In psychophysical experiments time and the limited goodwill of participants is usually a major constraint. This has been the main motivation behind the early development of adaptive methods for the measurements of psychometric thresholds. More recently methods have been developed to measure whole psychometric functions in an adaptive way. Here we describe a Bayesian method to measure adaptively any aspect of a psychophysical function, taking inspiration from Kontsevich and Tyler's optimal Bayesian measurement method. Our method is implemented in a complete and easy-to-use MATLAB package.
Sorbonne Université（索邦大学）；INSERM（法国国家健康与医学研究院）；CNRS（法国国家科学研究中心）；Institut de la Vision（视觉研究所）
Bayesian optimization (BO) is an efficient method to optimize expensive black-box functions. It has been generalized to scenarios where objective function evaluations return stochastic binary feedback, such as success/failure in a given test, or preference between different parameter settings. In many real-world situations, the objective function can be evaluated in controlled 'contexts' or 'environments' that directly influence the observations. For example, one could directly alter the 'difficulty' of the test that is used to evaluate a system's performance. With binary feedback, the context…
Stan is an open-source probabilistic programing language, primarily designed to do Bayesian data analysis. Its main inference algorithm is an adaptive Hamiltonian Monte Carlo sampler, supported by state of the art gradient computation. Stan's strengths include efficient computation, an expressive language which offers a great deal of flexibility, and numerous diagnostics that allow modelers to check whether the inference is reliable. Torsten extends Stan with a suite of functions that facilitate the specification of pharmacokinetic and pharmacodynamic models, and makes it straightforward to sp…
Reliable mortality estimates at the subnational level are essential in the study of health inequalities within a country. One of the difficulties in producing such estimates is the presence of small populations, where the stochastic variation in death counts is relatively high, and so the underlying mortality levels are unclear. We present a Bayesian hierarchical model to estimate mortality at the subnational level. The model builds on characteristic age patterns in mortality curves, which are constructed using principal components from a set of reference mortality curves. Information on morta…
We study objective Bayesian inference for linear regression models with residual errors distributed according to the class of two-piece scale mixtures of normal distributions. These models allow for capturing departures from the usual assumption of normality of the errors in terms of heavy tails, asymmetry, and certain types of heteroscedasticity. We propose a general noninformative, scale-invariant, prior structure and provide sufficient conditions for the propriety of the posterior distribution of the model parameters, which cover cases when the response variables are censored. These results…
In order to implement disease-specific interventions in young age groups, policy makers in low- and middle-income countries require timely and accurate estimates of age- and cause-specific child mortality. High quality data is not available in settings where these interventions are most needed, but there is a push to create sample registration systems that collect detailed mortality information. Current methods that estimate mortality from this data employ multistage frameworks without rigorous statistical justification that separately estimate all-cause and cause-specific mortality and are no…
The joint modeling of longitudinal and time-to-event data is an important tool of growing popularity to gain insights into the association between a biomarker and an event process. We develop a general framework of flexible additive joint models that allows the specification of a variety of effects, such as smooth nonlinear, time-varying and random effects, in the longitudinal and survival parts of the models. Our extensions are motivated by the investigation of the relationship between fluctuating disease-specific markers, in this case autoantibodies, and the progression to the autoimmune dis…
Generalized autoregressive moving average (GARMA) models are a class of models that was developed for extending the univariate Gaussian ARMA time series model to a flexible observation-driven model for non-Gaussian time series data. This work presents Bayesian approach for GARMA models with Poisson, binomial and negative binomial distributions. A simulation study was carried out to investigate the performance of Bayesian estimation and Bayesian model selection criteria. Also three real datasets were analysed using the Bayesian approach on GARMA models.
