本文在嵌套抽样的随机游走搜索中引入 mean shift 聚类识别并集成于 NestedFit，以应对多局部似然极大值问题，显著降低计算时间并减小贝叶斯证据不确定性。
摘要：
嵌套抽样是一种用于计算贝叶斯证据和后验参数概率分布的高效算法。它基于通过蒙特卡罗抽样对参数空间进行逐步探索，使用一系列被称为活点的值集合，这些活点向感兴趣区域（即似然函数最大的区域）演化。在存在多个局部似然极大值时，该算法难以收敛。一些未经探索的参数空间体区域还可能引入系统误差。为避免这一问题，文献中提出了不同方法，以便即使在存在局部极大值的情况下也能高效搜索新的活点。本文提出一种新的解决方案，该方案基于在随机游走搜索算法中实现的 mean shift 聚类识别方法。聚类识别被集成到贝叶斯分析程序 NestedFit 中。它通过对若干困难案例的分析进行了测试。与未采用聚类识别的分析结果相比，计算时间显著减少。同时，整个参数空间得到高效探索，这转化为所提取贝叶斯证据值的更小不确定性。
英文摘要：
Nested sampling is an efficient algorithm for the calculation of the Bayesian evidence and posterior parameter probability distributions. It is based on the step-by-step exploration of the parameter space by Monte Carlo sampling with a series of values sets called live points that evolve towards the region of interest, i.e. where the likelihood function is maximal. In presence of several local likelihood maxima, the algorithm converges with difficulty. Some systematic errors can also be introduced by unexplored parameter volume regions. In order to avoid this, different methods are proposed in the literature for an efficient search of new live points, even in presence of local maxima. Here we present a new solution based on the mean shift cluster recognition method implemented in a random walk search algorithm. The clustering recognition is integrated within the Bayesian analysis program NestedFit. It is tested with the analysis of some difficult cases. Compared to the analysis results without cluster recognition, the computation time is considerably reduced. At the same time, the entire parameter space is efficiently explored, which translates into a smaller uncertainty of the extracted value of the Bayesian evidence.
We present dynesty, a public, open-source, Python package to estimate Bayesian posteriors and evidences (marginal likelihoods) using Dynamic Nested Sampling. By adaptively allocating samples based on posterior structure, Dynamic Nested Sampling has the benefits of Markov Chain Monte Carlo algorithms that focus exclusively on posterior estimation while retaining Nested Sampling's ability to estimate evidences and sample from complex, multi-modal distributions. We provide an overview of Nested Sampling, its extension to Dynamic Nested Sampling, the algorithmic challenges involved, and the variou…
Nested sampling has emerged as a valuable tool for Bayesian analysis, in particular for determining the Bayesian evidence. The method is based on a specific type of random sampling of the likelihood function and prior volume of the parameter space. I study the statistical uncertainty in the evidence computed with nested sampling. I examine the uncertainty estimator from Skilling (2004, 2006) and introduce a new estimator based on a detailed analysis of the statistical properties of nested sampling. Both perform well in test cases and make it possible to obtain the statistical uncertainty in th…
Nested sampling is an increasingly popular technique for Bayesian computation, in particular for multimodal, degenerate problems of moderate to high dimensionality. Without appropriate settings, however, nested sampling software may fail to explore such posteriors correctly; for example producing correlated samples or missing important modes. This paper introduces new diagnostic tests to assess the reliability both of parameter estimation and evidence calculations using nested sampling software, and demonstrates them empirically. We present two new diagnostic plots for nested sampling, and giv…
Nested sampling is an important tool for conducting Bayesian analysis in Astronomy and other fields, both for sampling complicated posterior distributions for parameter inference, and for computing marginal likelihoods for model comparison. One technical obstacle to using nested sampling in practice is the requirement (for most common implementations) that prior distributions be provided in the form of transformations from the unit hyper-cube to the target prior density. For many applications - particularly when using the posterior from one experiment as the prior for another - such a transfor…
Metropolis Hastings nested sampling evolves a Markov chain, accepting new points along the chain according to a version of the Metropolis Hastings acceptance ratio, which has been modified to satisfy the nested sampling likelihood constraint. The geometric nested sampling algorithm I present here is based on the Metropolis Hastings 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 distribut…
Nested Slice Sampling: Vectorized Nested Sampling for GPU-Accelerated Inference
