Archive for CNRS

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.

Irène Waldspurger, CNRS bronze medal

Posted in Statistics with tags , , , , , , on February 14, 2020 by xi'an

My colleague at Paris Dauphine, Irène Waldspurger, got one of the prestigious CNRS bronze medals this year. Irène is working on inverse problems and machine learning, with applications to sensing and imaging. Congrats!

O’Bayes 19: registration and travel support

Posted in pictures, Running, Travel, University life with tags , , , , , , , on February 14, 2019 by xi'an

An update about the O’Bayes 19 conference next June-July:  the early registration period has now opened. And there should be funds for supporting early-career researchers, thanks to Google and CNRS sponsorships, as detailed below:

Early-career researchers less than four years from PhD, are invited to apply for early-career scholarships. If you are a graduate student, postdoctoral researcher or early-career academic and you are giving a poster, you are eligible to apply. Female researchers and underrepresented minorities are especially encouraged to apply. Selected applicants will receive up to £450, which can be used for any combination of fees, travel and accommodation costs, subject to receipts.

The deadline for applying is the 15th of March (which is also the deadline to submit the abstract for the poster) and it has to be done at the registration phase via the dedicated page. Those who have submitted an abstract before this information on scholarships was made available (11 Feb.) and applying for travel support should contact the organisers.

reading pile for X break

Posted in Books, pictures, Statistics, Travel, University life with tags , , , , , , , , , , , , , , on December 28, 2018 by xi'an

à la maison des mathématiciens [Jean Morlet chair, CIRM, Luminy]

Posted in pictures, Travel, University life with tags , , , , , , , , , , , , , on December 6, 2018 by xi'an