Archive for Nature

unimaginable scale culling

Posted in Books, pictures, Statistics, Travel with tags , , , , , , , , , , , , , on September 17, 2019 by xi'an

Despite the evidence brought by ABC on the inefficiency of culling in massive proportions the British Isles badger population against bovine tuberculosis, the [sorry excuse for a] United Kingdom government has permitted a massive expansion of badger culling, with up to 64,000 animals likely to be killed this autumn… Since the cows are the primary vectors of the disease, what about starting with these captive animals?!

Nature tidbits

Posted in Books, University life with tags , , , , , , , , , , , on September 7, 2019 by xi'an

Before returning a few older issues of Nature to the coffee room of the maths department, a quick look brought out the few following items of interests, besides the great cover above:

  • France showing the biggest decline in overal output among the top 10 countries in the Nature Index Annual Tables.
  • A tribune again the EU’s Plan S, towards funding (private) publishers directly from public (research) money. Why continuing to support commercial journals one way or another?!
  • A short debate on geo-engineering towards climate control, with the dire warning that “little is known about the consequences” [which could be further damaging the chances of human survival on this planet].
  • Another call for the accountability of companies designing AI towards fairness and unbiasedness [provided all agree on the meaning of these terms]
  • A study that argues that the obesity epidemics is more prevalent in rural than urban areas due to a higher recourse to junk food in the former.
  • A data mining venture in India to mine [not read] 73 million computerised journal articles, which is not yet clearly legal as the publishers object to it. Although the EU (and the UK) have laws authorising mining for non-commercial goals. (And India has looser regulations wrt copyright.)

FALL [book review]

Posted in Books, pictures, Travel with tags , , , , , , , , , , , , , , , , on August 30, 2019 by xi'an

The “last” book I took with me to Japan is Neal Stephenson’s FALL. With subtitle “Dodge in Hell”. It shares some characters with REAMDE but nothing prevents reading it independently as a single volume. Or not reading it at all! I am rather disappointed by the book and hence  sorry I had to carry it throughout Japan and back. And slightly X’ed at Nature writing such a positive review. And at The Guardian. (There is a theme there, as I took REAMDE for a trip to India with a similar feeling at the end. Maybe the sheer weight of the book is pulling my morale down…) The most important common feature to both books is the game industry, since the main (?) character is a game company manager, who is wealthy enough to ensure the rest of the story holds some financial likelihood. And whose training as a game designer impacts the construction of the afterlife that takes a good (or rather terrible) half of the heavy volume. The long minutes leading to his untimely death are also excruciatingly rendered (with none of the experimental nature of Leopold Bloom’s morning). With the side information that Dodge suffers from ocular migraine, a nuisance that visits me pretty regularly since my teenage years! The scientific aspects of the story are not particularly exciting either, since the core concept is that by registering the entire neuronal network of the brain of individuals after their death, a computer could revive them by simulating this network. With dead people keeping their personality if very little of their memories. And even more fanciful, interacting between them and producing a signal that can be understood by (living) humans. Despite having no sensory organs. The reconstruction of a world by the simulated NNs is unbearably slow and frankly uninteresting as it reproduces both living behaviours and borrows very heavily from the great myths, mostly Greek, with no discernible depth. The living side of the story is not much better, although with a little touch of the post-apocalyptic flavour I appreciated in Stephenson. But not enough to recover from the fall.

Among other things that set me off with the book, the complete lack of connection with the massive challenges currently facing humanity. Energy crisis? climate change? Nope. Keep taking an hydroplane to get from Seattle to islands on Puget Sound? Sure. Spending abyssal amounts of energy to animate this electronic Hades? By all means. More and more brittle democracies? Who cares, the Afterworld is a pantheon where gods clash and rule lower beings. Worse, the plot never reaches beyond America, from the heavily focused philosophical or religious background to the character life trajectories. Characters are surprisingly unidimensional, with no default until they become evil. Or die. Academics are not even unidimensional. For instance Sophie’s thesis defence is at best a chat in a café… And talks at a specialist workshop switch from impressive mathematical terms to a 3D representation of the activity of the simulated neuronal networks. Whille these few individuals keep impacting the whole World for their whole life. And beyond… By comparison, the Riverworld series of Phillip José Farmer (that I read forty years ago) is much more enjoyable as a tale of the Afterworld, even if one can object at “famous” people been central to the action. At least there are more of them and, judging from their (first) life, they may have interesting and innovative to say.

