Jarno Vanhatalo, Marcelo Hartmann, Lari Veneranta.

Source: Bayesian Analysis, Volume 15, Number 2, 415--447.

Abstract:
Species distribution models (SDM) are a key tool in ecology, conservation and management of natural resources. Two key components of the state-of-the-art SDMs are the description for species distribution response along environmental covariates and the spatial random effect that captures deviations from the distribution patterns explained by environmental covariates. Joint species distribution models (JSDMs) additionally include interspecific correlations which have been shown to improve their descriptive and predictive performance compared to single species models. However, current JSDMs are restricted to hierarchical generalized linear modeling framework. Their limitation is that parametric models have trouble in explaining changes in abundance due, for example, highly non-linear physical tolerance limits which is particularly important when predicting species distribution in new areas or under scenarios of environmental change. On the other hand, semi-parametric response functions have been shown to improve the predictive performance of SDMs in these tasks in single species models. Here, we propose JSDMs where the responses to environmental covariates are modeled with additive multivariate Gaussian processes coded as linear models of coregionalization. These allow inference for wide range of functional forms and interspecific correlations between the responses. We propose also an efficient approach for inference with Laplace approximation and parameterization of the interspecific covariance matrices on the Euclidean space. We demonstrate the benefits of our model with two small scale examples and one real world case study. We use cross-validation to compare the proposed model to analogous semi-parametric single species models and parametric single and joint species models in interpolation and extrapolation tasks. The proposed model outperforms the alternative models in all cases. We also show that the proposed model can be seen as an extension of the current state-of-the-art JSDMs to semi-parametric models.

Kelly C. M. Gonçalves, Hélio S. Migon, Leonardo S. Bastos.

Source: Bayesian Analysis, Volume 15, Number 2, 335--362.

Abstract:
The paper introduces a new class of models, named dynamic quantile linear models, which combines dynamic linear models with distribution-free quantile regression producing a robust statistical method. Bayesian estimation for the dynamic quantile linear model is performed using an efficient Markov chain Monte Carlo algorithm. The paper also proposes a fast sequential procedure suited for high-dimensional predictive modeling with massive data, where the generating process is changing over time. The proposed model is evaluated using synthetic and well-known time series data. The model is also applied to predict annual incidence of tuberculosis in the state of Rio de Janeiro and compared with global targets set by the World Health Organization.

Abhishek Bishoyi, Xiaojing Wang, Dipak K. Dey.

Source: Bayesian Analysis, Volume 15, Number 1, 215--239.

Abstract:
Missing data often appear as a practical problem while applying classical models in the statistical analysis. In this paper, we consider a semiparametric regression model in the presence of missing covariates for nonparametric components under a Bayesian framework. As it is known that Gaussian processes are a popular tool in nonparametric regression because of their flexibility and the fact that much of the ensuing computation is parametric Gaussian computation. However, in the absence of covariates, the most frequently used covariance functions of a Gaussian process will not be well defined. We propose an imputation method to solve this issue and perform our analysis using Bayesian inference, where we specify the objective priors on the parameters of Gaussian process models. Several simulations are conducted to illustrate effectiveness of our proposed method and further, our method is exemplified via two real datasets, one through Langmuir equation, commonly used in pharmacokinetic models, and another through Auto-mpg data taken from the StatLib library.

Fangzheng Xie, Yanxun Xu.

Source: Bayesian Analysis, Volume 15, Number 1, 159--186.

Abstract:
We propose a kernel mixture of polynomials prior for Bayesian nonparametric regression. The regression function is modeled by local averages of polynomials with kernel mixture weights. We obtain the minimax-optimal contraction rate of the full posterior distribution up to a logarithmic factor by estimating metric entropies of certain function classes. Under the assumption that the degree of the polynomials is larger than the unknown smoothness level of the true function, the posterior contraction behavior can adapt to this smoothness level provided an upper bound is known. We also provide a frequentist sieve maximum likelihood estimator with a near-optimal convergence rate. We further investigate the application of the kernel mixture of polynomials to partial linear models and obtain both the near-optimal rate of contraction for the nonparametric component and the Bernstein-von Mises limit (i.e., asymptotic normality) of the parametric component. The proposed method is illustrated with numerical examples and shows superior performance in terms of computational efficiency, accuracy, and uncertainty quantification compared to the local polynomial regression, DiceKriging, and the robust Gaussian stochastic process.

Antony Overstall, James McGree.

Source: Bayesian Analysis, Volume 15, Number 1, 103--131.

Abstract:
A Bayesian design is given by maximising an expected utility over a design space. The utility is chosen to represent the aim of the experiment and its expectation is taken with respect to all unknowns: responses, parameters and/or models. Although straightforward in principle, there are several challenges to finding Bayesian designs in practice. Firstly, the utility and expected utility are rarely available in closed form and require approximation. Secondly, the design space can be of high-dimensionality. In the case of intractable likelihood models, these problems are compounded by the fact that the likelihood function, whose evaluation is required to approximate the expected utility, is not available in closed form. A strategy is proposed to find Bayesian designs for intractable likelihood models. It relies on the development of an automatic, auxiliary modelling approach, using multivariate Gaussian process emulators, to approximate the likelihood function. This is then combined with a copula-based approach to approximate the marginal likelihood (a quantity commonly required to evaluate many utility functions). These approximations are demonstrated on examples of stochastic process models involving experimental aims of both parameter estimation and model comparison.