Many of the data, particularly in medicine and disease mapping are count. Indeed, the under or overdispersion problem in count data distrusts the performance of the classical Poisson model. For taking into account this problem, in this paper, we introduce a new Bayesian structured additive regression model, called gamma count, with enough flexibility in modeling dispersion. Setting convenient prior distributions on the model parameters is a momentous issue in Bayesian statistics that characterize the nature of our uncertainty parameters. Relying on a recently proposed class of penalized comple…
In employing spatial regression models for counts, we usually meet two issues. First, ignoring the inherent collinearity between covariates and the spatial effect would lead to causal inferences. Second, real count data usually reveal over or under-dispersion where the classical Poisson model is not appropriate to use. We propose a flexible Bayesian hierarchical modeling approach by joining non-confounding spatial methodology and a newly reconsidered dispersed count modeling from the renewal theory to control the issues. Specifically, we extend the methodology for analyzing spatial count data …
This paper considers the problem of estimating linear dynamic system models when the observations are corrupted by random disturbances with nonstandard distributions. The paper is particularly motivated by applications where sensor imperfections involve significant contribution of outliers or wrap-around issues resulting in multi-modal distributions such as commonly encountered in robotics applications. As will be illustrated, these nonstandard measurement errors can dramatically compromise the effectiveness of standard estimation methods, while a computational Bayesian approach developed here…
Bayesian adaptive inference is widely used in psychophysics to estimate psychometric parameters. Most applications used myopic one-step ahead strategy which only optimizes the immediate utility. The widely held expectation is that global optimization strategies that explicitly optimize over some horizon can largely improve the performance of the myopic strategy. With limited studies that compared myopic and global strategies, the expectation was not challenged and researchers are still investing heavily to achieve global optimization. Is that really worthwhile? This paper provides a discouragi…
Imperial College London（帝国理工学院）；Inria Nancy Grand - Est（法国国家信息与自动化研究所南锡-大东部研究中心）；CNRS（法国国家科学研究中心）；Université de Lorraine（洛林大学）
Limbo is an open-source C++11 library for Bayesian optimization which is designed to be both highly flexible and very fast. It can be used to optimize functions for which the gradient is unknown, evaluations are expensive, and runtime cost matters (e.g., on embedded systems or robots). Benchmarks on standard functions show that Limbo is about 2 times faster than BayesOpt (another C++ library) for a similar accuracy.
In this paper, we introduce a probabilistic model for learning nonnegative matrix factorization (NMF) that is commonly used for predicting missing values and finding hidden patterns in the data, in which the matrix factors are latent variables associated with each data dimension. The nonnegativity constraint for the latent factors is handled by choosing priors with support on the nonnegative subspace. Bayesian inference procedure based on Gibbs sampling is employed. We evaluate the model on several real-world datasets including MovieLens 100K and MovieLens 1M with different sizes and dimension…
Probability estimation is one of the fundamental tasks in statistics and machine learning. However, standard methods for probability estimation on discrete objects do not handle object structure in a satisfactory manner. In this paper, we derive a general Bayesian network formulation for probability estimation on leaf-labeled trees that enables flexible approximations which can generalize beyond observations. We show that efficient algorithms for learning Bayesian networks can be easily extended to probability estimation on this challenging structured space. Experiments on both synthetic and r…
Satellites and their instruments are subject to the motion stability throughout their lifetimes. The reliability of the large flexible space structures (LFSS) is particularly important for the motion stability of satellites and their instruments. In this paper, the reliability analysis of large flexible space structures is conducted based on Bayesian support vector regression (SVR). The kinematic model of a typical large flexible space structure is first established. Based on the kinematic model, the surrogate model of the motion of the large flexible space structure is then developed to furth…
Climbing grades are used to classify a climbing route based on its perceived difficulty, and have come to play a central role in the sport of rock climbing. Recently, the first statistically rigorous method for estimating climbing grades from whole-history ascent data was described, based on the dynamic Bradley-Terry model for games between players of time-varying ability. In this paper, we implement inference under the whole-history rating model using Markov chain Monte Carlo and apply the method to a curated data set made up of climbers who climb regularly. We use these data to get an estima…
Joint models of longitudinal and survival data have become an important tool for modeling associations between longitudinal biomarkers and event processes. The association between marker and log-hazard is assumed to be linear in existing shared random effects models, with this assumption usually remaining unchecked. We present an extended framework of flexible additive joint models that allows the estimation of nonlinear, covariate specific associations by making use of Bayesian P-splines. Our joint models are estimated in a Bayesian framework using structured additive predictors for all model…
Identifying Brexit voting patterns in the British House of Commons: an analysis based on Bayesian mixture models with flexible concomitant covariate effects
Flexible Empirical Bayesian Approaches to Pharmacovigilance for Simultaneous Signal Detection and Signal Strength Estimation in Spontaneous Reporting Systems Data
With advances in neural recording techniques, neuroscientists are now able to record the spiking activity of many hundreds of neurons simultaneously, and new statistical methods are needed to understand the structure of this large-scale neural population activity. Although previous work has tried to summarize neural activity within and between known populations by extracting low-dimensional latent factors, in many cases what determines a unique population may be unclear. Neurons differ in their anatomical location, but also, in their cell types and response properties. To identify populations …
A fast, flexible simulation framework for Bayesian adaptive designs -- the R package BATSS
MRC Biostatistics Unit, University of Cambridge（剑桥大学医学研究委员会生物统计学单位）；School of Public Health and Preventive Medicine, Monash University（莫纳什大学公共卫生与预防医学院）；Faculty of Informatics and Data Science, University of Regensburg（雷根斯堡大学信息科学与数据科学学院）
We present a class of sparse generalized linear models that include probit and logistic regression as special cases and offer some extra flexibility. We provide an EM algorithm for learning the parameters of these models from data. We apply our method in text classification and in simulated data and show that our method outperforms the logistic and probit models and also the elastic net, in general by a substantial margin.