Kavli Institute for Cosmology Cambridge（剑桥卡维利宇宙研究所）；Institute of Astronomy, University of Cambridge（剑桥大学天文研究所）；Cavendish Laboratory and Department of Engineering, University of Cambridge（剑桥大学卡文迪许实验室和工程系）
Sampling errors in nested sampling parameter estimation differ from those in Bayesian evidence calculation, but have been little studied in the literature. This paper provides the first explanation of the two main sources of sampling errors in nested sampling parameter estimation, and presents a new diagrammatic representation for the process. We find no current method can accurately measure the parameter estimation errors of a single nested sampling run, and propose a method for doing so using a new algorithm for dividing nested sampling runs. We empirically verify our conclusions and the acc…
Bayesian inference with nested sampling requires a likelihood-restricted prior sampling method, which draws samples from the prior distribution that exceed a likelihood threshold. For high-dimensional problems, Markov Chain Monte Carlo derivatives have been proposed. We numerically study ten algorithms based on slice sampling, hit-and-run and differential evolution algorithms in ellipsoidal, non-ellipsoidal and non-convex problems from 2 to 100 dimensions. Mixing capabilities are evaluated with the nested sampling shrinkage test. This makes our results valid independent of how heavy-tailed the…
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 pos…
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 t…
Improving Gradient-guided Nested Sampling for Posterior Inference
Mila – Québec Artificial Intelligence Institute（米拉-魁北克人工智能研究所）；Université de Montréal（蒙特利尔大学）；Ciela Institute（谢拉研究所）；CCA – Flatiron Institute（计算天体物理学中心-弗拉蒂伦研究所）；Cavendish Laboratory（卡文迪什实验室）；Kavli Institute for Cosmology（卡夫利宇宙学研究所）；Gonville and Caius College, University of Cambridge（剑桥大学冈维尔与凯斯学院）；Canadian Institute for Advanced Research (CIFAR)（加拿大高等研究院）
Nested sampling (NS) is a popular algorithm for Bayesian computation. We investigate statistical errors in NS both analytically and numerically. We show two analytic results. First, we show that the leading terms in Skilling's expression using information theory match the leading terms in Keeton's expression from an analysis of moments. This approximate agreement was previously only known numerically and was somewhat mysterious. Second, we show that the uncertainty in single NS runs approximately equals the standard deviation in repeated NS runs. Whilst intuitive, this was previously taken for…
In probabilistic (Bayesian) inferences, we typically want to compute properties of the posterior distribution, describing knowledge of unknown quantities in the context of a particular dataset and the assumed prior information. The marginal likelihood, also known as the "evidence", is a key quantity in Bayesian model selection. The Diffusive Nested Sampling algorithm, a variant of Nested Sampling, is a powerful tool for generating posterior samples and estimating marginal likelihoods. It is effective at solving complex problems including many where the posterior distribution is multimodal or h…
Many inference problems involve inferring the number $N$ of components in some region, along with their properties $\{\mathbf{x}_i\}_{i=1}^N$, from a dataset $\mathcal{D}$. A common statistical example is finite mixture modelling. In the Bayesian framework, these problems are typically solved using one of the following two methods: i) by executing a Monte Carlo algorithm (such as Nested Sampling) once for each possible value of $N$, and calculating the marginal likelihood or evidence as a function of $N$; or ii) by doing a single run that allows the model dimension $N$ to change (such as Marko…
Massachusetts Institute of Technology（麻省理工学院）；Woods Hole Oceanographic Institution（伍兹霍尔海洋研究所）
We present nested sampling for factor graphs (NSFG), a novel nested sampling approach to approximate inference for posterior distributions expressed over factor-graphs. Performing such inference is a key step in simultaneous localization and mapping (SLAM). Although the Gaussian approximation often works well, in other more challenging SLAM situations, the posterior distribution is non-Gaussian and cannot be explicitly represented with standard distributions. Our technique applies to settings where the posterior distribution is substantially non-Gaussian (e.g., multi-modal) and thus needs a mo…
