Archive for subsampling

on Markov chain Monte Carlo methods for tall data

Posted in Books, Statistics, University life with tags , , , , , on June 22, 2015 by xi'an

Rémi Bardenet, Arnaud Doucet, and Chris Holmes arXived a long paper (with the above title) a month ago, paper that I did not have time to read in detail till today. The paper is quite comprehensive in its analysis of the current literature on MCMC for huge, tall, or big data. Even including our delayed acceptance paper! Now, it is indeed the case that we are all still struggling with this size difficulty. Making proposals in a wide range of directions, hopefully improving the efficiency of dealing with tall data. However, we are not there yet in that the outcome is either about as costly as the original MCMC implementation or its degree of approximation is unknown, even when bounds are available.

Most of the paper proposal is based on aiming at an unbiased estimator of the likelihood function in a pseudo-marginal manner à la Andrieu and Roberts (2009) and on a random subsampling scheme that presumes (a) iid-ness and (b) a lower bound on each term in the likelihood. It seems to me slightly unrealistic to assume that a much cheaper and tight lower bound on those terms could be available. Firmly set in the iid framework, the problem itself is unclear: do we need 10⁸ observations of a logistic model with a few parameters? The real challenge is rather in non-iid hierarchical models with random effects and complex dependence structures. For which subsampling gets much more delicate. None of the methods surveyed in the paper broaches upon such situations where the entire data cannot be explored at once.

An interesting experiment therein, based on the Glynn and Rhee (2014) unbiased representation, shows that the approach does not work well. This could lead the community to reconsider the focus on unbiasedness by coming full circle to the opposition  between bias and variance. And between intractable likelihood and representative subsample likelihood.

Reading the (superb) coverage of earlier proposals made me trace back on the perceived appeal of the decomposition of Neiswanger et al. (2014) as I came to realise that the product of functions renormalised into densities has no immediate probabilistic connection with its components. As an extreme example, terms may fail to integrate. (Of course, there are many Monte Carlo features that exploit such a decomposition, from the pseudo-marginal to accept-reject algorithms. And more to come.) Taking samples from terms in the product is thus not directly related to taking samples from each term, in opposition with the arithmetic mixture representation. I was first convinced by using a fraction of the prior in each term but now find it unappealing because there is no reason the prior should change for a smaller sampler and no equivalent to the prohibition of using the data several times. At this stage, I would be much more in favour of raising a random portion of the likelihood function to the right power. An approach that I suggested to a graduate student earlier this year and which is also discussed in the paper. And considered too naïve and a “very poor approach” (Section 6, p.18), even though there must be versions that do not run afoul of the non-Gaussian nature of the log likelihood ratio. I am certainly going to peruse more thoroughly this Section 6 of the paper.

Another interesting suggestion in this definitely rich paper is the foray into an alternative bypassing the uniform sampling in the Metropolis-Hastings step, using instead the subsampled likelihood ratio. The authors call this “exchanging acceptance noise for subsampling noise” (p.22). However, there is no indication about the resulting stationary and I find the notion of only moving to higher likelihoods (or estimates of) counter to the spirit of Metropolis-Hastings algorithms. (I have also eventually realised the meaning of the log-normal “difficult” benchmark that I missed in the earlier : it means log-normal data is modelled by a normal density.)  And yet another innovation along the lines of a control variate for the log likelihood ratio, no matter it sounds somewhat surrealistic.

light and widely applicable MCMC: approximate Bayesian inference for large datasets

Posted in Books, Statistics, University life, Wines with tags , , , , , , , , , , on March 24, 2015 by xi'an

Florian Maire (whose thesis was discussed in this post), Nial Friel, and Pierre Alquier (all in Dublin at some point) have arXived today a paper with the above title, aimed at quickly analysing large datasets. As reviewed in the early pages of the paper, this proposal follows a growing number of techniques advanced in the past years, like pseudo-marginals, Russian roulette, unbiased likelihood estimators. firefly Monte Carlo, adaptive subsampling, sub-likelihoods, telescoping debiased likelihood version, and even our very own delayed acceptance algorithm. (Which is incorrectly described as restricted to iid data, by the way!)

The lightweight approach is based on an ABC idea of working through a summary statistic that plays the role of a pseudo-sufficient statistic. The main theoretical result in the paper is indeed that, when subsampling in an exponential family, subsamples preserving the sufficient statistics (modulo a rescaling) are optimal in terms of distance to the true posterior. Subsamples are thus weighted in terms of the (transformed) difference between the full data statistic and the subsample statistic, assuming they are both normalised to be comparable. I am quite (positively) intrigued by this idea in that it allows to somewhat compare inference based on two different samples. The weights of the subsets are then used in a pseudo-posterior that treats the subset as an auxiliary variable (and the weight as a substitute to the “missing” likelihood). This may sound a wee bit convoluted (!) but the algorithm description is not yet complete: simulating jointly from this pseudo-target is impossible because of the huge number of possible subsets. The authors thus suggest to run an MCMC scheme targeting this joint distribution, with a proposed move on the set of subsets and a proposed move on the parameter set conditional on whether or not the proposed subset has been accepted.

From an ABC perspective, the difficulty in calibrating the tolerance ε sounds more accute than usual, as the size of the subset comes as an additional computing parameter. Bootstrapping options seem impossible to implement in a large size setting.