University of Oslo（奥斯陆大学）；Norwegian Computing Center（挪威计算中心）；Medical University of Vienna（维也纳医科大学）
Regression models are used in a wide range of applications providing a powerful scientific tool for researchers from different fields. Linear, or simple parametric, models are often not sufficient to describe complex relationships between input variables and a response. Such relationships can be better described through flexible approaches such as neural networks, but this results in less interpretable models and potential overfitting. Alternatively, specific parametric nonlinear functions can be used, but the specification of such functions is in general complicated. In this paper, we introdu…
Several bivariate beta distributions have been proposed in the literature. In particular, Olkin and Liu (2003) proposed a 3 parameter bivariate beta model, which Arnold and Ng (2011) extend to 5 and 8 parameter models. The 3 parameter model allows for only positive correlation, while the latter models can accommodate both positive and negative correlation. However, these come at the expense of a density that is mathematically intractable. The focus of this research is on Bayesian estimation for the 5 and 8 parameter models. Since the likelihood does not exist in closed form, we apply approxima…
Item response theory (IRT) models typically rely on a normality assumption for subject-specific latent traits, which is often unrealistic in practice. Semiparametric extensions based on Dirichlet process mixtures offer a more flexible representation of the unknown distribution of the latent trait. However, the use of such models in the IRT literature has been extremely limited, in good part because of the lack of comprehensive studies and accessible software tools. This paper provides guidance for practitioners on semiparametric IRT models and their implementation. In particular, we rely on NI…
Modelling time-order effects in haptic perception with a Bayesian dynamical framework
Instituto Balseiro, Centro Atómico Bariloche（巴尔塞罗研究所，巴里洛切原子中心）；Department of Applications of Physics and Biology to Health Sciences, Centro Atómico Bariloche（巴里洛切原子中心应用物理与生物健康科学系）；Department of Translational Research, Centro Atómico Bariloche（巴里洛切原子中心转化研究系）；Institute for Intelligent Interactive Systems, Department of Computer Science, ETH Zürich（苏黎世联邦理工学院计算机学院智能交互系统研究所）
In this paper, we write the time-varying parameter (TVP) regression model involving K explanatory variables and T observations as a constant coefficient regression model with KT explanatory variables. In contrast with much of the existing literature which assumes coefficients to evolve according to a random walk, a hierarchical mixture model on the TVPs is introduced. The resulting model closely mimics a random coefficients specification which groups the TVPs into several regimes. These flexible mixtures allow for TVPs that feature a small, moderate or large number of structural breaks. We dev…
In computer experiments, a mathematical model implemented on a computer is used to represent complex physical phenomena. These models, known as computer simulators, enable experimental study of a virtual representation of the complex phenomena. Simulators can be thought of as complex functions that take many inputs and provide an output. Often these simulators are themselves expensive to compute, and may be approximated by "surrogate models" such as statistical regression models. In this paper we consider a new kind of surrogate model, a Bayesian ensemble of trees (Chipman et al. 2010), with t…
This work introduces a novel methodology based on finite mixtures of Student-t distributions to model the errors' distribution in linear regression models. The novelty lies on a particular hierarchical structure for the mixture distribution in which the first level models the number of modes, responsible to accommodate multimodality and skewness features, and the second level models tail behavior. Moreover, the latter is specified in a way that no degrees of freedom parameters are estimated and, therefore, the known statistical difficulties when dealing with those parameters is mitigated, and …
We propose a Bayesian approach using improper priors for hierarchical linear mixed models with flexible random effects and residual error distributions. The error distribution is modelled using scale mixtures of normals, which can capture tails heavier than those of the normal distribution. This generalisation is useful to produce models that are robust to the presence of outliers. The case of asymmetric residual errors is also studied. We present general results for the propriety of the posterior that also cover cases with censored observations, allowing for the use of these models in the con…
Modeling correlation (and covariance) matrices can be challenging due to the positive-definiteness constraint and potential high-dimensionality. Our approach is to decompose the covariance matrix into the correlation and variance matrices and propose a novel Bayesian framework based on modeling the correlations as products of unit vectors. By specifying a wide range of distributions on a sphere (e.g. the squared-Dirichlet distribution), the proposed approach induces flexible prior distributions for covariance matrices (that go beyond the commonly used inverse-Wishart prior). For modeling real-…
