Archive for nonparametric probability density estimation

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!

deep learning ABC summary statistics

Posted in Books, Statistics, University life with tags , , , , , , , , on October 19, 2015 by xi'an

“The main task of this article is to construct low-dimensional and informative summary statistics for ABC methods.”

The idea in the paper “Learning Summary Statistic for ABC via Deep Neural Network”, arXived a few days ago, is to start from the raw data and build a “deep neural network” (meaning a multiple layer neural network) to provide a non-linear regression of the parameters over the data. (There is a rather militant tone to the justification of the approach, not that unusual with proponents of deep learning approaches, I must add…) Whose calibration never seems an issue. The neural construct is called to produce an estimator (function) of θ, θ(x). Which is then used as the summary statistics. Meaning, if Theorem 1 is to be taken as the proposal, that a different ABC needs to be run for every function of interest. Or, in other words, that the method is not reparameterisation invariant.

The paper claims to achieve the same optimality properties as in Fearnhead and Prangle (2012). These are however moderate optimalities in that they are obtained for the tolerance ε equal to zero. And using the exact posterior expectation as a summary statistic, instead of a non-parametric estimate.  And an infinite functional basis in Theorem 2. I thus see little added value in results like Theorem 2 and no real optimality: That the ABC distribution can be arbitrarily close to the exact posterior is not an helpful statement when implementing the method.

The first example in the paper is the posterior distribution associated with the Ising model, which enjoys a sufficient statistic of dimension one. The issue of generating pseudo-data from the Ising model is evacuated by a call to a Gibbs sampler, but remains an intrinsic problem as the convergence of the Gibbs sampler depends on the value of the parameter θ and especially its location wrt the critical point. Both ABC posteriors are shown to be quite close.

The second example is the posterior distribution associated with an MA(2) model, apparently getting into a benchmark in the ABC literature. The comparison between an ABC based on the first two autocorrelations, an ABC based on the semi-automatic solution of Fearnhead and Prangle (2012) [for which collection of summaries?], and the neural network proposal, leads to the dismissal of the semi-automatic solution and the neural net being closest to the exact posterior [with the same tolerance quantile ε for all approaches].

A discussion crucially missing from the paper—from my perspective—is an accounting for size: First, what is the computing cost of fitting and calibrating and storing a neural network for the sole purpose of constructing a summary statistic? Once the neural net is constructed, I would assume most users would see little need in pursuing the experiment any further. (This was also why we stopped at our random forest output rather than using it as a summary statistic.) Second, how do cost and performances evolve as the dimension of the parameter θ grows? I would deem necessary to understand when the method fails. As for instance in latent variable models such as HMMs. Third, how does the size of the sample impact cost and performances? In many realistic cases when ABC applies, it is not possible to use the raw data, given its size, and summary statistics are a given. For such examples, neural networks should be compared with other ABC solutions, using the same reference table.

Bayesian optimization for likelihood-free inference of simulator-based statistical models [guest post]

Posted in Books, Statistics, University life with tags , , , , , , , on February 17, 2015 by xi'an

[The following comments are from Dennis Prangle, about the second half of the paper by Gutmann and Corander I commented last week.]

Here are some comments on the paper of Gutmann and Corander. My brief skim read through this concentrated on the second half of the paper, the applied methodology. So my comments should be quite complementary to Christian’s on the theoretical part!

ABC algorithms generally follow the template of proposing parameter values, simulating datasets and accepting/rejecting/weighting the results based on similarity to the observations. The output is a Monte Carlo sample from a target distribution, an approximation to the posterior. The most naive proposal distribution for the parameters is simply the prior, but this is inefficient if the prior is highly diffuse compared to the posterior. MCMC and SMC methods can be used to provide better proposal distributions. Nevertheless they often still seem quite inefficient, requiring repeated simulations in parts of parameter space which have already been well explored.

