Archive for diabetes

a first 5k [since last one]

Posted in pictures, Running with tags , , , , , , , , on June 15, 2022 by xi'an

machine-learning harmonic mean

Posted in Books, Statistics with tags , , , , , , on February 25, 2022 by xi'an

In a recent arXival, Jason McEwen propose a resurrection of the “infamous” harmonic mean estimator. In Machine learning assisted Bayesian model comparison: learnt harmonic mean estimator, they propose to aim at the “optimal importance function”. The paper provides a fair coverage of the literature on that topic, incl. our 2009 paper with Darren Wraith (although I do not follow the criticism of using a uniform over an HPD region, esp. since one of the learnt targets is also a uniform over an hypersphere, presumably optimised in terms of the chosen parameterisation).

“…the learnt harmonic mean estimator, a variant of the original estimator that solves its large variance problem. This is achieved by interpreting the harmonic mean estimator as importance sampling and introducing a new target distribution (…) learned to approximate the optimal but inaccessible target, while minimising the variance of the resulting estimator. Since the estimator requires samples of the posterior only it is agnostic to the strategy used to generate posterior samples.”

The method thus builds upon Gelfand and Dey (1994) general proposal that is a form of inverse importance sampling since the numerator [the new target] is free while the denominator is the unnormalised posterior. The optimal target being the complete posterior (since it lead to a null variance), the authors propose to try to approximate this posterior by various means. (Note however that an almost Dirac mass at a value with positive posterior would work as well!, at least in principle…) as the sections on moment approximations sound rather standard (and assume the estimated variances are finite) while the reason for the inclusion of the Bayes factor approximation is rather unclear. However, I am rather skeptical at the proposals made therein towards approximating the posterior distribution, from a Gaussian mixture [for which parameterisation?] to KDEs, or worse ML tools like neural nets [not explored there, which makes one wonder about the title], as the estimands will prove very costly, and suffer from the curse of dimensionality (3 hours for d=2¹⁰…).The Pima Indian women’s diabetes dataset and its quasi-Normal posterior are used as a benchmark, meaning that James and Nicolas did not shout loud enough! And I find surprising that most examples include the original harmonic mean estimator despite its complete lack of trustworthiness.

Leave the Pima Indians alone!

Posted in Books, R, Statistics, University life with tags , , , , , , , , , , , , , , , , on July 15, 2015 by xi'an

“…our findings shall lead to us be critical of certain current practices. Specifically, most papers seem content with comparing some new algorithm with Gibbs sampling, on a few small datasets, such as the well-known Pima Indians diabetes dataset (8 covariates). But we shall see that, for such datasets, approaches that are even more basic than Gibbs sampling are actually hard to beat. In other words, datasets considered in the literature may be too toy-like to be used as a relevant benchmark. On the other hand, if ones considers larger datasets (with say 100 covariates), then not so many approaches seem to remain competitive” (p.1)

Nicolas Chopin and James Ridgway (CREST, Paris) completed and arXived a paper they had “threatened” to publish for a while now, namely why using the Pima Indian R logistic or probit regression benchmark for checking a computational algorithm is not such a great idea! Given that I am definitely guilty of such a sin (in papers not reported in the survey), I was quite eager to read the reasons why! Beyond the debate on the worth of such a benchmark, the paper considers a wider perspective as to how Bayesian computation algorithms should be compared, including the murky waters of CPU time versus designer or programmer time. Which plays against most MCMC sampler.

As a first entry, Nicolas and James point out that the MAP can be derived by standard a Newton-Raphson algorithm when the prior is Gaussian, and even when the prior is Cauchy as it seems most datasets allow for Newton-Raphson convergence. As well as the Hessian. We actually took advantage of this property in our comparison of evidence approximations published in the Festschrift for Jim Berger. Where we also noticed the awesome performances of an importance sampler based on the Gaussian or Laplace approximation. The authors call this proposal their gold standard. Because they also find it hard to beat. They also pursue this approximation to its logical (?) end by proposing an evidence approximation based on the above and Chib’s formula. Two close approximations are provided by INLA for posterior marginals and by a Laplace-EM for a Cauchy prior. Unsurprisingly, the expectation-propagation (EP) approach is also implemented. What EP lacks in theoretical backup, it seems to recover in sheer precision (in the examples analysed in the paper). And unsurprisingly as well the paper includes a randomised quasi-Monte Carlo version of the Gaussian importance sampler. (The authors report that “the improvement brought by RQMC varies strongly across datasets” without elaborating for the reasons behind this variability. They also do not report the CPU time of the IS-QMC, maybe identical to the one for the regular importance sampling.) Maybe more surprising is the absence of a nested sampling version.

pimcisIn the Markov chain Monte Carlo solutions, Nicolas and James compare Gibbs, Metropolis-Hastings, Hamiltonian Monte Carlo, and NUTS. Plus a tempering SMC, All of which are outperformed by importance sampling for small enough datasets. But get back to competing grounds for large enough ones, since importance sampling then fails.

“…let’s all refrain from now on from using datasets and models that are too simple to serve as a reasonable benchmark.” (p.25)

This is a very nice survey on the theme of binary data (more than on the comparison of algorithms in that the authors do not really take into account design and complexity, but resort to MSEs versus CPus). I however do not agree with their overall message to leave the Pima Indians alone. Or at least not for the reason provided therein, namely that faster and more accurate approximations methods are available and cannot be beaten. Benchmarks always have the limitation of “what you get is what you see”, i.e., the output associated with a single dataset that only has that many idiosyncrasies. Plus, the closeness to a perfect normal posterior makes the logistic posterior too regular to pause a real challenge (even though MCMC algorithms are as usual slower than iid sampling). But having faster and more precise resolutions should on the opposite be  cause for cheers, as this provides a reference value, a golden standard, to check against. In a sense, for every Monte Carlo method, there is a much better answer, namely the exact value of the integral or of the optimum! And one is hardly aiming at a more precise inference for the benchmark itself: those Pima Indians [whose actual name is Akimel O’odham] with diabetes involved in the original study are definitely beyond help from statisticians and the model is unlikely to carry out to current populations. When the goal is to compare methods, as in our 2009 paper for Jim Berger’s 60th birthday, what matters is relative speed and relative ease of implementation (besides the obvious convergence to the proper target). In that sense bigger and larger is not always relevant. Unless one tackles really big or really large datasets, for which there is neither benchmark method nor reference value.

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