Matthew Moores, Geoff Nicholls, Anthony Pettitt, Kerrie Mengersen.

Source: Bayesian Analysis, Volume 15, Number 1, 1--27.

Abstract:
The inverse temperature parameter of the Potts model governs the strength of spatial cohesion and therefore has a major influence over the resulting model fit. A difficulty arises from the dependence of an intractable normalising constant on the value of this parameter and thus there is no closed-form solution for sampling from the posterior distribution directly. There is a variety of computational approaches for sampling from the posterior without evaluating the normalising constant, including the exchange algorithm and approximate Bayesian computation (ABC). A serious drawback of these algorithms is that they do not scale well for models with a large state space, such as images with a million or more pixels. We introduce a parametric surrogate model, which approximates the score function using an integral curve. Our surrogate model incorporates known properties of the likelihood, such as heteroskedasticity and critical temperature. We demonstrate this method using synthetic data as well as remotely-sensed imagery from the Landsat-8 satellite. We achieve up to a hundredfold improvement in the elapsed runtime, compared to the exchange algorithm or ABC. An open-source implementation of our algorithm is available in the R package bayesImageS .

Andrea Cremaschi, Raffaele Argiento, Katherine Shoemaker, Christine Peterson, Marina Vannucci.

Source: Bayesian Analysis, Volume 14, Number 4, 1271--1301.

Abstract:
Gaussian graphical models are useful tools for exploring network structures in multivariate normal data. In this paper we are interested in situations where data show departures from Gaussianity, therefore requiring alternative modeling distributions. The multivariate $t$ -distribution, obtained by dividing each component of the data vector by a gamma random variable, is a straightforward generalization to accommodate deviations from normality such as heavy tails. Since different groups of variables may be contaminated to a different extent, Finegold and Drton (2014) introduced the Dirichlet $t$ -distribution, where the divisors are clustered using a Dirichlet process. In this work, we consider a more general class of nonparametric distributions as the prior on the divisor terms, namely the class of normalized completely random measures (NormCRMs). To improve the effectiveness of the clustering, we propose modeling the dependence among the divisors through a nonparametric hierarchical structure, which allows for the sharing of parameters across the samples in the data set. This desirable feature enables us to cluster together different components of multivariate data in a parsimonious way. We demonstrate through simulations that this approach provides accurate graphical model inference, and apply it to a case study examining the dependence structure in radiomics data derived from The Cancer Imaging Atlas.

Abhirup Datta, Sudipto Banerjee, James S. Hodges, Leiwen Gao.

Source: Bayesian Analysis, Volume 14, Number 4, 1221--1244.

Abstract:
Hierarchical models for regionally aggregated disease incidence data commonly involve region specific latent random effects that are modeled jointly as having a multivariate Gaussian distribution. The covariance or precision matrix incorporates the spatial dependence between the regions. Common choices for the precision matrix include the widely used ICAR model, which is singular, and its nonsingular extension which lacks interpretability. We propose a new parametric model for the precision matrix based on a directed acyclic graph (DAG) representation of the spatial dependence. Our model guarantees positive definiteness and, hence, in addition to being a valid prior for regional spatially correlated random effects, can also directly model the outcome from dependent data like images and networks. Theoretical results establish a link between the parameters in our model and the variance and covariances of the random effects. Simulation studies demonstrate that the improved interpretability of our model reaps benefits in terms of accurately recovering the latent spatial random effects as well as for inference on the spatial covariance parameters. Under modest spatial correlation, our model far outperforms the CAR models, while the performances are similar when the spatial correlation is strong. We also assess sensitivity to the choice of the ordering in the DAG construction using theoretical and empirical results which testify to the robustness of our model. We also present a large-scale public health application demonstrating the competitive performance of the model.

Lutz F. Gruber, Erica F. Stuber, Lyndsie S. Wszola, Joseph J. Fontaine.

Source: Bayesian Analysis, Volume 14, Number 4, 1173--1199.

Abstract:
We present an integrated open population model where the population dynamics are defined by a differential equation, and the related statistical model utilizes a Poisson binomial convolution likelihood. Key advantages of the proposed approach over existing open population models include the flexibility to predict related, but unobserved quantities such as total immigration or emigration over a specified time period, and more computationally efficient posterior simulation by elimination of the need to explicitly simulate latent immigration and emigration. The viability of the proposed method is shown in an in-depth analysis of outdoor recreation participation on public lands, where the surveyed populations changed rapidly and demographic population closure cannot be assumed even within a single day.

Nadja Klein, Michael Stanley Smith.

Source: Bayesian Analysis, Volume 14, Number 4, 1143--1171.

Abstract:
We show how to extract the implicit copula of a response vector from a Bayesian regularized regression smoother with Gaussian disturbances. The copula can be used to compare smoothers that employ different shrinkage priors and function bases. We illustrate with three popular choices of shrinkage priors—a pairwise prior, the horseshoe prior and a g prior augmented with a point mass as employed for Bayesian variable selection—and both univariate and multivariate function bases. The implicit copulas are high-dimensional, have flexible dependence structures that are far from that of a Gaussian copula, and are unavailable in closed form. However, we show how they can be evaluated by first constructing a Gaussian copula conditional on the regularization parameters, and then integrating over these. Combined with non-parametric margins the regularized smoothers can be used to model the distribution of non-Gaussian univariate responses conditional on the covariates. Efficient Markov chain Monte Carlo schemes for evaluating the copula are given for this case. Using both simulated and real data, we show how such copula smoothing models can improve the quality of resulting function estimates and predictive distributions.

