Archive for Montpellier

likelihood-free model choice

Posted in Books, pictures, Statistics, University life, Wines with tags , , , , , , , on March 27, 2015 by xi'an

Jean-Michel Marin, Pierre Pudlo and I just arXived a short review on ABC model choice, first version of a chapter for the incoming Handbook of Approximate Bayesian computation edited by Scott Sisson, Yannan Fan, and Mark Beaumont. Except for a new analysis of a Human evolution scenario, this survey mostly argues for the proposal made in our recent paper on the use of random forests and [also argues] about the lack of reliable approximations to posterior probabilities. (Paper that was rejected by PNAS and that is about to be resubmitted. Hopefully with a more positive outcome.) The conclusion of the survey is  that

The presumably most pessimistic conclusion of this study is that the connections between (i) the true posterior probability of a model, (ii) the ABC version of this probability, and (iii) the random forest version of the above, are at best very loose. This leaves open queries for acceptable approximations of (i), since the posterior predictive error is instead an error assessment for the ABC RF model choice procedure. While a Bayesian quantity that can be computed at little extra cost, it does not necessarily compete with the posterior probability of a model.

reflecting my hope that we can eventually come up with a proper approximation to the “true” posterior probability…

Domaine de Mortiès [in the New York Times]

Posted in Mountains, Travel, Wines with tags , , , , , , , , , , , , , on March 7, 2015 by xi'an

IMG_0245

“I’m not sure how we found Domaine de Mortiès, an organic winery at the foothills of Pic St. Loup, but it was the kind of unplanned, delightful discovery our previous trips to Montpellier never allowed.”

Last year,  I had the opportunity to visit and sample (!) from Domaine de Mortiès, an organic Pic Saint-Loup vineyard and winemaker. I have not yet opened the bottle of Jamais Content I bought then. Today I spotted in The New York Times a travel article on A visit to the in-laws in Montpellier that takes the author to Domaine de Mortiès, Pic Saint-Loup, Saint-Guilhem-du-Désert and other nice places, away from the overcrowded centre of town and the rather bland beach-town of Carnon, where she usually stays when visiting. And where we almost finished our Bayesian Essentials with R! To quote from the article, “Montpellier, France’s eighth-largest city, is blessed with a Mediterranean sun and a beautiful, walkable historic centre, a tourist destination in its own right, but because it is my husband’s home city, a trip there never felt like a vacation to me.” And when the author mentions the owner of Domaine de Mortiès, she states that “Mme. Moustiés looked about as enthused as a teenager working the checkout at Rite Aid”, which is not how I remember her from last year. Anyway, it is fun to see that visitors from New York City can unexpectedly come upon this excellent vineyard!

Moonset near Montpellier

Posted in pictures, Travel with tags , , , , , on February 2, 2015 by xi'an

merry Yule!

Posted in Kids, pictures, Travel with tags , , , , , , , on December 21, 2014 by xi'an

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Methodological developments in evolutionary genomic [3 years postdoc in Montpellier]

Posted in pictures, Statistics, Travel, University life, Wines with tags , , , , , , , , , on November 26, 2014 by xi'an

[Here is a call for a post-doctoral position in Montpellier, South of France, not Montpelier, Vermont!, in a population genetics group with whom I am working. Highly recommended if you are currently looking for a postdoc!]

Three-year post-doctoral position at the Institute of Computational Biology (IBC), Montpellier (France) :
Methodological developments in evolutionary genomics.

One young investigator position opens immediately at the Institute for Computational Biology (IBC) of Montpellier (France) to work on the development of innovative inference methods and software in population genomics or phylogenetics to analyze large-scale genomic data in the fields of health, agronomy and environment (Work Package 2 « evolutionary genomics » of the IBC). The candidate will develop its own research on some of the following topics : selective processes, demographic history, spatial genetic processes, very large phylogenies reconstruction, gene/species tree reconciliation, using maximum likelihood, Bayesian and simulation-based inference. We are seeking a candidate with a strong background in mathematical and computational evolutionary biology, with interest in applications and software development. The successfull candidate will work on his own project, build in collaboration with any researcher involved in the WP2 project and working at the IBC labs (AGAP, CBGP, ISEM, I3M, LIRMM, MIVEGEC).