The strategy of this paper is to instead attempt to fit a non-parametric model to the target distribution (or in fact to a slight variation of it). Hopefully this will require many fewer simulations. This approach is quite similar to Richard Wilkinson’s recent paper. Richard fitted a Gaussian process to the ABC analogue of the log-likelihood. Gutmann and Corander introduce two main novelties:

  1. They model the expected discrepancy (i.e. distance) Δθ between the simulated and observed summary statistics. This is then transformed to estimate the likelihood. This is in contrast to Richard who transformed the discrepancy before modelling. This is the standard ABC approach of weighting the discrepancy depending on how close to 0 it is. The drawback of the latter approach is it requires picking a tuning parameter (the ABC acceptance threshold or bandwidth) in advance of the algorithm. The new approach still requires a tuning parameter but its choice can be delayed until the transformation is performed.
  2. They generate the θ values on-line using “Bayesian optimisation”. The idea is to pick θ to concentrate on the region near the minimum of the objective function, and also to reduce uncertainty in the Gaussian process. Thus well explored regions can usually be neglected. This is in contrast to Richard who chose θs using space filling design prior to performing any simulations.

I didn’t read the paper’s theory closely enough to decide whether (1) is a good idea. Certainly the results for the paper’s examples look convincing. Also, one issue with Richard‘s approach was that because the log-likelihood varied over such a wide variety of magnitudes, he needed to fit several “waves” of GPs. It would be nice to know if the approach of modelling the discrepancy has removed this problem, or if a single GP is still sometimes an insufficiently flexible model.

Novelty (2) is a very nice and natural approach to take here. I did wonder why the particular criterion in Equation (45) was used to decide on the next θ. Does this correspond to optimising some information theoretic quantity? Other practical questions were whether it’s possible to parallelise the method (I seem to remember talking to Michael Gutmann about this at NIPS but can’t remember his answer!), and how well the approach scales up with the dimension of the parameters.

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.

why do we maximise the weights in empirical likelihood?

Posted in Books, Statistics, University life with tags , , , , on October 29, 2013 by xi'an

Mark Johnson sent me the following question a few days ago:

I have one question about EL: how important is it to maximise the probabilities pi on the data items in the formula (stolen from the Wikipedia page on EL)?

\max_{\pi,\theta} \sum_{i=1}^n \ln\pi_i

You’re already replacing the max over θ with a distribution over θ.  What about the πi

It would seem to be “more Bayesian” to put a prior on the data item probabilities pi_i, and it would also seem to “do the right thing” in situations where there are several different pi that have the same empirical likelihood.

This is a fairly reasonable question, which first reminds me of an issue we had examined with Costas Goutis, on his very last trip to Paris in 1996, a few months before he died in a diving accident near Seattle. We were wondering if treating the bandwidth in a non-parametric density estimator as a regular parameter was making sense. After experimenting for a few days with different priors we found that it was not such a great idea and that, instead, the prior on the bandwidth needed to depend on the sample size. This led to Costas’ posthumous paper, Nonparametric Estimation of a Mixing Density via the Kernel Method, in JASA in 1997 (with the kind help of Jianqing Fan).

Now, more to the point (of empirical likelihood), I am afraid that putting (almost) any kind of prior on the weights πi would be hopeless. For one thing, the πi are of the same size as the sample (modulo the identifying equation constraints) so estimating them based on a prior that does not depend on the sample size does not produce consistent estimators of the weights. (Search Bayesian nonparametric likelihood estimation for more advanced reasons.) Intuitively, it seems to me that the (true) parameter θ of the (unknown or unavailable) distribution of the data does not make sense in the non-parametric setting or, conversely, that the weights πi have no meaning for the inference on θ. It thus sounds difficult to treat them together and on an equal footing. The approximation

\max_{\pi} \sum_{i=1}^n \ln\pi_i

is a function of θ that replaces the unknown or unavailable likelihood, in which the weights have no statistical meaning. But this is a wee of a weak argument as other solutions than the maximisation of the entropy could be used to determine the weights.

In the end, this remains a puzzling issue (and hence a great question), hitting at the difficulty of replacing the true model with an approximation on the one hand and aiming at estimating the true parameter(s) on the other hand.