on anonymisation

Posted in Books, pictures, Statistics, University life with tags , , , , , , , , , , , on August 2, 2019 by xi'an

An article in the New York Times covering a recent publication in Nature Communications on the ability to identify 99.98% of Americans from almost any dataset with fifteen covariates. And mentioning the French approach of INSEE, more precisely CASD (a branch of GENES, as ENSAE and CREST to which I am affiliated), where my friend Antoine worked for a few years, and whose approach is to vet researchers who want access to non-anonymised data, by creating local working environments on the CASD machines  so that data does not leave the site. The approach is to provide the researcher with a dedicated interface, which “enables access remotely to a secure infrastructure where confidential data is safe from harm”. It further delivers reproducibility certificates for publications, a point apparently missed by the New York Times which advances the lack of reproducibility as a drawback of the method. It also mentions the possibility of doing cryptographic data analysis, again missing the finer details with a lame objection.

“Our paper shows how the likelihood of a specific individual to have been correctly re-identified can be estimated with high accuracy even when the anonymized dataset is heavily incomplete.”

The Nature paper is actually about the probability for an individual to be uniquely identified from the given dataset, which somewhat different from the NYT headlines. Using a copula for the distribution of the covariates. And assessing the model with a mean square error evaluation when what matters are false positives and false negatives. Note that the model need be trained for each new dataset, which reduces the appeal of the claim, especially when considering that individuals tagged as uniquely identified about 6% are not. The statistic of 99.98% posted in the NYT is actually a count on a specific dataset,  the 5% Public Use Microdata Sample files, and Massachusetts residents, and not a general statistic [which would not make much sense!, as I can easily imagine 15 useless covariates] or prediction from the authors’ model. And a wee bit anticlimactic.

Nature snapshots

Posted in Books, pictures with tags , , , , , , , , , on July 16, 2019 by xi'an

In this 6 June issue of Nature, which I read on my way to O’Bayes, an editorial on the scary move by the WHO to incorporate traditional Chinese medicine remedies in its classification as this includes drugs made from protected and endangered species and as such remedies have not been evidence tested. A news brief on India abandoning the requirement for PhD students to get a paper published prior to been awarded the degree, presumably much to the sorrow of predatory publishers. A delay to Plan S (a European project to make all funded research freely available) reported to 21 January 2021. A review of the latest and yet unpublished book by Neal Stephenson, Fall. Which I obviously ordered immediately! A paper in the British Journal of Anasthesia published along with an independent assessment of the same study (methods and results). Some letters protesting the “public’s phobia” induced by the series Chernobyl. Which recoups an email from one of my colleagues on the same complaining theme, since “only 20 deaths” can be attributed to the disaster with certainty! A revisit of the “cold fusion” with no evidence of the claimed phenomenon that led to a scientific outcry in 1989.

natural LaTeX

Posted in Books, Statistics, University life with tags , , , , , , on July 13, 2019 by xi'an

Nature must have been out of inspiration in the past weeks for running a two-page article on LaTeX [as the toolbox column] and how it compares with… Word! Which is not so obvious since most articles in Nature are not involving equations (much) and are from fields where Word prevails. Besides the long-running whine that LaTeX is not he selling argument for this article seemed to be the increasing facility to use (basic) LaTeX commands in forums (like Stack Exchange) and blogs (like WordPress) via MathJax. But the author also pushes for the lighter (R?)Markdown as, “in LaTeX, there is a greater risk that contributors will make changes that prevent the code compiling into a PDF” (which does not make sense to me). This tribune also got me to find out that there is a blog dedicated to the “LaTeX fetish”, which sounds to me like an perfect illustration of Internet vigilantism, especially with arguments like “free and open source software has a strong tendency towards being difficult to install and get up and running”.

aftermaths of retiring significance

Posted in Books, pictures, Statistics, University life with tags , , , , , , on April 10, 2019 by xi'an


Beyond mentions in the general press of the retire significance paper, as in Retraction Watch, Bloomberg, The Guardian, Vox, and NPR, not to mention the large number of comments on Andrew’s blog, and Deborah Mayo’s tribune on a ban on free speech (!), Nature of “the week after” contained three letters from Ioannidis, calling for more stringent thresholds, Johnson, essentially if unclearly stating the same, and my friends from Amsterdam, Alexander Ly and E.J. Wagenmakers, along with Julia Haaf, getting back to the Great Old Ones, to defend the usefulness of testing versus estimation.