Archive for ODEs

probabilistic numerics [book review]

Posted in Books, pictures, Statistics, Travel with tags , , , , , , , , , , , , , , , , , , , , on July 28, 2023 by xi'an

Probabilistic numerics: Computation as machine learning is a 2022 book by Philipp Henning, Michael Osborne, and Hans Kersting that was sent to me by CUP (upon my request and almost free of charge, as I had to pay custom charges, thanks to Brexit!). With the important message of bringing statistical tools to numerics. I remember Persi Diaconis calling for (such) actions in the 1980’s (and even reading a paper of his on the topic along with George Casella in Ithaca while waiting for his car to get serviced!).

From a purely aesthetic view point, the book reads well, offers a beautiful cover and sells for a quite reasonable price for an academic book. Plus it is associated with a website containing draft version of the book. Code, links to courses, research, conferences are also available there. Just a side remark that it enjoys very wide margins that may have encouraged an inflation of footnotes (but also exercises). Except when formulas get in the way (as e.g. on p.40).

The figure below is an excerpt from the introduction that sets the scene of probabilistic numerics involving algorithms as agents, gathering data and making decisions, with an obvious analogy with standard Bayesian decision theory. Modelling uncertainty missing from the picture (if not from the book, as explained later by the authors as an argument against attaching the label Bayesian to the field). Also referring to Henri Poincaré for the origination of the prior vs posterior uncertainty about a mathematical quantity. Followed by early works from the Russian school of probability, somewhat ignored until the machine-learning revolution and a 2012 NIPS workshop organised by the authors. (I participated to a follow-up workshop at NIPS 2015.)

In this nicely written section, I have an objection to the authors’ argument that a frequentist, as opposed to a Bayesian, “has the loss function in mind from the outset” (p.9), since the loss function is logically inseparable from the prior and considered from the onset. I also like very much the conclusion to that introduction, namely that the main messages (from the book) are that (verbatim)

  • classical methods are probabilist (p.10)
  • numerical methods are autonomous agents (p.11)
  • numerics should not be random (if not a rejection of the concept of Monte Carlo methods, p.1, but probabilistic numerics being opposed to stochastic numerics, p.67)
  • numerics must report calibrated uncertainty (p.12)
  • imprecise computation is to be embraced (p.12)
  • probabilistic numerics consolidates numerical computation and statistical inference (p.13)
  • probabilistic numerical algorithms are already adding value (p.13)
  • pipelines of computation demand harmonisation

“Is it still reasonable to labour under computational constraints conceived in the 1940s?” (p.113)

“rather than being equally good for any number of dimensions, Monte Carlo is perhaps better thought of as being equally bad” (p.110)

Chapter I is a 40p infodump (!) on mathematical concepts needed for the following parts. Chapter II is about integration, opposing again PN and Monte Carlo (with strange remark that MCMC does not achieve √N convergence rate, p.72). In the sense that the later is frequentist in that it does not use a prior [unless considering a limiting improper version as in Section 12.2, an intriguing concept in this setup as I wonder whether or not improper priors can at all be contemplated] on the object of interest and hence that the stochasticity does not reflect uncertainty but rather the impact of the simulated sample. Advocating Bayesian quadrature (with some weird convergence graphs exhibiting a high variability with the number of iterations that apparently is not discussed) and bringing in the fascinating perspective of model choice in that framework (leading to compute a posterior probability for each model!). Being evidently biased towards Monte Carlo, I find the opposition in Chapter 12 unnecessarily antagonistic, while presenting Monte Carlo methods as a form of minimax solution, the more because quasi-Monte Carlo methods are hardly discussed (or dismissed). As illustrated by the following picture (p.115) and the above quotes. (And I won’t even go into the absurdity of §12.3 trashing pseudo-random generators as “painfully dumb”.)

