Archive for INRA

crowd-based peer review

Posted in Statistics with tags , , , , , , , , , , on June 20, 2017 by xi'an

In clear connection with my earlier post on Peer Community In… and my visit this week to Montpellier towards starting a Peer Community In Computational Statistics, I read a tribune in Nature (1 June, p.9) by the editor of Synlett, Benjamin List, describing an experiment conducted by this journal in chemical synthesis. The approach was to post (volunteered) submitted papers on a platform accessible to a list of 100 reviewers, nominated by the editorial board, who could anonymously comment on the papers and read others’ equally anonymous comments. With a 72 hours deadline! According to Benjamin List (and based on  a large dataset of … 10 papers!), the outcome of the experiment is one of better quality return than with traditional reviewing policies. While Peer Community In… does not work exactly this way, and does not aim at operating as a journal, it is exciting and encouraging to see such experiments unfold!

trip to Montpellier

Posted in pictures, Statistics, Travel, University life, Wines with tags , , , , , , on February 27, 2014 by xi'an

IMG_2477Last week, I flew down to Montpellier for two days of work on ABC model choice with Jean-Michel Marin and Pierre Pudlo. Although we missed the COLT 2014 deadline, we are now close to completing this work that will propose a rather radical change in our advocacy of how ABC model choice should be conducted. We actually spent the second day on the wonderful campus of INRA at Montferrier-sur-Lez, just outside Montpellier, discussing of the implications of this approach with our friends at CBGP, Jean-Marie Cornuet and Arnaud Estoup. With possible impact on the DIYABC software. It was a very profitable trip (not mentioning tasting great Grés de Montpellier wine!) and I hope to manage completing the paper with Pierre during the next week in Banff. Unfortunately, when I came back to my train station, I found some idiots had a go at my bike and bent the back wheel which then needed to be replaced…

tenured research position on ABC in Paris!

Posted in Statistics, University life with tags , , , , , , on February 2, 2013 by xi'an

Paris and la Seine, from Pont du Garigliano, Oct. 20, 2011Just to make sure this fabulous announcement has not gone undetected: there is a permanent research (I repeat, permanent research!) position in statistics is open at AgroParisTech/INRA (a French institute/school on biology, agronomy, veterinary sciences, environmental sciences) with the profile ‘Approximate inference methods for complex systems’ (Hence my title!). Applications must be received by February 28th. See here for more details on the profile and there for the application process. Please contact Eric PARENT for further information. (There are other tenured positions posted by INRA, and there will be a regular lecturer position at Paris-Dauphine opening soon.)

tenured research position with ABC skills!

Posted in R, Statistics, Travel, University life with tags , , , , , on February 2, 2012 by xi'an

I just received this announcement for the opening of a (tenured/civil servant) position in the national research institute in biostatistics, genetics, and agronomy, INRA:

Position opening with profile Approximate inference techniques in complex systems

Key activities and required skills: You will develop methodological research in the field of statistical inference for models used in environmental sciences. These inference techniques will account for the complex dependency structure due to the temporal, spatial and evolutionary organisation of the observations, for the heterogeneity of the data and for the existence of unobserved variables or incomplete data. Solid experience in statistical modelling of complex data (graphic models, multi-scale spatio-temporal data) and a strong orientation towards the applications in environment and biology would be appreciated. Skills in approximation techniques (variational inference, ABC techniques) will be welcome.

Contact person: Stéphane Robin (robin [chez] agroparistech [lepoint] fr)

Location:  Versailles-Grignon (Paris)

Deadline: February 25, 2012

Website: INRA offer

This should appeal to (some) readers of the blog, esp. since the offer has no nationality constraint.