Muteb Alharthi, Theodore Kypraios, Philip D. O’Neill.

Source: Bayesian Analysis, Volume 14, Number 3, 927--956.

Abstract:
We consider the problem of model choice for stochastic epidemic models given partial observation of a disease outbreak through time. Our main focus is on the use of Bayes factors. Although Bayes factors have appeared in the epidemic modelling literature before, they can be hard to compute and little attention has been given to fundamental questions concerning their utility. In this paper we derive analytic expressions for Bayes factors given complete observation through time, which suggest practical guidelines for model choice problems. We adapt the power posterior method for computing Bayes factors so as to account for missing data and apply this approach to partially observed epidemics. For comparison, we also explore the use of a deviance information criterion for missing data scenarios. The methods are illustrated via examples involving both simulated and real data.

Ioannis Ntzoufras, Claudia Tarantola, Monia Lupparelli.

Source: Bayesian Analysis, Volume 14, Number 3, 797--823.

Abstract:
We introduce a novel Bayesian approach for quantitative learning for graphical log-linear marginal models. These models belong to curved exponential families that are difficult to handle from a Bayesian perspective. The likelihood cannot be analytically expressed as a function of the marginal log-linear interactions, but only in terms of cell counts or probabilities. Posterior distributions cannot be directly obtained, and Markov Chain Monte Carlo (MCMC) methods are needed. Finally, a well-defined model requires parameter values that lead to compatible marginal probabilities. Hence, any MCMC should account for this important restriction. We construct a fully automatic and efficient MCMC strategy for quantitative learning for such models that handles these problems. While the prior is expressed in terms of the marginal log-linear interactions, we build an MCMC algorithm that employs a proposal on the probability parameter space. The corresponding proposal on the marginal log-linear interactions is obtained via parameter transformation. We exploit a conditional conjugate setup to build an efficient proposal on probability parameters. The proposed methodology is illustrated by a simulation study and a real dataset.

L. F. South, A. N. Pettitt, C. C. Drovandi.

Source: Bayesian Analysis, Volume 14, Number 3, 773--796.

Abstract:
Sequential Monte Carlo (SMC) methods for sampling from the posterior of static Bayesian models are flexible, parallelisable and capable of handling complex targets. However, it is common practice to adopt a Markov chain Monte Carlo (MCMC) kernel with a multivariate normal random walk (RW) proposal in the move step, which can be both inefficient and detrimental for exploring challenging posterior distributions. We develop new SMC methods with independent proposals which allow recycling of all candidates generated in the SMC process and are embarrassingly parallelisable. A novel evidence estimator that is easily computed from the output of our independent SMC is proposed. Our independent proposals are constructed via flexible copula-type models calibrated with the population of SMC particles. We demonstrate through several examples that more precise estimates of posterior expectations and the marginal likelihood can be obtained using fewer likelihood evaluations than the more standard RW approach.

Stefano Peluso, Siddhartha Chib, Antonietta Mira.

Source: Bayesian Analysis, Volume 14, Number 3, 727--751.

Abstract:
We develop a general Bayesian semiparametric change-point model in which separate groups of structural parameters (for example, location and dispersion parameters) can each follow a separate multiple change-point process, driven by time-dependent transition matrices among the latent regimes. The distribution of the observations within regimes is unknown and given by a Dirichlet process mixture prior. The properties of the proposed model are studied theoretically through the analysis of inter-arrival times and of the number of change-points in a given time interval. The prior-posterior analysis by Markov chain Monte Carlo techniques is developed on a forward-backward algorithm for sampling the various regime indicators. Analysis with simulated data under various scenarios and an application to short-term interest rates are used to show the generality and usefulness of the proposed model.

Sohan Seth, Iain Murray, Christopher K. I. Williams.

Source: Bayesian Analysis, Volume 14, Number 3, 703--725.

Abstract:
Model criticism is usually carried out by assessing if replicated data generated under the fitted model looks similar to the observed data, see e.g. Gelman, Carlin, Stern, and Rubin (2004, p. 165). This paper presents a method for latent variable models by pulling back the data into the space of latent variables, and carrying out model criticism in that space. Making use of a model's structure enables a more direct assessment of the assumptions made in the prior and likelihood. We demonstrate the method with examples of model criticism in latent space applied to factor analysis, linear dynamical systems and Gaussian processes.

Yushu Shi, Michael Martens, Anjishnu Banerjee, Purushottam Laud.

Source: Bayesian Analysis, Volume 14, Number 3, 677--702.

Abstract:
Dirichlet process mixture (DPM) models provide flexible modeling for distributions of data as an infinite mixture of distributions from a chosen collection. Specifying priors for these models in individual data contexts can be challenging. In this paper, we introduce a scheme which requires the investigator to specify only simple scaling information. This is used to transform the data to a fixed scale on which a low information prior is constructed. Samples from the posterior with the rescaled data are transformed back for inference on the original scale. The low information prior is selected to provide a wide variety of components for the DPM to generate flexible distributions for the data on the fixed scale. The method can be applied to all DPM models with kernel functions closed under a suitable scaling transformation. Construction of the low information prior, however, is kernel dependent. Using DPM-of-Gaussians and DPM-of-Weibulls models as examples, we show that the method provides accurate estimates of a diverse collection of distributions that includes skewed, multimodal, and highly dispersed members. With the recommended priors, repeated data simulations show performance comparable to that of standard empirical estimates. Finally, we show weak convergence of posteriors with the proposed priors for both kernels considered.

