Archive for Hong Kong

This is the worst of times

Posted in Statistics with tags , , , , , , on June 19, 2021 by xi'an

the pillar of shame [04 June 1989]

Posted in Kids, pictures with tags , , , , , , , , , on June 4, 2021 by xi'an

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.

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

Save the kids

Posted in Statistics with tags , , , , , , , , , on November 19, 2019 by xi'an