Bayesian Fall school in La Rochelle

Posted in Kids, R, Statistics, Travel, University life with tags , , , , , on June 27, 2011 by xi'an

The French agronomy research institute INRA is organising a Fall school in La Rochelle, Nov. 28 – Dec. 02, on Bayesian methods, oriented towards the applications in food sciences, environmental sciences, and biology. The provisional program (in French) is

■ Initiation aux outils informatiques R et WinBUGS (TP et réalisation de projets sur ordinateur)
■ Rappels en probabilité et initiation aux modèles graphiques
■ Introduction de la démarche bayésienne à travers des exemples simples
■ Quelques aspects et anecdotes sur l’histoire passée et récente de la statistique bayésienne
■ Estimation des distributions a posteriori à l’aide de méthodes numériques (MCMC etc.)
■ Evaluation et sélection de modèles en statistique bayésienne
■ Distributions a priori et élicitation
■ Exposés prospectifs sur les méthodes bayésiennes

The instructors will be Sophie Ancelet, Chantal Guihenneuc-Jouyaux, and Jean-Michel Marin. There are still a few places available and the registration deadline is June 30. (The above picture is a painting by Henri-Paul Motte of Richelieu during the year long siege of La Rochelle in 1628, painting that was included in my primary school history book and that I then found fascinating…)

PhD+postdoc grant on ABC

Posted in Statistics, University life with tags , , , , , , on April 3, 2010 by xi'an

I have received the following email announcement about a joint INRA/INRIA PhD grant on statistical methods for high frequency genomics, backed by an additional two year postdoc contract:

“Identifier les signatures de sélection dans les données issues de la génomique haut-débit : développement de modèles et de méthodes d’analyse statistique”.
Le développement rapide des technologies de séquençage et de génotypage à haut débit permet désormais de produire de très grandes quantités de données de polymorphisme génétique à une échelle populationnelle, y compris chez des espèces « non-modèles ». Dans ce contexte, la recherche de marqueurs moléculaires portant des signatures de sélection est primordiale pour comprendre la dynamique de l’adaptation. Cette thèse aura donc pour objet de développer des méthodes d’analyse statistique innovantes, pour caractériser la typologie des marqueurs génétiques vis-à-vis de leur statut évolutif. Ces méthodes seront développées dans un cadre bayésien, et se concentreront sur les outils stochastiques afférents (méthodes MCMC et approche ABC lorsque la vraisemblance n’est pas accessible) et les techniques de sélection de variables.

whose google translation is

The fast development of high-frequency sequencing and genotyping technologies allows henceforth to produce very large quantities  of genetic polymorphism data in a populationnal scale, including “non-model” species. In this context, the search for molecular markers carrying selection signatures is essential to understand the dynamics of the adaptation. This thesis will thus have for its goal to develop innovative statistical analysis methods, to characterize the typology of the genetic markers towards their evolutionary status. These methods will be developed in a Bayesian framework, and will concentrate on the relative stochastic tools (MCMC and ABC methods when the likelihood is not available) and the techniques of variable selection.

It involves my friend and coauthor Gilles Celeux (Paris Sud, Orsay) as one of the advisors, as well as two researchers from the place that taught me everything about ABC, the INRA CBGP (Centre de Biologie et de Gestion des Populations)  lab in Montpelliers: Mathieu Gautier and Renaud Vitalis. It is thus a highly interesting proposal whose deadline is April 23.

Another ABC thesis

Posted in University life with tags , , , , on December 19, 2009 by xi'an

Yesterday, my PhD student Aude Grelaud defended her thesis in Dauphine, in front of a wide audience of fans and quite brilliantly! Aude was working both with Francois Rodolphe from INRA and with me on both statistical and biological aspects of ABC (what else?!) at both CREST and INRIA, while teaching at both Dauphine and ENSAE, which made for a rather diverse environment. Besides the ABC paper for model choice we wrote together, she wrote a very good synthesis on the current state of ABC algorithms that will be soon submitted. Plus an application of SMC-ABC to selection pressure in evolution genetics. Aude is leaving in a few days for Rutgers University, and a joint postdoc between Statistics and Biology, where I wish her the best! This makes for a second brilliant ABC thesis in one week!