Archive for Asian lady beetle

would you wear those tee-shirts?!

Posted in Kids, pictures with tags , , , , , on January 25, 2015 by xi'an

Here are two examples of animal “face” tee-shirts I saw advertised in The New York Times and that I would not consider wearing. At any time.

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!

ABC in Le Monde?

Posted in Books, pictures, Statistics, Travel, University life, Wines with tags , , , , , , , , , , on October 29, 2012 by xi'an

In the plane to Chicago, while being stuck on the tarmac at Roissy airport for an hour, I went through my newspapers, only to have the pleasant surprise find in the science leaflet of Le Monde that my co-author Arnaud Estoup, senior researcher at INRA in Montpellier (CBGP), was mentioned in a full page article for his work on the multi-colored Asian lady beetle (Harmonia axyridis, HA), establishing “that the recent burst of worldwide invasions of HA followed a bridgehead scenario, in which an invasive population in eastern North America acted as the source of the colonists that invaded the European, South American and African continents, with some admixture with a biocontrol strain in Europe“. Obviously, Le Monde does not goes as far as mentioning ABC, which was used in our paper to compare scenarios, i.e. to make ABC model choice! (I may also add that the invasion of those Asian bettles in our neighbourhood is a real nuisance and, each Fall, I keep checking for any sign of black beetles inside the house before disaster strikes…)

Despite an inauspicious start (RER B train finishing its trip in Paris and forcing me to board in a hurry a taxi to the airport, abyssal mess at Roissy airport [now, that’s a surprise!], departure delayed by 90 minutes), I got some work done during the nine hour flight, including reading and reviewing a PhD thesis, and I even managed to get my connection from Chicago to Des Moines despite a tight 45 minutes transfer time! At a personal level, this reminded me of the very first time I flew to the US, in August 1987, as it also was through O’Hare and I also had to rush to get my connection to Lafayette, Indiana. Even more anecdotally, this AF0664 flight from Paris to Chicago happened to be the very last one, as the route is discontinued by Air France. The second flight to Des Moines was on a small propeller plane and, despite sitting next to an obnoxious drunk woman who wanted me to know everything about her [dull, so very dull] life, quite pleasant: I finished reading in the Midwest sun the highly entertaining thriller by Cédric Villani, Le Théorème vivant. (Obviously soon to be reviewed on The ‘Og!)