Archive for desert locust

Nature tidbits [the Bayesian brain]

Posted in Statistics with tags , , , , , , , , , , , , , , on March 8, 2020 by xi'an

In the latest Nature issue, a long cover of Asimov’s contributions to science and rationality. And a five page article on the dopamine reward in the brain seen as a probability distribution, seen as distributional reinforcement learning by researchers from DeepMind, UCL, and Harvard. Going as far as “testing” for this theory with a p-value of 0.008..! Which could be as well a signal of variability between neurons to dopamine rewards (with a p-value of 10⁻¹⁴, whatever that means). Another article about deep learning about protein (3D) structure prediction. And another one about learning neural networks via specially designed devices called memristors. And yet another one on West Africa population genetics based on four individuals from the Stone to Metal age (8000 and 3000 years ago), SNPs, PCA, and admixtures. With no ABC mentioned (I no longer have access to the journal, having missed renewal time for my subscription!). And the literal plague of a locust invasion in Eastern Africa. Making me wonder anew as to why proteins could not be recovered from the swarms of locust to partly compensate for the damages. (Locusts eat their bodyweight in food every day.) And the latest news from NeurIPS about diversity and inclusion. And ethics, as in checking for responsibility and societal consequences of research papers. Reviewing the maths of a submitted paper or the reproducibility of an experiment is already challenging at times, but evaluating the biases in massive proprietary datasets or the long-term societal impact of a classification algorithm may prove beyond the realistic.

locusts in a random forest

Posted in pictures, Statistics, University life with tags , , , , , , , , , , , on July 19, 2019 by xi'an

My friends from Montpellier, where I am visiting today, Arnaud Estoup, Jean-Michel Marin, and Louis Raynal, along with their co-authors, have recently posted on biorXiv a paper using ABC-RF (Random Forests) to analyse the divergence of two populations of desert locusts in Africa. (I actually first heard of their paper by an unsolicited email from one of these self-declared research aggregates.)

“…the present study is the first one using recently developed ABC-RF algorithms to carry out inferences about both scenario choice and parameter estimation, on a real multi-locus microsatellite dataset. It includes and illustrates three novelties in statistical analyses (…): model grouping analyses based on several key evolutionary events, assessment of the quality of predictions to evaluate the robustness of our inferences, and incorporation of previous information on the mutational setting of the used microsatellite markers”.

The construction of the competing models (or scenarios) is built upon data of past precipitations and desert evolution spanning several interglacial periods, back to the middle Pleistocene, concluding at a probable separation in the middle-late stages of the Holocene, which corresponds to the last transition from humid to arid conditions in the African continent. The probability of choosing the wrong model is exploited to determine which model(s) lead(s) to a posterior [ABC] probability lower than the corresponding prior probability, and only one scenario stands this test. As in previous ABC-RF implementations, the summary statistics are complemented by pure noise statistics in order to determine a barrier in the collection of statistics, even though those just above the noise elements (which often cluster together) may achieve better Gini importance by mere chance. An aspect of the paper that I particularly like is the discussion of the various prior modellings one can derive from existing information (or lack thereof) and the evaluation of the impact of these modellings on the resulting inference based on simulated pseudo-data.