Archive for recurrence

Monte Carlo Markov chains

Posted in Books, Statistics, University life with tags , , , , , , , , , , , , , , , , , , , , , , on May 12, 2020 by xi'an

Darren Wraith pointed out this (currently free access) Springer book by Massimiliano Bonamente [whose family name means good spirit in Italian] to me for its use of the unusual Monte Carlo Markov chain rendering of MCMC.  (Google Trend seems to restrict its use to California!) This is a graduate text for physicists, but one could nonetheless expect more rigour in the processing of the topics. Particularly of the Bayesian topics. Here is a pot-pourri of memorable quotes:

“Two major avenues are available for the assignment of probabilities. One is based on the repetition of the experiments a large number of times under the same conditions, and goes under the name of the frequentist or classical method. The other is based on a more theoretical knowledge of the experiment, but without the experimental requirement, and is referred to as the Bayesian approach.”

“The Bayesian probability is assigned based on a quantitative understanding of the nature of the experiment, and in accord with the Kolmogorov axioms. It is sometimes referred to as empirical probability, in recognition of the fact that sometimes the probability of an event is assigned based upon a practical knowledge of the experiment, although without the classical requirement of repeating the experiment for a large number of times. This method is named after the Rev. Thomas Bayes, who pioneered the development of the theory of probability.”

“The likelihood P(B/A) represents the probability of making the measurement B given that the model A is a correct description of the experiment.”

“…a uniform distribution is normally the logical assumption in the absence of other information.”

“The Gaussian distribution can be considered as a special case of the binomial, when the number of tries is sufficiently large.”

“This clearly does not mean that the Poisson distribution has no variance—in that case, it would not be a random variable!”

“The method of moments therefore returns unbiased estimates for the mean and variance of every distribution in the case of a large number of measurements.”

“The great advantage of the Gibbs sampler is the fact that the acceptance is 100 %, since there is no rejection of candidates for the Markov chain, unlike the case of the Metropolis–Hastings algorithm.”

Let me then point out (or just whine about!) the book using “statistical independence” for plain independence, the use of / rather than Jeffreys’ | for conditioning (and sometimes forgetting \ in some LaTeX formulas), the confusion between events and random variables, esp. when computing the posterior distribution, between models and parameter values, the reliance on discrete probability for continuous settings, as in the Markov chain chapter, confusing density and probability, using Mendel’s pea data without mentioning the unlikely fit to the expected values (or, as put more subtly by Fisher (1936), “the data of most, if not all, of the experiments have been falsified so as to agree closely with Mendel’s expectations”), presenting Fisher’s and Anderson’s Iris data [a motive for rejection when George was JASA editor!] as a “a new classic experiment”, mentioning Pearson but not Lee for the data in the 1903 Biometrika paper “On the laws of inheritance in man” (and woman!), and not accounting for the discrete nature of this data in the linear regression chapter, the three page derivation of the Gaussian distribution from a Taylor expansion of the Binomial pmf obtained by differentiating in the integer argument, spending endless pages on deriving standard properties of classical distributions, this appalling mess of adding over the conditioning atoms with no normalisation in a Poisson experiment

P(X=4|\mu=0,1,2) = \sum_{\mu=0}^2 \frac{\mu^4}{4!}\exp\{-\mu\},

botching the proof of the CLT, which is treated before the Law of Large Numbers, restricting maximum likelihood estimation to the Gaussian and Poisson cases and muddling its meaning by discussing unbiasedness, confusing a drifted Poisson random variable with a drift on its parameter, as well as using the pmf of the Poisson to define an area under the curve (Fig. 5.2), sweeping the improperty of a constant prior under the carpet, defining a null hypothesis as a range of values for a summary statistic, no mention of Bayesian perspectives in the hypothesis testing, model comparison, and regression chapters, having one-dimensional case chapters followed by two-dimensional case chapters, reducing model comparison to the use of the Kolmogorov-Smirnov test, processing bootstrap and jackknife in the Monte Carlo chapter without a mention of importance sampling, stating recurrence results without assuming irreducibility, motivating MCMC by the intractability of the evidence, resorting to the term link to designate the current value of a Markov chain, incorporating the need for a prior distribution in a terrible description of the Metropolis-Hastings algorithm, including a discrete proof for its stationarity, spending many pages on early 1990’s MCMC convergence tests rather than discussing the adaptive scaling of proposal distributions, the inclusion of numerical tables [in a 2017 book] and turning Bayes (1763) into Bayes and Price (1763), or Student (1908) into Gosset (1908).

[Usual disclaimer about potential self-plagiarism: this post or an edited version of it could possibly appear later in my Books Review section in CHANCE. Unlikely, though!]

survivalists [a Riddler’s riddle]

Posted in Books, Kids, R, Statistics with tags , , , , , , on April 22, 2019 by xi'an

A neat question from The Riddler on a multi-probability survival rate:

Nine processes are running in a loop with fixed survivals rates .99,….,.91. What is the probability that the first process is the last one to die? Same question with probabilities .91,…,.99 and the probability that the last process is the last one to die.

