Archive for China

a journal of the plague year [post-december reviews]

Posted in Books, Kids, pictures, Travel with tags , , , , , , , , , , , , , , , , , , , , , , , , , , , , , on February 13, 2021 by xi'an

Read a (French) novel by Fred Vargas, Sous les Vents de Neptune, after finding it in the book depository near my office. And enjoyed it very much, partly because it was partly taking place near Ottawa [which I visited many times while my wife was completing her EE Master there] and partly because of the author’s ability to make us doubt the main character and to keep the suspense tight enough for most of the book. There are a trip to Montréal to attend a concert and a journey to Detroit and back to find a lost relation, both reminding me of drives on these roads more than 30 years ago. What annoyed me though was the caricaturesque depiction of the locals, with a Québecois French that sounded overdone. Checking for a local perspective on that aspect, I found a book review in Le Devoir of 2004 sharing the reservation on that aspect, if with humour.  (I would also have rather done without the super-hacker character à la Lisbeth Salander.)

Watched Still Life (三峡好人) a 2006 film by Jia Zhangke, as it was proposed in the list of my local cinema (which I support during the endless lockdown of cinemas and theatres in France). This is an amazing film, which at the same time feels incredibly remote or alien… It follows two characters arriving by boat on the at the Three Gorges Dam under construction in search of a runaway spouse. The search for their respective spouse takes place among the demolition of the old Fengjie, soon to be drowned under 150 meters of dam water. This demolition makes for a unique soundtrack, workers hammering in cadence as blurred black shades against the sky. The dialogues are full of long silences, except for the background hammering, and it often feels theatrical. But the characters maintain a strong dignity throughout the film and the depiction of the last days of Fengjie is gripping. The film received the 2006 Venezia Golden Lion.

Cooked a few Venetian dishes from a Venetian cookbook that was my Xmas gift. And finished that way past-the-date polenta boxes. Managed to escape unscathed from both the bûche and galette weeks! And found that cooking spelt bread with spelt yeast was unbelievably easy, taking less time to work on the dough than to reach the closest bakery!

Could not manage to achieve a coherent discussion with some anti-vaxxer relatives over the Xmas break. And gave up, still hoping they would change their mind.

Watched the first episodes of The Expanse, which started as a collection of eight novels and eight shorter works, before turning into a TV series which won the 2020 Hugo Award. Enjoyable if a rather conventional setting, with the usual disregard for space physics! Reminded me very much of the Takeshi Kovacs novels.  To quote from Wikipedia, “Ty Franck began developing the world of The Expanse initially as the setting for a MMORPG and, after a number of years, for a tabletop roleplaying game.” Some of the actors are terrific (even though Steven Strait’s Holden painfully reminds me of Kit Harrington’s Jon Snow, to the point I wondered for a while if they were the same actor…)

Bayesian phylogeographic inference of SARS-CoV-2

Posted in Books, Statistics, Travel, University life with tags , , , , , , , , , , , , , , , , , on December 14, 2020 by xi'an

Nature Communications of 10 October has a paper by Philippe Lemey et al. (incl. Marc Suchard) on including travel history and removing sampling bias on the study of the virus spread. (Which I was asked to review for a CNRS COVID watch platform, Bibliovid.)

The data is made of curated genomes available in GISAID on March 10, that is, before lockdown even started in France. With (trustworthy?) travel history data for over 20% of the sampled patients. (And an unwelcome reminder that Hong Kong is part of China, at a time of repression and “mainlandisation” by the CCP.)

“we model a discrete diffusion process between 44 locations within China, including 13 provinces, one municipality (Beijing), and one special administrative area (Hong Kong). We fit a generalized linear model (GLM) parameterization of the discrete diffusion process…”

The diffusion is actually a continuous-time Markov process, with a phylogeny that incorporates nodes associated with location. The Bayesian analysis of the model is made by MCMC, since, contrary to ABC, the likelihood can be computed by Felsenstein’s pruning algorithm. The covariates are used to calibrate the Markov process transitions between locations. The paper also includes a posterior predictive accuracy assessment.