We review Skilling's nested sampling (NS) algorithm for Bayesian inference and more broadly multi-dimensional integration. After recapitulating the principles of NS, we survey developments in implementing efficient NS algorithms in practice in high-dimensions, including methods for sampling from the so-called constrained prior. We outline the ways in which NS may be applied and describe the application of NS in three scientific fields in which the algorithm has proved to be useful: cosmology, gravitational-wave astronomy, and materials science. We close by making recommendations for best pract…
Bayesian inference involves two main computational challenges. First, in estimating the parameters of some model for the data, the posterior distribution may well be highly multi-modal: a regime in which the convergence to stationarity of traditional Markov Chain Monte Carlo (MCMC) techniques becomes incredibly slow. Second, in selecting between a set of competing models the necessary estimation of the Bayesian evidence for each is, by definition, a (possibly high-dimensional) integration over the entire parameter space; again this can be a daunting computational task, although new Monte Carlo…
Gaussian Process (GPs) models are a rich distribution over functions with inductive biases controlled by a kernel function. Learning occurs through the optimisation of kernel hyperparameters using the marginal likelihood as the objective. This classical approach known as Type-II maximum likelihood (ML-II) yields point estimates of the hyperparameters, and continues to be the default method for training GPs. However, this approach risks underestimating predictive uncertainty and is prone to overfitting especially when there are many hyperparameters. Furthermore, gradient based optimisation make…
Bayesian inference methods rely on numerical algorithms for both model selection and parameter inference. In general, these algorithms require a high computational effort to yield reliable estimates. One of the major challenges in phylogenetics is the estimation of the marginal likelihood. This quantity is commonly used for comparing different evolutionary models, but its calculation, even for simple models, incurs high computational cost. Another interesting challenge relates to the estimation of the posterior distribution. Often, long Markov chains are required to get sufficient samples to c…
Priors in Bayesian analyses often encode informative domain knowledge that can be useful in making the inference process more efficient. Occasionally, however, priors may be unrepresentative of the parameter values for a given dataset, which can result in inefficient parameter space exploration, or even incorrect inferences, particularly for nested sampling (NS) algorithms. Simply broadening the prior in such cases may be inappropriate or impossible in some applications. Hence our previous solution to this problem, known as posterior repartitioning (PR), redefines the prior and likelihood whil…
Nested error regression models are useful tools for analysis of grouped data, especially in the case of small area estimation. This paper suggests a nested error regression model using uncertain random effects in which the random effect in each area is expressed as a mixture of a normal distribution and a positive mass at $0$. For estimation of the model parameters and prediction of the random effects, an objective Bayesian inference is proposed by setting non-informative prior distributions on the model parameters. Under mild sufficient conditions, it is shown that the posterior distribution …
We introduce dynamic nested sampling: a generalisation of the nested sampling algorithm in which the number of "live points" varies to allocate samples more efficiently. In empirical tests the new method significantly improves calculation accuracy compared to standard nested sampling with the same number of samples; this increase in accuracy is equivalent to speeding up the computation by factors of up to ~72 for parameter estimation and ~7 for evidence calculations. We also show that the accuracy of both parameter estimation and evidence calculations can be improved simultaneously. In additio…
Nested sampling is a simulation method for approximating marginal likelihoods proposed by Skilling (2006). We establish that nested sampling has an approximation error that vanishes at the standard Monte Carlo rate and that this error is asymptotically Gaussian. We show that the asymptotic variance of the nested sampling approximation typically grows linearly with the dimension of the parameter. We discuss the applicability and efficiency of nested sampling in realistic problems, and we compare it with two current methods for computing marginal likelihood. We propose an extension that avoids r…
