Archive for nested sampling

unbiased consistent nested sampling via sequential Monte Carlo [a reply]

Posted in pictures, Statistics, Travel with tags , , , , , , , , on June 13, 2018 by xi'an

Rob Salomone sent me the following reply on my comments of yesterday about their recently arXived paper.

Our main goal in the paper was to show that Nested Sampling (when interpreted a certain way) is really just a member of a larger class of SMC algorithms, and exploring the consequences of that. We should point out that the section regarding calibration applies generally to SMC samplers, and hope that people give those techniques a try regardless of their chosen SMC approach.
Regarding your question about “whether or not it makes more sense to get completely SMC and forego any nested sampling flavour!”, this is an interesting point. After all, if Nested Sampling is just a special form of SMC, why not just use more standard SMC approaches? It seems that the Nested Sampling’s main advantage is its ability to cope with problems that have “phase transition’’ like behaviour, and thus is robust to a wider range of difficult problems than annealing approaches. Nevertheless, we hope this way of looking at NS (and showing that there may be variations of SMC with certain advantages) leads to improved NS and SMC methods down the line.  
Regarding your post, I should clarify a point regarding unbiasedness. The largest likelihood bound is actually set to infinity. Thus, for the fixed version of NS—SMC, one has an unbiased estimator of the “final” band. Choosing a final band prematurely will of course result in very high variance. However, the estimator is unbiased. For example, consider NS—SMC with only one strata. Then, the method reduces to simply using the prior as an importance sampling distribution for the posterior (unbiased, but often high variance).
Comments related to two specific parts of your post are below (your comments in italicised bold):
“Which never occurred as the number one difficulty there, as the simplest implementation runs a Markov chain from the last removed entry, independently from the remaining entries. Even stationarity is not an issue since I believe that the first occurrence within the level set is distributed from the constrained prior.”
This is an interesting point that we had not considered! In practice, and in many papers that apply Nested Sampling with MCMC, the common approach is to start the MCMC at one of the randomly selected “live points”, so the discussion related to independence was in regard to these common implementations.
Regarding starting the chain from outside of the level set. This is likely not done in practice as it introduces an additional difficulty of needing to propose a sample inside the required region (Metropolis–Hastings will have non—zero probability of returning a sample that is still outside the constrained region for any fixed number of iterations). Forcing the continuation of MCMC until a valid point is proposed I believe will be a subtle violation of detailed balance. Of course, the bias of such a modification may be small in practice, but it is an additional awkwardness introduced by the requirement of sample independence!
“And then, in a twist that is not clearly explained in the paper, the focus moves to an improved nested sampler that moves one likelihood value at a time, with a particle step replacing a single  particle. (Things get complicated when several particles may take the very same likelihood value, but randomisation helps.) At this stage the algorithm is quite similar to the original nested sampler. Except for the unbiased estimation of the constants, the  final constant, and the replacement of exponential weights exp(-t/N) by powers of (N-1/N)”
Thanks for pointing out that this isn’t clear, we will try to do better in the next revision! The goal of this part of the paper wasn’t necessarily to propose a new version of nested sampling. Our focus here was to demonstrate that NS–SMC is not simply the Nested Sampling idea with an SMC twist, but that the original NS algorithm with MCMC (and restarting the MCMC sampling at one of the “live points’” as people do in practice) actually is a special case of SMC (with the weights replaced with a suboptimal choice).
The most curious thing is that, as you note, the estimates of remaining prior mass in the SMC context come out as powers of (N-1)/N and not exp(-t/N). In the paper by Walter (2017), he shows that the former choice is actually superior in terms of bias and variance. It was a nice touch that the superior choice of weights came out naturally in the SMC interpretation! 
That said, as the fixed version of NS-SMC is the one with the unbiasedness and consistency properties, this was the version we used in the main statistical examples.

unbiased consistent nested sampling via sequential Monte Carlo

Posted in pictures, Statistics, Travel with tags , , , , , , , , on June 12, 2018 by xi'an

“Moreover, estimates of the marginal likelihood are unbiased.” (p.2)

Rob Salomone, Leah South, Chris Drovandi and Dirk Kroese (from QUT and UQ, Brisbane) recently arXived a paper that frames the nested sampling in such a way that marginal likelihoods can be unbiasedly (and consistently) estimated.