“…we generate Markov jump estimates of the transition histories that are averaged over the entire posterior in our Bayesian inference.”

In particular the paper describes “travel-aware reconstruction” analyses that track the spatial path followed by a virus until collection, as below. The top graph represents the posterior probability distribution of this path.Given the lack of representativity, the authors also develop an additional “approach that adds unsampled taxa to assess the sensitivity of inferences to sampling bias”, although it mostly reflects the assumptions made in producing the artificial data. (With a possible connection with ABC?). If I understood correctly, they added 458 taxa for 14 locations,

An interesting opening made in the conclusion about the scalability of the approach:

“With the large number of SARS-CoV-2 genomes now available, the question arises how scalable the incorporation of un-sampled taxa will be. For computationally expensive Bayesian inferences, the approach may need to go hand in hand with down-sampling procedures or more detailed examination of specific sub-lineages.”

In the end, I find it hard, as with other COVID-related papers I read, to check how much the limitations, errors, truncations, &tc., attached with the data at hand impact the validation of this philogeographic reconstruction, and how the model can help further than reconstructing histories of contamination at the (relatively) early stage.

oops…!

Posted in Statistics with tags , , , , , , , , , , on September 22, 2020 by xi'an

Hong Kong under CPC iron fist

Posted in Kids, Travel with tags , , , , , , , on July 14, 2020 by xi'an

“Students in Hong Kong are now banned from any political activity in schools including singing, posting slogans and boycotting classes, the territory’s education minister has said.” BBC, 8 July

“Books by prominent Hong Kong pro-democracy figures have become unavailable in the Chinese-ruled city’s public libraries as they are being reviewed to see whether they violate a new national security law, a government department said.” ABC, 6 July

“Lawyers and legal experts have said China’s national security law for Hong Kong will fundamentally change the territory’s legal system. It introduces new crimes with severe penalties – up to life in prison – and allows mainland security personnel to legally operate in Hong Kong with impunity. The legislation gives Beijing extensive powers it has never had before to shape life in the territory far beyond the legal system.” BBC, 1 July

“Based on the [new] law, the Hong Kong authorities can dictate the way people around the world talk about the city’s contested politics. A Facebook employee could potentially be arrested in Hong Kong if the company failed to hand over user data on someone based in the United States whom Chinese authorities deemed a threat to national security.” NYT, 7 July

Bernoulli-IMS One World Symposium 2020 [accessible to everyone from everywhere!]

Posted in Statistics with tags , , , , , , , on June 25, 2020 by xi'an

[Since the Bernoulli-IMS meeting in Seoul had to be postponed till August 2021, the IMS, the Bernoulli society and the founding organisers of the One World webinars got together to hastily patch up a virtual substitute, resulting in this exciting event, a first on many different reality planes, with a surprisingly positive return from contacted speakers and co-organisers. The first Bernoulli-IMS meeting where the sun never sets! Free of fees and travel costs. Hopefully accessible for “everyone from everywhere”, that is, even from countries with restrictions on Internet access like China and Cuba. Or with poor broadband access.]

Join the Bernoulli Society and IMS for the first-ever, Bernoulli-IMS One World Symposium 2020 August 24-28, 2020! The meeting will be virtual with many new experimental features. Participation at the symposium is free, but registration is mandatory to get the passwords for the Zoom sessions.

Live talks by plenary speakers include Emmanuel Candes, Martin Hairer, Kerrie Mengersen, and Wendelin Werner. The symposium will also include live talks by early career speakers, prerecorded 10-minute talks with discussion sessions, posters, experimental interactive events, and problem solving sessions. Topics from probability and  mathematical statistics are arranged in 23 sessions (with 23 Zoom rooms) to which all researchers are warmly invited to contribute and discuss their original research results. Live talks will be set at two different times in order to reach the most time zones.

Accessible to Everyone from Everywhere!