An MCMC issue with this proposal is that designing the move across the subset space is both paramount for its convergence properties and lacking in geometric intuition. Indeed, two subsets with similar summary statistics may be very far apart… Funny enough, in the representation of the joint Markov chain, the parameter subchain is secondary if crucial to avoid intractable normalising constants. It is also unclear for me from reading the paper maybe too quickly whether or not the separate moves when switching and when not switching subsets retain the proper balance condition for the pseudo-joint to still be the stationary distribution. The stationarity for the subset Markov chain is straightforward by design, but it is not so for the parameter. In case of switched subset, simulating from the true full conditional given the subset would work, but not simulated  by a fixed number L of MCMC steps.

The lightweight technology therein shows its muscles on an handwritten digit recognition example where it beats regular MCMC by a factor of 10 to 20, using only 100 datapoints instead of the 10⁴ original datapoints. While very nice and realistic, this example may be misleading in that 100 digit realisations may be enough to find a tolerable approximation to the true MAP. I was also intrigued by the processing of the probit example, until I realised the authors had integrated the covariate out and inferred about the mean of that covariate, which means it is not a genuine probit model.

the fundamental incompatibility of HMC and data subsampling

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

the pond in front of the Zeeman building, University of Warwick, July 01, 2014Last week, Michael Betancourt, from WarwickarXived a neat wee note on the fundamental difficulties in running HMC on a subsample of the original data. The core message is that using only one fraction of the data to run an HMC with the hope that it will preserve the stationary distribution does not work. The only way to recover from the bias is to use a Metropolis-Hastings step using the whole data, a step that both kills most of the computing gain and has very low acceptance probabilities. Even the strategy that subsamples for each step in a single trajectory fails: there cannot be a significant gain in time without a significant bias in the outcome. Too bad..! Now, there are ways of accelerating HMC, for instance by parallelising the computation of gradients but, just as in any other approach (?), the information provided by the whole data is only available when looking at the whole data.

Importance sampling schemes for evidence approximation in mixture models

Posted in R, Statistics, University life with tags , , , , , , , , , on November 27, 2013 by xi'an

boximpJeong Eun (Kate) Lee and I completed this paper, “Importance sampling schemes for evidence approximation in mixture models“, now posted on arXiv. (With the customary one-day lag for posting, making me bemoan the days of yore when arXiv would give a definitive arXiv number at the time of submission.) Kate came twice to Paris in the past years to work with me on this evaluation of Chib’s original marginal likelihood estimate (also called the candidate formula by Julian Besag). And on the improvement proposed by Berkhof, van Mechelen, and Gelman (2003), based on averaging over all permutations, idea that we rediscovered in an earlier paper with Jean-Michel Marin. (And that Andrew seemed to have completely forgotten. Despite being the very first one to publish [in English] a paper on a Gibbs sampler for mixtures.) Given that this averaging can get quite costly, we propose a preliminary step to reduce the number of relevant permutations to be considered in the averaging, removing far-away modes that do not contribute to the Rao-Blackwell estimate and called dual importance sampling. We also considered modelling the posterior as a product of k-component mixtures on the components, following a vague idea I had in the back of my mind for many years, but it did not help. In the above boxplot comparison of estimators, the marginal likelihood estimators are

  1. Chib’s method using T = 5000 samples with a permutation correction by multiplying by k!.
  2. Chib’s method (1), using T = 5000 samples which are randomly permuted.
  3. Importance sampling estimate (7), using the maximum likelihood estimate (MLE) of the latents as centre.
  4. Dual importance sampling using q in (8).
  5. Dual importance sampling using an approximate in (14).
  6. Bridge sampling (3). Here, label switching is imposed in hyperparameters.

Asymptotically Exact, Embarrassingly Parallel MCMC

Posted in Books, Statistics, University life with tags , , , , , , on November 26, 2013 by xi'an

Departamento de Matemática, Universidad Complutense de Madrid, 11/11/11Willie Neiswanger, Chong Wang, and Eric Xing (from CMU) recently arXived a paper entitled as above. The “embarrassing” in the title refers to the “embarrassingly simple” solution proposed therein, namely to solve the difficulty in handling very large datasets by running completely independent parallel MCMC samplers on parallel threads or computers and using the outcomes of those samplers as density estimates, pulled together as a product towards an approximation of the true posterior density. In other words, the idea is to break the posterior as

p(\theta|x) = \prod_{i=1}^m p_i(\theta|x)

and to use the estimate

\hat p(\theta|x) = \prod_{i=1}^m \hat p_i(\theta|x)

where the individual estimates are obtained by, say, non-parametric estimates. The method is then “asymptotically exact” in the weak (and unsurprising) sense of being converging in the number of MCMC iterations. Still, there is a theoretical justification that is not found in previous parallel methods that mixed all resulting samples without accounting for the subsampling. And I also appreciate the point that, in many cases, running MCMC samplers with subsamples produces faster convergence.

In the paper, the division of p into its components is done by partitioning the iid data into m subsets. And taking a power 1/m of the prior in each case. (Which may induce improperness issues.) However, the subdivision is arbitrary and can thus be implemented in other cases than the fairly restrictive iid setting. Because each (subsample)  non-parametric estimate involves T terms, the resulting overall estimate contains Tm terms and the authors suggest using an independent Metropolis-within-Gibbs sampler to handle this complexity. Which is necessary [took me a while to realise this!] for producing a final sample from the (approximate) true posterior distribution. As an aside, I wonder why the bandwidths are all equal across all subsamples, as they should depend on those. And as it would not make much of a difference. It would also be interesting to build a typology of cases where subsampling leads to subposteriors that are close to orthogonal, preventing the implementation of the method.

As it happened, I read this paper on the very day Nial Friel (University College Dublin) gave a seminar at the Big’MC seminar on the convergence of approximations to ergodic transition kernels, based on the recent results of Mitrophanov on the stability of Markov chains, where he introduced the topic by the case of datasets large enough to prevent the computation of the likelihood function.