Archive for PNAS

conditioning on insufficient statistics in Bayesian regression

Posted in Books, Statistics, University life with tags , , , , , , , , , , , , on October 23, 2021 by xi'an

“…the prior distribution, the loss function, and the likelihood or sampling density (…) a healthy skepticism encourages us to question each of them”

A paper by John Lewis, Steven MacEachern, and Yoonkyung Lee has recently appeared in Bayesian Analysis. Starting with the great motivation of a misspecified model requiring the use of a (thus necessarily) insufficient statistic and moving to their central concern of simulating the posterior based on that statistic.

Model misspecification remains understudied from a B perspective and this paper is thus most welcome in addressing the issue. However, when reading through, one of my criticisms is in defining misspecification as equivalent to outliers in the sample. An outlier model is an easy case of misspecification, in the end, since the original model remains meaningful. (Why should there be “good” versus “bad” data) Furthermore, adding a non-parametric component for the unspecified part of the data would sound like a “more Bayesian” alternative. Unrelated, I also idly wondered at whether or not normalising flows could be used in this instance..

The problem in selecting a T (Darjeeling of course!) is not really discussed there, while each choice of a statistic T leads to a different signification to what misspecified means and suggests a comparison with Bayesian empirical likelihood.

“Acceptance rates of this [ABC] algorithm can be intolerably low”

Erm, this is not really the issue with ABC, is it?! Especially when the tolerance is induced by the simulations themselves.

When I reached the MCMC (Gibbs?) part of the paper, I first wondered at its relevance for the mispecification issues before realising it had become the focus of the paper. Now, simulating the observations conditional on a value of the summary statistic T is a true challenge. I remember for instance George Casella mentioning it in association with a Student’s t sample in the 1990’s and Kerrie and I having an unsuccessful attempt at it in the same period. Persi Diaconis has written several papers on the problem and I am thus surprised at the dearth of references here, like the rather recent Byrne and Girolami (2013), Florens and Simoni (2015), or Bornn et al. (2019). In the present case, the  linear model assumed as the true model has the exceptional feature that it leads to a feasible transform of an unconstrained simulation into a simulation with fixed statistics, with no measure theoretic worries if not free from considerable efforts to establish the operation is truly valid… And, while simulating (θ,y) makes perfect sense in an insufficient setting, the cost is then precisely the same as when running a vanilla ABC. Which brings us to the natural comparison with ABC. While taking ε=0 may sound as optimal for being “exact”, it is not from an ABC perspective since the convergence rate of the (summary) statistic should be roughly the one of the tolerance (Fearnhead and Liu, Frazier et al., 2018).

“[The Borel Paradox] shows that the concept of a conditional probability with regard to an isolated given hypothesis whose probability equals 0 is inadmissible.” A. Колмого́ров (1933)

As a side note for measure-theoretic purists, the derivation of the conditional of y given T(y)=T⁰ is arbitrary since the event has probability zero (ie, the conditioning set is of measure zero). See the Borel-Kolmogorov paradox. The computations in the paper are undoubtedly correct, but this is only one arbitrary choice of a transform (or conditioning σ-algebra).

variational approximation to empirical likelihood ABC

Posted in Statistics with tags , , , , , , , , , , , , , , , , , , on October 1, 2021 by xi'an

Sanjay Chaudhuri and his colleagues from Singapore arXived last year a paper on a novel version of empirical likelihood ABC that I hadn’t yet found time to read. This proposal connects with our own, published with Kerrie Mengersen and Pierre Pudlo in 2013 in PNAS. It is presented as an attempt at approximating the posterior distribution based on a vector of (summary) statistics, the variational approximation (or information projection) appearing in the construction of the sampling distribution of the observed summary. (Along with a weird eyed-g symbol! I checked inside the original LaTeX file and it happens to be a mathbbmtt g, that is, the typewriter version of a blackboard computer modern g…) Which writes as an entropic correction of the true posterior distribution (in Theorem 1).

