Archive for Biometrika

a journal of the plague, sword, and famine year

Posted in Books, Kids, Mountains, pictures, Running, Travel, University life with tags , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , on December 9, 2022 by xi'an

Read two successive books about seeking lost sisters, The Last House on Needless Street and Second Sister, after finishing the third book in a row involving a dead god, aptly named Three parts dead. This third one was rather enjoyable, thanks to the world construction, except for a blah ending. The first one, by Catriona Ward, is perplexing, complex and frankly a bit stretched in its gradual exposition of a multiple personality (disorder) patient. The “horror” side never really set for me, which is fine as it never does. Furthermore, this is the very first book I ever read where I saw a few words (correctly) written in Breton, as well as a thread with the Breton myth of ar Ankou, the local Death personification. Kudos for that! The second one, a physical book that I picked rather instinctively / hurriedly in a Barnes & Noble in Philadelphia is a thriller set in Hong Kong. Despite a bit too much of infodump on internet (in)security and hacking, and some caricaturesque sides, incl. the final coup de théâtre!, I enjoyed it as a page-turner. (But I now wonder if I am not getting prejudiced against Kindle books..!) Except for the anti-protest paragraph. Also read a nice BD, Les Animaux Dénaturés, borrowed from Andrew, which is an adaptation the 1952 book by Vercors, that I saw eons ago as a theatre play. The interrogation on what constitutes humanity (vs. simianity) is the driving force of the story, but it is somewhat marred by the killing of a newborn child that seems to negate the whole fight of the main characters.

Thanks to a short (train) visit to Coventry, I stayed overnight in the center of the city and enjoyed a fabulous dinner with friends at Jinseon Korean BBQ Restaurant, recently reviewed by Jay Rayner in The Guardian. Marinated thin slices of beef, pork, and lamb almost immediately cooked on the white hot (ring) coals, along rice and plenty of kimchi and hot sauce. And a sip of soju. Not an everyday fare, for sure, but quite delightful (and even more as my single true meal over two days!)

Watched a fraction of Swedish Black Crab, with Naomi Rapace playing the central character, but despite potential connections with the current survival war of Ukraine against the Russian terror, I quickly lost interest in the very shallow plot and in the accumulation of unrealistic scenes and heavily programmed eliminations of the characters (sorry for the spoiler!). For one thing, expert skaters skating 100km should not take days to cover the distance. For another, a military commando operating in the far North should wear appropriate clothes, not a sweater and a loose scarf!  Luckily enough, I have had no screen nearby [me] to distract me on my round trip flight to NYC from reviewing Biometrika submissions. (The flight back to Paris amazingly took less than 6 hours, thanks to extremely strong tail winds.)

diffusions, sampling, and transport

Posted in Books, pictures, Statistics, Travel, University life with tags , , , , , , , , , , , , , on November 21, 2022 by xi'an

The third and final day of the workshop was shortened for me as I had to catch an early flight back to Paris (and as I got overly conservative in my estimation for returning to JFK, catching a train with no delay at Penn Station and thus finding myself with two hours free before boarding, hence reviewing remaining Biometrika submission at the airport while waiting). As a result I missed the afternoon talks.

The morning was mostly about using scores for simulation (a topic of which I was mostly unaware), with Yang Song giving the introductory lecture on creating better [cf pix left] generative models via the score function, with a massive production of his on the topic (but too many image simulations of dogs, cats, and celebrities!). Estimating directly the score is feasible via Fisher divergence or score matching à la Hyvärinen (with a return of Stein’s unbiased estimator of the risk!). And relying on estimated scores to simulate / generate by Langevin dynamics or other MCMC methods that do not require density evaluations. Due to poor performances in low density / learning regions a fix is randomization / tempering but the resolution (as exposed) sounded clumsy. (And made me wonder at using some more advanced form of deconvolution since the randomization pattern is controlled.) The talk showed some impressive text to image simulations used by an animation studio!


And then my friend Arnaud Doucet continued on the same theme, motivating by estimating normalising constant through annealed importance sampling [Yuling’s meta-perspective comes back to mind in that the geometric mixture is not the only choice, but with which objective]. In AIS, as in a series of Arnaud’s works, like the 2006 SMC Read Paper with Pierre Del Moral and Ajay Jasra, the importance (!) of some auxiliary backward kernels goes beyond theoretical arguments, with the ideally sequence being provided by a Langevin diffusion. Hence involving a score, learned as in the previous talk. Arnaud reformulated this issue as creating a transportation map and its reverse, which is leading to their recent Schrödinger bridge generative model. Which [imho] both brings a unification perspective to his work and an efficient way to bridge prior to posterior in AIS. A most profitable morn for me!