Marko Järvenpää, Michael U. Gutmann, Arijus Pleska, Aki Vehtari, Pekka Marttinen.

Source: Bayesian Analysis, Volume 14, Number 2, 595--622.

Abstract:
Approximate Bayesian computation (ABC) is a method for Bayesian inference when the likelihood is unavailable but simulating from the model is possible. However, many ABC algorithms require a large number of simulations, which can be costly. To reduce the computational cost, Bayesian optimisation (BO) and surrogate models such as Gaussian processes have been proposed. Bayesian optimisation enables one to intelligently decide where to evaluate the model next but common BO strategies are not designed for the goal of estimating the posterior distribution. Our paper addresses this gap in the literature. We propose to compute the uncertainty in the ABC posterior density, which is due to a lack of simulations to estimate this quantity accurately, and define a loss function that measures this uncertainty. We then propose to select the next evaluation location to minimise the expected loss. Experiments show that the proposed method often produces the most accurate approximations as compared to common BO strategies.

Quan Zhou, Yongtao Guan.

Source: Bayesian Analysis, Volume 14, Number 2, 573--594.

Abstract:
Bayesian variable selection regression (BVSR) is able to jointly analyze genome-wide genetic datasets, but the slow computation via Markov chain Monte Carlo (MCMC) hampered its wide-spread usage. Here we present a novel iterative method to solve a special class of linear systems, which can increase the speed of the BVSR model-fitting tenfold. The iterative method hinges on the complex factorization of the sum of two matrices and the solution path resides in the complex domain (instead of the real domain). Compared to the Gauss-Seidel method, the complex factorization converges almost instantaneously and its error is several magnitude smaller than that of the Gauss-Seidel method. More importantly, the error is always within the pre-specified precision while the Gauss-Seidel method is not. For large problems with thousands of covariates, the complex factorization is 10–100 times faster than either the Gauss-Seidel method or the direct method via the Cholesky decomposition. In BVSR, one needs to repetitively solve large penalized regression systems whose design matrices only change slightly between adjacent MCMC steps. This slight change in design matrix enables the adaptation of the iterative complex factorization method. The computational innovation will facilitate the wide-spread use of BVSR in reanalyzing genome-wide association datasets.

Alberto Cassese, Weixuan Zhu, Michele Guindani, Marina Vannucci.

Source: Bayesian Analysis, Volume 14, Number 2, 553--572.

Abstract:
In many applications, investigators monitor processes that vary in space and time, with the goal of identifying temporally persistent and spatially localized departures from a baseline or “normal” behavior. In this manuscript, we consider the monitoring of pneumonia and influenza (P&I) mortality, to detect influenza outbreaks in the continental United States, and propose a Bayesian nonparametric model selection approach to take into account the spatio-temporal dependence of outbreaks. More specifically, we introduce a zero-inflated conditionally identically distributed species sampling prior which allows borrowing information across time and to assign data to clusters associated to either a null or an alternate process. Spatial dependences are accounted for by means of a Markov random field prior, which allows to inform the selection based on inferences conducted at nearby locations. We show how the proposed modeling framework performs in an application to the P&I mortality data and in a simulation study, and compare with common threshold methods for detecting outbreaks over time, with more recent Markov switching based models, and with spike-and-slab Bayesian nonparametric priors that do not take into account spatio-temporal dependence.

Łukasz Rajkowski.

Source: Bayesian Analysis, Volume 14, Number 2, 477--494.

Abstract:
Mixture models are a natural choice in many applications, but it can be difficult to place an a priori upper bound on the number of components. To circumvent this, investigators are turning increasingly to Dirichlet process mixture models (DPMMs). It is therefore important to develop an understanding of the strengths and weaknesses of this approach. This work considers the MAP (maximum a posteriori) clustering for the Gaussian DPMM (where the cluster means have Gaussian distribution and, for each cluster, the observations within the cluster have Gaussian distribution). Some desirable properties of the MAP partition are proved: ‘almost disjointness’ of the convex hulls of clusters (they may have at most one point in common) and (with natural assumptions) the comparability of sizes of those clusters that intersect any fixed ball with the number of observations (as the latter goes to infinity). Consequently, the number of such clusters remains bounded. Furthermore, if the data arises from independent identically distributed sampling from a given distribution with bounded support then the asymptotic MAP partition of the observation space maximises a function which has a straightforward expression, which depends only on the within-group covariance parameter. As the operator norm of this covariance parameter decreases, the number of clusters in the MAP partition becomes arbitrarily large, which may lead to the overestimation of the number of mixture components.

Suprateek Kundu, Bani K. Mallick, Veera Baladandayuthapani.

Source: Bayesian Analysis, Volume 14, Number 2, 449--476.

