Archive for Melbourne

warp-U bridge sampling

Posted in Books, Statistics, Travel, University life with tags , , , , , , , , , , on October 12, 2016 by xi'an

[I wrote this set of comments right after MCqMC 2016 on a preliminary version of the paper so mileage may vary in terms of the adequation to the current version!]

In warp-U bridge sampling, newly arXived and first presented at MCqMC 16, Xiao-Li Meng continues (in collaboration with Lahzi Wang) his exploration of bridge sampling techniques towards improving the estimation of normalising constants and ratios thereof. The bridge sampling estimator of Meng and Wong (1996) is an harmonic mean importance sampler that requires iterations as it depends on the ratio of interest. Given that the normalising constant of a density does not depend on the chosen parameterisation in the sense that the Jacobian transform preserves this constant, a degree of freedom is in the choice of the parameterisation. This is the idea behind warp transformations. The initial version of Meng and Schilling (2002) used location-scale transforms, while the warp-U solution goes for a multiple location-scale transform that can be seen as based on a location-scale mixture representation of the target. With K components. This approach can also be seen as a sort of artificial reversible jump algorithm when one model is fully known. A strategy Nicolas and I also proposed in our nested sampling Biometrika paper.

Once such a mixture approximation is obtained. each and every component of the mixture can be turned into the standard version of the location-scale family by the appropriate location-scale transform. Since the component index k is unknown for a given X, they call this transform a random transform, which I find somewhat more confusing that helpful. The conditional distribution of the index given the observable x is well-known for mixtures and it is used here to weight the component-wise location-scale transforms of the original distribution p into something that looks rather similar to the standard version of the location-scale family. If no mode has been forgotten by the mixture. The simulations from the original p are then rescaled by one of those transforms, which index k is picked according to the conditional distribution. As explained later to me by XL, the random[ness] in the picture is due to the inclusion of a random ± sign. Still, in the notation introduced in (13), I do not get how the distribution Þ [sorry for using different symbols, I cannot render a tilde on a p] is defined since both ψ and W are random. Is it the marginal? In which case it would read as a weighted average of rescaled versions of p. I have the same problem with Theorem 1 in that I do not understand how one equates Þ with the joint distribution.

Equation (21) is much more illuminating (I find) than the previous explanation in that it exposes the fact that the principle is one of aiming at a new distribution for both the target and the importance function, with hopes that the fit will get better. It could have been better to avoid the notion of random transform, then, but this is mostly a matter of conveying the notion.

On more specifics points (or minutiae), the unboundedness of the likelihood is rarely if ever a problem when using EM. An alternative to the multiple start EM proposal would then be to get sequential and estimate the mixture in a sequential manner, only adding a component when it seems worth it. See eg Chopin and Pelgrin (2004) and Chopin (2007). This could also help with the bias mentioned therein since only a (tiny?) fraction of the data would be used. And the number of components K has an impact on the accuracy of the approximation, as in not missing a mode, and on the computing time. However my suggestion would be to avoid estimating K as this must be immensely costly.

Section 6 obviously relates to my folded Markov interests. If I understand correctly, the paper argues that the transformed density Þ does not need to be computed when considering the folding-move-unfolding step as a single step rather than three steps. I fear the description between equations (30) and (31) is missing the move step over the transformed space. Also on a personal basis I still do not see how to add this approach to our folding methodology, even though the different transforms act as as many replicas of the original Markov chain.

speaker for the dead [book review]

Posted in Books, Kids, Travel with tags , , , , , , , , , , , on October 8, 2016 by xi'an

Here is another book I bought for next to nothing at Beers Book Center in Sacramento. I have read several times Ender’s Game, which I consider as a major science-fiction book, for the fantastic plot, the psychological analysis of the main character, and the deeper reflections about the nature of war and the extermination of other forms of life, even when those are extremely alien. For one reason or another, I never had the opportunity to read the sequel trilogy, which starts with Speaker for the Dead. The 37 hour trip back home from Melbourne was a perfect opportunity to catch up and I read this 1986 instalment in the plane, once I was too tired to read statistics papers on my computer screen. It is a very good (if not major) book, with a lot of threads to philosophy, ethics, ethnology, and (almost) no hard science-fi’ line in that most of the story takes place in a very limited universe, a town on a monotone planet (monotone as in mono-tone, for it enjoys no diversity in both flaura and fauna), with a prohibited access to the rest of the planet, and sentient if alien autochtones. The main plot is thus centred on uncovering the culture and specifics of those autochtones, under strict regulations (from the central planet) preventing cultural contaminations. Or aimed at preventing, as contamination does occur nonetheless. The new culture is quite fascinating in the intricate symbiosis between flaura and fauna, a theme repeated (differently) in Avatar. This progressive uncovering of what first appears as primitive, then cruel, is great. The influence of the Catholic Church is well-rendered, if hard to believe that many centuries in the future, as is the pan- and extra-humanist vision of Ender himself. The concept of Speaker for the Dead is by itself just brilliant! What I like less in the story is the very homely feeling of being in a small provincial town with gossips from everyone about everyone and a lack of broader views. Not that I particularly lean towards space operas, but this secluded atmosphere is at odds with the concept of hundreds of colonised planets by colons from Earth. In particular, assuming that each planet is colonised by people from the same place and culture (Portugal in the current case) does not sound realistic. Anyway, this is a good book and I would have read the sequel Xenocide, had I had it with me during this looong trip.

