ABC for COVID spread reconstruction

A recent Nature paper by Jessica Davis et al. (with an assessment by Simon Cauchemez and X from INSERM) reassessed the appearance of COVID in European and American States. Accounting for the massive under-reporting in the early days since there was no testing. The approach is based on a complex dynamic model whose parameters are estimated by an ABC algorithm (the reference being the PLoS article that initiated the ABC Wikipedia page). Results are quite interesting in that the distribution of the entry dates covers a calendar as early as December 2019 in most cases. And a proportion of missed cases as high as 99%.

“As evidence, E, we considered the cumulative number of SARS-CoV-2 cases internationally imported from China up to January 21, 2020″

The model behind remain a classical SLIR model but with a discrete and stochastic dynamical and a geographical compartmentalization based on a Voronoi tessellation centred at airports, commuting intensity and population density. Interventions by local and State authorities are also accounted for. The ABC version is a standard rejection algorithm with distance based on the evidence as quoted above. Which is a form of cdf distance (as in our Wasserstein ABC paper). For the posterior distribution of the IFR,  a second ABC algorithm uses the relative distance between observed and generated deaths (per country). The paper further investigates different introduction sources (countries) before local transmission was established. For instance, China is shown to be the dominant source for the first EU countries impacted by the pandemics such as Italy, UK, Germany, France and Spain. Using a “counterfactual scenario where the surveillance systems of the US states and European countries are imagined to operate at levels able to identify 50% of all imported and locally generated infections”, the authors conclude that

“broadening testing specifications could have considerably slowed the pandemic progression, buying considerable time to prepare mitigation responses.”

another poor infographics [from Nature, with a warning]

another terrible infographic [jatg]

out-standing scientist

I noticed quite recently that the [Nature] journal Heredity [managed by the Genetics Society] had published an historical / opinion piece on Ronald Fisher and his views on eugenics and race. The authors are all trustees of the Fisher Memorial Trust. The core of the paper contents was also contained in [one of the authors] Stephen Senn’s talk at the JSM round table (I also took part in) and later at the RSS. This is mostly an attempt at resetting Fisher’s position within the era when he lived, in terms of prevalent racism, nationalism, and imperialism. At the core of these woes was a generalised belief in the superiority of some nations, creeds, human groups, even social classes, over others, that was used as a justification in the tragedies of large scale colonialism, the first World War, systemic racism, Nazism, and widespread forced sterilisations….

“More attention to the History of Science is needed, as much by scientists as by historians, and especially by biologists, and this should mean a deliberate attempt to understand the thoughts of the great masters of the past, to see in what circumstances or intellectual milieu their ideas were formed, where they took the wrong turning  track or stopped short of the right.”  R.A. Fisher (1959)

While I am thinking the authors are somewhat stretching the arguments isolating Ronald from the worst manifestations of eugenism and racism, as the concept of “voluntary sterilisation” is more than debatable when applied to patients with limited intellectual abilities, as Fisher considered (in 1943) that the Nazi racial laws “have been successful with the best type of German” (which stands as a fairly stupid statement on so many levels, starting with the one that this racial selection had only started a few years before!) and “that the Party sincerely wished to benefit the German racial stock” (in 1948), my already made point is rather that the general tendency of turning genii into saints is bound to meet with disappointment. (Hence, if we have to stick with them, named lectures, prizes, memorials, &tc., should come with an expiration date!)

Nature & predatory publishers

Nature of 26 October has another article (comment) that I found of general interest, namely a long report on one of the most prolific predatory publishers, OMICS, which got sued by the US Federal Trade Commission for “deceptive business practice”. The authors built a database of articles from fringe publishers. Exhibiting a rebranding of OMICS journals.

“The number of [OMICS] journals has grown faster than the number of publications, suggesting that many journals are shells with little content.”

They also found a massive number of re-published “papers from legitimate sources without crediting the original journal, and sometimes not the original author”. With all kinds of very shoddy attempts at hiding the plagiarism. The obvious problem is that such papers get evaluated by committees and reviewers without being ever read, with the name of the journal playing on the easy confusion with a legitimate journal. Except in the glaringly obvious cases. The recommendations from the authors include requesting for open peer reviews, linking funded publication costs to an adherence to some minimal transparency rules, moving to low-cost institutional platforms, and, more importantly, rewind the evaluation rules in academia so that low-quality, plagiarising, or otherwise illegitimate papers get identified as such, rather than betting on the reviewers spotting an already-known predatory journal or conference…