Archive for data generating process

variational approximation to empirical likelihood ABC

Posted in Statistics with tags , , , , , , , , , , , , , , , , , , on October 1, 2021 by xi'an

Sanjay Chaudhuri and his colleagues from Singapore arXived last year a paper on a novel version of empirical likelihood ABC that I hadn’t yet found time to read. This proposal connects with our own, published with Kerrie Mengersen and Pierre Pudlo in 2013 in PNAS. It is presented as an attempt at approximating the posterior distribution based on a vector of (summary) statistics, the variational approximation (or information projection) appearing in the construction of the sampling distribution of the observed summary. (Along with a weird eyed-g symbol! I checked inside the original LaTeX file and it happens to be a mathbbmtt g, that is, the typewriter version of a blackboard computer modern g…) Which writes as an entropic correction of the true posterior distribution (in Theorem 1).

“First, the true log-joint density of the observed summary, the summaries of the i.i.d. replicates and the parameter have to be estimated. Second, we need to estimate the expectation of the above log-joint density with respect to the distribution of the data generating process. Finally, the differential entropy of the data generating density needs to be estimated from the m replicates…”

The density of the observed summary is estimated by empirical likelihood, but I do not understand the reasoning behind the moment condition used in this empirical likelihood. Indeed the moment made of the difference between the observed summaries and the observed ones is zero iff the true value of the parameter is used in the simulation. I also fail to understand the connection with our SAME procedure (Doucet, Godsill & X, 2002), in that the empirical likelihood is based on a sample made of pairs (observed,generated) where the observed part is repeated m times, indeed, but not with the intent of approximating a marginal likelihood estimator… The notion of using the actual data instead of the true expectation (i.e. as a unbiased estimator) at the true parameter value is appealing as it avoids specifying the exact (or analytical) value of this expectation (as in our approach), but I am missing the justification for the extension to any parameter value. Unless one uses an ancillary statistic, which does not sound pertinent… The differential entropy is estimated by a Kozachenko-Leonenko estimator implying k-nearest neighbours.

“The proposed empirical likelihood estimates weights by matching the moments of g(X¹), , g(X) with that of
g(X), without requiring a direct relationship with the parameter. (…) the constraints used in the construction of the empirical likelihood are based on the identity in (7), which can only be satisfied when θ = θ⁰. “

Although I am feeling like missing one argument, the later part of the paper seems to comfort my impression, as quoted above. Meaning that the approximation will fare well only in the vicinity of the true parameter. Which makes it untrustworthy for model choice purposes, I believe. (The paper uses the g-and-k benchmark without exploiting Pierre Jacob’s package that allows for exact MCMC implementation.)

asymptotics of synthetic likelihood

Posted in pictures, Statistics, Travel with tags , , , , , , , , , , on March 11, 2019 by xi'an

David Nott, Chris Drovandi and Robert Kohn just arXived a paper on a comparison between ABC and synthetic likelihood, which is both interesting and timely given that synthetic likelihood seems to be lacking behind in terms of theoretical evaluation. I am however as puzzled by the results therein as I was by the earlier paper by Price et al. on the same topic. Maybe due to the Cambodia jetlag, which is where and when I read the paper.

My puzzlement, thus, comes from the difficulty in comparing both approaches on a strictly common ground. The paper first establishes convergence and asymptotic normality for synthetic likelihood, based on the 2003 MCMC paper of Chernozukov and Hong [which I never studied in details but that appears like the MCMC reference in the econometrics literature]. The results are similar to recent ABC convergence results, unsurprisingly when assuming a CLT on the summary statistic vector. One additional dimension of the paper is to consider convergence for a misspecified covariance matrix in the synthetic likelihood [and it will come back with a revenge]. And asymptotic normality of the synthetic score function. Which is obviously unavailable in intractable models.

The first point I have difficulty with is how the computing time required for approximating mean and variance in the synthetic likelihood, by Monte Carlo means, is not accounted for in the comparison between ABC and synthetic likelihood versions. Remember that ABC only requires one (or at most two) pseudo-samples per parameter simulation. The latter requires M, which is later constrained to increase to infinity with the sample size. Simulations that are usually the costliest in the algorithms. If ABC were to use M simulated samples as well, since it already relies on a kernel, it could as well construct [at least on principle] a similar estimator of the [summary statistic] density. Or else produce M times more pairs (parameter x pseudo-sample). The authors pointed out (once this post out) that they do account for the factor M when computing the effective sample size (before Lemma 4, page 12), but I still miss why the ESS converging to N=MN/M when M goes to infinity is such a positive feature.

