewhat similar to posterior predictives if the samples are simulated from the associated predictives. But the issue was not raised during the visit to Bristol, which possibly reflects on how unfrequentist the audience was [the Statistics group is], as it apparently accepted with no further ado the use of a posterior distribution as a soft assessment of the comparative fits of the different models. If not necessarily agreeing the need of conducting hypothesis testing (especially in the case of the Pima Indian dataset!).

approximating evidence with missing data

Posted in Books, pictures, Statistics, University life with tags , , , , , , , , , , , , , , , on December 23, 2015 by xi'an

University of Warwick, May 31 2010Panayiota Touloupou (Warwick), Naif Alzahrani, Peter Neal, Simon Spencer (Warwick) and Trevelyan McKinley arXived a paper yesterday on Model comparison with missing data using MCMC and importance sampling, where they proposed an importance sampling strategy based on an early MCMC run to approximate the marginal likelihood a.k.a. the evidence. Another instance of estimating a constant. It is thus similar to our Frontier paper with Jean-Michel, as well as to the recent Pima Indian survey of James and Nicolas. The authors give the difficulty to calibrate reversible jump MCMC as the starting point to their research. The importance sampler they use is the natural choice of a Gaussian or t distribution centred at some estimate of θ and with covariance matrix associated with Fisher’s information. Or derived from the warmup MCMC run. The comparison between the different approximations to the evidence are done first over longitudinal epidemiological models. Involving 11 parameters in the example processed therein. The competitors to the 9 versions of importance samplers investigated in the paper are the raw harmonic mean [rather than our HPD truncated version], Chib’s, path sampling and RJMCMC [which does not make much sense when comparing two models]. But neither bridge sampling, nor nested sampling. Without any surprise (!) harmonic means do not converge to the right value, but more surprisingly Chib’s method happens to be less accurate than most importance solutions studied therein. It may be due to the fact that Chib’s approximation requires three MCMC runs and hence is quite costly. The fact that the mixture (or defensive) importance sampling [with 5% weight on the prior] did best begs for a comparison with bridge sampling, no? The difficulty with such study is obviously that the results only apply in the setting of the simulation, hence that e.g. another mixture importance sampler or Chib’s solution would behave differently in another model. In particular, it is hard to judge of the impact of the dimensions of the parameter and of the missing data.

the problem of assessing statistical methods

Posted in Books, pictures, Statistics, University life with tags , , , , , , on November 4, 2015 by xi'an

A new arXival today by Abigail Arnold and Jason Loeppky that discusses how simulations studies are and should be conducted when assessing statistical methods.

“Obviously there is no one model that will universally outperform the rest. Recognizing the “No Free Lunch” theorem, the logical question to ask is whether one model will perform best over a given class of problems. Again, we feel that the answer to this question is of course no. But we do feel that there are certain methods that will have a better chance than other methods.”

I find the assumptions or prerequisites of the paper arguable [in the sense of 2. open to disagreement; not obviously correct]—not even mentioning the switch from models to methods in the above—in that I will not be convinced that a method outperforms another method by simply looking at a series of simulation experiments. (Which is why I find some machine learning papers unconvincing, when they introduce a new methodology and run it through a couple benchmarks.) This also reminds me of Samaniego’s Comparison of the Bayesian and frequentist approaches, which requires a secondary prior to run the comparison. (And hence is inconclusive.)

“The papers above typically show the results as a series of side-by-side boxplots (…) for each method, with one plot for each test function and sample size. Conclusions are then drawn from looking at a handful of boxplots which often look very cluttered and usually do not provide clear evidence as to the best method(s). Alternatively, the results will be summarized in a table of average performance (…) These tables are usually overwhelming to look at and interpretations are incredibly inefficient.”

Agreed boxplots are terrible (my friend Jean-Michel is forever arguing against them!). Tables are worse. But why don’t we question RMSE as well? This is most often a very reductive way of comparing methods. I also agree with the point that the design of the simulation studies is almost always overlooked and induces a false sense of precision, while failing to cover a wide enough range of cases. However, and once more, I question the prerequisites for comparing methods through simulations for the purpose of ranking those methods. (Which is not the perspective adopted by James and Nicolas when criticising the use of the Pima Indian dataset.)

“The ECDF allows for quick assessments of methods over a large array of problems to get an overall view while of course not precluding comparisons on individual functions (…) We hope that readers of this paper agree with our opinions and strongly encourage everyone to rely on the ECDF, at least as a starting point, to display relevant statistical information from simulations.”

Drawing a comparison with the benchmarking of optimisation methods, the authors suggest to rank statistical methods via the empirical cdf of their performances or accuracy across (benchmark) problems. Arguing that “significant benefit is gained by [this] collapsing”. I am quite sceptical [as often] of the argument, first because using a (e)cdf means the comparison is unidimensional, second because I see no reason why two cdfs should be easily comparable, third because the collapsing over several problems only operates when the errors for those different problems do not overlap.