Archive for ABC

AI and Statistics 2014

Posted in Kids, Mountains, Statistics, Travel, University life with tags , , , , , on April 18, 2014 by xi'an

Today, I am leaving Paris for a 8 day stay in Iceland! This is quite exciting, for many reasons: first, I missed the AISTATS 2013 last year as I was still in the hospital;  second, I am giving a short short tutorial on ABC methods which will be more like a long (two hours)  talk; third, it gives me the fantastic opportunity to visit Iceland for a few days, a place that was top of my wish list of countries to visit. The weather forecast is rather bleak but I am carrying enough waterproof layers to withstand a wee bit of snow and rain… The conference proper starts next Tuesday, April 22, with the tutorials taking place next Friday, April 25. Hence leaving me three completely free days for exploring the area near Reykjavik.

MCqMC 2014 [day #3]

Posted in pictures, Running, Statistics, Travel, University life, Wines with tags , , , , , , , , , , , , , , , , on April 10, 2014 by xi'an


As the second day at MCqMC 2014, was mostly on multi-level Monte Carlo and quasi-Monte Carlo methods, I did not attend many talks but had a long run in the countryside (even saw a pheasant and a heron), worked at “home” on pressing recruiting evaluations and had a long working session with Pierre Jacob. Plus an evening out sampling (just) a few Belgian beers in the shade of the city hall…

Today was more in my ballpark as there were MCMC talks the whole day! The plenary talk was not about MCMC as Erich Novak presented a survey on the many available results bounding the complexity of approximating an integral based on a fixed number of evaluations of the integrand, some involving the dimension (and its curse), some not, some as fast as √n and some not as fast, all this depending on the regularity and the size of the classes of integrands considered. In some cases, the solution was importance sampling, in other cases, quasi-Monte Carlo, and yet other cases were still unsolved. Then Yves Atchadé gave a new perspective on computing the asymptotic variance in the central limit theorem on Markov chains when truncating the autocovariance, Matti Vihola talked about theoretical orderings of Markov chains that transmuted into the very practical consequence that using more simulations in a pseudo-marginal likelihood approximation improved acceptance rate and asymptotic variances (and this applies to aBC-MCMC as well), Radu Craiu proposed a novel processing of adaptive MCMC by treating various approximations to the true target as food for a multiple-try Metropolis algorithm, and Luca Martino had a go at resuscitating the ARMS algorithm of Gilks and Wild (used for a while in BUGS), although the talk did not dissipate all of my misgivings about the multidimensional version! I had more difficulties following the “Warwick session” which was made of four talks by current or former students from Warwick, although I appreciated the complexity of the results in infinite dimensional settings and novel approximations to diffusion based Metropolis algorithms. No further session this afternoon as the “social” activity was to visit the nearby Stella Artois brewery! This activity made us very social, for certain, even though there was hardly a soul around in this massively automated factory. (Maybe an ‘Og post to come one of those days…)

data scientist position

Posted in R, Statistics, University life with tags , , , , , , , , , , on April 8, 2014 by xi'an

Université Paris-DauphineOur newly created Chaire “Economie et gestion des nouvelles données” in Paris-Dauphine, ENS Ulm, École Polytechnique and ENSAE is recruiting a data scientist starting as early as May 1, the call remaining open till the position is filled. The location is in one of the above labs in Paris, the duration for at least one year, salary is varying, based on the applicant’s profile, and the contacts are Stephane Gaiffas (stephane.gaiffas AT cmap DOT, Robin Ryder (ryder AT ceremade DOT and Gabriel Peyré (peyre AT ceremade DOT Here are more details:

Job description

The chaire “Economie et gestion des nouvelles données” is recruiting a talented young engineer specialized in large scale computing and data processing. The targeted applications include machine learning, imaging sciences and finance. This is a unique opportunity to join a newly created research group between the best Parisian labs in applied mathematics and computer science (ParisDauphine, ENS Ulm, Ecole Polytechnique and ENSAE) working hand in hand with major industrial companies (Havas, BNP Paribas, Warner Bros.). The proposed position consists in helping researchers of the group to develop and implement large scale data processing methods, and applying these methods on real life problems in collaboration with the industrial partners.