Another point deals with the use of multiple approximate posteriors in the comparison. Since the approximations differ, it is unclear that convergence to a given approximation is all that should matter, if the approximation is less efficient [when compared with the original and out-of-reach posterior distribution]. Especially for a finite sample size n. This chasm in the targets becomes more evident when the authors discuss the use of a constrained synthetic likelihood covariance matrix towards requiring less pseudo-samples, i.e. lower values of M, because of a smaller number of parameters to estimate. This should be balanced against the loss in concentration of the synthetic approximation, as exemplified by the realistic examples in the paper. (It is also hard to see why M could be not of order √n for Monte Carlo reasons.)

The last section in the paper is revolving around diverse issues for misspecified models, from wrong covariance matrix to wrong generating model. As we just submitted a paper on ABC for misspecified models, I will not engage into a debate on this point but find the proposed strategy that goes through an approximation of the log-likelihood surface by a Gaussian process and a derivation of the covariance matrix of the score function apparently greedy in both calibration and computing. And not so clearly validated when the generating model is misspecified.

Bayesian gan [gan style]

Posted in Books, pictures, Statistics, University life with tags , , , , , , , , , , , , , on June 26, 2018 by xi'an

In their paper Bayesian GANS, arXived a year ago, Saatchi and Wilson consider a Bayesian version of generative adversarial networks, putting priors on both the model and the discriminator parameters. While the prospect seems somewhat remote from genuine statistical inference, if the following statement is representative

“GANs transform white noise through a deep neural network to generate candidate samples from a data distribution. A discriminator learns, in a supervised manner, how to tune its parameters so as to correctly classify whether a given sample has come from the generator or the true data distribution. Meanwhile, the generator updates its parameters so as to fool the discriminator. As long as the generator has sufficient capacity, it can approximate the cdf inverse-cdf composition required to sample from a data distribution of interest.”

I figure the concept can also apply to a standard statistical model, where x=G(z,θ) rephrases the distributional assumption x~F(x;θ) via a white noise z. This makes resorting to a prior distribution on θ more relevant in the sense of using potential prior information on θ (although the successes of probabilistic numerics show formal priors can be used on purely numerical ground).

The “posterior distribution” that is central to the notion of Bayesian GANs is however unorthodox in that the distribution is associated with the following conditional posteriors

where D(x,θ) is the “discriminator”, that is, in GAN lingo, the probability to be allocated to the “true” data generating mechanism rather than to the one associated with G(·,θ). The generative conditional posterior (1) then aims at fooling the discriminator, i.e. favours generative parameter values that raise the probability of wrong allocation of the pseudo-data. The discriminative conditional posterior (2) is a standard Bayesian posterior based on the original sample and the generated sample. The authors then iteratively sample from these posteriors, effectively implementing a two-stage Gibbs sampler.

“By iteratively sampling from (1) and (2) at every step of an epoch one can, in the limit, obtain samples from the approximate posteriors over [both sets of parameters].”

What worries me about this approach is that  just cannot work, in the sense that (1) and (2) cannot be compatible conditional (posterior) distributions. There is no joint distribution for which (1) and (2) would be the conditionals, since the pseudo-data appears in D for (1) and (1-D) in (2). This means that the convergence of a Gibbs sampler is at best to a stationary σ-finite measure. And hence that the meaning of the chain is delicate to ascertain… Am I missing any fundamental point?! [I checked the reviews on NIPS webpage and could not spot this issue being raised.]

ABCDE for approximate Bayesian conditional density estimation

Posted in Books, pictures, Statistics, Travel, University life with tags , , , , , , , , , , , , , on February 26, 2018 by xi'an

Another arXived paper I surprisingly (?) missed, by George Papamakarios and Iain Murray, on an ABCDE (my acronym!) substitute to ABC for generative models. The paper was reviewed [with reviews made available!] and accepted by NIPS 2016. (Most obviously, I was not one of the reviewers!)

