Archive for Montpellier

a senseless taxi-ride

Posted in pictures, Travel with tags , , , , on May 23, 2015 by xi'an

This morning, on my way to the airport (and to Montpellier for a seminar), Rock, my favourite taxi-driver, told me of a strange ride he endured the night before, so strange that he had not yet fully got over it! As it happened, he had picked an elderly lady with two large bags in the vicinity after a radio-call and drove her to a sort of catholic hostel in down-town Paris, near La Santé jail, a pastoral place housing visiting nuns and priests. However, when they arrived there, she asked the taxi to wait before leaving, quite appropriately as she had apparently failed to book the place. She then asked my friend to take her to another specific address, an hotel located nearby at Denfert-Rochereau. While Rock was waiting and the taxi counter running, the passenger literally checked in by visiting the hotel room and deciding she did not like it so she gave my taxi yet another hotel address near Saint-Honoré where she repeated the same process, namely visited the hotel room with the same outcome that she did not like the place. My friend was then getting worried about the meaning of this processionary trip all over Paris, the more because the lady did not have a particularly coherent discourse. And could not stop talking. The passenger then made him stop for food and drink, and, while getting back in the taxi, ordered him to drive her back to her starting place. After two hours and half, they thus came back to the place, with a total bill of 113 euros. The lady then handled a 100 euro bill to the taxi-driver, declaring she did not have any further money and that he should have brought her home directly from the first place they had stopped… In my friend’s experience, this was the weirdest passenger he ever carried and he thought the true point of the ride was to escape solitude and loneliness for one evening, even if chatting about non-sense the whole time.

speed seminar-ing

Posted in Books, pictures, Statistics, Travel, University life, Wines with tags , , , , , , , , , , on May 20, 2015 by xi'an

harbour in the morning, Carnon, June 15, 2012Yesterday, I  made a quick afternoon trip to Montpellier as replacement of a seminar speaker who had cancelled at the last minute. Most obviously, I gave a talk about our “testing as mixture” proposal. And as previously, the talk generated a fair amount of discussion and feedback from the audience. Providing me with additional aspects to include in a revision of the paper. Whether or not the current submission is rejected, new points made and received during those seminars will have to get in a revised version as they definitely add to the appeal to the perspective. In that seminar, most of the discussion concentrated on the connection with decisions based on such a tool as the posterior distribution of the mixture weight(s). My argument for sticking with the posterior rather than providing a hard decision rule was that the message is indeed in arguing hard rules that end up mimicking the p- or b-values. And the catastrophic consequences of fishing for significance and the like. Producing instead a validation by simulating under each model pseudo-samples shows what to expect for each model under comparison. The argument did not really convince Jean-Michel Marin, I am afraid! Another point he raised was that we could instead use a distribution on α with support {0,1}, to avoid the encompassing model he felt was too far from the original models. However, this leads back to the Bayes factor as the weights in 0 and 1 are the marginal likelihoods, nothing more. However, this perspective on the classical approach has at least the appeal of completely validating the use of improper priors on common (nuisance or not) parameters. Pierre Pudlo also wondered why we could not conduct an analysis on the mixture of the likelihoods. Instead of the likelihood of the mixture. My first answer was that there was not enough information in the data for estimating the weight(s). A few more seconds of reflection led me to the further argument that the posterior on α with support (0,1) would then be a mixture of Be(2,1) and Be(1,2) with weights the marginal likelihoods, again (under a uniform prior on α). So indeed not much to gain. A last point we discussed was the case of the evolution trees we analyse with population geneticists from the neighbourhood (and with ABC). Jean-Michel’s argument was that the scenari under comparison were not compatible with a mixture, the models being exclusive. My reply involved an admixture model that contained all scenarios as special cases. After a longer pondering, I think his objection was more about the non iid nature of the data. But the admixture construction remains valid. And makes a very strong case in favour of our approach, I believe.

masbruguiere2After the seminar, Christian Lavergne and Jean-Michel had organised a doubly exceptional wine-and-cheese party: first because it is not usually the case there is such a post-seminar party and second because they had chosen a terrific series of wines from the Mas Bruguière (Pic Saint-Loup) vineyards. Ending up with a great 2007 L’Arbouse. Perfect ending for an exciting day. (I am not even mentioning a special Livarot from close to my home-town!)

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

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“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

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