“First, the true log-joint density of the observed summary, the summaries of the i.i.d. replicates and the parameter have to be estimated. Second, we need to estimate the expectation of the above log-joint density with respect to the distribution of the data generating process. Finally, the differential entropy of the data generating density needs to be estimated from the m replicates…”

The density of the observed summary is estimated by empirical likelihood, but I do not understand the reasoning behind the moment condition used in this empirical likelihood. Indeed the moment made of the difference between the observed summaries and the observed ones is zero iff the true value of the parameter is used in the simulation. I also fail to understand the connection with our SAME procedure (Doucet, Godsill & X, 2002), in that the empirical likelihood is based on a sample made of pairs (observed,generated) where the observed part is repeated m times, indeed, but not with the intent of approximating a marginal likelihood estimator… The notion of using the actual data instead of the true expectation (i.e. as a unbiased estimator) at the true parameter value is appealing as it avoids specifying the exact (or analytical) value of this expectation (as in our approach), but I am missing the justification for the extension to any parameter value. Unless one uses an ancillary statistic, which does not sound pertinent… The differential entropy is estimated by a Kozachenko-Leonenko estimator implying k-nearest neighbours.

“The proposed empirical likelihood estimates weights by matching the moments of g(X¹), , g(X) with that of
g(X), without requiring a direct relationship with the parameter. (…) the constraints used in the construction of the empirical likelihood are based on the identity in (7), which can only be satisfied when θ = θ⁰. “

Although I am feeling like missing one argument, the later part of the paper seems to comfort my impression, as quoted above. Meaning that the approximation will fare well only in the vicinity of the true parameter. Which makes it untrustworthy for model choice purposes, I believe. (The paper uses the g-and-k benchmark without exploiting Pierre Jacob’s package that allows for exact MCMC implementation.)

frontier of simulation-based inference

Posted in Books, Statistics, University life with tags , , , , , , , , , , , , , on June 11, 2020 by xi'an

“This paper results from the Arthur M. Sackler Colloquium of the National Academy of Sciences, `The Science of Deep Learning,’ held March 13–14, 2019, at the National Academy of Sciences in Washington, DC.”

A paper by Kyle Cranmer, Johann Brehmer, and Gilles Louppe just appeared in PNAS on the frontier of simulation-based inference. Sounding more like a tribune than a research paper producing new input. Or at least like a review. Providing a quick introduction to simulators, inference, ABC. Stating the shortcomings of simulation-based inference as three-folded:

  1. costly, since required a large number of simulated samples
  2. loosing information through the use of insufficient summary statistics or poor non-parametric approximations of the sampling density.
  3. wasteful as requiring new computational efforts for new datasets, primarily for ABC as learning the likelihood function (as a function of both the parameter θ and the data x) is only done once.

And the difficulties increase with the dimension of the data. While the points made above are correct, I want to note that ideally ABC (and Bayesian inference as a whole) only depends on a single dimension observation, which is the likelihood value. Or more practically that it only depends on the distance from the observed data to the simulated data. (Possibly the Wasserstein distance between the cdfs.) And that, somewhat unrealistically, that ABC could store the reference table once for all. Point 3 can also be debated in that the effort of learning an approximation can only be amortized when exactly the same model is re-employed with new data, which is likely in industrial applications but less in scientific investigations, I would think. About point 2, the paper misses part of the ABC literature on selecting summary statistics, e.g., the culling afforded by random forests ABC, or the earlier use of the score function in Martin et al. (2019).

The paper then makes a case for using machine-, active-, and deep-learning advances to overcome those blocks. Recouping other recent publications and talks (like Dennis on One World ABC’minar!). Once again presenting machine-learning techniques such as normalizing flows as more efficient than traditional non-parametric estimators. Of which I remain unconvinced without deeper arguments [than the repeated mention of powerful machine-learning techniques] on the convergence rates of these estimators (rather than extolling the super-powers of neural nets).

“A classifier is trained using supervised learning to discriminate two sets of data, although in this case both sets come from the simulator and are generated for different parameter points θ⁰ and θ¹. The classifier output function can be converted into an approximation of the likelihood ratio between θ⁰ and θ¹ (…) learning the likelihood or posterior is an unsupervised learning problem, whereas estimating the likelihood ratio through a classifier is an example of supervised learning and often a simpler task.”

The above comment is highly connected to the approach set by Geyer in 1994 and expanded in Gutmann and Hyvärinen in 2012. Interestingly, at least from my narrow statistician viewpoint!, the discussion about using these different types of approximation to the likelihood and hence to the resulting Bayesian inference never engages into a quantification of the approximation or even broaches upon the potential for inconsistent inference unlocked by using fake likelihoods. While insisting on the information loss brought by using summary statistics.

