Archive for thinning

scalable Langevin exact algorithm [armchair Read Paper]

Posted in Books, pictures, Statistics, Travel, University life with tags , , , , , , , , , , , on June 26, 2020 by xi'an

So, Murray Pollock, Paul Fearnhead, Adam M. Johansen and Gareth O. Roberts presented their Read Paper with discussions on the Wednesday aft! With a well-sized if virtual audience of nearly a hundred people. Here are a few notes scribbled during the Readings. And attempts at keeping the traditional structure of the meeting alive.

In their introduction, they gave the intuition of a quasi-stationary chain as the probability to be in A at time t while still alice as π(A) x exp(-λt) for a fixed killing rate λ. The concept is quite fascinating if less straightforward than stationarity! The presentation put the stress on the available recourse to an unbiased estimator of the κ rate whose initialisation scaled as O(n) but allowed a subsampling cost reduction afterwards. With a subsampling rat connected with Bayesian asymptotics, namely on how quickly the posterior concentrates. Unfortunately, this makes the practical construction harder, since n is finite and the concentration rate is unknown (although a default guess should be √n). I wondered if the link with self-avoiding random walks was more than historical.

The initialisation of the method remains a challenge in complex environments. And hence one may wonder if and how better it does when compared with SMC. Furthermore, while the motivation for using a Brownian motion stems from the practical side, this simulation does not account for the target π. This completely blind excursion sounds worse than simulating from the prior in other settings.

One early illustration for quasi stationarity was based on an hypothetical distribution of lions and wandering (Brownian) antelopes. I found that the associated concept of soft killing was not necessarily well received by …. the antelopes!

As it happens, my friend and coauthor Natesh Pillai was the first discussant! I did no not get the details of his first bimodal example. But he addressed my earlier question about how large the running time T should be. Since the computational cost should be exploding with T. He also drew a analogy with improper posteriors as to wonder about the availability of convergence assessment.

And my friend and coauthor Nicolas Chopin was the second discussant! Starting with a request to… leave the Pima Indians (model)  alone!! But also getting into a deeper assessment of the alternative use of SMCs.

scalable Langevin exact algorithm [Read Paper]

Posted in Books, pictures, Statistics, University life with tags , , , , , , , , , , , , , , , , on June 23, 2020 by xi'an


Murray Pollock, Paul Fearnhead, Adam M. Johansen and Gareth O. Roberts (CoI: all with whom I have strong professional and personal connections!) have a Read Paper discussion happening tomorrow [under relaxed lockdown conditions in the UK, except for the absurd quatorzine on all travelers|, but still in a virtual format] that we discussed together [from our respective homes] at Paris Dauphine. And which I already discussed on this blog when it first came out.

Here are quotes I spotted during this virtual Dauphine discussion but we did not come up with enough material to build a significant discussion, although wondering at the potential for solving the O(n) bottleneck, handling doubly intractable cases like the Ising model. And noticing the nice features of the log target being estimable by unbiased estimators. And of using control variates, for once well-justified in a non-trivial environment.

“However, in practice this simple idea is unlikely to work. We can see this most clearly with the rejection sampler, as the probability of survival will decrease exponentially with t—and thus the rejection probability will often be prohibitively large.”

“This can be viewed as a rejection sampler to simulate from μ(x,t), the distribution of the Brownian motion at time  t conditional on its surviving to time t. Any realization that has been killed is ‘rejected’ and a realization that is not killed is a draw from μ(x,t). It is easy to construct an importance sampling version of this rejection sampler.”

is there such a thing as optimal subsampling?

Posted in Books, Statistics, University life with tags , , , , , , , , , , , , , on June 12, 2020 by xi'an

This idea of optimal thinnin and burnin has been around since the early days of the MCMC revolution and did not come up with a definite answer. For instance, from a pure estimation perspective, subsampling always increases the variance of the resulting estimator. My personal approach is to ignore both burnin and thinnin and rather waste time on running several copies of the code to check for potential discrepancies and get a crude notion of the variability. And to refuse to answer to questions like is 5000 iterations long enough for burnin?

A recent arXival by Riabiz et al. readdresses the issue. In particular concerning this notion that the variance of the subsampled version is higher: this only applies to a deterministic subsampling, as opposed to an MCMC-based subsampling (although this intricacy only makes the problem harder!). I however fail to understand the argument in favour of subsampling based on storage issues (p.4), as a dynamic storage of the running mean for all quantities of interest does not cost anything if the integrand is not particularly demanding. I also disagree at the pessimistic view that the asymptotic variance of the MCMC estimate is hard to estimate: papers by Flegal, Hobert, Jones, Vat and others have rather clearly shown how batch means can produce converging estimates of this asymptotic variance.

“We do not to attempt to solve a continuous optimisation problem for selection of the next point [in the sample]. Such optimisation problems are fundamentally difficult and can at best be approximately solved. Instead, we exactly solve the discrete optimisation problem of selecting a suitable element from a supplied MCMC output.”

