Archive for knn estimator

finding our way in the dark

Posted in Books, pictures, Statistics with tags , , , , , , , , , on November 18, 2021 by xi'an

The paper Finding our Way in the Dark: Approximate MCMC for Approximate Bayesian Methods by Evgeny Levi and (my friend) Radu Craiu, recently got published in Bayesian Analysis. The central motivation for their work is that both ABC and synthetic likelihood are costly methods when the data is large and does not allow for smaller summaries. That is, when summaries S of smaller dimension cannot be directly simulated. The idea is to try to estimate


since this is the substitute for the likelihood used for ABC. (A related idea is to build an approximate and conditional [on θ] distribution on the distance, idea with which Doc. Stoehr and I played a wee bit without getting anything definitely interesting!) This is a one-dimensional object, hence non-parametric estimates could be considered… For instance using k-nearest neighbour methods (which were already linked with ABC by Gérard Biau and co-authors.) A random forest could also be used (?). Or neural nets. The method still requires a full simulation of new datasets, so I wonder at the gain unless the replacement of the naïve indicator with h(θ) brings clear improvement to the approximation. Hence much fewer simulations. The ESS reduction is definitely improved, esp. since the CPU cost is higher. Could this be associated with the recourse to independent proposals?

In a sence, Bayesian synthetic likelihood does not convey the same appeal, since is a bit more of a tough cookie: approximating the mean and variance is multidimensional. (BSL is always more expensive!)

As a side remark, the authors use two chains in parallel to simplify convergence proofs, as we did a while ago with AMIS!

evaluating stochastic algorithms

Posted in Books, R, Statistics, University life with tags , , , , , , , , on February 20, 2014 by xi'an

Reinaldo sent me this email a long while ago

Could you recommend me a nice reference about 
measures to evaluate stochastic algorithms (in 
particular focus in approximating posterior 

and I hope he is still reading the ‘Og, despite my lack of prompt reply! I procrastinated and procrastinated in answering this question as I did not have a ready reply… We have indeed seen (almost suffered from!) a flow of MCMC convergence diagnostics in the 90’s.  And then it dried out. Maybe because of the impossibility to be “really” sure, unless running one’s MCMC much longer than “necessary to reach” stationarity and convergence. The heat of the dispute between the “single chain school” of Geyer (1992, Statistical Science) and the “multiple chain school” of Gelman and Rubin (1992, Statistical Science) has since long evaporated. My feeling is that people (still) run their MCMC samplers several times and check for coherence between the outcomes. Possibly using different kernels on parallel threads. At best, but rarely, they run (one or another form of) tempering to identify the modal zones of the target. And instances where non-trivial control variates are available are fairly rare. Hence, a non-sequitur reply at the MCMC level. As there is no automated tool available, in my opinion. (Even though I did not check the latest versions of BUGS.)

As it happened, Didier Chauveau from Orléans gave today a talk at Big’MC on convergence assessment based on entropy estimation, a joint work with Pierre Vandekerkhove. He mentioned SamplerCompare which is an R package that appeared in 2010. Soon to come is their own EntropyMCMC package, using parallel simulation. And k-nearest neighbour estimation.

If I re-interpret the question as focussed on ABC algorithms, it gets both more delicate and easier. Easy because each ABC distribution is different. So there is no reason to look at the unreachable original target. Delicate because there are several parameters to calibrate (tolerance, choice of summary, …) on top of the number of MCMC simulations. In DIYABC, the outcome is always made of the superposition of several runs to check for stability (or lack thereof). But this tells us nothing about the distance to the true original target. The obvious but impractical answer is to use some basic bootstrapping, as it is generally much too costly.

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