Archive for philogenic trees

JSM 2015 [day #4]

Posted in pictures, Running, Statistics, Travel, University life with tags , , , , , , , , , , , , , , , , , , on August 13, 2015 by xi'an

My first session today was Markov Chain Monte Carlo for Contemporary Statistical Applications with a heap of interesting directions in MCMC research! Now, without any possible bias (!), I would definitely nominate Murray Pollock (incidentally from Warwick) as the winner for best slides, funniest presentation, and most enjoyable accent! More seriously, the scalable Langevin algorithm he developed with Paul Fearnhead, Adam Johansen, and Gareth Roberts, is quite impressive in avoiding computing costly likelihoods. With of course caveats on which targets it applies to. Murali Haran showed a new proposal to handle high dimension random effect models by a projection trick that reduces the dimension. Natesh Pillai introduced us (or at least me!) to a spectral clustering that allowed for an automated partition of the target space, itself the starting point to his parallel MCMC algorithm. Quite exciting, even though I do not perceive partitions as an ideal solution to this problem. The final talk in the session was Galin Jones’ presentation of consistency results and conditions for multivariate quantities which is a surprisingly unexplored domain. MCMC is still alive and running!

The second MCMC session of the morning, Monte Carlo Methods Facing New Challenges in Statistics and Science, was equally diverse, with Lynn Kuo’s talk on the HAWK approach, where we discovered that harmonic mean estimators are still in use, e.g., in MrBayes software employed in phylogenetic inference. The proposal to replace this awful estimator that should never be seen again (!) was rather closely related to an earlier solution of us for marginal likelihood approximation, based there on a partition of the whole space rather than an HPD region in our case… Then, Michael Betancourt brilliantly acted as a proxy for Andrew to present the STAN language, with a flashy trailer he most recently designed. Featuring Andrew as the sole actor. And with great arguments for using it, including the potential to run expectation propagation (as a way of life). In fine, Faming Liang proposed a bootstrap subsampling version of the Metropolis-Hastings algorithm, where the likelihood acknowledging the resulting bias in the limiting distribution.

My first afternoon session was another entry on Statistical Phylogenetics, somewhat continued from yesterday’s session. Making me realised I had not seen a single talk on ABC for the entire meeting! The issues discussed in the session were linked with aligning sequences and comparing  many trees. Again in settings where likelihoods can be computed more or less explicitly. Without any expertise in the matter, I wondered at a construction that would turn all trees, like  into realizations of a continuous model. For instance by growing one branch at a time while removing the MRCA root… And maybe using a particle like method to grow trees. As an aside, Vladimir Minin told me yesterday night about genetic mutations that could switch on and off phenotypes repeatedly across generations… For instance  the ability to glow in the dark for species of deep sea fish.

When stating that I did not see a single talk about ABC, I omitted Steve Fienberg’s Fisher Lecture R.A. Fisher and the Statistical ABCs, keeping the morceau de choix for the end! Even though of course Steve did not mention the algorithm! A was for asymptotics, or ancilarity, B for Bayesian (or biducial??), C for causation (or cuffiency???)… Among other germs, I appreciated that Steve mentioned my great-grand father Darmois in connection with exponential families! And the connection with Jon Wellner’s LeCam Lecture from a few days ago. And reminding us that Savage was a Fisher lecturer himself. And that Fisher introduced fiducial distributions quite early. And for defending the Bayesian perspective. Steve also set some challenges like asymptotics for networks, Bayesian model assessment (I liked the notion of stepping out of the model), and randomization when experimenting with networks. And for big data issues. And for personalized medicine, building on his cancer treatment. No trace of the ABC algorithm, obviously, but a wonderful Fisher’s lecture, also most obviously!! Bravo, Steve, keep thriving!!!

Ebola virus [and Mr. Bayes]

Posted in Statistics, Travel, University life with tags , , , , , , , on August 12, 2014 by xi'an

Just like after the Malaysian Airlines flight 370 disappearance, the current Ebola virus outbreak makes me feel we are sorely missing an emergency statistical force to react on urgent issues… It would indeed be quite valuable to have a team of statisticians at the ready to quantify risks and posterior probabilities and avoid media approximations. The situations calling for this reactive force abound. A few days ago I was reading about the unknown number of missing pro-West activists in Eastern Ukraine. Maybe statistical societies could join forces to set such an emergency team?! Whose goals are somewhat different from the great Statistics without Borders

As a side remark, the above philogeny is taken from Dudas and Rambaut’s recent paper in PLOS reassessing the family tree of the current Ebola virus(es) acting in Guinea. The tree is found using MrBayes, which delivers a posterior probability of 1 to this filiation! And concluding “that the rooting of this clade using the very divergent other ebolavirus species is very problematic.”

Advances in scalable Bayesian computation [day #4]

Posted in Books, Mountains, pictures, R, Statistics, University life with tags , , , , , , , , , , , , , , , , , on March 7, 2014 by xi'an

polyptych painting within the TransCanada Pipeline Pavilion, Banff Centre, Banff, March 21, 2012Final day of our workshop Advances in Scalable Bayesian Computation already, since tomorrow morning is an open research time ½ day! Another “perfect day in paradise”, with the Banff Centre campus covered by a fine snow blanket, still falling…, and making work in an office of BIRS a dream-like moment.