“Why isn’t nested sampling more popular with statisticians?” (p.7)

A most interesting question, especially given its popularity in cosmology and other branches of physics. A first drawback pointed out in the c is the requirement of independence between the elements of the sample produced at each iteration. Which never occurred as the number one difficulty there, as the simplest implementation runs a Markov chain from the last removed entry, independently from the remaining entries. Even stationarity is not an issue since I believe that the first occurrence within the level set is distributed from the constrained prior.

A second difficulty is the use of quadrature which turns integrand into step functions at random slices. Indeed, mixing Monte Carlo with numerical integration makes life much harder, as shown by the early avatars of nested sampling that only accounted for the numerical errors. (And which caused Nicolas and I to write our critical paper in Biometrika.) There are few studies of that kind in the literature, the only one I can think of being [my former PhD student] Anne Philippe‘s thesis twenty years ago.

The third issue stands with the difficulty in parallelising the method. Except by jumping k points at once, rather than going one level at a time. While I agree this makes life more complicated, I am also unsure about the severity of that issue as k nested sampling algorithms can be run in parallel and aggregated in the end, from simple averaging to something more elaborate.

The final blemish is that the nested sampling estimator has a stopping mechanism that induces a truncation error, again maybe a lesser problem given the overall difficulty in assessing the total error.

The paper takes advantage of the ability of SMC to produce unbiased estimates of a sequence of normalising constants (or of the normalising constants of a sequence of targets). For nested sampling, the sequence is made of the prior distribution restricted to an embedded sequence of level sets. With another sequence restricted to bands (likelihood between two likelihood boundaries). If all restricted posteriors of the second kind and their normalising constant are known, the full posterior is known. Apparently up to the main normalising constant, i.e. the marginal likelihood., , except that it is also the sum of all normalising constants. Handling this sequence by SMC addresses the four concerns of the four authors, apart from the truncation issue, since the largest likelihood bound need be set for running the algorithm.

When the sequence of likelihood bounds is chosen based on the observed likelihoods so far, the method becomes adaptive. Requiring again the choice of a stopping rule that may induce bias if stopping occurs too early. And then, in a twist that is not clearly explained in the paper, the focus moves to an improved nested sampler that moves one likelihood value at a time, with a particle step replacing a single particle. (Things get complicated when several particles may take the very same likelihood value, but randomisation helps.) At this stage the algorithm is quite similar to the original nested sampler. Except for the unbiased estimation of the constants, the final constant, and the replacement of exponential weights exp(-t/N) by powers of (N-1/N).

The remainder of this long paper (61 pages!) is dedicated to practical implementation, calibration and running a series of comparisons. A nice final touch is the thanks to the ‘Og for its series of posts on nested sampling, which “helped influence this work, and played a large part in inspiring it.”

In conclusion, this paper is certainly a worthy exploration of the nested sampler, providing further arguments towards a consistent version, with first and foremost an (almost?) unbiased resolution. The comparison with a wide range of alternatives remains open, in particular time-wise, if evidence is the sole target of the simulation. For instance, the choice of this sequence of targets in an SMC may be improved by another sequence, since changing one particle at a time does not sound efficient. The complexity of the implementation and in particular of the simulation from the prior under more and more stringent constraints need to be addressed.

nested sampling when prior and likelihood clash

Posted in Books, Statistics with tags , , , , , , , , , on April 3, 2018 by xi'an

A recent arXival by Chen, Hobson, Das, and Gelderblom makes the proposal of a new nested sampling implementation when prior and likelihood disagree, making simulations from the prior inefficient. The paper holds the position that a single given prior is used over and over all datasets that come along:

“…in applications where one wishes to perform analyses on many thousands (or even millions) of different datasets, since those (typically few) datasets for which the prior is unrepresentative can absorb a large fraction of the computational resources.” Chen et al., 2018

My reaction to this situation, provided (a) I want to implement nested sampling and (b) I realise there is a discrepancy, would be to resort to an importance sampling resolution, as we proposed in our Biometrika paper with Nicolas. Since one objection [from the authors] is that identifying outlier datasets is complicated (it should not be when the likelihood function can be computed) and time-consuming, sequential importance sampling could be implemented.

