Archive for MCMC

deterministic moves in Metropolis-Hastings

Posted in Books, Kids, R, Statistics with tags , , , , , , , , on July 10, 2020 by xi'an

A curio on X validated where an hybrid Metropolis-Hastings scheme involves a deterministic transform, once in a while. The idea is to flip the sample from one mode, ν, towards the other mode, μ, with a symmetry of the kind

μ-α(x+μ) and ν-α(x+ν)

with α a positive coefficient. Or the reciprocal,

-μ+(μ-x)/α and -ν+(ν-x)/α

for… reversibility reasons. In that case, the acceptance probability is simply the Jacobian of the transform to the proposal, just as in reversible jump MCMC.

Why the (annoying) Jacobian? As explained in the above slides (and other references), the Jacobian is there to account for the change of measure induced by the transform.

Returning to the curio, the originator of the question had spotted some discrepancy between the target and the MCMC sample, as the moments did not fit well enough. For a similar toy model, a balanced Normal mixture, and an artificial flip consisting of

x’=±1-x/2 or x’=±2-2x

implemented by

  u=runif(5)
  if(u[1]<.5){
    mhp=mh[t-1]+2*u[2]-1
    mh[t]=ifelse(u[3]<gnorm(mhp)/gnorm(mh[t-1]),mhp,mh[t-1])
  }else{
    dx=1+(u[4]<.5)
    mhp=ifelse(dx==1,
               ifelse(mh[t-1]<0,1,-1)-mh[t-1]/2,
               2*ifelse(mh[t-1]<0,-1,1)-2*mh[t-1])
    mh[t]=ifelse(u[5]<dx*gnorm(mhp)/gnorm(mh[t-1])/(3-dx),mhp,mh[t-1])

I could not spot said discrepancy beyond Monte Carlo variability.

scalable Langevin exact algorithm [armchair Read Paper]

Posted in Books, pictures, Statistics, Travel, University life with tags , , , , , , , , , , , on June 26, 2020 by xi'an

So, Murray Pollock, Paul Fearnhead, Adam M. Johansen and Gareth O. Roberts presented their Read Paper with discussions on the Wednesday aft! With a well-sized if virtual audience of nearly a hundred people. Here are a few notes scribbled during the Readings. And attempts at keeping the traditional structure of the meeting alive.

In their introduction, they gave the intuition of a quasi-stationary chain as the probability to be in A at time t while still alice as π(A) x exp(-λt) for a fixed killing rate λ. The concept is quite fascinating if less straightforward than stationarity! The presentation put the stress on the available recourse to an unbiased estimator of the κ rate whose initialisation scaled as O(n) but allowed a subsampling cost reduction afterwards. With a subsampling rat connected with Bayesian asymptotics, namely on how quickly the posterior concentrates. Unfortunately, this makes the practical construction harder, since n is finite and the concentration rate is unknown (although a default guess should be √n). I wondered if the link with self-avoiding random walks was more than historical.

The initialisation of the method remains a challenge in complex environments. And hence one may wonder if and how better it does when compared with SMC. Furthermore, while the motivation for using a Brownian motion stems from the practical side, this simulation does not account for the target π. This completely blind excursion sounds worse than simulating from the prior in other settings.

One early illustration for quasi stationarity was based on an hypothetical distribution of lions and wandering (Brownian) antelopes. I found that the associated concept of soft killing was not necessarily well received by …. the antelopes!

As it happens, my friend and coauthor Natesh Pillai was the first discussant! I did no not get the details of his first bimodal example. But he addressed my earlier question about how large the running time T should be. Since the computational cost should be exploding with T. He also drew a analogy with improper posteriors as to wonder about the availability of convergence assessment.

And my friend and coauthor Nicolas Chopin was the second discussant! Starting with a request to… leave the Pima Indians (model)  alone!! But also getting into a deeper assessment of the alternative use of SMCs.

scalable Langevin exact algorithm [Read Paper]

Posted in Books, pictures, Statistics, University life with tags , , , , , , , , , , , , , , , , on June 23, 2020 by xi'an


Murray Pollock, Paul Fearnhead, Adam M. Johansen and Gareth O. Roberts (CoI: all with whom I have strong professional and personal connections!) have a Read Paper discussion happening tomorrow [under relaxed lockdown conditions in the UK, except for the absurd quatorzine on all travelers|, but still in a virtual format] that we discussed together [from our respective homes] at Paris Dauphine. And which I already discussed on this blog when it first came out.

Here are quotes I spotted during this virtual Dauphine discussion but we did not come up with enough material to build a significant discussion, although wondering at the potential for solving the O(n) bottleneck, handling doubly intractable cases like the Ising model. And noticing the nice features of the log target being estimable by unbiased estimators. And of using control variates, for once well-justified in a non-trivial environment.

