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Register a new userImproving the efficiency and robustness of nested sampling using posterior repartitioning
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In real-world Bayesian inference applications, prior assumptions regarding the parameters of interest may be unrepresentative of their actual values for a given dataset. In particular, if the likelihood is concentrated far out in the wings of the assumed prior distribution, this can lead to extremely inefficient exploration of the resulting posterior by nested sampling algorithms, with unnecessarily high associated computational costs. Simple solutions such as broadening the prior range in such cases might not be appropriate or possible in real-world applications, for example when one wishes to assume a single standardised prior across the analysis of a large number of datasets for which the true values of the parameters of interest may vary. This work therefore introduces a posterior repartitioning (PR) method for nested sampling algorithms, which addresses the problem by redefining the likelihood and prior while keeping their product fixed, so that the posterior inferences and evidence estimates remain unchanged but the efficiency of the nested sampling process is significantly increased. Numerical results show that the PR method provides a simple yet powerful refinement for nested sampling algorithms to address the issue of unrepresentative priors.
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Nested sampling (NS) computes parameter posterior distributions and makes Bayesian model comparison computationally feasible. Its strengths are the unsupervised navigation of complex, potentially multi-modal posteriors until a well-defined termination point. A systematic literature review of nested sampling algorithms and variants is presented. We focus on complete algorithms, including solutions to likelihood-restricted prior sampling, parallelisation, termination and diagnostics. The relation between number of live points, dimensionality and computational cost is studied for two complete algorithms. A new formulation of NS is presented, which casts the parameter space exploration as a search on a tree. Previously published ways of obtaining robust error estimates and dynamic variations of the number of live points are presented as special cases of this formulation. A new on-line diagnostic test is presented based on previous insertion rank order work. The survey of nested sampling methods concludes with outlooks for future research.
It was recently emphasised by Riley (2019); Schittenhelm & Wacker (2020) that that in the presence of plateaus in the likelihood function nested sampling (NS) produces faulty estimates of the evidence and posterior densities. After informally explaining the cause of the problem, we present a modified version of NS that handles plateaus and can be applied retrospectively to NS runs from popular NS software using anesthetic. In the modified NS, live points in a plateau are evicted one by one without replacement, with ordinary NS compression of the prior volume after each eviction but taking into account the dynamic number of live points. The live points are replenished once all points in the plateau are removed. We demonstrate it on a number of examples. Since the modification is simple, we propose that it becomes the canonical version of Skillings NS algorithm.
The Shannon entropy, and related quantities such as mutual information, can be used to quantify uncertainty and relevance. However, in practice, it can be difficult to compute these quantities for arbitrary probability distributions, particularly if the probability mass functions or densities cannot be evaluated. This paper introduces a computational approach, based on Nested Sampling, to evaluate entropies of probability distributions that can only be sampled. I demonstrate the method on three examples: a simple gaussian example where the key quantities are available analytically; (ii) an experimental design example about scheduling observations in order to measure the period of an oscillating signal; and (iii) predicting the future from the past in a heavy-tailed scenario.
Metropolis nested sampling evolves a Markov chain from a current livepoint and accepts new points along the chain according to a version of the Metropolis acceptance ratio modified to satisfy the likelihood constraint, characteristic of nested sampling algorithms. The geometric nested sampling algorithm we present here is a based on the Metropolis method, but treats parameters as though they represent points on certain geometric objects, namely circles, tori and spheres. For parameters which represent points on a circle or torus, the trial distribution is `wrapped around the domain of the posterior distribution such that samples cannot be rejected automatically when evaluating the Metropolis ratio due to being outside the sampling domain. Furthermore, this enhances the mobility of the sampler. For parameters which represent coordinates on the surface of a sphere, the algorithm transforms the parameters into a Cartesian coordinate system before sampling which again makes sure no samples are automatically rejected, and provides a physically intutive way of the sampling the parameter space. We apply the geometric nested sampler to two types of toy model which include circular, toroidal and spherical parameters. We find that the geometric nested sampler generally outperforms textsc{MultiNest} in both cases. %We also apply the algorithm to a gravitational wave detection model which includes circular and spherical parameters, and find that the geometric nested sampler and textsc{MultiNest} appear to perform equally well as one another. Our implementation of the algorithm can be found at url{https://github.com/SuperKam91/nested_sampling}.
Nested sampling (NS) is an invaluable tool in data analysis in modern astrophysics, cosmology, gravitational wave astronomy and particle physics. We identify a previously unused property of NS related to order statistics: the insertion indexes of new live points into the existing live points should be uniformly distributed. This observation enabled us to create a novel cross-check of single NS runs. The tests can detect when an NS run failed to sample new live points from the constrained prior and plateaus in the likelihood function, which break an assumption of NS and thus leads to unreliable results. We applied our cross-check to NS runs on toy functions with known analytic results in 2 - 50 dimensions, showing that our approach can detect problematic runs on a variety of likelihoods, settings and dimensions. As an example of a realistic application, we cross-checked NS runs performed in the context of cosmological model selection. Since the cross-check is simple, we recommend that it become a mandatory test for every applicable NS run.
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