Archive for grants

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.

Citation abuses

Posted in Statistics with tags , , , , , , on October 21, 2009 by xi'an

“There is a belief that citation statistics are
inherently more accurate because they
substitute simple numbers for complex
judgments, and hence overcome the
possible subjectivity of peer review.
But this belief is unfounded.”

A very interesting report appeared in the latest issue of Statistical Science about bibliometrics and its abuses (or “bibliometrics as an abuse per se”!). It was commissioned by the IMS, the IMU and the ICIAM. Along with the set of comments (by Bernard Silverman, David Spiegelhalter, Peter Hall and others) also posted in arXiv, it is a must-read!

“even a casual inspection of the h-index and its variants shows
that these are naïve attempts to understand complicated citation
records. While they capture a small amount of information about
the distribution of a scientist’s citations, they lose crucial
information that is essential for the assessment of research.”

The issue is not gratuitous. While having Series B ranked with a high impact factor is an indicator of the relevance of a majority of papers published in the journal, there are deeper and more important issues at stake. Our grant allocations, our promotions, our salary are more and more dependent on these  “objective” summary or “comprehensive” factors. The misuse of bibliometrics stems from government bodies and other funding agencies wishing to come up with assessments of the quality of a researcher that bypass peer reviews and, more to the point, are easy to come by.

The report points out the many shortcomings of journal impact factors. Its two-year horizon is very short-sighted in mathematics and statistics. As an average, it is strongly influenced by outliers, like controversial papers or broad surveys, as shown by the yearly variations of the thing. Commercial productions like Thomson’s misses a large part of the journals that could quote a given paper and this is particularly true for fields at the interface between disciplines and for emergent topics. The variation in magnitude between disciplines is enormous and based on the impact factor I’d rather publish one paper in Bioinformatics than four in the Annals of Statistics… The second issue is that the “quality” of the journal does not automatically extend to all papers it publishes: multiplying papers by the journal impact factor is thus ignoring variation to an immense extent. The report illustrates this with the fact that a paper published in a journal with half the impact factor of another journal has a 62% probability to be more quoted than if it had been published in this other journal! The h-factor is similarly criticised by the report.  More fundamentally, the report also analyses the multicriteria nature of citations, which cannot be reflected (only) as a measure of worth of the quoted papers.

Vielä Helsingissä!

Posted in Travel, University life with tags , , , on September 25, 2009 by xi'an

Helsinki1The meeting of the panel at the Academy of Finland is quite interesting with panelists from such a very wide range of disciplines, covering most aspects of computational sciences. In particular, the approach to reviewing grant proposals appears to be highly dependent on the discipline in the sense that the arguments are more or less theoretical depending on the referee’s discipline. At the mathematical end of the gamut, I have stronger inclinations to be severe with proposals that are missing a minimal probabilistic background to validate simulation experiments, while bioinformaticians will most likely bite at projects with poorly motivated protein structures… This makes for interesting debates, when compared with an NSF statisticians-only panel. Overall, I am quite impressed by the extremely high quality of most proposals, some of which are  clearly internationally leading-edge projects. A point of further interest I discovered this morning when entering its building is that the Academy of Finland is distinct from the Finnish Academy of Science: the former is in fact the funding body for public research in Finland while the later is working on the same principles as the National Academy of Science or The Royal Society… (Two Academy members with strong connections with Bayesian Statistics and MCMC are Elja Arjas and Esa Nummelin.)

Lyhyt matka Helsinkiin

Posted in Travel, University life with tags , , on September 23, 2009 by xi'an

This is the (possibly mistaken) Google translation for “A short trip to Helsinki” into Finnish! Indeed, being involved into an evaluation panel for the Finnish Academy of Sciences, I will be away to Helsinki, Finland, for the two next days. Although this activity is time-consuming, I always find this kind of experience rewarding as the evaluation of grant applications brings forward current (and future) directions of research in our field. In the current case, although I cannot unveil too much, the panel is broader than in the NSF Statistics and Probability grant panel I was involved with, say, but this is also interesting since colleagues from other fields will necessarily have different perspectives on which directions are more relevant. Contrary to a “popular” belief, I have never had the feeling that some panel members in those situations were clearly biased towards a subfield or a group of researchers, but on the opposite that discussions were quite open and objective. (Of course this may reflect my naïvety rather than truth!)

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