Archive for nested sampling

trans-dimensional nested sampling and a few planets

Posted in Books, Statistics, Travel, University life with tags , , , , , , , , , on March 2, 2015 by xi'an

This morning, in the train to Dauphine (train that was even more delayed than usual!), I read a recent arXival of Brendon Brewer and Courtney Donovan. Entitled Fast Bayesian inference for exoplanet discovery in radial velocity data, the paper suggests to associate Matthew Stephens’ (2000)  birth-and-death MCMC approach with nested sampling to infer about the number N of exoplanets in an exoplanetary system. The paper is somewhat sparse in its description of the suggested approach, but states that the birth-date moves involves adding a planet with parameters simulated from the prior and removing a planet at random, both being accepted under a likelihood constraint associated with nested sampling. I actually wonder if this actually is the birth-date version of Peter Green’s (1995) RJMCMC rather than the continuous time birth-and-death process version of Matthew…

“The traditional approach to inferring N also contradicts fundamental ideas in Bayesian computation. Imagine we are trying to compute the posterior distribution for a parameter a in the presence of a nuisance parameter b. This is usually solved by exploring the joint posterior for a and b, and then only looking at the generated values of a. Nobody would suggest the wasteful alternative of using a discrete grid of possible a values and doing an entire Nested Sampling run for each, to get the marginal likelihood as a function of a.”

This criticism is receivable when there is a huge number of possible values of N, even though I see no fundamental contradiction with my ideas about Bayesian computation. However, it is more debatable when there are a few possible values for N, given that the exploration of the augmented space by a RJMCMC algorithm is often very inefficient, in particular when the proposed parameters are generated from the prior. The more when nested sampling is involved and simulations are run under the likelihood constraint! In the astronomy examples given in the paper, N never exceeds 15… Furthermore, by merging all N’s together, it is unclear how the evidences associated with the various values of N can be computed. At least, those are not reported in the paper.

The paper also omits to provide the likelihood function so I do not completely understand where “label switching” occurs therein. My first impression is that this is not a mixture model. However if the observed signal (from an exoplanetary system) is the sum of N signals corresponding to N planets, this makes more sense.

reading classics (The End)

Posted in Books, Kids, Statistics, University life with tags , , , , , , , , , on February 24, 2015 by xi'an

La Défense from Paris-Dauphine, Nov. 15, 2012Today was the final session of our Reading Classics Seminar for the academic year 2014-2015. I have not reported on this seminar much so far because it has had starting problems, namely hardly any student present on the first classes and therefore several re-starts until we reached a small group of interested students. And this is truly The End for this enjoyable experiment as this is the final year for my TSI Master at Paris-Dauphine, as it will become integrated within the new MASH Master next year.

As a last presentation for the entire series, my student picked John Skilling’s Nested Sampling, not that it was in my list of “classics”, but he had worked on the paper in a summer project and was thus reasonably fluent with the topic. As he did a good enough job (!), here are his slides.

Some of the questions that came to me during the talk were on how to run nested sampling sequentially, both in the data and in the number of simulated points, and on incorporating more deterministic moves in order to remove some of the Monte Carlo variability. I was about to ask about (!) the Hamiltonian version of nested sampling but then he mentioned his last summer internship on this very topic! I also realised during that talk that the formula (for positive random variables)

\int_0^\infty(1-F(x))\text{d}x = \mathbb{E}_F[X]

does not require absolute continuity of the distribution F.

nested sampling for systems biology

Posted in Books, Statistics, University life with tags , , , , on January 14, 2015 by xi'an

In conjunction with the recent PNAS paper on massive model choice, Rob Johnson†, Paul Kirk and Michael Stumpf published in Bioinformatics an implementation of nested sampling that is designed for biological applications, called SYSBIONS. Hence the NS for nested sampling! The C software is available on-line. (I had planned to post this news next to my earlier comments but it went under the radar…)

