Archive for PNAS

workshop in Columbia [talk]

Posted in Statistics, Travel, University life with tags , , , , , , , , , on September 25, 2011 by xi'an

Here are the slides of my talk yesterday at the Computational Methods in Applied Sciences workshop in Columbia:

The last section of the talk covers our new results with Jean-Michel Marin, Natesh Pillai and Judith Rousseau on the necessary and sufficient conditions for a summary statistic to be used in ABC model choice. (The paper is about to be completed.) This obviously comes as the continuation of our reflexions on  ABC model choice started last January. The major message of the paper is that the statistics used for running model choice cannot have a mean value common to both models, which strongly implies using ancillary statistics with different means under each model. (I am afraid that, thanks to the mixture of no-jetlag fatigue and of slide inflation [95 vs. 40mn] and of asymptotics technicalities in the last part, the talk was far from comprehensible. I started on the wrong foot with not getting an XL [Xiao-Li’s] comment on the measure-theory problem with the limit in ε going to zero. A peak given that great debate we had in Banff with Jean-Michel, David Balding, and Mark Beaumont, years ago. And our more recent paper about the arbitrariness of the density value in the Savage-Dickey paradox. I then compounded the confusion by stating the empirical mean was sufficient in the Laplace case…which is not even an exponential family. I hope I will be more articulate next week in Zürich where at least I will not speak past my bedtime!)

Bayes-250, Edinburgh

Posted in Mountains, Statistics, Travel, University life with tags , , , , , , , on September 6, 2011 by xi'an

       

On September 5-7, I am attending Bayes-250 at the University of Edinburgh. I arrived under a blazing sun that showed Arthur’s Seat in full glory! (I realised I had never seen it in the sun before!)

My talk is a short version of the ABC in London talk about ABC model choice, in connection with the recently published PNAS paper.

On Monday afternoon, David Dunson gave a plenary talk on the use of tensors in Bayesian non-parametric modeling and the possibilities offered by this highly malleable tool that made me look forward reading his 2009 JASA paper with Xing. In the evening, David Spiegelhalter delivered a great (and well-attended) public lecture on the Bayesian nature of risk that made me think further about the de Finetti‘s “probability does not exist”, a declaration that had irked me until then. (And on which I will expand in a later comment on Error and Inference.) We ended up the day in Blonde, a nice restaurant we had already enjoyed during the mixture meeting in 2009.

published in PNAS!

Posted in Statistics, University life with tags , , , , on August 30, 2011 by xi'an

The paper “Lack of confidence in approximate Bayesian computation model choice“, with  Jean-Marie Cornuet, Jean-Michel Marin, and Natesh S. Pillai, has now appeared in the Early Edition of PNAS! It is in Open Access, so fully accessible to everyone. Thanks to the referees and to the PNAS editor, Steve Fienberg, for their support. A very fitting ending for a paper started around a (fake) log-fire in Park City! (And my very first paper in PNAS!)

Natbib error

Posted in Statistics, University life with tags , , , on July 21, 2011 by xi'an

When compiling my papers with the PNAS options,

[sourcecode gutter=”false” language=”tex”]
\documentclass{pnastwo}
\usepackage{amssymb,amsfonts,amsmath}
\usepackage[numbers,round]{natbib}
\bibpunct{(}{)}{,}{a}{,}{,}
\bibliographystyle{pnas}
[/sourcecode]

I would get a compilation error

! Package natbib Error: Bibliography not compatible with author-year citations.
(natbib) Press  <return> to continue in numerical citation style.
See the natbib package documentation for explanation.

that was quite minor (just press <return>!) but nonetheless annoying. This seemed to be due to the latest version of natbib. I eventually found a solution by Ulrike Fisher on this forum, namely to replace {a} with {n} in the above \bibpunct line.

[sourcecode gutter=”false” language=”tex”]
\bibpunct{(}{)}{,}{n}{,}{,}
[/sourcecode]

Accepted lack of confidence

Posted in R, Statistics, University life with tags , , , , on July 17, 2011 by xi'an

I just got the following email from PNAS about our Lack of confidence in ABC model choice.

Editor's Remarks to Author: 

both referees now find the manuscript acceptable for publication as do I. Each
suggests small changes which I encourage the authors to make prior to having the
manuscript go into production. 

Congratulations on an interesting and provocative paper.

This is terrific news (and my first true paper in PNAS)! The small changes are indeed very minor and involve (a) reverting to the inclusion of the above graph comparing 1000 with 50,000 importance sampling simulation in the large population genetic experiment (b) mentioning that the ABC-based model choice actually produced the proper conclusion in those population genetic experiments. We now have to work hard to complete our paper with Jean-Michel Marin, Natesh Pillai and Judith Rousseau towards a partial resolution of the issues raised in this paper.