“However, in practice this simple idea is unlikely to work. We can see this most clearly with the rejection sampler, as the probability of survival will decrease exponentially with t—and thus the rejection probability will often be prohibitively large.”

“This can be viewed as a rejection sampler to simulate from μ(x,t), the distribution of the Brownian motion at time  t conditional on its surviving to time t. Any realization that has been killed is ‘rejected’ and a realization that is not killed is a draw from μ(x,t). It is easy to construct an importance sampling version of this rejection sampler.”

sequential neural likelihood estimation as ABC substitute

Posted in Books, Kids, Statistics, University life with tags , , , , , , , , , , , , , , , , , , on May 14, 2020 by xi'an

A JMLR paper by Papamakarios, Sterratt, and Murray (Edinburgh), first presented at the AISTATS 2019 meeting, on a new form of likelihood-free inference, away from non-zero tolerance and from the distance-based versions of ABC, following earlier papers by Iain Murray and co-authors in the same spirit. Which I got pointed to during the ABC workshop in Vancouver. At the time I had no idea as to autoregressive flows meant. We were supposed to hold a reading group in Paris-Dauphine on this paper last week, unfortunately cancelled as a coronaviral precaution… Here are some notes I had prepared for the meeting that did not take place.

A simulator model is a computer program, which takes a vector of parameters θ, makes internal calls to a random number generator, and outputs a data vector x.”

Just the usual generative model then.

“A conditional neural density estimator is a parametric model q(.|φ) (such as a neural network) controlled by a set of parameters φ, which takes a pair of datapoints (u,v) and outputs a conditional probability density q(u|v,φ).”

Less usual, in that the outcome is guaranteed to be a probability density.

“For its neural density estimator, SNPE uses a Mixture Density Network, which is a feed-forward neural network that takes x as input and outputs the parameters of a Gaussian mixture over θ.”

In which theoretical sense would it improve upon classical or Bayesian density estimators? Where are the error evaluation, the optimal rates, the sensitivity to the dimension of the data? of the parameter?

“Our new method, Sequential Neural Likelihood (SNL), avoids the bias introduced by the proposal, by opting to learn a model of the likelihood instead of the posterior.”

I do not get the argument in that the final outcome (of using the approximation within an MCMC scheme) remains biased since the likelihood is not the exact likelihood. Where is the error evaluation? Note that in the associated Algorithm 1, the learning set is enlarged on each round, as in AMIS, rather than set back to the empty set ∅ on each round.

…given enough simulations, a sufficiently flexible conditional neural density estimator will eventually approximate the likelihood in the support of the proposal, regardless of the shape of the proposal. In other words, as long as we do not exclude parts of the parameter space, the way we propose parameters does not bias learning the likelihood asymptotically. Unlike when learning the posterior, no adjustment is necessary to account for our proposing strategy.”

This is a rather vague statement, with the only support being that the Monte Carlo approximation to the Kullback-Leibler divergence does converge to its actual value, i.e. a direct application of the Law of Large Numbers! But an interesting point I informally made a (long) while ago that all that matters is the estimate of the density at x⁰. Or at the value of the statistic at x⁰. The masked auto-encoder density estimator is based on a sequence of bijections with a lower-triangular Jacobian matrix, meaning the conditional density estimate is available in closed form. Which makes it sounds like a form of neurotic variational Bayes solution.

The paper also links with ABC (too costly?), other parametric approximations to the posterior (like Gaussian copulas and variational likelihood-free inference), synthetic likelihood, Gaussian processes, noise contrastive estimation… With experiments involving some of the above. But the experiments involve rather smooth models with relatively few parameters.

“A general question is whether it is preferable to learn the posterior or the likelihood (…) Learning the likelihood can often be easier than learning the posterior, and it does not depend on the choice of proposal, which makes learning easier and more robust (…) On the other hand, methods such as SNPE return a parametric model of the posterior directly, whereas a further inference step (e.g. variational inference or MCMC) is needed on top of SNL to obtain a posterior estimate”

A fair point in the conclusion. Which also mentions the curse of dimensionality (both for parameters and observations) and the possibility to work directly with summaries.

Getting back to the earlier and connected Masked autoregressive flow for density estimation paper, by Papamakarios, Pavlakou and Murray:

“Viewing an autoregressive model as a normalizing flow opens the possibility of increasing its flexibility by stacking multiple models of the same type, by having each model provide the source of randomness for the next model in the stack. The resulting stack of models is a normalizing flow that is more flexible than the original model, and that remains tractable.”

Which makes it sound like a sort of a neural network in the density space. Optimised by Kullback-Leibler minimisation to get asymptotically close to the likelihood. But a form of Bayesian indirect inference in the end, namely an MLE on a pseudo-model, using the estimated model as a proxy in Bayesian inference…

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!]