Archive for phylogenetic tree

reversible chain[saw] massacre

Posted in Books, pictures, R, Statistics, University life with tags , , , , , , , , on May 16, 2016 by xi'an

A paper in Nature this week that uses reversible-jump MCMC, phylogenetic trees, and Bayes factors. And that looks at institutionalised or ritual murders in Austronesian cultures. How better can it get?!

“by applying Bayesian phylogenetic methods (…) we find strong support for models in which human sacrifice stabilizes social stratification once stratification has arisen, and promotes a shift to strictly inherited class systems.” Joseph Watts et al.

The aim of the paper is to establish that societies with human sacrifices are more likely to have become stratified and stable than societies without such niceties. The hypothesis to be tested is then about the evolution towards more stratified societies rather the existence of a high level of stratification.

“The social control hypothesis predicts that human sacrifice (i) co-evolves with social stratification, (ii) increases the chance of a culture gaining social stratification, and (iii) reduces the chance of a culture losing social stratification once stratification has arisen.” Joseph Watts et al.

The methodological question is then how can this be tested when considering those are extinct societies about which little is known. Grouping together moderate and high stratification societies against egalitarian societies, the authors tested independence of both traits versus dependence, with a resulting Bayes factor of 3.78 in favour of the latest. Other hypotheses of a similar flavour led to Bayes factors in the same range. Which is thus not overwhelming. Actually, given that the models are quite simplistic, I do not agree that those Bayes factors prove anything of the magnitude of such anthropological conjectures. Even if the presence/absence of human sacrifices is confirmed in all of the 93 societies, and if the stratification of the cultures is free from uncertainties, the evolutionary part is rather involved, from my neophyte point of view: the evolutionary structure (reproduced above) is based on a sample of 4,200 trees based on Bayesian analysis of Austronesian basic vocabulary items, followed by a call to the BayesTrait software to infer about evolution patterns between stratification levels, concluding (with p-values!) at a phylogenetic structure of the data. BayesTrait was also instrumental in deriving MLEs for the various transition rates, “in order to inform our choice of priors” (!). BayesTrait has an MCMC function used by the authors “to test for correlated evolution between traits” and derive the above Bayes factors. Using a stepping-stone method I am unaware of. And 10⁹ iterations (repeated 3 times for checking consistency)… Reversible jump is apparently used to move between constrained and unconstrained models, leading to the pie charts at the inner nodes of the above picture. Again a by-product of BayesTrait. The trees on the left and the right are completely identical, the difference being in the inference about stratification evolution (right) and sacrifice evolution (left). While the overall hypothesis makes sense at my layman level (as a culture has to be stratified enough to impose sacrifices from its members), I am not convinced that this involved statistical analysis brings that strong a support. (But it would make a fantastic topic for an undergraduate or a Master thesis!)

JSM 2015 [day #3]

Posted in Books, Statistics, University life with tags , , , , , , , , , , on August 12, 2015 by xi'an

My first morning session was about inference for philogenies. While I was expecting some developments around Kingman’s  coalescent models my coauthors needed and developped ABC for, I was surprised to see models that were producing closed form (or close enough to) likelihoods. Due to strong restrictions on the population sizes and migration possibilities, as explained later to me by Vladimir Minin. No need for ABC there since MCMC was working on the species trees, with Vladimir Minin making use of [the Savage Award winner] Vinayak Rao’s approach on trees that differ from the coalescent. And enough structure to even consider and demonstrate tree identifiability in Laura Kubatko’s case.

I then stopped by the astrostatistics session as the first talk by Gwendolin Eddie was about galaxy mass estimation, a problem I may actually be working on in the Fall, but it ended up being a completely different problem and I was further surprised that the issue of whether or not the data was missing at random was not considered by the authors.searise3

Christening a session Unifying foundation(s) may be calling for trouble, at least from me! In this spirit, Xiao Li Meng gave a talk attempting at a sort of unification of the frequentist, Bayesian, and fiducial paradigms by introducing the notion of personalized inference, which is a notion I had vaguely thought of in the past. How much or how far do you condition upon? However, I have never thought of this justifying fiducial inference in any way and Xiao Li’s lively arguments during and after the session not enough to convince me of the opposite: Prior-free does not translate into (arbitrary) choice-free. In the earlier talk about confidence distributions by Regina Liu and Minge Xie, that I partly missed for Galactic reasons, I just entered into the room at the very time when ABC was briefly described as a confidence distribution because it was not producing a convergent approximation to the exact posterior, a logic that escapes me (unless those confidence distributions are described in such a loose way as to include about any method f inference). Dongchu Sun also gave us a crash course on reference priors, with a notion of random posteriors I had not heard of before… As well as constructive posteriors… (They seemed to mean constructible matching priors as far as I understood.)

The final talk in this session by Chuanhei Liu on a new approach (modestly!) called inferential model was incomprehensible, with the speaker repeatedly stating that the principles were too hard to explain in five minutes and needed an incoming book… I later took a brief look at an associated paper, which relates to fiducial inference and to Dempster’s belief functions. For me, it has the same Münchhausen feeling of creating a probability out of nothing, creating a distribution on the parameter by ignoring the fact that the fiducial equation x=a(θ,u) modifies the distribution of u once x is observed.

NIPS 2014

Posted in Kids, pictures, Statistics, Travel, University life with tags , , , , , , , , , , , on December 15, 2014 by xi'an

mugSecond and last day of the NIPS workshops! The collection of topics was quite broad and would have made my choosing an ordeal, except that I was invited to give a talk at the probabilistic programming workshop, solving my dilemma… The first talk by Kathleen Fisher was quite enjoyable in that it gave a conceptual discussion of the motivations for probabilistic languages, drawing an analogy with the early days of computer programming that saw a separation between higher level computer languages and machine programming, with a compiler interface. And calling for a similar separation between the models faced by statistical inference and machine-learning and the corresponding code, if I understood her correctly. This was connected with Frank Wood’s talk of the previous day where he illustrated the concept through a generation of computer codes to approximately generate from standard distributions like Normal or Poisson. Approximately as in ABC, which is why the organisers invited me to talk in this session. However, I was a wee bit lost in the following talks and presumably lost part of my audience during my talk, as I realised later to my dismay when someone told me he had not perceived the distinction between the trees in the random forest procedure and the phylogenetic trees in the population genetic application. Still, while it had for me a sort of Twilight Zone feeling of having stepped in another dimension, attending this workshop was an worthwhile experiment as an eye-opener into a highly different albeit connected field, where code and simulator may take the place of a likelihood function… To the point of defining Hamiltonian Monte Carlo directly on the former, as Vikash Mansinghka showed me at the break.

I completed the day with the final talks in the variational inference workshop, if only to get back on firmer ground! Apart from attending my third talk by Vikash in the conference (but on a completely different topic on variational approximations for discrete particle-ar distributions), a talk by Tim Salimans linked MCMC and variational approximations, using MCMC and HMC to derive variational bounds. (He did not expand on the opposite use of variational approximations to build better proposals.) Overall, I found these two days and my first NIPS conference quite exciting, if somewhat overpowering, with a different atmosphere and a different pace compared with (small or large) statistical meetings. (And a staggering gender imbalance!)