Archive for Student’s t distribution

fiducial simulation

Posted in Books, Kids, pictures, Statistics, Travel, University life with tags , , , , , , , , , , , on April 19, 2018 by xi'an

While reading Confidence, Likelihood, Probability), by Tore Schweder and Nils Hjort, in the train from Oxford to Warwick, I came upon this unexpected property shown by Lindqvist and Taraldsen (Biometrika, 2005) that to simulate a sample y conditional on the realisation of a sufficient statistic, T(y)=t⁰, it is sufficient (!!!) to simulate the components of  y as y=G(u,θ), with u a random variable with fixed distribution, e.g., a U(0,1), and to solve in θ the fixed point equation T(y)=t⁰. Assuming there exists a single solution. Brilliant (like an aurora borealis)! To borrow a simple example from the authors, take an exponential sample to be simulated given the sum statistics. As it is well-known, the conditional distribution is then a (rescaled) Beta and the proposed algorithm ends up being a standard Beta generator. For the method to work in general, T(y) must factorise through a function of the u’s, a so-called pivotal condition which brings us back to my post title. If this condition does not hold, the authors once again brilliantly introduce a pseudo-prior distribution on the parameter θ to make it independent from the u’s conditional on T(y)=t⁰. And discuss the choice of the Jeffreys prior as optimal in this setting even when this prior is improper. While the setting is necessarily one of exponential families and of sufficient conditioning statistics, I find it amazing that this property is not more well-known [at least by me!]. And wonder if there is an equivalent outside exponential families, for instance for simulating a t sample conditional on the average of this sample.

a programming bug with weird consequences

Posted in Kids, pictures, R, Statistics, University life with tags , , , , , , on November 25, 2015 by xi'an

One student of mine coded by mistake an independent Metropolis-Hastings algorithm with too small a variance in the proposal when compared with the target variance. Here is the R code of this implementation:

#target is N(0,1)
#proposal is N(0,.01)
for (t in 2:T){
  if (logu[t]>ratav){

It produces outputs of the following shape
smalvarwhich is quite amazing because of the small variance. The reason for the lengthy freezes of the chain is the occurrence with positive probability of realisations from the proposal with very small proposal density values, as they induce very small Metropolis-Hastings acceptance probabilities and are almost “impossible” to leave. This is due to the lack of control of the target, which is flat over the domain of the proposal for all practical purposes. Obviously, in such a setting, the outcome is unrelated with the N(0,1) target!

It is also unrelated with the normal proposal in that switching to a t distribution with 3 degrees of freedom produces a similar outcome:

It is only when using a Cauchy proposal that the pattern vanishes:

Sequentially Constrained Monte Carlo

Posted in Books, Mountains, pictures, Statistics, University life with tags , , , , , , , , , , on November 7, 2014 by xi'an

This newly arXived paper by S. Golchi and D. Campbell from Vancouver (hence the above picture) considers the (quite) interesting problem of simulating from a target distribution defined by a constraint. This is a question that have bothered me for a long while as I could not come up with a satisfactory solution all those years… Namely, when considering a hard constraint on a density, how can we find a sequence of targets that end up with the restricted density? This is of course connected with the zero measure case posted a few months ago. For instance, how do we efficiently simulate a sample from a Student’s t distribution with a fixed sample mean and a fixed sample variance?

“The key component of SMC is the filtering sequence of distributions through which the particles evolve towards the target distribution.” (p.3)

This is indeed the main issue! The paper considers using a sequence of intermediate targets hardening progressively the constraint(s), along with an SMC sampler, but this recommendation remains rather vague and hence I am at loss as to how to make it work when the exact constraint implies a change of measure. The first example is monotone regression where y has mean f(x) and f is monotone. (Everything is unidimensional here.) The sequence is then defined by adding a multiplicative term that is a function of ∂f/∂x, for instance


with τ growing to infinity to make the constraint moving from soft to hard. An interesting introduction, even though the hard constraint does not imply a change of parameter space or of measure. The second example is about estimating the parameters of an ODE, with the constraint being the ODE being satisfied exactly. Again, not exactly what I was looking for. But with an exotic application to deaths from the 1666 Black (Death) plague.

And then the third example is about ABC and the choice of summary statistics! The sequence of constraints is designed to keep observed and simulated summary statistics close enough when the dimension of those summaries increases, which means they are considered simultaneously rather than jointly. (In the sense of Ratmann et al., 2009. That is, with a multidimensional distance.) The model used for the application of the SMC is the dynamic model of Wood (2010, Nature). The outcome of this specific implementation is not that clear compared with alternatives… And again sadly does not deal with the/my zero measure issue.

recycling accept-reject rejections (#2)

Posted in R, Statistics, University life with tags , , , , , , on July 2, 2014 by xi'an

Following yesterday’s post on Rao’s, Liu’s, and Dunson’s paper on a new approach to intractable normalising constants, and taking advantage of being in Warwick, I tested the method on a toy model, namely the posterior associated with n Student’s t observations with unknown location parameter μ and a flat prior,

x_1,\ldots,x_n \sim p(x|\mu) \propto \left[ 1+(x-\mu)^2/\nu \right]^{-(\nu+1)/2}

which is “naturally” bounded by a Cauchy density with scale √ν. The constant M is then easily derived and running the new algorithm follows from a normal random walk proposal targeting the augmented likelihood (R code below).

dunsonAs shown by the above graph, the completion-by-rejection scheme produces a similar outcome (tomato) as the one based on the sole observations (steelblue). With a similar acceptance rate. However, the computing time is much much degraded:

> system.time(g8())
   user  system elapsed
 53.751   0.056  54.103
> system.time(g9())
   user  system elapsed
  1.156   0.000   1.161

when compared with the no-completion version. Here is the entire R code that produced both MCMC samples: Continue reading