“The posterior repartitioning (PR) method takes advantage of the fact that nested sampling makes use of the likelihood L(θ) and prior π(θ) separately in its exploration of the parameter space, in contrast to Markov chain Monte Carlo (MCMC) sampling methods or genetic algorithms which typically deal solely in terms of the product.” Chen et al., 2018

The above salesman line does not ring a particularly convincing chime in that nested sampling is about as myopic as MCMC since based on the similar notion of a local proposal move, starting from the lowest likelihood argument (the minimum likelihood estimator!) in the nested sample.

“The advantage of this extension is that one can choose (π’,L’) so that simulating from π’ under the constraint L'(θ) > l is easier than simulating from π under the constraint L(θ) > l. For instance, one may choose an instrumental prior π’ such that Markov chain Monte Carlo steps adapted to the instrumental constrained prior are easier to implement than with respect to the actual constrained prior. In a similar vein, nested importance sampling facilitates contemplating several priors at once, as one may compute the evidence for each prior by producing the same nested sequence, based on the same pair (π’,L’), and by simply modifying the weight function.” Chopin & Robert, 2010

Since the authors propose to switch to a product (π’,L’) such that π’.L’=π.L, the solution appears like a special case of importance sampling, with the added drwaback that when π’ is not normalised, its normalised constant must be estimated as well. (With an extra nested sampling implementation?) Furthermore, the advocated solution is to use tempering, which is not so obvious as it seems in small dimensions. As the mass does not always diffuse to relevant parts of the space. A more “natural” tempering would be to use a subsample in the (sub)likelihood for nested sampling and keep the remainder of the sample for weighting the evaluation of the evidence.

divide & reconquer

Posted in Books, Statistics, University life with tags , , , , , , , , , , on February 5, 2018 by xi'an

Qi Liu, Anindya Bhadra, and William Cleveland from Purdue have arXived a paper entitled Divide and Recombine for Large and Complex Data: Model Likelihood Functions using MCMC. Which is a variation on the earlier divide & … papers attempting at handling large datasets. The beginning is quite similar to these earlier papers in that the likelihood is split into sub-likelihoods, approximated from MCMC samples and recombined into an approximate full likelihood. As in for instance Scott et al. one approximation use for the subsample is to replace the likelihood with a Normal approximation, or a skew Normal generalisation, which remains  a limited choice for heavy tailed likelihoods. Producing a Normal and skew-Normal approximation for the whole [data] likelihood, respectively. If I understand correctly, these approximations are missing a normalising constant to bring them to scale with the true likelihood, which I do not completely understand as the likelihood only needs to be defined up to a [constant] constant for most purposes, including Bayesian ones. The  method of estimation of this constant proposed therein is called the contour probability algorithm and it consists in using a highest density region to compare a likelihood and its approximation. (Nothing to do with our adaptation of Gelfand and Dey (1994) based on HPDs, with Darren Wright. Nor with nested sampling.) Returning a form of qq-plot. This is rather exploratory, while hardly addressing the issue of the precision of such approximations and the resolution of conflicting proposals. And the comparison with all these other recent proposals for splitting likelihoods into manageable bits (proposals that are mentioned in the final section, including our recentering scheme with my student Changye Wu).

WBIC, practically

Posted in Statistics with tags , , , , , , , , , on October 20, 2017 by xi'an

“Thus far, WBIC has received no more than a cursory mention by Gelman et al. (2013)”

I had missed this 2015  paper by Nial Friel and co-authors on a practical investigation of Watanabe’s WBIC. Where WBIC stands for widely applicable Bayesian information criterion. The thermodynamic integration approach explored by Nial and some co-authors for the approximation of the evidence, thermodynamic integration that produces the log-evidence as an integral between temperatures t=0 and t=1 of a powered evidence, is eminently suited for WBIC, as the widely applicable Bayesian information criterion is associated with the specific temperature t⁰ that makes the power posterior equidistant, Kullback-Leibler-wise, from the prior and posterior distributions. And the expectation of the log-likelihood under this very power posterior equal to the (genuine) evidence. In fact, WBIC is often associated with the sub-optimal temperature 1/log(n), where n is the (effective?) sample size. (By comparison, if my minimalist description is unclear!, thermodynamic integration requires a whole range of temperatures and associated MCMC runs.) In an ideal Gaussian setting, WBIC improves considerably over thermodynamic integration, the larger the sample the better. In more realistic settings, though, including a simple regression and a logistic [Pima Indians!] model comparison, thermodynamic integration may do better for a given computational cost although the paper is unclear about these costs. The paper also runs a comparison with harmonic mean and nested sampling approximations. Since the integral of interest involves a power of the likelihood, I wonder if a safe version of the harmonic mean resolution can be derived from simulations of the genuine posterior. Provided the exact temperature t⁰ is known…

