running in circles

Posted in Mountains, pictures, Running, Travel with tags , , , , , , , , on May 31, 2020 by xi'an

As lockdown rules concerning outdoor activities were rather restrictive (run alone, away from other people, at most one hour and at most 1km away from home), I used the network of streets around my house to design a 13km circuit that was never replicating more than intersecting previously visited roads. And I ran it every one of the 60 days of the lockdown.

This was a purely urban run on pavement only, but offered nice views of the neighbouring suburbs, with three hills to climb.


And hardly anyone in the streets, except for the occasional soul walking her dog. And never a single control of the laisser-passer I had to print every morn.


Going by the park and the local swimming pool every day and unrealistically wishing they would open soon…

Murderbot 2.0 [book review]

Posted in Kids, Books with tags , , , , , , , , , , , on May 30, 2020 by xi'an

After reading (for free) the (fab) four “murderbot diaries”, I got enough infected to fall for the fifth installment, Network Effect, and buy it upon release on May 5. This is definitely a continuation of the on-going development of the growth of the central character, SecUnit, a rogue android operating free-lance after it hacked its own OS. With private name Murderbot. And  with biological human parts and a more and more human way of thinking. Except it is faster and seriously multitasking. Characters that came to life in All Systems Red (an Amazon bestseller in Science Fiction!) and the following diaries are still around and active, including the super AI ART which is the closest to a friend Murderbot can think of. Corporate entities are still revolving around the story, with an unlimited greed that leads to catastrophes on new planets they turn into mines and often abandon if the economy does not come their way. As previously, a large part of the plot is hardwired in that it involves hacking, killerwares, unfortunate reboots, and hidden recovery files, which sounds like lazy plot lines at times but remains enjoyable. The fact (!) that some characters are androids means that they can even die and be rebooted if a safe copy of their OS is available. Which makes for a schizophrenic and hilarious inner dialogue at a point of the book. The part I found the least convincing cannot be divulged without being a spoiler, but it made the explanation for the bad guys being bad guys lame. And reminded of a terrible short story I had written in high school involving a sentient blurb which… (Well, it was getting worse from there!) But overall, this is quite a fun and enjoyable if rather geeky novel, with witty exchanges (although AIs with deep minds should have been able to come up with better ones!).

fit data to your model [bobologie]

Posted in Kids, Running, Travel with tags , , , , , , , , , , , , on May 29, 2020 by xi'an

A few weeks ago, I contacted my general (and sport) practitioner for a mild issue with hurting toes, as they were indeed hurting and not only during or after my daily runs (!). Since the beginning of lockdown. I thought he would tell me to contact him later and stop running in the meanwhile but instead he told me to come to his office and after a rather cursory glance at said toes started discussing on a rare occurrence of COVID-19 induced frostbite-like toes. He then ordered a blood test which I took the next morn. Right after my (legit and solitary) one hour run. The results of the test were within the “normal” boundaries, except for the D-dimer test which was above the limit and is usually intended for detecting deep venous thrombosis. (As reported on Wikipedia, “a four-fold increase in the D-Dimer protein is a strong indicator of mortality in those suffering from COVID-19.”) This caused my physician to react quickly by prescribing me a cocktail of anticoagulants, corticosteroids and antibiotics. And another test four days later, incl. one for COVID-19. While anticoagulants made sense wrt to the coagulation issues, the corticosteroids were a surprise as they had been earlier pointed out as a potential aggravating cause for younger patients. Including by the French Ministry of Health. I thus asked my daughter for advice, as she had been triaging potential COVID-19 patients in the emergency room for the past month and she was strongly negative about the treatment, both because of the corticosteroids and of the antibiotics. Treatment that was apparently advocated by my practitioner on his own. I thus waited for the second round of blood tests, which returned a lower D-Dimer level and a negative signal for COVID-19. (In the meanwhile, I had spotted a BMJ paper on the possible impact of extended running on the D-Dimer levels and hence waited till the mid-afternoon to take the test!) While this ended up as a non-story, only made more exciting by the lack of competitive events during the lockdown!, I find it interesting that my doctor, who was most reasonably worried about the rising number of COVID-19 among his patients, leaned towards a viral conclusion with little data, as my month-old return to intensive (daily) running was a more likely explanation for sore toes…

a photographer’s demise

Posted in Books, Mountains, pictures, Travel with tags , , , , , on May 28, 2020 by xi'an

ABC in Kuala Lumpur [alas not!]