Topological sensitivity analysis for systems biology

Posted in Books, Statistics, Travel, University life with tags , , , , , , on December 17, 2014 by xi'an

Michael Stumpf sent me Topological sensitivity analysis for systems biology, written by Ann Babtie and Paul Kirk,  en avant-première before it came out in PNAS and I read it during the trip to NIPS in Montréal. (The paper is published in open access, so everyone can read it now!) The topic is quite central to a lot of debates about climate change, economics, ecology, finance, &tc., namely to assess the impact of using the wrong model to draw conclusions and make decisions about a real phenomenon. (Which reminded me of the distinction between mechanical and phenomenological models stressed by Michael Blum in his NIPS talk.) And it is of much interest from a Bayesian point of view since assessing the worth of a model requires modelling the “outside” of a model, using for instance Gaussian processes as in the talk Tony O’Hagan gave in Warwick earlier this term. I would even go as far as saying that the issue of assessing [and compensating for] how wrong a model is, given available data, may be the (single) most under-assessed issue in statistics. We (statisticians) have yet to reach our Boxian era.

In Babtie et al., the space or universe of models is represented by network topologies, each defining the set of “parents” in a semi-Markov representation of the (dynamic) model. At which stage Gaussian processes are also called for help. Alternative models are ranked in terms of fit according to a distance between simulated data from the original model (sounds like a form of ABC?!). Obviously, there is a limitation in the number and variety of models considered this way, I mean there are still assumptions made on the possible models, while this number of models is increasing quickly with the number of nodes. As pointed out in the paper (see, e.g., Fig.4), the method has a parametric bootstrap flavour, to some extent.

What is unclear is how one can conduct Bayesian inference with such a collection of models. Unless all models share the same “real” parameters, which sounds unlikely. The paper mentions using uniform prior on all parameters, but this is difficult to advocate in a general setting. Another point concerns the quantification of how much one can trust a given model, since it does not seem models are penalised by a prior probability. Hence they all are treated identically. This is a limitation of the approach (or an indication that it is only a preliminary step in the evaluation of models) in that some models within a large enough collection will eventually provide an estimate that differs from those produced by the other models. So the assessment may become altogether highly pessimistic for this very reason.

“If our parameters have a real, biophysical interpretation, we therefore need to be very careful not to assert that we know the true values of these quantities in the underlying system, just because–for a given model–we can pin them down with relative certainty.”

In addition to its relevance for moving towards approximate models and approximate inference, and in continuation of yesterday’s theme, the paper calls for nested sampling to generate samples from the posterior(s) and to compute the evidence associated with each model. (I realised I had missed this earlier paper by Michael and co-authors on nested sampling for system biology.) There is no discussion in the paper on why nested sampling was selected, compared with, say, a random walk Metropolis-Hastings algorithm. Unless it is used in a fully automated way,  but the paper is rather terse on that issue… And running either approach on 10⁷ models in comparison sounds like an awful lot of work!!! Using importance [sampling] nested sampling as we proposed with Nicolas Chopin could be a way to speed up this exploration if all parameters are identical between all or most models.

an extension of nested sampling

Posted in Books, Statistics, University life with tags , , , , , , , on December 16, 2014 by xi'an

I was reading [in the Paris métro] Hastings-Metropolis algorithm on Markov chains for small-probability estimation, arXived a few weeks ago by François Bachoc, Lionel Lenôtre, and Achref Bachouch, when I came upon their first algorithm that reminded me much of nested sampling: the following was proposed by Guyader et al. in 2011,

To approximate a tail probability P(H(X)>h),

  • start from an iid sample of size N from the reference distribution;
  • at each iteration m, select the point x with the smallest H(x)=ξ and replace it with a new point y simulated under the constraint H(y)≥ξ;
  • stop when all points in the sample are such that H(X)>h;
  • take

\left(1-\dfrac{1}{N}\right)^{m-1}

as the unbiased estimator of P(H(X)>h).