The first question means that the realisation of a Geometric G(.99) has to be strictly larger than the largest of eight Geometric G(.98),…,G(.91). Given that the cdf of a Geometric G(a) is [when counting the number of attempts till failure, included, i.e. the Geometric with support the positive integers]

F(x)=\Bbb P(X\le x)=1-a^{x}

the probability that this happens has the nice (?!) representation

\sum_{x=2}^\infty a_1^{x-1}(1-a_1)\prod_{j\ge 2}(1-a_j^{x-1})=(1-a_1)G(a_1,\ldots,a_9)

which leads to an easy resolution by recursion since

G(a_1,\ldots,a_9)=G(a_1,\ldots,a_8)-G(a_1a_9,\ldots,a_8)

and G(a)=a/(1-a)

and a value of 0.5207 returned by R (Monte Carlo evaluation of 0.5207 based on 10⁷ replications). The second question is quite similar, with solution

\sum_{x=2}^\infty a_1^{x-1}(1-a_1)\prod_{j\ge 1}(1-a_j^{x})=a^{-1}(1-a_1)G(a_1,\ldots,a_9)

and value 0.52596 (Monte Carlo evaluation of 0.52581 based on 10⁷ replications).

Gibbs for kidds

Posted in Books, Kids, Statistics, University life with tags , , , , , , , , , , , , , , , on February 12, 2018 by xi'an

 

A chance (?) question on X validated brought me to re-read Gibbs for Kids, 25 years after it was written (by my close friends George and Ed). The originator of the question had difficulties with the implementation, apparently missing the cyclic pattern of the sampler, as in equations (2.3) and (2.4), and with the convergence, which is only processed for a finite support in the American Statistician paper. The paper [which did not appear in American Statistician under this title!, but inspired an animal bredeer, Dan Gianola, to write a “Gibbs for pigs” presentation in 1993 at the 44th Annual Meeting of the European Association for Animal Production, Aarhus, Denmark!!!] most appropriately only contains toy examples since those can be processed and compared to know stationary measures. This is for instance the case for the auto-exponential model

f(x,y) \propto exp(-xy)

which is only defined as a probability density for a compact support. (The paper does not identify the model as a special case of auto-exponential model, which apparently made the originator of the model, Julian Besag in 1974, unhappy, as George and I found out when visiting Bath, where Julian was spending the final year of his life, many years later.) I use the limiting case all the time in class to point out that a Gibbs sampler can be devised and operate without a stationary probability distribution. However, being picky!, I would like to point out that, contrary, to a comment made in the paper, the Gibbs sampler does not “fail” but on the contrary still “converges” in this case, in the sense that a conditional ergodic theorem applies, i.e., the ratio of the frequencies of visits to two sets A and B with finite measure do converge to the ratio of these measures. For instance, running the Gibbs sampler 10⁶ steps and ckecking for the relative frequencies of x’s in (1,2) and (1,3) gives 0.685, versus log(2)/log(3)=0.63, since 1/x is the stationary measure. One important and influential feature of the paper is to stress that proper conditionals do not imply proper joints. George would work much further on that topic, in particular with his PhD student at the time, my friend Jim Hobert.

With regard to the convergence issue, Gibbs for Kids points out to Schervish and Carlin (1990), which came quite early when considering Gelfand and Smith published their initial paper the very same year, but which also adopts a functional approach to convergence, along the paper’s fixed point perspective, somehow complicating the matter. Later papers by Tierney (1994), Besag (1995), and Mengersen and Tweedie (1996) considerably simplified the answer, which is that irreducibility is a necessary and sufficient condition for convergence. (Incidentally, the reference list includes a technical report of mine’s on latent variable model MCMC implementation that never got published.)

A repulsive random walk

Posted in R, Statistics with tags , , , , on May 28, 2010 by xi'an

Matt Asher posted an R experiment on R-bloggers yesterday simulating the random walk

x_{t+1} = x_t + \varepsilon_t / x_t

which has the property of avoiding zero by quickly switching to a large value as soon as x_t is small. He was then wondering about the “convergence” of the random walk given that it moves very little once x_t is large enough. The values he found for various horizons t seemed to indicate a stable regime.

I reran the same experiment as Matt in a Monte Carlo perspective, using the R program

resu=matrix(0,ncol=100,nrow=25)
sampl=rnorm(100)
for (i in 1:25){
  for (t in 2^(i-1):2^i) sampl=sampl+rnorm(100)/sampl
     resu[i,]=sampl
     }
boxplot(as.data.frame(t(abs(resu))),name=as.character(1:25),col="wheat3")

The outcome of this R code plotted above shows that the range and the average of the 100 replications is increasing with t. This behaviour indicates a transient behaviour of the Markov chain, which almost surely goes to infinity and never comes back (because at infinity the variance is zero). Another indication for transience is shown by the fact that x_t comes back to the interval (-1,1) with probability \Phi(-|x_t|), a probability which goes to zero with x_t. As suggested to me by Randal Douc, this transience can be established rigorously by considering

x_{t+1}^2 = x_t^2 + 2\epsilon_t + \epsilon_t^2/x_t^2 > x_t^2 + 2\epsilon_t>2\sum_{i=1}^t \epsilon_t

which is thus bounded from below by a null recurrent process, which almost surely goes to infinity. Therefore the above Markov chain cannot have a stationary distribution or even a stationary measure: it almost surely goes to (plus or minus) infinity.