Abstract:
There has been an intense development in the Bayesian graphical model literature over the past decade; however, most of the existing methods are restricted to moderate dimensions. We propose a novel graphical model selection approach for large dimensional settings where the dimension increases with the sample size, by decoupling model fitting and covariance selection. First, a full model based on a complete graph is fit under a novel class of mixtures of inverse–Wishart priors, which induce shrinkage on the precision matrix under an equivalence with Cholesky-based regularization, while enabling conjugate updates. Subsequently, a post-fitting model selection step uses penalized joint credible regions to perform model selection. This allows our methods to be computationally feasible for large dimensional settings using a combination of straightforward Gibbs samplers and efficient post-fitting inferences. Theoretical guarantees in terms of selection consistency are also established. Simulations show that the proposed approach compares favorably with competing methods, both in terms of accuracy metrics and computation times. We apply this approach to a cancer genomics data example.

M. W. McLean, M. P. Wand.

Source: Bayesian Analysis, Volume 14, Number 2, 371--398.

Abstract:
We build on recent work concerning message passing approaches to approximate fitting and inference for arbitrarily large regression models. The focus is on regression models where the response variable is modeled to have an elaborate distribution, which is loosely defined to mean a distribution that is more complicated than common distributions such as those in the Bernoulli, Poisson and Normal families. Examples of elaborate response families considered here are the Negative Binomial and $t$ families. Variational message passing is more challenging due to some of the conjugate exponential families being non-standard and numerical integration being needed. Nevertheless, a factor graph fragment approach means the requisite calculations only need to be done once for a particular elaborate response distribution family. Computer code can be compartmentalized, including that involving numerical integration. A major finding of this work is that the modularity of variational message passing extends to elaborate response regression models.

Lloyd T. Elliott, Maria De Iorio, Stefano Favaro, Kaustubh Adhikari, Yee Whye Teh.

Source: Bayesian Analysis, Volume 14, Number 2, 313--339.

Abstract:
We propose a Bayesian nonparametric model to infer population admixture, extending the hierarchical Dirichlet process to allow for correlation between loci due to linkage disequilibrium. Given multilocus genotype data from a sample of individuals, the proposed model allows inferring and classifying individuals as unadmixed or admixed, inferring the number of subpopulations ancestral to an admixed population and the population of origin of chromosomal regions. Our model does not assume any specific mutation process, and can be applied to most of the commonly used genetic markers. We present a Markov chain Monte Carlo (MCMC) algorithm to perform posterior inference from the model and we discuss some methods to summarize the MCMC output for the analysis of population admixture. Finally, we demonstrate the performance of the proposed model in a real application, using genetic data from the ectodysplasin-A receptor (EDAR) gene, which is considered to be ancestry-informative due to well-known variations in allele frequency as well as phenotypic effects across ancestry. The structure analysis of this dataset leads to the identification of a rare haplotype in Europeans. We also conduct a simulated experiment and show that our algorithm outperforms parametric methods.

Thomas Staudt, Timo Aspelmeier, Oskar Laitenberger, Claudia Geisler, Alexander Egner, Axel Munk.

Source: Statistical Science, Volume 35, Number 1, 92--111.

Abstract:
Super-resolution microscopy is rapidly gaining importance as an analytical tool in the life sciences. A compelling feature is the ability to label biological units of interest with fluorescent markers in (living) cells and to observe them with considerably higher resolution than conventional microscopy permits. The images obtained this way, however, lack an absolute intensity scale in terms of numbers of fluorophores observed. In this article, we discuss state of the art methods to count such fluorophores and statistical challenges that come along with it. In particular, we suggest a modeling scheme for time series generated by single-marker-switching (SMS) microscopy that makes it possible to quantify the number of markers in a statistically meaningful manner from the raw data. To this end, we model the entire process of photon generation in the fluorophore, their passage through the microscope, detection and photoelectron amplification in the camera, and extraction of time series from the microscopic images. At the heart of these modeling steps is a careful description of the fluorophore dynamics by a novel hidden Markov model that operates on two timescales (HTMM). Besides the fluorophore number, information about the kinetic transition rates of the fluorophore’s internal states is also inferred during estimation. We comment on computational issues that arise when applying our model to simulated or measured fluorescence traces and illustrate our methodology on simulated data.

Chao Du, S. C. Kou.

Source: Statistical Science, Volume 35, Number 1, 75--91.

Abstract:
Toward the last quarter of the 20th century, the emergence of single-molecule experiments enabled scientists to track and study individual molecules’ dynamic properties in real time. Unlike macroscopic systems’ dynamics, those of single molecules can only be properly described by stochastic models even in the absence of external noise. Consequently, statistical methods have played a key role in extracting hidden information about molecular dynamics from data obtained through single-molecule experiments. In this article, we survey the major statistical methodologies used to analyze single-molecule experimental data. Our discussion is organized according to the types of stochastic models used to describe single-molecule systems as well as major experimental data collection techniques. We also highlight challenges and future directions in the application of statistical methodologies to single-molecule experiments.

Peter J. Diggle, Emanuele Giorgi, Julienne Atsame, Sylvie Ntsame Ella, Kisito Ogoussan, Katherine Gass.

Source: Statistical Science, Volume 35, Number 1, 42--50.

