Archive for cosmoPMC

astroABC: ABC SMC sampler for cosmological parameter estimation

Posted in Books, R, Statistics, University life with tags , , , , , , , , on September 6, 2016 by xi'an

“…the chosen statistic needs to be a so-called sufficient statistic in that any information about the parameter of interest which is contained in the data, is also contained in the summary statistic.”

Elise Jenningsa and Maeve Madigan arXived a paper on a new Python code they developed for implementing ABC-SMC, towards astronomy or rather cosmology applications. They stress the parallelisation abilities of their approach which leads to “crucial speed enhancement” against the available competitors, abcpmc and cosmoabc. The version of ABC implemented there is “our” ABC PMC where particle clouds are shifted according to mixtures of random walks, based on each and every point of the current cloud, with a scale equal to twice the estimated posterior variance. (The paper curiously refers to non-astronomy papers through their arXiv version, even when they have been published. Like our 2008 Biometrika paper.) A large part of the paper is dedicated to computing aspects that escape me, like the constant reference to MPIs. The algorithm is partly automated, except for the choice of the summary statistics and of the distance. The tolerance is chosen as a (large) quantile of the previous set of simulated distances. Getting comments from the designers of abcpmc and cosmoabc would be great.

“It is clear that the simple Gaussian Likelihood assumption in this case, which neglects the effects of systematics yields biased cosmological constraints.”

The last part of the paper compares ABC and MCMC on a supernova simulated dataset. Which is somewhat a dubious comparison since the model used for producing the data and running ABC is not the same as the Gaussian version used with MCMC. Unsurprisingly, MCMC then misses the true value of the cosmological parameters and most likely and more importantly the true posterior HPD region. While ABC SMC (or PMC) proceeds to a concentration around the genuine parameter values. (There is no additional demonstration of how accelerated the approach is.)

Initializing adaptive importance sampling with Markov chains

Posted in Statistics with tags , , , , , , , , , , , on May 6, 2013 by xi'an

Another paper recently arXived by Beaujean and Caldwell elaborated on our population Monte Carlo papers (Cappé et al., 2005, Douc et al., 2007, Wraith et al., 2010) to design a more thorough starting distribution. Interestingly, the authors mention the fact that PMC is an EM-type algorithm to emphasize the importance of the starting distribution, as with “poor proposal, PMC fails as proposal updates lead to a consecutively poorer approximation of the target” (p.2). I had not thought of this possible feature of PMC, which indeed proceeds along integrated EM steps, and thus could converge to a local optimum (if not poorer than the start as the Kullback-Leibler divergence decreases).

The solution proposed in this paper is similar to the one we developed in our AMIS paper. An important part of the simulation is dedicated to the construction of the starting distribution, which is a mixture deduced from multiple Metropolis-Hastings runs. I find the method spends an unnecessary long time on refining this mixture by culling the number of components: down-the-shelf clustering techniques should be sufficient, esp. if one considers that the value of the target is available at every simulated point. This has been my pet (if idle) theory for a long while: we do not take (enough) advantage of this informative feature in our simulation methods… I also find the Student’s t versus Gaussian kernel debate (p.6) somehow superfluous: as we shown in Douc et al., 2007, we can process Student’s t distributions so we can as well work with those. And rather worry about the homogeneity assumption this choice implies: working with any elliptically symmetric kernel assumes a local Euclidean structure on the parameter space, for all components, and does not model properly highly curved spaces. Another pet theory of mine’s. As for picking the necessary number of simulations at each PMC iteration, I would add to the ESS and the survival rate of the components a measure of the Kullback-Leibler divergence, as it should decrease at each iteration (with an infinite number of particles).

Another interesting feature is in the comparison with Multinest, the current version of nested sampling, developed by Farhan Feroz. This is the second time I read a paper involving nested sampling in the past two days. While this PMC implementation does better than nested sampling on the examples processed in the paper, the Multinest outcome remains relevant, particularly because it handles multi-modality fairly well. The authors seem to think parallelisation is an issue with nested sampling, while I do see why: at the most naïve stage, several nested samplers can be run in parallel and the outcomes pulled together.

cosmoPMC in action

Posted in Statistics, University life with tags , , on March 18, 2011 by xi'an

Martin Kilbinger pointed out to me this morning that a recent posting on arXiv, Forecasts of non-Gaussian parameter spaces using Box-Cox transformations by Joachimi and Taylor from Edinburgh, is using cosmoPMC, apparently with very good performances. Here is the abstract:

Forecasts of statistical constraints on model parameters using the Fisher matrix abound in many fields of astrophysics. The Fisher matrix formalism involves the assumption of Gaussianity in parameter space and hence fails to predict complex features of posterior probability distributions. Combining the standard Fisher matrix with Box-Cox transformations, we propose a novel method that accurately predicts arbitrary posterior shapes. The Box-Cox transformations are applied to parameter space to render it approximately multivariate Gaussian, performing the Fisher matrix calculation on the transformed parameters. We demonstrate that, after the Box-Cox parameters have been determined from an initial likelihood evaluation, the method correctly predicts changes in the posterior when varying various parameters of the experimental setup and the data analysis, with marginally higher computational cost than a standard Fisher matrix calculation. We apply the Box-Cox-Fisher formalism to forecast cosmological parameter constraints by future weak gravitational lensing surveys. The characteristic non-linear degeneracy between matter density parameter and normalisation of matter density fluctuations is reproduced for several cases, and the capabilities of breaking this degeneracy by weak lensing three-point statistics is investigated. Possible applications of Box-Cox transformations of posterior distributions are discussed, including the prospects for performing statistical data analysis steps in the transformed gaussianised parameter space.