Posted in Statistics, Travel, University life with tags , , , , , , , on May 28, 2020 by xi'an

While attending an “ABC in…” conference in Malaysia would have been most exciting, barring the current difficulties with traveling, especially since I had not heard of it at an earlier stage and also had never visited Malaysia (except when considering that Singapore was was one of the 14 states of Malaysia from 1963 to 1965), the “International Conference on Approximate Bayesian Computation in Science and Engineering”, scheduled for Feb 2021 is alas not the right opportunity! As a fake conference run by WASET, the “World Academy of Science, Engineering and Technology”, which runs thousands of conferences every year, usually cramming several of them in the very same room at the very same time in a periphery motel..! As attendees, if any, are not expected to… attend. Judging from the current list of “selected papers”, none of them has any connection with ABC. It would be funny, were it not a swindle of sorts…

PhD position for research in ABC in Chalmers University

Posted in Statistics with tags , , , , , , , , , on May 27, 2020 by xi'an

[Posting a call for PhD candidates from Umberto Piccini as the deadline is June 1, next Monday!]

A PhD student position in mathematical statistics on simulation-based inference methods for models with an “intractable” likelihood is available at the Dept. Mathematical Sciences, Chalmers University, Gothenburg (Sweden).

You will be part of an international collaboration to create new methodology bridging between simulation-based inference (such as approximate Bayesian computation and other likelihood-free methods) and deep neuronal networks. The goal is to ease inference for stochastic modelling.

Details on the project and the essential requirements are at

The PhD student position is fully funded and is up to 5 years, in the dynamic and international city of Gothenburg, the second largest city in Sweden, As a PhD student in Mathematical Sciences you will have opportunities for many inspiring conversations, a lot of autonomous work and some travel.

The position will be supervised by Assoc. Prof. Umberto Picchini.

Apply by 01 June 2020 following the instructions at

For informal enquiries, please get in touch with Umberto Picchini

Naturally amazed at non-identifiability

Posted in Books, Statistics, University life with tags , , , , , , , , , , , on May 27, 2020 by xi'an

A Nature paper by Stilianos Louca and Matthew W. Pennell,  Extant time trees are consistent with a myriad of diversification histories, comes to the extraordinary conclusion that birth-&-death evolutionary models cannot distinguish between several scenarios given the available data! Namely, stem ages and daughter lineage ages cannot identify the speciation rate function λ(.), the extinction rate function μ(.)  and the sampling fraction ρ inherently defining the deterministic ODE leading to the number of species predicted at any point τ in time, N(τ). The Nature paper does not seem to make a point beyond the obvious and I am rather perplexed at why it got published [and even highlighted]. A while ago, under the leadership of Steve, PNAS decided to include statistician reviewers for papers relying on statistical arguments. It could time for Nature to move there as well.

“We thus conclude that two birth-death models are congruent if and only if they have the same rp and the same λp at some time point in the present or past.” [S.1.1, p.4]

Or, stated otherwise, that a tree structured dataset made of branch lengths are not enough to identify two functions that parameterise the model. The likelihood looks like

\frac{\rho^{n-1}\Psi(\tau_1,\tau_0)}{1-E(\tau)}\prod_{i=1}^n \lambda(\tau_i)\Psi(s_{i,1},\tau_i)\Psi(s_{i,2},\tau_i)$

where E(.) is the probability to survive to the present and ψ(s,t) the probability to survive and be sampled between times s and t. Sort of. Both functions depending on functions λ(.) and  μ(.). (When the stem age is unknown, the likelihood changes a wee bit, but with no changes in the qualitative conclusions. Another way to write this likelihood is in term of the speciation rate λp


where Λp is the integrated rate, but which shares the same characteristic of being unable to identify the functions λ(.) and μ(.). While this sounds quite obvious the paper (or rather the supplementary material) goes into fairly extensive mode, including “abstract” algebra to define congruence.


“…we explain why model selection methods based on parsimony or “Occam’s razor”, such as the Akaike Information Criterion and the Bayesian Information Criterion that penalize excessive parameters, generally cannot resolve the identifiability issue…” [S.2, p15]

As illustrated by the above quote, the supplementary material also includes a section about statistical model selections techniques failing to capture the issue, section that seems superfluous or even absurd once the fact that the likelihood is constant across a congruence class has been stated.