Abstract:
Vector-borne diseases have long presented major challenges to the health of rural communities in the wet tropical regions of the world, but especially in sub-Saharan Africa. In this paper, we describe the contribution that statistical modelling has made to the global elimination programme for one vector-borne disease, onchocerciasis. We explain why information on the spatial distribution of a second vector-borne disease, Loa loa, is needed before communities at high risk of onchocerciasis can be treated safely with mass distribution of ivermectin, an antifiarial medication. We show how a model-based geostatistical analysis of Loa loa prevalence survey data can be used to map the predictive probability that each location in the region of interest meets a WHO policy guideline for safe mass distribution of ivermectin and describe two applications: one is to data from Cameroon that assesses prevalence using traditional blood-smear microscopy; the other is to Africa-wide data that uses a low-cost questionnaire-based method. We describe how a recent technological development in image-based microscopy has resulted in a change of emphasis from prevalence alone to the bivariate spatial distribution of prevalence and the intensity of infection among infected individuals. We discuss how statistical modelling of the kind described here can contribute to health policy guidelines and decision-making in two ways. One is to ensure that, in a resource-limited setting, prevalence surveys are designed, and the resulting data analysed, as efficiently as possible. The other is to provide an honest quantification of the uncertainty attached to any binary decision by reporting predictive probabilities that a policy-defined condition for action is or is not met.

Adam R. Brentnall, Jack Cuzick.

Source: Statistical Science, Volume 35, Number 1, 14--30.

Abstract:
Strategies to prevent cancer and diagnose it early when it is most treatable are needed to reduce the public health burden from rising disease incidence. Risk assessment is playing an increasingly important role in targeting individuals in need of such interventions. For breast cancer many individual risk factors have been well understood for a long time, but the development of a fully comprehensive risk model has not been straightforward, in part because there have been limited data where joint effects of an extensive set of risk factors may be estimated with precision. In this article we first review the approach taken to develop the IBIS (Tyrer–Cuzick) model, and describe recent updates. We then review and develop methods to assess calibration of models such as this one, where the risk of disease allowing for competing mortality over a long follow-up time or lifetime is estimated. The breast cancer risk model model and calibration assessment methods are demonstrated using a cohort of 132,139 women attending mammography screening in the State of Washington, USA.

Zhixiang Lin, Mahdi Zamanighomi, Timothy Daley, Shining Ma, Wing Hung Wong.

Source: Statistical Science, Volume 35, Number 1, 2--13.

Abstract:
Unsupervised methods, including clustering methods, are essential to the analysis of single-cell genomic data. Model-based clustering methods are under-explored in the area of single-cell genomics, and have the advantage of quantifying the uncertainty of the clustering result. Here we develop a model-based approach for the integrative analysis of single-cell chromatin accessibility and gene expression data. We show that combining these two types of data, we can achieve a better separation of the underlying cell types. An efficient Markov chain Monte Carlo algorithm is also developed.

T. Tony Cai.

Source: Statistical Science, Volume 34, Number 4, 635--656.

Abstract:
A wide range of nonparametric function estimation models have been studied individually in the literature. Among them the homoscedastic nonparametric Gaussian regression is arguably the best known and understood. Inspired by the asymptotic equivalence theory, Brown, Cai and Zhou ( Ann. Statist. 36 (2008) 2055–2084; Ann. Statist. 38 (2010) 2005–2046) and Brown et al. ( Probab. Theory Related Fields 146 (2010) 401–433) developed a unified approach to turn a collection of non-Gaussian function estimation models into a standard Gaussian regression and any good Gaussian nonparametric regression method can then be used. These Gaussianization Machines have two key components, binning and transformation. When combined with BlockJS, a wavelet thresholding procedure for Gaussian regression, the procedures are computationally efficient with strong theoretical guarantees. Technical analysis given in Brown, Cai and Zhou ( Ann. Statist. 36 (2008) 2055–2084; Ann. Statist. 38 (2010) 2005–2046) and Brown et al. ( Probab. Theory Related Fields 146 (2010) 401–433) shows that the estimators attain the optimal rate of convergence adaptively over a large set of Besov spaces and across a collection of non-Gaussian function estimation models, including robust nonparametric regression, density estimation, and nonparametric regression in exponential families. The estimators are also spatially adaptive. The Gaussianization Machines significantly extend the flexibility and scope of the theories and methodologies originally developed for the conventional nonparametric Gaussian regression. This article aims to provide a concise account of the Gaussianization Machines developed in Brown, Cai and Zhou ( Ann. Statist. 36 (2008) 2055–2084; Ann. Statist. 38 (2010) 2005–2046), Brown et al. ( Probab. Theory Related Fields 146 (2010) 401–433).

Andreas Buja, Arun Kumar Kuchibhotla, Richard Berk, Edward George, Eric Tchetgen Tchetgen, Linda Zhao.

Source: Statistical Science, Volume 34, Number 4, 606--620.

Abstract:
We respond to the discussants of our articles emphasizing the importance of inference under misspecification in the context of the reproducibility/replicability crisis. Along the way, we discuss the roles of diagnostics and model building in regression as well as connections between our well-specification framework and semiparametric theory.

Dalia Ghanem, Todd A. Kuffner.

Source: Statistical Science, Volume 34, Number 4, 604--605.

David Whitney, Ali Shojaie, Marco Carone.

Source: Statistical Science, Volume 34, Number 4, 591--598.

Anthony C. Davison, Erwan Koch, Jonathan Koh.

Source: Statistical Science, Volume 34, Number 4, 584--590.