Hence, except for the stopping rule, this is the same implementation as nested sampling. Furthermore, Guyader et al. (2011) also take advantage of the bested sampling fact that, if direct simulation under the constraint H(y)≥ξ is infeasible, simulating via one single step of a Metropolis-Hastings algorithm is as valid as direct simulation. (I could not access the paper, but the reference list of Guyader et al. (2011) includes both original papers by John Skilling, so the connection must be made in the paper.) What I find most interesting in this algorithm is that it even achieves unbiasedness (even in the MCMC case!).

nested sampling with a test

Posted in Books, pictures, Statistics, Travel, University life with tags , , , , , on December 5, 2014 by xi'an

backhomeOn my way back from Warwick, I read through a couple preprints, including this statistical test for nested sampling algorithms by Johannes Buchner. As it happens, I had already read and commented it in July! However, without the slightest memory of it (sad, isn’t it?!), I focussed this time much more on the modification proposed to MultiNest than on the test itself, which is in fact a Kolmogorov-Smirnov test applied to a specific target function.

Indeed, when reading the proposed modification of Buchner, I thought of a modification to the modification that sounded more appealing. Without getting back  to defining nested sampling in detail, this algorithm follows a swarm of N particles within upper-level sets of the likelihood surface, each step requiring a new simulation above the current value of the likelihood. The remark that set me on this time was that we should exploit the fact that (N-1) particles were already available within this level set. And uniformly distributed herein. Therefore this particle cloud should be exploited as much as possible to return yet another particle distributed just as uniformly as the other ones (!). Buchner proposes an alternative to MultiNest based on a randomised version of the maximal distance to a neighbour and a ball centre picked at random (but not uniformly). But it would be just as feasible to draw a distance from the empirical cdf of the distances to the nearest neighbours or to the k-nearest neighbours. With some possible calibration of k. And somewhat more accurate, because this distribution represents the repartition of the particle within the upper-level set. Although I looked at it briefly in the [sluggish] metro from Roissy airport, I could not figure out a way to account for the additional point to be included in the (N-1) existing particles. That is, how to deform the empirical cdf of those distances to account for an additional point. Unless one included the just-removed particle, which is at the boundary of this upper-level set. (Or rather, which defines the boundary of this upper-level set.) I have no clear intuition as to whether or not this would amount to a uniform generation over the true upper-level set. But simulating from the distance distribution would remove (I think) the clustering effect mentioned by Buchner.

“Other priors can be mapped [into the uniform prior over the unit hypercube] using the inverse of the cumulative prior distribution.”

Hence another illustration of the addictive features of nested sampling! Each time I get back to this notion, a new understanding or reinterpretation comes to mind. In any case, an equally endless source of projects for Master students. (Not that I agree with the above quote, mind you!)

a statistical test for nested sampling

Posted in Books, Statistics, University life with tags , , , , , on July 25, 2014 by xi'an

A new arXival on nested sampling: “A statistical test for nested sampling algorithms” by Johannes Buchner. The point of the test is to check if versions of the nested sampling algorithm that fail to guarantee increased likelihood (or nesting) at each step are not missing parts of the posterior mass. and hence producing biased evidence approximations. This applies to MultiNest for instance. This version of nest sampling evaluates the above-threshold region by drawing hyper-balls around the remaining points. A solution which is known to fail in one specific but meaningful case. Buchner’s  arXived paper proposes an hyper-pyramid distribution for which the volume of any likelihood constrained set is known. Hence allowing for a distribution test like Kolmogorov-Smirnov. Confirming the findings of Beaujean and Caldwell (2013). The author then proposes an alternative to MultiNest that is more robust but also much more costly as it computes distances between all pairs of bootstrapped samples. This solution passes the so-called “shrinkage test”, but it is orders of magnitude less efficient than MultiNest. And also simply shows that its coverage is fine for a specific target rather than all possible targets. I wonder if a solution to the problem is at all possible given that evaluating a support or a convex hull is a complex problem which complexity explodes with the dimension.

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