Archive for R.A. Fisher

JSM 2015 [day #4]

Posted in pictures, Running, Statistics, Travel, University life with tags , , , , , , , , , , , , , , , , , , on August 13, 2015 by xi'an

My first session today was Markov Chain Monte Carlo for Contemporary Statistical Applications with a heap of interesting directions in MCMC research! Now, without any possible bias (!), I would definitely nominate Murray Pollock (incidentally from Warwick) as the winner for best slides, funniest presentation, and most enjoyable accent! More seriously, the scalable Langevin algorithm he developed with Paul Fearnhead, Adam Johansen, and Gareth Roberts, is quite impressive in avoiding computing costly likelihoods. With of course caveats on which targets it applies to. Murali Haran showed a new proposal to handle high dimension random effect models by a projection trick that reduces the dimension. Natesh Pillai introduced us (or at least me!) to a spectral clustering that allowed for an automated partition of the target space, itself the starting point to his parallel MCMC algorithm. Quite exciting, even though I do not perceive partitions as an ideal solution to this problem. The final talk in the session was Galin Jones’ presentation of consistency results and conditions for multivariate quantities which is a surprisingly unexplored domain. MCMC is still alive and running!

The second MCMC session of the morning, Monte Carlo Methods Facing New Challenges in Statistics and Science, was equally diverse, with Lynn Kuo’s talk on the HAWK approach, where we discovered that harmonic mean estimators are still in use, e.g., in MrBayes software employed in phylogenetic inference. The proposal to replace this awful estimator that should never be seen again (!) was rather closely related to an earlier solution of us for marginal likelihood approximation, based there on a partition of the whole space rather than an HPD region in our case… Then, Michael Betancourt brilliantly acted as a proxy for Andrew to present the STAN language, with a flashy trailer he most recently designed. Featuring Andrew as the sole actor. And with great arguments for using it, including the potential to run expectation propagation (as a way of life). In fine, Faming Liang proposed a bootstrap subsampling version of the Metropolis-Hastings algorithm, where the likelihood acknowledging the resulting bias in the limiting distribution.

My first afternoon session was another entry on Statistical Phylogenetics, somewhat continued from yesterday’s session. Making me realised I had not seen a single talk on ABC for the entire meeting! The issues discussed in the session were linked with aligning sequences and comparing  many trees. Again in settings where likelihoods can be computed more or less explicitly. Without any expertise in the matter, I wondered at a construction that would turn all trees, like  into realizations of a continuous model. For instance by growing one branch at a time while removing the MRCA root… And maybe using a particle like method to grow trees. As an aside, Vladimir Minin told me yesterday night about genetic mutations that could switch on and off phenotypes repeatedly across generations… For instance  the ability to glow in the dark for species of deep sea fish.

When stating that I did not see a single talk about ABC, I omitted Steve Fienberg’s Fisher Lecture R.A. Fisher and the Statistical ABCs, keeping the morceau de choix for the end! Even though of course Steve did not mention the algorithm! A was for asymptotics, or ancilarity, B for Bayesian (or biducial??), C for causation (or cuffiency???)… Among other germs, I appreciated that Steve mentioned my great-grand father Darmois in connection with exponential families! And the connection with Jon Wellner’s LeCam Lecture from a few days ago. And reminding us that Savage was a Fisher lecturer himself. And that Fisher introduced fiducial distributions quite early. And for defending the Bayesian perspective. Steve also set some challenges like asymptotics for networks, Bayesian model assessment (I liked the notion of stepping out of the model), and randomization when experimenting with networks. And for big data issues. And for personalized medicine, building on his cancer treatment. No trace of the ABC algorithm, obviously, but a wonderful Fisher’s lecture, also most obviously!! Bravo, Steve, keep thriving!!!

reflections on the probability space induced by moment conditions with implications for Bayesian Inference [slides]

Posted in Books, Statistics, University life with tags , , , , , , , , , , , , on December 4, 2014 by xi'an

defsunset2Here are the slides of my incoming discussion of Ron Gallant’s paper, tomorrow.

reflections on the probability space induced by moment conditions with implications for Bayesian Inference [discussion]

Posted in Books, Statistics, University life with tags , , , , , , on December 1, 2014 by xi'an

[Following my earlier reflections on Ron Gallant’s paper, here is a more condensed set of questions towards my discussion of next Friday.]

“If one specifies a set of moment functions collected together into a vector m(x,θ) of dimension M, regards θ as random and asserts that some transformation Z(x,θ) has distribution ψ then what is required to use this information and then possibly a prior to make valid inference?” (p.4)

The central question in the paper is whether or not given a set of moment equations


(where both the Xi‘s and θ are random), one can derive a likelihood function and a prior distribution compatible with those. It sounds to me like a highly complex question since it implies the integral equation

\int_{\Theta\times\mathcal{X}^n} m(x_1,\ldots,x_n,\theta)\,\pi(\theta)f(x_1|\theta)\cdots f(x_n|\theta) \text{d}\theta\text{d}x_1\cdots\text{d}x_n=0

must have a solution for all n’s. A related question that was also remanent with fiducial distributions is how on Earth (or Middle Earth) the concept of a random theta could arise outside Bayesian analysis. And another one is how could the equations make sense outside the existence of the pair (prior,likelihood). A question that may exhibit my ignorance of structural models. But which may also relate to the inconsistency of Zellner’s (1996) Bayesian method of moments as exposed by Geisser and Seidenfeld (1999).