A non exhaustive list of methods that are currently investigated by researchers of the group, and that will play a key role in the computational framework developed by the recruited engineer, includes :
● Large scale non smooth optimization methods (proximal schemes, interior points, optimization on manifolds).
● Machine learning problems (kernelized methods, Lasso, collaborative filtering, deep learning, learning for graphs, learning for timedependent systems), with a particular focus on large scale problems and stochastic methods.
● Imaging problems (compressed sensing, superresolution).
● Approximate Bayesian Computation (ABC) methods.
● Particle and Sequential Monte Carlo methods

Candidate profile

The candidate should have a very good background in computer science with various programming environments (e.g. Matlab, Python, C++) and knowledge of high performance computing methods (e.g. GPU, parallelization, cloud computing). He/she should adhere to the open source philosophy and possibly be able to interact with the relevant communities (e.g. scikitlearn initiative). Typical curriculum includes engineering school or Master studies in computer science / applied maths / physics, and possibly a PhD (not required).

Working environment

The recruited engineer will work within one of the labs of the chaire. He will benefit from a very stimulating working environment and all required computing resources. He will work in close interaction with the 4 research labs of the chaire, and will also have regular meetings with the industrial partners. More information about the chaire can be found online at

talk in Orsay (message in a beetle)

Posted in Kids, Statistics, Travel, University life with tags , , , , , , , , on April 5, 2014 by xi'an

IMG_0161Yesterday (March 27), I gave a seminar at Paris-Sud University, Orsay, in the stats department, on ABC model choice. It was an opportunity to talk about recent advances we have made with Jean-Michel Marin and Pierre Pudlo on using machine-learning devices to improve ABC. (More to come soon!) And to chat with Gilles Celeux about machine learning and classification. Actually, given that one of my examples was about the Asian lady beetle invasion and that the buildings of the Paris-Sud University have suffered from this invasion, I should have advertised the talk with the more catchy title of “message in a beetle”…

This seminar was also an opportunity to experiment with mixed transportation. Indeed, since I had some errands to run in Paris in morning I decided to bike there (in Paris), work at CREST, and then take my bike in the RER train down to Orsay as I did not have the time and leisure to bike all the 20k there. Since it was the middle of the day, the carriage was mostly empty and I managed to type a blog entry without having to worry about the bike being a nuisance…. The only drag was to enter the platform in Paris (Cité Universitaire) as there was no clear access for bike. Fortunately, a student kindly helped me to get over the gate with my bike, as I could not manage on my own… Nonetheless, I will certainly repeat the experience on my next trip to Orsay (but would not dare take the bike inside/under Paris per se because of the (over-)crowded carriages there).

Pre-processing for approximate Bayesian computation in image analysis

Posted in R, Statistics, University life with tags , , , , , , , , , , , , , on March 21, 2014 by xi'an

ridge6With Matt Moores and Kerrie Mengersen, from QUT, we wrote this short paper just in time for the MCMSki IV Special Issue of Statistics & Computing. And arXived it, as well. The global idea is to cut down on the cost of running an ABC experiment by removing the simulation of a humongous state-space vector, as in Potts and hidden Potts model, and replacing it by an approximate simulation of the 1-d sufficient (summary) statistics. In that case, we used a division of the 1-d parameter interval to simulate the distribution of the sufficient statistic for each of those parameter values and to compute the expectation and variance of the sufficient statistic. Then the conditional distribution of the sufficient statistic is approximated by a Gaussian with these two parameters. And those Gaussian approximations substitute for the true distributions within an ABC-SMC algorithm à la Del Moral, Doucet and Jasra (2012).


Across 20 125 × 125 pixels simulated images, Matt’s algorithm took an average of 21 minutes per image for between 39 and 70 SMC iterations, while resorting to pseudo-data and deriving the genuine sufficient statistic took an average of 46.5 hours for 44 to 85 SMC iterations. On a realistic Landsat image, with a total of 978,380 pixels, the precomputation of the mapping function took 50 minutes, while the total CPU time on 16 parallel threads was 10 hours 38 minutes. By comparison, it took 97 hours for 10,000 MCMC iterations on this image, with a poor effective sample size of 390 values. Regular SMC-ABC algorithms cannot handle this scale: It takes 89 hours to perform a single SMC iteration! (Note that path sampling also operates in this framework, thanks to the same precomputation: in that case it took 2.5 hours for 10⁵ iterations, with an effective sample size of 10⁴…)

Since my student’s paper on Seaman et al (2012) got promptly rejected by TAS for quoting too extensively from my post, we decided to include me as an extra author and submitted the paper to this special issue as well.


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