Astrostatistics school

Posted in Mountains, pictures, R, Statistics, Travel, University life with tags , , , , , , , , , , , , , , , , , , , , , on October 17, 2017 by xi'an

What a wonderful week at the Astrostat [Indian] summer school in Autrans! The setting was superb, on the high Vercors plateau overlooking both Grenoble [north] and Valence [west], with the colours of the Fall at their brightest on the foliage of the forests rising on both sides of the valley and a perfect green on the fields at the centre, with sun all along, sharp mornings and warm afternoons worthy of a late Indian summer, too many running trails [turning into X country ski trails in the Winter] to contemplate for a single week [even with three hours of running over two days], many climbing sites on the numerous chalk cliffs all around [but a single afternoon for that, more later in another post!]. And of course a group of participants eager to learn about Bayesian methodology and computational algorithms, from diverse [astronomy, cosmology and more] backgrounds, trainings and countries. I was surprised at the dedication of the participants travelling all the way from Chile, Péru, and Hong Kong for the sole purpose of attending the school. David van Dyk gave the first part of the school on Bayesian concepts and MCMC methods, Roberto Trotta the second part on Bayesian model choice and hierarchical models, and myself a third part on, surprise, surprise!, approximate Bayesian computation. Plus practicals on R.

As it happens Roberto had to cancel his participation and I turned for a session into Christian Roberto, presenting his slides in the most objective possible fashion!, as a significant part covered nested sampling and Savage-Dickey ratios, not exactly my favourites for estimating constants. David joked that he was considering postponing his flight to see me talk about these, but I hope I refrained from engaging into controversy and criticisms… If anything because this was not of interest for the participants. Indeed when I started presenting ABC through what I thought was a pedestrian example, namely Rasmus Baath’s socks, I found that the main concern was not running an MCMC sampler or a substitute ABC algorithm but rather an healthy questioning of the construction of the informative prior in that artificial setting, which made me quite glad I had planned to cover this example rather than an advanced model [as, e.g., one of those covered in the packages abc, abctools, or abcrf]. Because it generated those questions about the prior [why a Negative Binomial? why these hyperparameters? &tc.] and showed how programming ABC turned into a difficult exercise even in this toy setting. And while I wanted to give my usual warning about ABC model choice and argue for random forests as a summary selection tool, I feel I should have focussed instead on another example, as this exercise brings out so clearly the conceptual difficulties with what is taught. Making me quite sorry I had to leave one day earlier. [As did missing an extra run!] Coming back by train through the sunny and grape-covered slopes of Burgundy hills was an extra reward [and no one in the train commented about the local cheese travelling in my bag!]


and another one on nested sampling

Posted in Books, Statistics with tags , , , on May 2, 2017 by xi'an

The same authors as those of the paper discussed last week arXived a paper on dynamic nested sampling.

“We propose modifying the nested sampling algorithm by dynamically varying the number of “live points” in order to maximise the accuracy of a calculation for some number of posterior sample.”

Some of the material is actually quite similar to the previous paper (to the point I had to check they were not the same paper). The authors rightly point out that the main source of variation in the nested sampling approximation is due to the Monte Carlo variability in the estimated volume of the level sets.

The main notion in that paper is that it is acceptable to have a varying number of “live” points in nested sampling provided the weights are correctly accordingly. Adding more of those points as a new “thread” in a region where the likelihood changes rapidly. Addition may occur at any level of the likelihood, in fact, and is determined  in the paper by an importance weight being in the upper tail of the importance weights… While the description is rather vague [for instance I do not get the notation in (9)] and the criteria for adding threads somewhat arbitrary, I find interesting that several passes at different precision levels can improve the efficiency of the nested approximation at a given simulation cost. Remains the issue of whether or not this is a sufficient perk for attracting users of other simulation techniques to the nested galaxy…