For instance, the paper starts (why?) with the Fisherian example of the t distribution of

Z(x,\theta) = \frac{\bar{x}_n-\theta}{s/\sqrt{n}}

which is truly is a t variable when θ is fixed at the true mean value. Now, if we assume that the joint distribution of the Xi‘s and θ is such that this projection is a t variable, is there any other case than the Dirac mass on θ? For all (large enough) sample sizes n? I cannot tell and the paper does not bring [me] an answer either.

When I look at the analysis made in the abstraction part of the paper, I am puzzled by the starting point (17), where

p(x|\theta) = \psi(Z(x,\theta))

since the lhs and rhs operate on different spaces. In Fisher’s example, x is an n-dimensional vector, while Z is unidimensional. If I apply blindly the formula on this example, the t density does not integrate against the Lebesgue measure in the n-dimension Euclidean space… If a change of measure allows for this representation, I do not see so much appeal in using this new measure and anyway wonder in which sense this defines a likelihood function, i.e. the product of n densities of the Xi‘s conditional on θ. To me this is the central issue, which remains unsolved by the paper.

marauders of the lost sciences

Posted in Books, Statistics, University life with tags , , , , , , on October 26, 2014 by xi'an

The editors of a new blog entitled Marauders of the Lost Sciences (Learn from the giants) sent me an email to signal the start of this blog with a short excerpt from a giant in maths or stats posted every day:

There is  a new blog I wanted to tell you 
about which  excerpts one  interesting or 
classic  paper  or  book  a day  from the 
mathematical  sciences.  We plan on daily
posting across the  range of mathematical 
fields and at any level, but about 20-30% 
of the posts in queue are from statistics.

The goal is to entice people to read the great 
works of old.

The first post today was from an old paper by 
Fisher applying Group Theory to the design of 

Interesting concept, which will hopefully generate comments to put the quoted passage into context. Somewhat connected to my Reading Statistical Classics posts. Which incidentally if sadly will not take place this year since only two students registered. should take place in the end since more students registered! (I am unsure about the references behind the title of that blog, besides Spielberg’s Raiders of the Lost Ark and Norman’s Marauders of Gor… I just hope Statistics does not qualify as a lost science!)

epidemiology in Le Monde

Posted in Books, Statistics, University life with tags , , , , , , , , , on February 19, 2012 by xi'an

Quite an interesting weekend Le Monde issue: a fourth (2 pages!) of the science folder is devoted to epidemiology… In the statistical sense. (The subtitle is actually Strengths and limitations of Statistics.) The paper does not delve into technical statistical issues but points out the logical divergence between a case-by-case study and an epidemiological study. The impression that the higher the conditioning (i.e. the more covariates), the better the explanation is a statistical fallacy some of the opponents interviewed in the paper do not grasp. (Which reminded me of Keynes seemingly going the same way.) The short paragraph written on causality and Hill’s criteria is vague enough to concur to the overall remark that causality can never been proved or disproved… The fourth examples illustrating the strengths and limitations are tobacco vs. lung cancer, a clear case except for R.A. Fisher!, mobile phones vs. brain tumors, a not yet conclusive setting, hepatitis B vaccine vs. sclerosis, lacking data (the pre-2006 records were destroyed for legal reasons), and leukemia vs. nuclear plants, with a significant [?!] correlation between the number of cases and the distance to a nuclear plant. (The paper was inspired by a report recently published by the French Académie de Médecine on epidemiology in France.) The science folder also includes a review of a recent Science paper by Wilhite and Fong on the coercive strategies used by some journals/editors to increase their impact factor, e.g., “you cite Leukemia [once in 42 references]. Consequently, we kindly ask you to add references of articles published in Leukemia to your present article”.

Error and Inference [arXived]

Posted in Books, Statistics, University life with tags , , , , , , , on November 29, 2011 by xi'an

Following my never-ending series of posts on the book Error and Inference, (edited) by Deborah Mayo and Ari Spanos (and kindly sent to me by Deborah), I decided to edit those posts into a (slightly) more coherent document, now posted on arXiv. And to submit it as a book review to Siam Review, even though I had not high expectations it fits the purpose of the journal: the review was rejected between the submission to arXiv and the publication of this post!

the cult of significance

Posted in Books, Statistics, University life with tags , , , , , , , , , , , , , on October 18, 2011 by xi'an

Statistical significance is not a scientific test. It is a philosophical, qualitative test. It asks “whether”. Existence, the question of whether, is interesting. But it is not scientific.” S. Ziliak and D. McCloskey, p.5

The book, written by economists Stephen Ziliak and Deirdre McCloskey, has a theme bound to attract Bayesians and all those puzzled by the absolute and automatised faith in significance tests. The main argument of the authors is indeed that an overwhelming majority of papers stop at rejecting variables (“coefficients”) on the sole and unsupported basis of non-significance at the 5% level. Hence the subtitle “How the standard error costs us jobs, justice, and lives“… This is an argument I completely agree with, however, the aggressive style of the book truly put me off! As with Error and Inference, which also addresses a non-Bayesian issue, I could have let the matter go, however I feel the book may in the end be counter-productive and thus endeavour to explain why through this review.  (I wrote the following review in batches, before and during my trip to Dublin, so the going is rather broken, I am afraid…) Continue reading