One definitely positive aspect of the paper is that the (thinning) method is called Stein thinning, in connection with Stein’s discrepancy, and this honours Charles Stein. The method looks at the optimal subsample, with optimality defined in terms of minimising Stein’s discrepancy from the true target over a reproducible kernel Hilbert space. And then over a subsample to minimise the distance from the empirical distribution to the theoretical distribution. The kernel (11) is based on the gradient of the target log density and the solution is determined by greedy algorithms that determine which next entry to add to the empirical distribution. Which is of complexity O(nm2) if the subsample is of size m. Some entries may appear more than once and the burnin step could be automatically included as (relatively) unlikely values are never selected (at least this was my heuristic understanding). While the theoretical backup for the construct is present and backed by earlier papers of some of the authors, I do wonder at the use of the most rudimentary representation of an approximation to the target when smoother versions could have been chosen and optimised on the same ground. And I am also surprised at the dependence of both estimators and discrepancies on the choice of the (sort-of) covariance matrix in the inner kernel, as the ODE examples provided in the paper (see, e.g., Figure 7). (As an aside and at a shallow level, the approach also reminded me of the principal points of my late friend Bernhard Flury…) Storage of all MCMC simulations for a later post-processing is of course costly in terms of storage, at O(nm). Unless a “secretary problem” approach can be proposed to get sequential. Another possible alternate would be to consider directly the chain of the accepted values (à la vanilla Rao-Blackwellisation). Overall, since the stopping criterion is based on a fixed sample size, and hence depends on the sub-efficiency of evaluating the mass of different modes, I am unsure the method is anything but what-you-get-is-what-you-see, i.e. prone to get misled by a poor exploration of the complete support of the target.

“This paper focuses on nonuniform subsampling and shows that it is more efficiency than uniform subsampling.”

Two weeks later, Guanyu Hu and Hai Ying Wang arXived their Most Likely Optimal Subsampled Markov Chain Monte Carlo, in what I first thought as an answer to the above! But both actually have little in common as this second paper considers subsampling on the data, rather than the MCMC output, towards producing scalable algorithms. Building upon Bardenet et al. (2014) and Korattikara et al. (2014).  Replacing thus the log-likelihood with a random sub-sampled version and deriving the sample size based on a large deviation inequality. By a Cauchy-Schwartz inequality, the authors find sampling probabilities proportional to the individual log-likelihooods. Which depend on the running value of the MCMC’ed parameters. And thus replaced with the values at a fixed parameter, with cost O(n) but only once, but no so much optimal. (The large deviation inequality therein is only concerned with an approximation to the log-likelihood, without examining the long term impact on the convergence of the approximate Markov chain as this is no longer pseudo-marginal MCMC. For instance, both current and prospective log-likelihoods are re-estimated at each iteration. The paper compares with uniform sampling on toy examples,  to demonstrate a smaller estimation error for the statistical problem, rather than convergence to the true posterior.)

simulating hazard

Posted in Books, Kids, pictures, Statistics, Travel with tags , , , , , , , , , , , , on May 26, 2020 by xi'an

A rather straightforward X validated question that however leads to an interesting simulation question: when given the hazard function h(·), rather than the probability density f(·), how does one simulate this distribution? Mathematically h(·) identifies the probability distribution as much as f(·),

1-F(x)=\exp\left\{ \int_{-\infty}^x h(t)\,\text{d}t \right\}=\exp\{H(x)\}

which means cdf inversion could be implemented in principle. But in practice, assuming the integral is intractable, what would an exact solution look like? Including MCMC versions exploiting one fixed point representation or the other.. Since

f(x)=h(x)\,\exp\left\{ \int_{-\infty}^x h(t)\,\text{d}t \right\}

using an unbiased estimator of the exponential term in a pseudo-marginal algorithm would work. And getting an unbiased estimator of the exponential term can be done by Glynn & Rhee debiasing. But this is rather costly… Having Devroye’s book under my nose [at my home desk] should however have driven me earlier to the obvious solution to… simply open it!!! A whole section (VI.2) is indeed dedicated to simulations when the distribution is given by the hazard rate. (Which made me realise this problem is related with PDMPs in that thinning and composition tricks are common to both.) Besides the inversion method, ie X=H⁻¹(U), Devroye suggests thinning a Poisson process when h(·) is bounded by a manageable g(·). Or a generic dynamic thinning approach that converges when h(·) is non-increasing.

generalised Poisson difference autoregressive processes

Posted in pictures, Statistics, Travel, University life with tags , , , , , , , , on February 14, 2020 by xi'an

Yesterday, Giulia Carallo arXived the paper on generalised Poisson difference autoregressive processes that is a component of her Ph.D. thesis at Ca’ Foscari Universita di Venezia and to which I contributed while visiting Venezia last Spring. The stochastic process under study is integer valued as a difference of two generalised Poisson variates, made dependent by an INGARCH process that expresses the mean as a regression over past values of the process and past means. Which can be easily simulated as a difference of (correlated) Poisson variates. These two variates can in their turn be (re)defined through a thinning operator that I find most compelling, namely as a sum of Poisson variates with a number of terms being a (quasi-) Binomial variate depending on the previous value. This representation proves useful in establishing stationarity conditions on the process. Beyond establishing various properties of the process, the paper also examines how to conduct Bayesian inference in this context, with specialised Gibbs samplers in action. And comparing models on real datasets via Geyer‘s (1994) logistic approximation to Bayes factors.