IBC hires young investigators, typically with a PhD plus some post-doc experience, a high level of publishing, strong communication abilities, and a taste for multidisciplinary research. Working full-time at IBC, these young researchers will play a key role in Institute life. Most of their time will be devoted to scientific projects. In addition, they are expected to actively participate in the coordination of workpackages, in the hosting of foreign researchers and in the organization of seminars and events (summer schools, conferences…). In exchange, these young researchers will benefit from an exceptional environment thanks to the presence of numerous leading international researchers, not to mention significant autonomy for their work. Montpellier hosts one of the most vibrant communities of biodiversity research in Europe with several research centers of excellence in the field. This positions is open for up to 3 years with a salary well above the French post-doc standards. Starting date is open to discussion.

 The application deadline is January 31, 2015.

Living in Montpellier: http://www.agropolis.org/english/guide/index.html

 

Contacts at WP2 « Evolutionary Genetics » :

 

Jean-Michel Marin : http://www.math.univ-montp2.fr/~marin/

François Rousset : http://www.isem.univ-montp2.fr/recherche/teams/evolutionary-genetics/staff/roussetfrancois/?lang=en

Vincent Ranwez : https://sites.google.com/site/ranwez/

Olivier Gascuel : http://www.lirmm.fr/~gascuel/

Submit my application : http://www.ibc-montpellier.fr/open-positions/young-investigators#wp2-evolution

ABC model choice by random forests

Posted in pictures, R, Statistics, Travel, University life with tags , , , , , , , , , , , , , on June 25, 2014 by xi'an

treerise6After more than a year of collaboration, meetings, simulations, delays, switches,  visits, more delays, more simulations, discussions, and a final marathon wrapping day last Friday, Jean-Michel Marin, Pierre Pudlo,  and I at last completed our latest collaboration on ABC, with the central arguments that (a) using random forests is a good tool for choosing the most appropriate model and (b) evaluating the posterior misclassification error rather than the posterior probability of a model is an appropriate paradigm shift. The paper has been co-signed with our population genetics colleagues, Jean-Marie Cornuet and Arnaud Estoup, as they provided helpful advice on the tools and on the genetic illustrations and as they plan to include those new tools in their future analyses and DIYABC software.  ABC model choice via random forests is now arXived and very soon to be submitted…

truePPOne scientific reason for this fairly long conception is that it took us several iterations to understand the intrinsic nature of the random forest tool and how it could be most naturally embedded in ABC schemes. We first imagined it as a filter from a set of summary statistics to a subset of significant statistics (hence the automated ABC advertised in some of my past or future talks!), with the additional appeal of an associated distance induced by the forest. However, we later realised that (a) further ABC steps were counterproductive once the model was selected by the random forest and (b) including more summary statistics was always beneficial to the performances of the forest and (c) the connections between (i) the true posterior probability of a model, (ii) the ABC version of this probability, (iii) the random forest version of the above, were at best very loose. The above picture is taken from the paper: it shows how the true and the ABC probabilities (do not) relate in the example of an MA(q) model… We thus had another round of discussions and experiments before deciding the unthinkable, namely to give up the attempts to approximate the posterior probability in this setting and to come up with another assessment of the uncertainty associated with the decision. This led us to propose to compute a posterior predictive error as the error assessment for ABC model choice. This is mostly a classification error but (a) it is based on the ABC posterior distribution rather than on the prior and (b) it does not require extra-computations when compared with other empirical measures such as cross-validation, while avoiding the sin of using the data twice!

last Big MC [seminar] before summer [June 19, 3pm]

Posted in pictures, Statistics, University life with tags , , , , , , , , , , , on June 17, 2014 by xi'an

crossing Rue Soufflot on my way to IHP from Vieux Campeur, March 28, 2013Last session of our Big’MC seminar at Institut Henri Poincaré this year, on Tuesday Thursday, June 19, with

Chris Holmes (Oxford) at 3pm on

Robust statistical decisions via re-weighted Monte Carlo samples

and Pierre Pudlo (iC3M, Université de Montpellier 2) at 4:15pm on [our joint work]

ABC and machine learning

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