Archive for Montpellier

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!

peer community in evolutionary biology

Posted in Statistics with tags , , , , , , , on May 18, 2017 by xi'an

My friends (and co-authors) from Montpellier pointed out the existence of PCI Evolutionary Biology, which is a preprint and postprint validation forum [so far only] in the field of Evolutionary Biology. Authors of a preprint or of a published paper request a recommendation from the forum. If someone from the board finds the paper of interest, this person initiates a quick refereeing process with one or two referees and returns a review to the authors, with possible requests for modification, and if the lead reviewer is happy with the new version, the link to the paper and the reviews are published on PCI Evol Biol, which thus gives a stamp of validation to the contents in the paper. The paper can then be submitted for publication in any journal, as can be seen from the papers in the list.

This sounds like a great initiative and since PCI is calling for little brothers and sisters to PCI Evol Biol, I think we should try to build its equivalent in Statistics or maybe just Computational Statistics.

The Grothendieck papers

Posted in Books, Kids, Mountains, pictures, University life with tags , , , , , , , , on December 28, 2016 by xi'an

Running back towards Carnon, along the expressway (!), with pink flamingoes in the distance, June 15, 2012Following the death of the mathematician Alexandre Grothendieck in 2014, his former maths department at the University of Montpellier decided to digitise in very high resolution the 28,000 pages of notes he had left to the department. Under the supervision of Jean-Michel Marin, Head of the said department! However, thanks to the French laws governing succession, those notes cannot be posted on-line without the authorisation of the five children of Grothendieck, who keep a moral right on those notes, even though they were given to the department. Grothendieck’s children want to recover all their father’s notes—which amount to more than 90,000 handwritten pages—presumably towards a bulk sale to a prestigious American university, but the succession is in limbo while the monetary value of those notes is not ascertained. And the digitised notes are stuck in this legal no man’s land as well. It is fairly ironical that those notes are at the centre of a financial conundrum, when Grothendieck’s anarchist principles led him to refuse awards and positions and to lead a recluse and frugal life in an isolated mountain village. And to prohibit the publication of those notes… Jean-Michel remains confident though that a solution can soon be reached between Grothendieck’s children, the University, the IHES, and the French National Library. I hope those notes can be made public, so that anyone could consult them. In paper or digitised format. Even though most of these pages may just be unexploitable. But at least they will be available rather than stuck in a storage for another 25 years.

Argentan half-marathon 2016 [1:23:28-23/380-V2 2/74-16⁰]

Posted in Running, Travel, Wines with tags , , , , , , , , , , , , on October 2, 2016 by xi'an

And yet another Argentan half-marathon! Which started this blog, so to speak, 8 years ago… Although I could not repeat my feat at the San Francisco half-marathon, as I had lost my high altitude benefits, I managed well enough, with a good overall time of 1:23:28 and a second place in the V2 category, once again. I gained more than one minute from last year time, despite a strong face wind and thanks to sticking to a small group of younger runners. This is one of my best times since the start of the blog in 2008, so I am clearly very happy with the result. And plan to celebrate tonight with a top Montpellier wine!

ignorami rule

Posted in Kids, Travel, University life with tags , , , , , on May 12, 2016 by xi'an

plane2There has already been many blog entries [incl. Andrew’s] on that story of a plane passenger calling security about a neighbour solving differential equations next seat and many jokes will certainly stem from it. My closest encounter with such a passenger was a while ago, when flying to Manchester for a visit to Lancaster, when the man next to me suddenly asked if I was working on particle physics because he would not tolerate it. Or something like this. As I did not want to get arrested upon arrival I refrained from smashing his head into the seat and muttered something indistinct between a curse and a comment that this was statistics, but I now regret I had not confronted this holier-than-thou (to keep polite) attitude! This story also reminds me of another flight, from Montpelier to Paris, when I was discussing ABC with Jean-Michel Marin and Jean-Marie Cornuet, when an AF flight attendant came by and added an x at random in one of my equations! This did not solve the problem but we had a good laugh and did not end up questioned by security!

Anyway, my reaction to this PDE (or is it ODE?!) scandal is of a more sombre tone: I find the fact that airline personal paid any attention to the complaint deeply worrying. Rather that dismissing the worries of this ignorant (or myopic) passenger [and possibly contacting a psychiatrist], they called security and the PDE had to be produced before the economics professor could resume his seat and the flight take off… This incident shows both (i) a trend in irrationality (if associating maths equations with terrorist threat) or ignorance (if confusing maths equation with Arabic writing), not to mention xenophobia and (ii) a readiness of companies and administrations to pester, detain, question and bother anyone with any exotic characteristics. Including solving PDEs or even trying to. [But what can we expect when bottled water or orange marmalade is treated as a potential threat by security checks?] Beside sticking to writing maths in my notebook when I travel, I think I should start signalling to flight attendants truly irrational behaviours of my fellow passengers, like reading newspapers that seem solely concerned by the anatomy of reality TV shows or muttering prayers to a deity at take-off and landing…

ABC model choice via random forests accepted!

Posted in Books, pictures, Statistics, University life with tags , , , , , on October 21, 2015 by xi'an

treerise6“This revision represents a very nice response to the earlier round of reviews, including a significant extension in which the posterior probability of the selected model is now estimated (whereas previously this was not included). The extension is a very nice one, and I am happy to see it included.” Anonymous

Great news [at least for us], our paper on ABC model choice has been accepted by Bioninformatics! With the pleasant comment above from one anonymous referee. This occurs after quite a prolonged gestation, which actually contributed to a shift in our understanding and our implementation of the method. I am still a wee bit unhappy at the rejection by PNAS, but it paradoxically led to a more elaborate article. So all is well that ends well! Except the story is not finished and we have still exploring the multiple usages of random forests in ABC.

SPA 2015 Oxford

Posted in pictures, Statistics, Travel, University life with tags , , , , , , , , , , , , , , on July 14, 2015 by xi'an

Today I gave a talk on Approximate Bayesian model choice via random forests at the yearly SPA (Stochastic Processes and their Applications) 2015 conference, taking place in Oxford (a nice town near Warwick) this year. In Keble College more precisely. The slides are below and while they are mostly repetitions of earlier slides, there is a not inconsequential novelty in the presentation, namely that I included our most recent and current perspective on ABC model choice. Indeed, when travelling to Montpellier two weeks ago, we realised that there was a way to solve our posterior probability conundrum!

campusDespite the heat wave that rolled all over France that week, we indeed figured out a way to estimate the posterior probability of the selected (MAP) model, way that we had deemed beyond our reach in previous versions of the talk and of the paper. The fact that we could not provide an estimate of this posterior probability and had to rely instead on a posterior expected loss was one of the arguments used by the PNAS reviewers in rejecting the paper. While the posterior expected loss remains a quantity worth approximating and reporting, the idea that stemmed from meeting together in Montpellier is that (i) the posterior probability of the MAP is actually related to another posterior loss, when conditioning on the observed summary statistics and (ii) this loss can be itself estimated via a random forest, since it is another function of the summary statistics. A posteriori, this sounds trivial but we had to have a new look at the problem to realise that using ABC samples was not the only way to produce an estimate of the posterior probability! (We are now working on the revision of the paper for resubmission within a few week… Hopefully before JSM!)