Overall, this was an exhilarating workshop, full of discoveries for me and providing me with the opportunity to meet and exchange with mostly people I had not met before. Thanks to Bob Carpenter and Michael Albergo for organising and running the workshop!

transport, diffusions, and sampling

Posted in pictures, Statistics, Travel, University life with tags , , , , , , , , , , , , , , , , , , , , , , on November 19, 2022 by xi'an

At the Sampling, Transport, and Diffusions workshop at the Flatiron Institute, on Day #2, Marilou Gabrié (École Polytechnique) gave the second introductory lecture on merging sampling and normalising flows targeting the target distribution, when driven by a divergence criterion like KL, that only requires the shape of the target density. I first wondered about ergodicity guarantees in simultaneous MCMC and map training due to the adaptation of the flow but the update of the map only depends on the current particle cloud in (8). From an MCMC perspective, it sounds somewhat paradoxical to see the independent sampler making such an unexpected come-back when considering that no insider information is available about the (complex) posterior to drive the [what-you-get-is-what-you-see] construction of the transport map. However, the proposed approach superposed local (random-walk like) and global (transport) proposals in Algorithm 1.

Qiang Liu followed on learning transport maps, with the  Interesting notion of causalizing a graph by removing intersections (which are impossible for an ODE, as discussed by Eric Vanden-Eijden’s talk yesterday) through  coupling. Which underlies his notion of rectified flows. Possibly connecting with the next lightning talk by Jonathan Weare on spurious modes created by a variational Monte Carlo sampler and the use of stochastic gradient, corrected by (case-dependent?) regularisation.

Then came a whole series of MCMC talks!

Sam Livingstone spoke on Barker’s proposal (an incoming Biometrika paper!) as part of a general class of transforms g of the MH ratio, using jump processes based on a nasty normalising constant related with g (tractable for the original Barker algorithm). I then realised I had missed his StatSci paper on how to speak to statistical physics researchers!

Charles Margossian spoke about using a massive number of short parallel runs (many-short-chain regime) from a recent paper written with Aki,  Andrew, and Lionel Riou-Durand (Warwick) among others. Which brings us back to the challenge of producing convergence diagnostics and precisely the Gelman-Rubin R statistic or its recent nR avatar (with its linear limitations and dependence on parameterisation, as opposed to fuller distributional criteria). The core of the approach is in using blocks of GPUs to improve and speed-up the estimation of the between-chain variance. (D for R².) I still wonder at a waste of simulations / computing power resulting from stopping the runs almost immediately after warm-up is over, since reaching the stationary regime or an approximation thereof should be exploited more efficiently. (Starting from a minimal discrepancy sample would also improve efficiency.)

Lu Zhang also talked on the issue of cutting down warmup, presenting a paper co-authored with Bob, Andrew, and Aki, recommending Laplace / variational approximations for reaching faster high-posterior-density regions, using an algorithm called Pathfinder that relies on ELBO checks to counter poor performances of Laplace approximations. In the spirit of the workshop, it could be profitable to further transform / push-forward the outcome by a transport map.

Yuling Yao (of stacking and Pareto smoothing fame!) gave an original and challenging (in a positive sense) talk on the many ways of bridging densities [linked with the remark he shared with me the day before] and their statistical significance. Questioning our usual reliance on arithmetic or geometric mixtures. Ignoring computational issues, selecting a bridging pattern sounds not different from choosing a parameterised family of embedding distributions. This new typology of models can then be endowed with properties that are more or less appealing. (Occurences of the Hyvärinen score and our mixtestin perspective in the talk!)

Miranda Holmes-Cerfon talked about MCMC on stratification (illustrated by this beautiful picture of nanoparticle random walks). Which means sampling under varying constraints and dimensions with associated densities under the respective Hausdorff measures. This sounds like a perfect setting for reversible jump and in a sense it is, as mentioned in the talks. Except that the moves between manifolds are driven by the proximity to said manifold, helping with a higher acceptance rate, and making the proposals easier to construct since projections (or the reverses) have a physical meaning. (But I could not tell from the talk why the approach was seemingly escaping the symmetry constraint set by Peter Green’s RJMCMC on the reciprocal moves between two given manifolds).