Abstract:
This discussion focuses on areas of disagreement with the papers, particularly the target of inference and the case for using the robust ‘sandwich’ variance estimator in the presence of moderate mis-specification. We also suggest that existing procedures may be appreciably more powerful for detecting mis-specification than the authors’ RAV statistic, and comment on the use of the pairs bootstrap in balanced situations.

Roderick J. Little.

Source: Statistical Science, Volume 34, Number 4, 580--583.

Dag Tjøstheim.

Source: Statistical Science, Volume 34, Number 4, 575--579.

Nikki L. B. Freeman, Xiaotong Jiang, Owen E. Leete, Daniel J. Luckett, Teeranan Pokaprakarn, Michael R. Kosorok.

Source: Statistical Science, Volume 34, Number 4, 572--574.

Jerald F. Lawless.

Source: Statistical Science, Volume 34, Number 4, 569--571.

Abstract:
I comment on the papers Models as Approximations I and II, by A. Buja, R. Berk, L. Brown, E. George, E. Pitkin, M. Traskin, L. Zhao and K. Zhang.

Sara van de Geer.

Source: Statistical Science, Volume 34, Number 4, 566--568.

Abstract:
We discuss the papers “Models as Approximations” I & II, by A. Buja, R. Berk, L. Brown, E. George, E. Pitkin, M. Traskin, L. Zao and K. Zhang (Part I) and A. Buja, L. Brown, A. K. Kuchibhota, R. Berk, E. George and L. Zhao (Part II). We present a summary with some details for the generalized linear model.

Andreas Buja, Lawrence Brown, Arun Kumar Kuchibhotla, Richard Berk, Edward George, Linda Zhao.

Source: Statistical Science, Volume 34, Number 4, 545--565.

Abstract:
We develop a model-free theory of general types of parametric regression for i.i.d. observations. The theory replaces the parameters of parametric models with statistical functionals, to be called “regression functionals,” defined on large nonparametric classes of joint ${x extrm{-}y}$ distributions, without assuming a correct model. Parametric models are reduced to heuristics to suggest plausible objective functions. An example of a regression functional is the vector of slopes of linear equations fitted by OLS to largely arbitrary ${x extrm{-}y}$ distributions, without assuming a linear model (see Part I). More generally, regression functionals can be defined by minimizing objective functions, solving estimating equations, or with ad hoc constructions. In this framework, it is possible to achieve the following: (1) define a notion of “well-specification” for regression functionals that replaces the notion of correct specification of models, (2) propose a well-specification diagnostic for regression functionals based on reweighting distributions and data, (3) decompose sampling variability of regression functionals into two sources, one due to the conditional response distribution and another due to the regressor distribution interacting with misspecification, both of order $N^{-1/2}$, (4) exhibit plug-in/sandwich estimators of standard error as limit cases of ${x extrm{-}y}$ bootstrap estimators, and (5) provide theoretical heuristics to indicate that ${x extrm{-}y}$ bootstrap standard errors may generally be preferred over sandwich estimators.

Andreas Buja, Lawrence Brown, Richard Berk, Edward George, Emil Pitkin, Mikhail Traskin, Kai Zhang, Linda Zhao.

Source: Statistical Science, Volume 34, Number 4, 523--544.

Abstract:
In the early 1980s, Halbert White inaugurated a “model-robust” form of statistical inference based on the “sandwich estimator” of standard error. This estimator is known to be “heteroskedasticity-consistent,” but it is less well known to be “nonlinearity-consistent” as well. Nonlinearity, however, raises fundamental issues because in its presence regressors are not ancillary, hence cannot be treated as fixed. The consequences are deep: (1) population slopes need to be reinterpreted as statistical functionals obtained from OLS fits to largely arbitrary joint ${x extrm{-}y}$ distributions; (2) the meaning of slope parameters needs to be rethought; (3) the regressor distribution affects the slope parameters; (4) randomness of the regressors becomes a source of sampling variability in slope estimates of order $1/sqrt{N}$; (5) inference needs to be based on model-robust standard errors, including sandwich estimators or the ${x extrm{-}y}$ bootstrap. In theory, model-robust and model-trusting standard errors can deviate by arbitrary magnitudes either way. In practice, significant deviations between them can be detected with a diagnostic test.

Daniele Durante, Tommaso Rigon.

Source: Statistical Science, Volume 34, Number 3, 472--485.

Abstract:
Variational Bayes (VB) is a common strategy for approximate Bayesian inference, but simple methods are only available for specific classes of models including, in particular, representations having conditionally conjugate constructions within an exponential family. Models with logit components are an apparently notable exception to this class, due to the absence of conjugacy among the logistic likelihood and the Gaussian priors for the coefficients in the linear predictor. To facilitate approximate inference within this widely used class of models, Jaakkola and Jordan ( Stat. Comput. 10 (2000) 25–37) proposed a simple variational approach which relies on a family of tangent quadratic lower bounds of the logistic log-likelihood, thus restoring conjugacy between these approximate bounds and the Gaussian priors. This strategy is still implemented successfully, but few attempts have been made to formally understand the reasons underlying its excellent performance. Following a review on VB for logistic models, we cover this gap by providing a formal connection between the above bound and a recent Pólya-gamma data augmentation for logistic regression. Such a result places the computational methods associated with the aforementioned bounds within the framework of variational inference for conditionally conjugate exponential family models, thereby allowing recent advances for this class to be inherited also by the methods relying on Jaakkola and Jordan ( Stat. Comput. 10 (2000) 25–37).