Generalized additive models (GAMs) are flexible non-linear regression models, which can be fitted efficiently using the approximate Bayesian methods provided by the mgcv R package. While the GAM methods provided by mgcv are based on the assumption that the response distribution is modelled parametrically, here we discuss more flexible methods that do not entail any parametric assumption. In particular, this article introduces the qgam package, which is an extension of mgcv providing fast calibrated Bayesian methods for fitting quantile GAMs (QGAMs) in R. QGAMs are based on a smooth version of …
Many real world applications can be framed as multi-objective optimization problems, where we wish to simultaneously optimize for multiple criteria. Bayesian optimization techniques for the multi-objective setting are pertinent when the evaluation of the functions in question are expensive. Traditional methods for multi-objective optimization, both Bayesian and otherwise, are aimed at recovering the Pareto front of these objectives. However, in certain cases a practitioner might desire to identify Pareto optimal points only in a subset of the Pareto front due to external considerations. In thi…
The problem we consider considers estimating a multivariate longitudinal panel data model whose outcomes can be a combination of discrete and continuous variables. This problem is challenging because the likelihood is usually analytically intractable. Our article makes both a methodological contribution and also a substantive contribution to the application. The methodological contribution is to introduce into the panel data literature a particle Metropolis within Gibbs method to carry out Bayesian inference, using a Hamiltonian Monte Carlo (Neal 2011} proposal for sampling the vector of unkno…
Objective: Brain networks have gained increasing recognition as potential biomarkers in mental health studies, but there are limited approaches that can leverage complex brain networks for accurate classification. Our goal is to develop a novel Bayesian Support Vector Machine (SVM) approach that incorporates high-dimensional networks as covariates and is able to overcome limitations of existing penalized methods. Methods: We develop a novel Dirichlet process mixture of double exponential priors on the coefficients in the Bayesian SVM model that is able to perform feature selection and uncertai…
Deep feedforward neural networks (DFNNs) are a powerful tool for functional approximation. We describe flexible versions of generalized linear and generalized linear mixed models incorporating basis functions formed by a DFNN. The consideration of neural networks with random effects is not widely used in the literature, perhaps because of the computational challenges of incorporating subject specific parameters into already complex models. Efficient computational methods for high-dimensional Bayesian inference are developed using Gaussian variational approximation, with a parsimonious but flex…
Most Item Response Theory (IRT) models for dichotomous responses are based on probit or logit link functions which assume a symmetric relationship between the probability of a correct response and the latent traits of individuals submitted to a test. This assumption restricts the use of those models to the case in which all items have a symmetric behaviour. On the other hand, asymmetric models proposed in the literature impose that all the items in a test have an asymmetric behaviour. This assumption is inappropriate for great part of the tests which are, in general, composed by both symmetric…
A multivariate distribution can be described by a triangular transport map from the target distribution to a simple reference distribution. We propose Bayesian nonparametric inference on the transport map by modeling its components using Gaussian processes. This enables regularization and uncertainty quantification of the map estimation, while still resulting in a closed-form and invertible posterior map. We then focus on inferring the distribution of a nonstationary spatial field from a small number of replicates. We develop specific transport-map priors that are highly flexible and are motiv…
Small area population estimates are useful for decision making in the private and public sectors. However, in small areas (i.e., those that are difficult to reach and with small population sizes) computing demographic quantities is complicated. Bayesian methods are an alternative for demographic population estimates which uses data from multiple administrative records. In this paper we explore a Bayesian approach which is simple and flexible and represents an alternative procedure for base population estimates particularly powerful for intercensal periods. The applicability of the methodologic…
Typical Bayesian inference requires parameter identification via likelihood parameterization, which has invited criticism for being less flexible than the Frequentist framework and subject to misspecification. Though misspecification may be avoided by functional parameter inference under a nonparametric model space, there does not exist a flexible Bayesian semiparametric model that would allow full control over the marginal prior over any general functional parameter. We present the technique of $θ$-augmentation which helps us manipulate nonparametric models into semiparametric ones that direc…