The Magicians [book review]

Posted in Books, Kids, Travel, Wines with tags , , , , , , , , , on September 17, 2016 by xi'an

While in Melbourne, I heard a recommendation for Lev Grossman’s The Magicians and the next day, while checking the Melbourne Writers Festival bookstore, found the book (rather than the Kristoff volume I was seeking), bought it, and read it within a few days.

‘Brakebills will remind readers of Hogwarts, though with more illicit fondling. Grossman has written what could crudely be labeled a Harry Potter for adults.” , NYT

So is this an Harry Potter for adults?! First, I think Harry Potter can be read by adults (if I qualify as adult!). This remark presumably means the book should not be read by young readers, maybe, due to recurrent sex and alcohol consumption, plus some drugs and an overall depressive tone.

Back to Harry Potter, there is the same magical boarding school feeling, even though it is located in upstate New York on the Hudson river.  And not in Scotland. With an equivalent to Quidditch, an evil magician, exams, surly teens, one or two love triangles, &tc. If in a more modern and American way. The difference with Harry Potter is that it also doubles as Narnia! A Narnia eventually turned wrong and sour, but nonetheless a strong similarity of stories and ideas. Of course, this parallel could be seen as an attempt at deconstruction, exhibiting the inconsistencies in the original novels, but it is so subtle it does not feel like it. There are the same encounters with sentient animal creatures, who never reappear after, the same call for Kings and Queens, as in Narnia. This lack of depth at exploring the connections between Harry Potter, Narnia and even some aspects of the Wheel of Time is frustrating in that something great could have come of it. And then… then… comes the worst literary trick in my list, the call to a subterranean quest with endless monsters and accidents! (I obviously exclude Tolkien’ Moria episode from this list!!!) Concluding with the evil character dumping information in the last battle to explain missing bits and pieces in the story.

So, in conclusion, not such a magical book, even though I read it within a few days thanks to my 39 hour trip back to Paris. The Magicians remains too teeny for my taste, hearing self-deprecating depressive monologues occurs way too often to make the main character congenial, and the story has not enough depth or structure to be compelling. A reviewer rightly pointed out it feels like fandom fiction. Rather than a universe on its own. (As for instance Aaronovitch’ Rivers of London series.)

Darwin’s radio [book review]

Posted in Books, Kids, pictures, University life with tags , , , , , , , , , , , , , , , , on September 10, 2016 by xi'an

When in Sacramento two weeks ago I came across the Beers Books Center bookstore, with a large collection of used and (nearly) new cheap books and among other books I bought Greg Bear’s Darwin Radio. I had (rather) enjoyed another book of his’, Hull Zero Three, not to mention one of his first books, Blood Music, I read in the mid 1980’s, and the premises of this novel sounded promising, not mentioning the Nebula award. The theme is of a major biological threat, apparently due to a new virus, and of the scientific unraveling of what the threat really means. (Spoilers alert!) In that respect it sounds rather similar to the (great) Crichton‘s The Andromeda Strain, which is actually mentioned by some characters in this book. As is Ebola, as a sort of contrapoint (since Ebola is a deadly virus, although the epidemic in Western Africa now seems to have vanished). The biological concept exploited here is dormant DNA in non-coding parts of the genome that periodically get awaken and induce massive steps in the evolution. So massive that carriers of those mutations are killed by locals. Until the day it happens in an all-connected World and the mutation can no longer be stopped. The concept is compelling if not completely convincing of course, while the outcome of a new human race, which is to Homo Sapiens what Homo Sapiens was to Neanderthal, is rather disappointing. (How could it be otherwise?!) But I did appreciate the postulate of a massive and immediate change in the genome, even though the details were disputable and the dismissal of Dawkins‘ perspective poorly defended. From a stylistic perspective, the style is at time heavy, while there are too many chance occurrences, like the main character happening to be in Georgia for a business deal (spoilers, spoilers!) at the times of the opening of collective graves, or the second main character coming upon a couple of Neanderthal mummies with a Sapiens baby, or yet this pair of main characters falling in love and delivering a live mutant baby-girl. But I enjoyed reading it between San Francisco and Melbourne, with a few hours of lost sleep and work. It is a page turner, no doubt! I also like the political undercurrents, from riots to emergency measures, to an effective dictatorship controlling pregnancies and detaining newborns and their mothers.

One important thread in the book deals with anthropology digs getting against Native claims to corpses and general opposition to such digs. This reminded me of a very recent article in Nature where a local Indian tribe had claimed rights to several thousand year old skeletons, whose DNA was then showed to be more related with far away groups than the claimants. But where the tribe was still granted the last word, in a rather worrying jurisprudence.

Melbourne coastline [jatp]

Posted in pictures, Running, Travel with tags , , , , , on August 31, 2016 by xi'an

Melbourne sunrise

Posted in pictures, Running, Travel with tags , , , , , , , , , , on August 28, 2016 by xi'an

off to Australia

Posted in pictures, Statistics, Travel, University life, Wines with tags , , , , , , , , , on August 22, 2016 by xi'an

south bank of the Yarra river, Melbourne, July 21, 2012Taking advantage of being in San Francisco, I flew yesterday to Australia over the Pacific, crossing for the first time the day line. The 15 hour Qantas flight to Sydney was remarkably smooth and quiet, with most passengers sleeping for most of the way, and it gave me a great opportunity to go over several papers I wanted to read and review. Over the next week or so, I will work with my friends and co-authors David Frazier and Gael Martin at Monash University (and undoubtedly enjoy the great food and wine scene!). Before flying back to Paris (alas via San Francisco rather than direct).