Anna L. Smith, Dena M. Asta, Catherine A. Calder.

Source: Statistical Science, Volume 34, Number 3, 428--453.

Abstract:
We review the class of continuous latent space (statistical) models for network data, paying particular attention to the role of the geometry of the latent space. In these models, the presence/absence of network dyadic ties are assumed to be conditionally independent given the dyads’ unobserved positions in a latent space. In this way, these models provide a probabilistic framework for embedding network nodes in a continuous space equipped with a geometry that facilitates the description of dependence between random dyadic ties. Specifically, these models naturally capture homophilous tendencies and triadic clustering, among other common properties of observed networks. In addition to reviewing the literature on continuous latent space models from a geometric perspective, we highlight the important role the geometry of the latent space plays on properties of networks arising from these models via intuition and simulation. Finally, we discuss results from spectral graph theory that allow us to explore the role of the geometry of the latent space, independent of network size. We conclude with conjectures about how these results might be used to infer the appropriate latent space geometry from observed networks.

Sijia Xiang, Weixin Yao, Guangren Yang.

Source: Statistical Science, Volume 34, Number 3, 391--404.

Abstract:
Finite mixture models have offered a very important tool for exploring complex data structures in many scientific areas, such as economics, epidemiology and finance. Semiparametric mixture models, which were introduced into traditional finite mixture models in the past decade, have brought forth exciting developments in their methodologies, theories, and applications. In this article, we not only provide a selective overview of the newly-developed semiparametric mixture models, but also discuss their estimation methodologies, theoretical properties if applicable, and some open questions. Recent developments are also discussed.

Roger Koenker, Jiaying Gu.

Source: Statistical Science, Volume 34, Number 2, 209--213.

Abstract:
Efron’s elegant approach to $g$-modeling for empirical Bayes problems is contrasted with an implementation of the Kiefer–Wolfowitz nonparametric maximum likelihood estimator for mixture models for several examples. The latter approach has the advantage that it is free of tuning parameters and consequently provides a relatively simple complementary method.

Nicole Bohme Carnegie.

Source: Statistical Science, Volume 34, Number 1, 90--93.

Abstract:
With a thorough exposition of the methods and results of the 2016 Atlantic Causal Inference Competition, Dorie et al. have set a new standard for reproducibility and comparability of evaluations of causal inference methods. In particular, the open-source R package aciccomp2016, which permits reproduction of all datasets used in the competition, will be an invaluable resource for evaluation of future methodological developments. Building upon results from Dorie et al., we examine whether a set of potential modifications to Bayesian Additive Regression Trees (BART)—multiple chains in model fitting, using the propensity score as a covariate, targeted maximum likelihood estimation (TMLE), and computing symmetric confidence intervals—have a stronger impact on bias, RMSE, and confidence interval coverage in combination than they do alone. We find that bias in the estimate of SATT is minimal, regardless of the BART formulation. For purposes of CI coverage, however, all proposed modifications are beneficial—alone and in combination—but use of TMLE is least beneficial for coverage and results in considerably wider confidence intervals.

The capacity to process information in conceptual form is a fundamental aspect of human cognition, yet little is known about how this type of information is encoded in the brain. Although the role of sensory and motor cortical areas has been a focus of recent debate, neuroimaging studies of concept representation consistently implicate a network of heteromodal areas that seem to support concept retrieval in general rather than knowledge related to any particular sensory-motor content. We used predictive machine learning on fMRI data to investigate the hypothesis that cortical areas in this "general semantic network" (GSN) encode multimodal information derived from basic sensory-motor processes, possibly functioning as convergence–divergence zones for distributed concept representation. An encoding model based on five conceptual attributes directly related to sensory-motor experience (sound, color, shape, manipulability, and visual motion) was used to predict brain activation patterns associated with individual lexical concepts in a semantic decision task. When the analysis was restricted to voxels in the GSN, the model was able to identify the activation patterns corresponding to individual concrete concepts significantly above chance. In contrast, a model based on five perceptual attributes of the word form performed at chance level. This pattern was reversed when the analysis was restricted to areas involved in the perceptual analysis of written word forms. These results indicate that heteromodal areas involved in semantic processing encode information about the relative importance of different sensory-motor attributes of concepts, possibly by storing particular combinations of sensory and motor features.

SIGNIFICANCE STATEMENT The present study used a predictive encoding model of word semantics to decode conceptual information from neural activity in heteromodal cortical areas. The model is based on five sensory-motor attributes of word meaning (color, shape, sound, visual motion, and manipulability) and encodes the relative importance of each attribute to the meaning of a word. This is the first demonstration that heteromodal areas involved in semantic processing can discriminate between different concepts based on sensory-motor information alone. This finding indicates that the brain represents concepts as multimodal combinations of sensory and motor representations.

London (33 Stillness Road, London SE23 1NG) : Cleanair, Campaign for a Smoke-free Environment, [1989?]

London (33 Stillness Rd, London, SE23 1NG) : Cleanair, Campaign for a Smoke-free Environment, [198-?]

London (33 Stllness Rd, London, SE23 1NG) : Cleanair, Campaign for a Smoke-free Environment, [198-?]

London (33 Stillness Rd, London, SE23 ING) : Cleanair, Campaign for a Smoke-free Environment, [198-?]