We introduce a general Monte Carlo method based on Nested Sampling (NS), for sampling complex probability distributions and estimating the normalising constant. The method uses one or more particles, which explore a mixture of nested probability distributions, each successive distribution occupying ~e^-1 times the enclosed prior mass of the previous distribution. While NS technically requires independent generation of particles, Markov Chain Monte Carlo (MCMC) exploration fits naturally into this technique. We illustrate the new method on a test problem and find that it can achieve four times …
Nested sampling is an iterative integration procedure that shrinks the prior volume towards higher likelihoods by removing a "live" point at a time. A replacement point is drawn uniformly from the prior above an ever-increasing likelihood threshold. Thus, the problem of drawing from a space above a certain likelihood value arises naturally in nested sampling, making algorithms that solve this problem a key ingredient to the nested sampling framework. If the drawn points are distributed uniformly, the removal of a point shrinks the volume in a well-understood way, and the integration of nested …
In performing a Bayesian analysis, two difficult problems often emerge. First, in estimating the parameters of some model for the data, the resulting posterior distribution may be multi-modal or exhibit pronounced (curving) degeneracies. Secondly, in selecting between a set of competing models, calculation of the Bayesian evidence for each model is computationally expensive using existing methods such as thermodynamic integration. Nested Sampling is a Monte Carlo method targeted at the efficient calculation of the evidence, but also produces posterior inferences as a by-product and therefore p…
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 exp…
We propose a novel method for computing $p$-values based on nested sampling (NS) applied to the sampling space rather than the parameter space of the problem, in contrast to its usage in Bayesian computation. The computational cost of NS scales as $\log^2{1/p}$, which compares favorably to the $1/p$ scaling for Monte Carlo (MC) simulations. For significances greater than about $4σ$ in both a toy problem and a simplified resonance search, we show that NS requires orders of magnitude fewer simulations than ordinary MC estimates. This is particularly relevant for high-energy physics, which adopts…
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…
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…
The Integrated Nested Laplace Approximation (INLA) is a deterministic approach to Bayesian inference on latent Gaussian models (LGMs) and focuses on fast and accurate approximation of posterior marginals for the parameters in the models. Recently, methods have been developed to extend this class of models to those that can be expressed as conditional LGMs by fixing some of the parameters in the models to descriptive values. These methods differ in the manner descriptive values are chosen. This paper proposes to combine importance sampling with INLA (IS-INLA), and extends this approach with the…
In this review, we address the use of Monte Carlo methods for approximating definite integrals of the form $Z = \int L(x) d P(x)$, where $L$ is a target function (often a likelihood) and $P$ a finite measure. We present vertical-likelihood Monte Carlo, which is an approach for designing the importance function $g(x)$ used in importance sampling. Our approach exploits a duality between two random variables: the random draw $X \sim g$, and the corresponding random likelihood ordinate $Y\equiv L(X)$ of the draw. It is natural to specify $g(x)$ and ask: what is the the implied distribution of $Y$?…
This paper addresses the issue of estimating the expectation of a real-valued random variable of the form $X = g(\mathbf{U})$ where $g$ is a deterministic function and $\mathbf{U}$ can be a random finite- or infinite-dimensional vector. Using recent results on rare event simulation, we propose a unified framework for dealing with both probability and mean estimation for such random variables, \emph{i.e.} linking algorithms such as Tootsie Pop Algorithm (TPA) or Last Particle Algorithm with nested sampling. Especially, it extends nested sampling as follows: first the random variable $X$ does no…