Still looking for a daily theme, parallelisation could be the right candidate, even though other talks this week went into parallelisation issues, incl. Steve’s talk yesterday. Indeed, Anthony Lee gave a talk this morning on interactive sequential Monte Carlo, where he motivated the setting by a formal parallel structure. Then, Darren Wilkinson surveyed the parallelisation issues in Monte Carlo, MCMC, SMC and ABC settings, before arguing in favour of a functional language called Scala. (Neat entries to those topics can be found on Darren’s blog.) And in the afternoon session, Sylvia Frühwirth-Schnatter exposed her approach to the (embarrassingly) parallel problem, in the spirit of Steve’s , David Dunson’s and Scott’s (a paper posted on the day I arrived in Chamonix and hence I missed!). There was plenty to learn from that talk (do not miss the Yin-Yang moment at 25 mn!), but it also helped me to break a difficulty I had with the consensus Bayes representation for two weeks (more on that later!). And, even though Marc Suchard mostly talked about flu and trees in a very pleasant and broad talk, he also had a slide on parallelisation to fit the theme! Although unrelated with parallelism,  Nicolas Chopin’s talk was on sequential quasi-Monte Carlo algorithms: while I had heard previous versions of this talk in Chamonix and BigMC, I found it full of exciting stuff. And it clearly got the room truly puzzled by this possibility, in a positive way! Similarly, Alex Lenkoski spoke about extreme rain events in Norway with no trace of parallelism, but the general idea behind the examples was to question the notion of the calibrated Bayesian (with possible connections with the cut models).

This has been a wonderful week and I am sure the participants got as much as I did from the talks and the informal exchanges. Thanks to BIRS for the sponsorship and the superb organisation of the week (and to the Banff Centre for providing such a paradisical environment). I feel very privileged to have benefited from this support, even though I deadly hope to be back in Banff within a few years.

Robin Ryder’s interview

Posted in Statistics, University life with tags , , , , on March 9, 2011 by xi'an

Robin Ryder—with whom I am sharing an office at CREST, and who is currently doing a postdoc on ABC methods—, got interviewed in the March issue of La Recherche. (The interviewer was Philippe Pajot who wrote “Parcours de mathématiciens”, reviewed in a recent post.) The interview is reproduced on Robin’s blog (in French) and gives in a few words the principles of Bayesian linguistics. This two-page interview also includes a few lines of a technical entry to MCMC (called Monte Carlo Markov chains rather than Markov chain Monte Carlo) that focus on the exploration of huge state-spaces associated with trees. Overall, a very good advertising for MCMC methods for the general public through the highly attractive story of the history of languages…

Incoherent phyleogeographic inference [reply]

Posted in Statistics, University life with tags , , , , , , , , , on September 29, 2010 by xi'an

“Logical overlap is the norm for the complex models analyzed with ABC, so many ABC posterior model probabilities published to date are wrong.” Alan R. Templeton, PNAS, doi:10.1073/pnas.1009012107

Our letter in PNAS about Templeton’s surprising diatribe on Bayesian inference is now appeared in the early edition, along with Templeton’s reply. This reply is unfortunately missing any novelty element compared with the original paper. First, he maintains that the critcism is about ABC (which is, in case you do not know, a computational technique and not a specific statistical methodology!). Second, he insists on the inappropriate Venn diagram analogy by reproducing the basic identity

P(A\cup B\cup C) = P(A)+P(B)+P(C)-P(A\cap B)-P(B\cap C)-P(C\cap A)+P(A\cap B\cap C)

(presumably in case we had lost sight of it!) to argue that using instead


is incoherent (hence rejecting Bayes factors, Bayesian model averaging and so on). I am not particularly surprised by this immutable stance, but it means that there is little point in debate when starting from such positions… Our main goal in publishing this letter was actually to stress that the earlier tribune had no statistical ground and I think we achieved this goal.

Welcome, Robin!

Posted in R, Statistics, University life with tags , , , on February 26, 2010 by xi'an

Robin Ryder started his new blog with his different solutions to Le Monde puzzle of last Saturday (about the algebraic sum of products…), solutions that are much more elegant than my pedestrian rendering. I particularly like the one based on the Jacobian of a matrix! (Robin is doing a postdoc in Dauphine and CREST—under my supervision—on ABC and other computational issues, after completing a PhD in Oxford on philogenic trees for language history with Geoff Nicholls. His talk at the Big’MC seminar last month is reproduced there.)

And, in a totally unrelated way, here is the Sudoku (in Le Monde) that started my post on simulated annealing, nicely represented on Revolutions. (Although I cannot see why the central columns are set in grey…) I must mention that I am quite surprised at the number of visits my post received, given that using simulated annealing for solving Sudokus has been around for a while. Even my R code, while original, does not compete with simulated annealing solutions that take a few seconds… I thus completely share Dirk Eddelbuettel‘s surprise in this respect (but point to him that Robin’s blog entry has nothing to do with Sudokus, but with another Le Monde puzzle!)


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