“Conventional ABC algorithms such as the above suffer from three drawbacks. First, they only represent the parameter posterior as a set of (possibly weighted or correlated) samples [for which] it is not obvious how to perform some other computations using samples, such as combining posteriors from two separate analyses. Second, the parameter samples do not come from the correct Bayesian posterior (…) Third, as the ε-tolerance is reduced, it can become impractical to simulate the model enough times to match the observed data even once [when] simulations are expensive to perform”

The above criticisms are a wee bit overly harsh as, well…, Monte Carlo approximations remain a solution worth considering for all Bayesian purposes!, while the approximation [replacing the data with a ball] in ABC is replaced with an approximation of the true posterior as a mixture. Both requiring repeated [and likely expensive] simulations. The alternative is in iteratively simulating from pseudo-predictives towards learning better pseudo-posteriors, then used as new proposals at the next iteration modulo an importance sampling correction.  The approximation to the posterior chosen therein is a mixture density network, namely a mixture distribution with parameters obtained as neural networks based on the simulated pseudo-observations. Which the authors claim [p.4] requires no tuning. (Still, there are several aspects to tune, from the number of components to the hyper-parameter λ [p.11, eqn (35)], to the structure of the neural network [20 tanh? 50 tanh?], to the number of iterations, to the amount of X checking. As usual in NIPS papers, it is difficult to assess how arbitrary the choices made in the experiments are. Unless one starts experimenting with the codes provided.) All in all, I find the paper nonetheless exciting enough (!) to now start a summer student project on it in Dauphine and hope to check the performances of ABCDE on different models, as well as comparing this ABC implementation with a synthetic likelihood version.

 As an addendum, let me point out the very pertinent analysis of this paper by Dennis Prangle, 18 months ago!

1500 nuances of gan [gan gan style]

Posted in Books, Statistics, University life with tags , , , , , , , , , , , on February 16, 2018 by xi'an

I recently realised that there is a currently very popular trend in machine learning called GAN [for generative adversarial networks] that strongly connects with ABC, at least in that it relies mostly on the availability of a generative model, i.e., a probability model that can be generated as in x=G(ϵ;θ), to draw inference about θ [or predictions]. For instance, there was a GANs tutorial at NIPS 2016 by Ian Goodfellow and many talks on the topic at recent NIPS, the 1500 in the title referring to the citations of the GAN paper by Goodfellow et al. (2014). (The name adversarial comes from opposing true model to generative model in the inference. )

If you remember Jeffreys‘s famous pique about classical tests as being based on improbable events that did not happen, GAN, like ABC,  is sort of the opposite in that it generates events until the one that was observed happens. More precisely, by generating pseudo-samples and switching parameters θ until these samples get as confused as possible between the data generating (“true”) distribution and the generative one. (In its original incarnation, GAN is indeed an optimisation scheme in θ.) A basic presentation of GAN is that it constructs a function D(x,ϕ) that represents the probability that x came from the true model p versus the generative model, ϕ being the parameter of a neural network trained to this effect, aimed at minimising in ϕ a two-term objective function

E[log D(x,ϕ)]+E[log(1D(G(ϵ;θ),ϕ))]

where the first expectation is taken under the true model and the second one under the generative model.

“The discriminator tries to best distinguish samples away from the generator. The generator tries to produce samples that are indistinguishable by the discriminator.” Edward

One ABC perception of this technique is that the confusion rate


is a form of distance between the data and the generative model. Which expectation can be approximated by repeated simulations from this generative model. Which suggests an extension from the optimisation approach to a ABCyesian version by selecting the smallest distances across a range of θ‘s simulated from the prior.

This notion relates to solution using classification tools as density ratio estimation, connecting for instance to Gutmann and Hyvärinen (2012). And ultimately with Geyer’s 1992 normalising constant estimator.

Another link between ABC and networks also came out during that trip. Proposed by Bishop (1994), mixture density networks (MDN) are mixture representations of the posterior [with component parameters functions of the data] trained on the prior predictive through a neural network. These MDNs can be trained on the ABC learning table [based on a specific if redundant choice of summary statistics] and used as substitutes to the posterior distribution, which brings an interesting alternative to Simon Wood’s synthetic likelihood. In a paper I missed Papamakarios and Murray suggest replacing regular ABC with this version…

%d bloggers like this: