Philippe Gagnon, Alain Desgagné, Mylène Bédard.

Source: Bayesian Analysis, Volume 15, Number 2, 389--414.

Abstract:
Linear regression is ubiquitous in statistical analysis. It is well understood that conflicting sources of information may contaminate the inference when the classical normality of errors is assumed. The contamination caused by the light normal tails follows from an undesirable effect: the posterior concentrates in an area in between the different sources with a large enough scaling to incorporate them all. The theory of conflict resolution in Bayesian statistics (O’Hagan and Pericchi (2012)) recommends to address this problem by limiting the impact of outliers to obtain conclusions consistent with the bulk of the data. In this paper, we propose a model with super heavy-tailed errors to achieve this. We prove that it is wholly robust, meaning that the impact of outliers gradually vanishes as they move further and further away from the general trend. The super heavy-tailed density is similar to the normal outside of the tails, which gives rise to an efficient estimation procedure. In addition, estimates are easily computed. This is highlighted via a detailed user guide, where all steps are explained through a simulated case study. The performance is shown using simulation. All required code is given.

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.

Aliaksandr Hubin, Geir Storvik, Florian Frommlet.

Source: Bayesian Analysis, Volume 15, Number 1, 263--333.

Abstract:
Logic regression was developed more than a decade ago as a tool to construct predictors from Boolean combinations of binary covariates. It has been mainly used to model epistatic effects in genetic association studies, which is very appealing due to the intuitive interpretation of logic expressions to describe the interaction between genetic variations. Nevertheless logic regression has (partly due to computational challenges) remained less well known than other approaches to epistatic association mapping. Here we will adapt an advanced evolutionary algorithm called GMJMCMC (Genetically modified Mode Jumping Markov Chain Monte Carlo) to perform Bayesian model selection in the space of logic regression models. After describing the algorithmic details of GMJMCMC we perform a comprehensive simulation study that illustrates its performance given logic regression terms of various complexity. Specifically GMJMCMC is shown to be able to identify three-way and even four-way interactions with relatively large power, a level of complexity which has not been achieved by previous implementations of logic regression. We apply GMJMCMC to reanalyze QTL (quantitative trait locus) mapping data for Recombinant Inbred Lines in Arabidopsis thaliana and from a backcross population in Drosophila where we identify several interesting epistatic effects. The method is implemented in an R package which is available on github.

Ilaria Bianchini, Alessandra Guglielmi, Fernando A. Quintana.

Source: Bayesian Analysis, Volume 15, Number 1, 187--214.

Abstract:
We consider mixture models where location parameters are a priori encouraged to be well separated. We explore a class of determinantal point process (DPP) mixture models, which provide the desired notion of separation or repulsion. Instead of using the rather restrictive case where analytical results are partially available, we adopt a spectral representation from which approximations to the DPP density functions can be readily computed. For the sake of concreteness the presentation focuses on a power exponential spectral density, but the proposed approach is in fact quite general. We later extend our model to incorporate covariate information in the likelihood and also in the assignment to mixture components, yielding a trade-off between repulsiveness of locations in the mixtures and attraction among subjects with similar covariates. We develop full Bayesian inference, and explore model properties and posterior behavior using several simulation scenarios and data illustrations. Supplementary materials for this article are available online (Bianchini et al., 2019).

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.

Jeong Eun Lee, Geoff K. Nicholls, Robin J. Ryder.

Source: Bayesian Analysis, Volume 14, Number 4, 1245--1269.

Abstract:
We develop and apply two calibration procedures for checking the coverage of approximate Bayesian credible sets, including intervals estimated using Monte Carlo methods. The user has an ideal prior and likelihood, but generates a credible set for an approximate posterior based on some approximate prior and likelihood. We estimate the realised posterior coverage achieved by the approximate credible set. This is the coverage of the unknown “true” parameter if the data are a realisation of the user’s ideal observation model conditioned on the parameter, and the parameter is a draw from the user’s ideal prior. In one approach we estimate the posterior coverage at the data by making a semi-parametric logistic regression of binary coverage outcomes on simulated data against summary statistics evaluated on simulated data. In another we use Importance Sampling from the approximate posterior, windowing simulated data to fall close to the observed data. We illustrate our methods on four examples.

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.

Julyan Arbel, Pierpaolo De Blasi, Igor Prünster.

Source: Bayesian Analysis, Volume 14, Number 3, 753--771.

Abstract:
In this paper we consider approximations to the popular Pitman–Yor process obtained by truncating the stick-breaking representation. The truncation is determined by a random stopping rule that achieves an almost sure control on the approximation error in total variation distance. We derive the asymptotic distribution of the random truncation point as the approximation error $epsilon$ goes to zero in terms of a polynomially tilted positive stable random variable. The practical usefulness and effectiveness of this theoretical result is demonstrated by devising a sampling algorithm to approximate functionals of the $epsilon$ -version of the Pitman–Yor process.

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.

Luis Gutiérrez, Eduardo Gutiérrez-Peña, Ramsés H. Mena.

Source: Bayesian Analysis, Volume 14, Number 2, 427--447.

Abstract:
This work presents a Bayesian predictive approach to statistical shape analysis. A modeling strategy that starts with a Gaussian distribution on the configuration space, and then removes the effects of location, rotation and scale, is studied. This boils down to an application of the projected normal distribution to model the configurations in the shape space, which together with certain identifiability constraints, facilitates parameter interpretation. Having better control over the parameters allows us to generalize the model to a regression setting where the effect of predictors on shapes can be considered. The methodology is illustrated and tested using both simulated scenarios and a real data set concerning eight anatomical landmarks on a sagittal plane of the corpus callosum in patients with autism and in a group of controls.

Peter D. Hoff

Source: Bayesian Anal., Volume 6, Number 2, 179--196.

Abstract:
Modern datasets are often in the form of matrices or arrays, potentially having correlations along each set of data indices. For example, data involving repeated measurements of several variables over time may exhibit temporal correlation as well as correlation among the variables. A possible model for matrix-valued data is the class of matrix normal distributions, which is parametrized by two covariance matrices, one for each index set of the data. In this article we discuss an extension of the matrix normal model to accommodate multidimensional data arrays, or tensors. We show how a particular array-matrix product can be used to generate the class of array normal distributions having separable covariance structure. We derive some properties of these covariance structures and the corresponding array normal distributions, and show how the array-matrix product can be used to define a semi-conjugate prior distribution and calculate the corresponding posterior distribution. We illustrate the methodology in an analysis of multivariate longitudinal network data which take the form of a four-way array.

Ruosi Guo, Chunming Zhang, Zhengjun Zhang.

Source: Statistical Science, Volume 35, Number 1, 145--157.

Abstract:
In many scientific disciplines, finding hidden influential factors behind observational data is essential but challenging. The majority of existing approaches, such as the independent component analysis (${mathrm{ICA}}$), rely on linear transformation, that is, true signals are linear combinations of hidden components. Motivated from analyzing nonlinear temporal signals in neuroscience, genetics, and finance, this paper proposes the “maximum independent component analysis” (${mathrm{MaxICA}}$), based on max-linear combinations of components. In contrast to existing methods, ${mathrm{MaxICA}}$ benefits from focusing on significant major components while filtering out ignorable components. A major tool for parameter learning of ${mathrm{MaxICA}}$ is an augmented genetic algorithm, consisting of three schemes for the elite weighted sum selection, randomly combined crossover, and dynamic mutation. Extensive empirical evaluations demonstrate the effectiveness of ${mathrm{MaxICA}}$ in either extracting max-linearly combined essential sources in many applications or supplying a better approximation for nonlinearly combined source signals, such as $mathrm{EEG}$ recordings analyzed in this paper.

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.

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.

Gregorio Quintana-Ortí, Amelia Simó.

Source: Statistical Science, Volume 34, Number 2, 236--252.

Abstract:
This paper is focused on kernel regression when the response variable is the shape of a 3D object represented by a configuration matrix of landmarks. Regression methods on this shape space are not trivial because this space has a complex finite-dimensional Riemannian manifold structure (non-Euclidean). Papers about it are scarce in the literature, the majority of them are restricted to the case of a single explanatory variable, and many of them are based on the approximated tangent space. In this paper, there are several methodological innovations. The first one is the adaptation of the general method for kernel regression analysis in manifold-valued data to the three-dimensional case of Kendall’s shape space. The second one is its generalization to the multivariate case and the addressing of the curse-of-dimensionality problem. Finally, we propose bootstrap confidence intervals for prediction. A simulation study is carried out to check the goodness of the procedure, and a comparison with a current approach is performed. Then, it is applied to a 3D database obtained from an anthropometric survey of the Spanish child population with a potential application to online sales of children’s wear.

The chic sneaks are part of Zappos' massive Cyber Monday sale.

Brian Zingg
Apr 15, 2020; 40:3250-3267
Systems/Circuits

KM Harris
Jul 1, 1992; 12:2685-2705
Articles

Randy L. Buckner
Feb 11, 2009; 29:1860-1873
Neurobiology of Disease

French translation of the BIS Quarterly Review, March 2018

French translation of the BIS press release about the BIS Quarterly Review, March 2018

French translation of the BIS Quarterly Review, June 2018

French translation of the Annual Economic Report 2018 of the BIS, June 2018 - Les responsables des politiques publiques peuvent prolonger la phase de croissance actuelle en engageant des réformes structurelles, en restaurant les marges de manœuvre monétaires et budgétaires pour faire face aux menaces futures et en encourageant une mise en œuvre rapide des réformes réglementaires, indique la Banque des Règlements Internationaux (BRI) dans son Rapport économique annuel.

French translation of the BIS press release about the BIS Quarterly Review, September 2018

French translation of the BIS Quarterly Review, September 2018

French translation of the BIS press release about the BIS Quarterly Review, December 2018

French translation of the BIS Quarterly Review, December 2018

French translation of the BIS press release about the BIS Quarterly Review, March 2019

French translation of the BIS Quarterly Review, March 2019

French translation of the BIS press release on the presentation of the Annual Economic Report 2019, 30 June 2019. La politique monétaire ne peut plus être le principal moteur de la croissance économique, et d'autres leviers de politique publique doivent être actionnés pour faire en sorte que l'économie mondiale connaisse une dynamique durable ...

To view more press releases, please visit http://www.snl.com/irweblinkx/news.aspx?iid=1024452.

The UK's plans to launch a smartphone application to track potential COVID-19 infections won't include Apple and Google. The country's National Health Service has designed its own mobile software to do contact tracing of people exposed to the coronavirus. The NHS reportedly found that its own tech works "sufficiently well." The NHS chose a centralized model for its data collection and storage.

Revealing the organization and function of neural circuits is greatly facilitated by viral tools that spread transsynaptically. Adeno-associated virus (AAV) exhibits anterograde transneuronal transport, however, the synaptic specificity of this spread and its broad application within a diverse set of circuits remains to be explored. Here, using anatomic, functional, and molecular approaches, we provide evidence for the preferential transport of AAV1 to postsynaptically connected neurons and reveal its spread is strongly dependent on synaptic transmitter release. In addition to glutamatergic pathways, AAV1 also spreads through GABAergic synapses to both excitatory and inhibitory cell types. We observed little or no transport, however, through neuromodulatory projections (e.g., serotonergic, cholinergic, and noradrenergic). In addition, we found that AAV1 can be transported through long-distance descending projections from various brain regions to effectively transduce spinal cord neurons. Combined with newly designed intersectional and sparse labeling strategies, AAV1 can be applied within a wide variety of pathways to categorize neurons according to their input sources, morphology, and molecular identities. These properties make AAV1 a promising anterograde transsynaptic tool for establishing a comprehensive cell-atlas of the brain, although its capacity for retrograde transport currently limits its use to unidirectional circuits.

SIGNIFICANCE STATEMENT The discovery of anterograde transneuronal spread of AAV1 generates great promise for its application as a unique tool for manipulating input-defined cell populations and mapping their outputs. However, several outstanding questions remain for anterograde transsynaptic approaches in the field: (1) whether AAV1 spreads exclusively or specifically to synaptically connected neurons, and (2) how broad its application could be in various types of neural circuits in the brain. This study provides several lines of evidence in terms of anatomy, functional innervation, and underlying mechanisms, to strongly support that AAV1 anterograde transneuronal spread is highly synapse specific. In addition, several potentially important applications of transsynaptic AAV1 in probing neural circuits are described.

MECP2 gain-of-function and loss-of-function in genetically engineered monkeys recapitulates typical phenotypes in patients with autism, yet where MECP2 mutation affects the monkey brain and whether/how it relates to autism pathology remain unknown. Here we report a combination of gene–circuit–behavior analyses including MECP2 coexpression network, locomotive and cognitive behaviors, and EEG and fMRI findings in 5 MECP2 overexpressed monkeys (Macaca fascicularis; 3 females) and 20 wild-type monkeys (Macaca fascicularis; 11 females). Whole-genome expression analysis revealed MECP2 coexpressed genes significantly enriched in GABA-related signaling pathways, whereby reduced β-synchronization within fronto-parieto-occipital networks was associated with abnormal locomotive behaviors. Meanwhile, MECP2-induced hyperconnectivity in prefrontal and cingulate networks accounted for regressive deficits in reversal learning tasks. Furthermore, we stratified a cohort of 49 patients with autism and 72 healthy controls of 1112 subjects using functional connectivity patterns, and identified dysconnectivity profiles similar to those in monkeys. By establishing a circuit-based construct link between genetically defined models and stratified patients, these results pave new avenues to deconstruct clinical heterogeneity and advance accurate diagnosis in psychiatric disorders.

SIGNIFICANCE STATEMENT Autism spectrum disorder (ASD) is a complex disorder with co-occurring symptoms caused by multiple genetic variations and brain circuit abnormalities. To dissect the gene–circuit–behavior causal chain underlying ASD, animal models are established by manipulating causative genes such as MECP2. However, it is unknown whether such models have captured any circuit-level pathology in ASD patients, as demonstrated by human brain imaging studies. Here, we use transgenic macaques to examine the causal effect of MECP2 overexpression on gene coexpression, brain circuits, and behaviors. For the first time, we demonstrate that the circuit abnormalities linked to MECP2 and autism-like traits in the monkeys can be mapped to a homogeneous ASD subgroup, thereby offering a new strategy to deconstruct clinical heterogeneity in ASD.

In 2015 we celebrated the “International Year of Soils” and with good reason. Soil sustains all our agricultural and livestock food production, wood for fuel production, filters water so that we can drink it and fish can live in it. We also use it for construction - therefore it sustains our homes and infrastructure. As we approach the end of #IYS [...]

In 2016 we celebrated the International Year of Pulses and it is obvious why. Pulses are good for you, beneficial to farmers' livelihoods and have a positive impact on the environment. It is clear that even though dried beans, lentils and peas have been around for centuries, they will play a fundamental role in our sustainable future. Even though #IYP2016 has [...]

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