Chapter III is a sort of dual of Chapter II for linear algebra numerics, primarily solving linear equations by Gaussian solvers, which introduces new concepts like Krylov sequences, although it sounds quite specific (for an outsider like me). Chapters IV and V deal with the more ambitious prospect of optimisation. Reconsidering classics and expanding into Bayesian optimisation, using Gaussian process priors and defining specific loss functions. Bringing in a strong link with machine learning tools and goals. [citation typo on p.277]. Chapter VII addresses the resolution of ODEs by a Bayesian state space model representation and (again!) Gaussian processes. Reaching to mentioning inverse problems and offering a short finale on prospective steps for interested readers.

[Disclaimer about potential self-plagiarism: this post or an edited version will eventually appear in my Books Review section in CHANCE.]

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.)

[Nature on] simulations driving the world’s response to COVID-19

Posted in Books, pictures, Statistics, Travel, University life with tags , , , , , , , , , , , on April 30, 2020 by xi'an

Nature of 02 April 2020 has a special section on simulation methods used to assess and predict the pandemic evolution. Calling for caution as the models used therein, like the standard ODE S(E)IR models, which rely on assumptions on the spread of the data and very rarely on data, especially in the early stages of the pandemic. One epidemiologist is quote stating “We’re building simplified representations of reality” but this is not dire enough, as “simplified” evokes “less precise” rather than “possibly grossly misleading”. (The graph above is unrelated to the Nature cover and appears to me as particularly appalling in mixing different types of data, time-scale, population at risk, discontinuous updates, and essentially returning no information whatsoever.)

“[the model] requires information that can be only loosely estimated at the start of an epidemic, such as the proportion of infected people who die, and the basic reproduction number (…) rough estimates by epidemiologists who tried to piece together the virus’s basic properties from incomplete information in different countries during the pandemic’s early stages. Some parameters, meanwhile, must be entirely assumed.”

The report mentions that the team at Imperial College, which predictions impacted the UK Government decisions, also used an agent-based model, with more variability or stochasticity in individual actions, which require even more assumptions or much more refined, representative, and trustworthy data.

“Unfortunately, during a pandemic it is hard to get data — such as on infection rates — against which to judge a model’s projections.”

Unfortunately, the paper was written in the early days of the rise of cases in the UK, which means predictions were not much opposed to actual numbers of deaths and hospitalisations. The following quote shows how far off they can fall from reality:

“the British response, Ferguson said on 25 March, makes him “reasonably confident” that total deaths in the United Kingdom will be held below 20,000.”

since the total number as of April 29 is above 21,000 24,000 29,750 and showing no sign of quickly slowing down… A quite useful general public article, nonetheless.

likelihood-free Bayesian design [SimStat 2019 discussion]

Posted in Statistics with tags , , , , , , , , , , on September 5, 2019 by xi'an

consistency of ABC

Posted in pictures, Statistics, Travel, University life with tags , , , , , , , , , on August 25, 2015 by xi'an

Along with David Frazier and Gael Martin from Monash University, Melbourne, we have just completed (and arXived) a paper on the (Bayesian) consistency of ABC methods, producing sufficient conditions on the summary statistics to ensure consistency of the ABC posterior. Consistency in the sense of the prior concentrating at the true value of the parameter when the sample size and the inverse tolerance (intolerance?!) go to infinity. The conditions are essentially that the summary statistics concentrates around its mean and that this mean identifies the parameter. They are thus weaker conditions than those found earlier consistency results where the authors considered convergence to the genuine posterior distribution (given the summary), as for instance in Biau et al. (2014) or Li and Fearnhead (2015). We do not require here a specific rate of decrease to zero for the tolerance ε. But still they do not hold all the time, as shown for the MA(2) example and its first two autocorrelation summaries, example we started using in the Marin et al. (2011) survey. We further propose a consistency assessment based on the main consistency theorem, namely that the ABC-based estimates of the marginal posterior densities for the parameters should vary little when adding extra components to the summary statistic, densities estimated from simulated data. And that the mean of the resulting summary statistic is indeed one-to-one. This may sound somewhat similar to the stepwise search algorithm of Joyce and Marjoram (2008), but those authors aim at obtaining a vector of summary statistics that is as informative as possible. We also examine the consistency conditions when using an auxiliary model as in indirect inference. For instance, when using an AR(2) auxiliary model for estimating an MA(2) model. And ODEs.