“Can the outcome be trusted in the presence of imperfections such as limited sample size, insufficient network capacity, or inefficient optimization?”

Interestingly [the more because the paper is classified as statistics] the above shows that the statistical question is set instead in terms of numerical error(s). With proposals to address it ranging from (unrealistic) parametric bootstrap to some forms of GANs.

Naturally amazed at non-identifiability

Posted in Books, Statistics, University life with tags , , , , , , , , , , , on May 27, 2020 by xi'an

A Nature paper by Stilianos Louca and Matthew W. Pennell,  Extant time trees are consistent with a myriad of diversification histories, comes to the extraordinary conclusion that birth-&-death evolutionary models cannot distinguish between several scenarios given the available data! Namely, stem ages and daughter lineage ages cannot identify the speciation rate function λ(.), the extinction rate function μ(.)  and the sampling fraction ρ inherently defining the deterministic ODE leading to the number of species predicted at any point τ in time, N(τ). The Nature paper does not seem to make a point beyond the obvious and I am rather perplexed at why it got published [and even highlighted]. A while ago, under the leadership of Steve, PNAS decided to include statistician reviewers for papers relying on statistical arguments. It could time for Nature to move there as well.

“We thus conclude that two birth-death models are congruent if and only if they have the same rp and the same λp at some time point in the present or past.” [S.1.1, p.4]

Or, stated otherwise, that a tree structured dataset made of branch lengths are not enough to identify two functions that parameterise the model. The likelihood looks like

\frac{\rho^{n-1}\Psi(\tau_1,\tau_0)}{1-E(\tau)}\prod_{i=1}^n \lambda(\tau_i)\Psi(s_{i,1},\tau_i)\Psi(s_{i,2},\tau_i)$

where E(.) is the probability to survive to the present and ψ(s,t) the probability to survive and be sampled between times s and t. Sort of. Both functions depending on functions λ(.) and  μ(.). (When the stem age is unknown, the likelihood changes a wee bit, but with no changes in the qualitative conclusions. Another way to write this likelihood is in term of the speciation rate λp

e^{-\Lambda_p(\tau_0)}\prod_{i=1}^n\lambda_p(\tau_I)e^{-\Lambda_p(\tau_i)}

where Λp is the integrated rate, but which shares the same characteristic of being unable to identify the functions λ(.) and μ(.). While this sounds quite obvious the paper (or rather the supplementary material) goes into fairly extensive mode, including “abstract” algebra to define congruence.

 

“…we explain why model selection methods based on parsimony or “Occam’s razor”, such as the Akaike Information Criterion and the Bayesian Information Criterion that penalize excessive parameters, generally cannot resolve the identifiability issue…” [S.2, p15]

As illustrated by the above quote, the supplementary material also includes a section about statistical model selections techniques failing to capture the issue, section that seems superfluous or even absurd once the fact that the likelihood is constant across a congruence class has been stated.

value of a chess game

Posted in pictures, Statistics, University life with tags , , , , , , , , , , , , on April 15, 2020 by xi'an

In our (internal) webinar at CEREMADE today, Miguel Oliu Barton gave a talk on the recent result his student Luc Attia and himself obtained, namely a tractable way of finding the value of a game (when minimax equals maximin), result that got recently published in PNAS:

“Stochastic games were introduced by the Nobel Memorial Prize winner Lloyd Shapley in 1953 to model dynamic interactions in which the environment changes in response to the players’ behavior. The theory of stochastic games and its applications have been studied in several scientific disciplines, including economics, operations research, evolutionary biology, and computer science. In addition, mathematical tools that were used and developed in the study of stochastic games are used by mathematicians and computer scientists in other fields. This paper contributes to the theory of stochastic games by providing a tractable formula for the value of finite competitive stochastic games. This result settles a major open problem which remained unsolved for nearly 40 years.”

While I did not see a direct consequence of this result in regular statistics, I found most interesting the comment made at one point that chess (with forced nullity after repetitions) had a value, by virtue of Zermelo’s theorem. As I had never considered the question (contrary to Shannon!). This value remains unknown.

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