BNP13

Posted in Mountains, pictures, Running, Statistics, Travel with tags , , , , , , , , , , , , , , , , on October 28, 2022 by xi'an

BNP13 is set in this incredible location on a massive lake (almost as large as Lac Saint Jean!) facing several tantalizing snow-capped volcanoes… My trip from Paris to Puerto Varas was quite smooth if relatively longish (but I slept close to 8 hours on the first leg and busied myself with Biometrika submissions the rest of the way). Leaving from Paris at midnight proved a double advantage as this was one of the last flights leaving, with hardly anyone in the airport. On Sunday, I arrived early enough to take a quick dip in Lake Llanquihue which was fairly cold and choppy!

Overall the conference is quite exhilarating as all talks are of interest and often covering on-going research. This may be one of the most engaging meetings I have attended in the past years! Plus a refreshing variety of topics and seniority in the speakers.

To start with a bang!, Sonia Petrone (Bocconi) gave a very nice plenary lecture in the most auspicious manner, covering her recent works on Bayesian prediction as an alternative way to run Bayesian inference (in connection with the incoming Read Paper by Fong et al.). She covered so much ground that I got lost before long (jetlag did not help!). However, an interesting feature underlying her talk is that, under exchangeability, the sequence of predictives converges to a random probability measure, a de Finetti way to construct the prior that is based on predictives. Avoiding in a sense the model and the prior on the parameters of that process. (The parameter is derived from the infinite exchangeable [or conditionally iid] sequence, but the sequence of predictives need be defined.) The drawback is that this approach involves infinite sequences, with practical truncation to a finite horizon being an approximation whose precision / error may prove elusive to characterise. The predictive approach also allows to recover a limiting Normal distribution (not a Bernstein-von Mises type!) and hence credible intervals on parameters and distributions.

While this is indeed a BNP conference (!), I was surprised to see lot of talks paying attention to clustering and even to mixtures, with again a recurrent imprecision on the meaning of a cluster. (Maybe this was already the case for BNP11 in Paris but I may have been too busy helping with catering to notice!) For instance, Brian Trippe (MIT) gave a quick intro on his (AISTATS 2022) work on parallel MCMC with coupling. As unbiased MCMC strongly improving upon naïve parallel MCMC relative to the computing cost. With an interesting example where coupling is agnostic to the labeling of random partitions in clustering problems, involving optimal transport, manageable in O(K³log(K)) time when K is the number of clusters.

a journal of the [tolerated] plague and [mostly] pestilence year

Posted in Books, Kids, Mountains, pictures, Travel, University life with tags , , , , , , , , , , , , , , , , , , , , , on August 31, 2022 by xi'an

Read Among Our Weapons by Ben Aaronovitch, the ninth installment in the Rivers of London urban fantasy series. Which I found superior to the earlier volumes. As the ninth novel in the series, it obviously shows some signs of fatigue in the relatively thin plot that painstakingly connects a series of no-spoilers with the Spanish Inquisition, in the convenient so convenient appearance of a new kind of magical being, and in the convoluted uncovering of this connection in the final pages. However, the witty remarks of Peter Grant still make me smile and his move to becoming a father is rather charming. Recommended for the comforting feeling of being reunited with a familiar.

Over the four week summer period “everyone” was away (on vacations), I managed to deal with long delayed projects, keep my Biometrika slate mostly clean, and work on an incoming grant. Plus, made an uninterrupted series of compotes from my neighbour’s fallen apples and rhubarb sticks from the local market, as I found a much faster way to bake them in the microwave oven, with no danger for kitchen pans! Observing in the process a phase transition phenomenon where the contents very suddenly change structure and the bowl overflows, despite my frequent stirring. And I found time to lazily bike with my wife on weekends to traffic-free Paris, incl. light dinners outside (except during heatwaves), like a nice and perfectly spicy Korean bulgogi near Denfert. Had some DIY experiences as well, incl. changing my 2000 Twingo car battery, which had run flat after at least three months of idleness (now that our children no longer drive it)! Which as usual induced several (dreaded) trips to the DIY store…

Watched Extraordinary Attorney Woo, which is a Korean TV series following an autistic attorney at law, which has some original features but leaves me uneasy about its rather charicaturesque depiction of autism. At least, addressing discrimination and sexism (albeit with mixed results, as in the stereotyped representation of both female heads of the law firms). And The Soul, a Taiwanese horror + sci-fi + noir movie whose foggy atmosphere was rather appealing but alas following a terrible scenario.

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