We present a Bayesian nonparametric model for conditional distribution estimation using Bayesian additive regression trees (BART). The generative model we use is based on rejection sampling from a base model. Typical of BART models, our model is flexible, has a default prior specification, and is computationally convenient. To address the distinguished role of the response in the BART model we propose, we further introduce an approach to targeted smoothing which is possibly of independent interest for BART models. We study the proposed model theoretically and provide sufficient conditions for the posterior distribution to concentrate at close to the minimax optimal rate adaptively over smoothness classes in the high-dimensional regime in which many predictors are irrelevant. To fit our model we propose a data augmentation algorithm which allows for existing BART samplers to be extended with minimal effort. We illustrate the performance of our methodology on simulated data and use it to study the relationship between education and body mass index using data from the medical expenditure panel survey (MEPS).
Modeling complex conditional distributions is critical in a variety of settings. Despite a long tradition of research into conditional density estimation, current methods employ either simple parametric forms or are difficult to learn in practice. This paper employs normalising flows as a flexible likelihood model and presents an efficient method for fitting them to complex densities. These estimators must trade-off between modeling distributional complexity, functional complexity and heteroscedasticity without overfitting. We recognize these trade-offs as modeling decisions and develop a Baye…
This paper gives upper and lower bounds on the minimum error probability of Bayesian $M$-ary hypothesis testing in terms of the Arimoto-Rényi conditional entropy of an arbitrary order $α$. The improved tightness of these bounds over their specialized versions with the Shannon conditional entropy ($α=1$) is demonstrated. In particular, in the case where $M$ is finite, we show how to generalize Fano's inequality under both the conventional and list-decision settings. As a counterpart to the generalized Fano's inequality, allowing $M$ to be infinite, a lower bound on the Arimoto-Rényi conditional…
Recent developments in statistical regression methodology shift away from pure mean regression towards distributional regression models. One important strand thereof is that of conditional transformation models (CTMs). CTMs infer the entire conditional distribution directly by applying a transformation function to the response conditionally on a set of covariates towards a simple log-concave reference distribution. Thereby, CTMs allow not only variance, kurtosis or skewness but the complete conditional distribution to depend on the explanatory variables. We propose a Bayesian notion of conditi…
Ensemble Conditional Variance Estimation (ECVE) is a novel sufficient dimension reduction (SDR) method in regressions with continuous response and predictors. ECVE applies to general non-additive error regression models. It operates under the assumption that the predictors can be replaced by a lower dimensional projection without loss of information. It is a semiparametric forward regression model based exhaustive sufficient dimension reduction estimation method that is shown to be consistent under mild assumptions. It is shown to outperform central subspace mean average variance estimation (c…
We consider the problem of comparing two Poisson parameters from the Bayesian perspective. Kawasaki and Miyaoka (2012b) proposed the Bayesian index $P(λ_1 < λ_2 | X_1,X_2)$ and expressed it using the hypergeometric series. In this paper, under some conditions, we give four other expressions of the Bayesian index in terms of the cumulative distribution functions of beta, $F$, binomial, and negative binomial distribution. Next, we investigate the relationship between the Bayesian index and the $p$-value of the conditional test with the null hypothesis $H_0: λ_1 \geq λ_2 $ versus an alternative h…
We present a novel Bayesian nonparametric regression model for covariates X and continuous, real response variable Y. The model is parametrized in terms of marginal distributions for Y and X and a regression function which tunes the stochastic ordering of the conditional distributions F(y|x). By adopting an approximate composite likelihood approach, we show that the resulting posterior inference can be decoupled for the separate components of the model. This procedure can scale to very large datasets and allows for the use of standard, existing, software from Bayesian nonparametric density est…
In many application areas, data are collected on a categorical response and high-dimensional categorical predictors, with the goals being to build a parsimonious model for classification while doing inferences on the important predictors. In settings such as genomics, there can be complex interactions among the predictors. By using a carefully-structured Tucker factorization, we define a model that can characterize any conditional probability, while facilitating variable selection and modeling of higher-order interactions. Following a Bayesian approach, we propose a Markov chain Monte Carlo al…
Methods based on Bayesian decision tree ensembles have proven valuable in constructing high-quality predictions, and are particularly attractive in certain settings because they encourage low-order interaction effects. Despite adapting to the presence of low-order interactions for prediction purpose, we show that Bayesian decision tree ensembles are generally anti-conservative for the purpose of conducting interaction detection. We address this problem by introducing Dirichlet process forests (DP-Forests), which leverage the presence of low-order interactions by clustering the trees so that tr…
Bivariate count data arise in several different disciplines (epidemiology, marketing, sports statistics, etc., to name but a few) and the bivariate Poisson distribution which is a generalization of the Poisson distribution plays an important role in modeling such data. In this article, we consider the inferential aspect of a bivariate Poisson conditionals distribution for which both the conditionals are Poisson but the marginals are typically non-Poisson. It has Poisson marginals only in the case of independence. It appears that a simple iterative procedure under the maximum likelihood method …
We propose a generalised framework for the updating of a prior ensemble to a posterior ensemble, an essential yet challenging part in ensemble-based filtering methods. The proposed framework is based on a generalised and fully Bayesian view on the traditional ensemble Kalman filter (EnKF). In the EnKF, the updating of the ensemble is based on Gaussian assumptions, whereas in our general setup the updating may be based on another parametric family. In addition, we propose to formulate an optimality criterion and to find the optimal update with respect to this criterion. The framework is fully B…
We introduce a novel regression model for the conditional left and right tail of a possibly heavy-tailed response. The proposed model can be used to learn the effect of covariates on an extreme value setting via a Lasso-type specification based on a Lagrangian restriction. Our model can be used to track if some covariates are significant for the lower values, but not for the (right) tail---and vice-versa; in addition to this, the proposed model bypasses the need for conditional threshold selection in an extreme value theory framework. We assess the finite-sample performance of the proposed met…
There has been growing interest in the AI community for precise uncertainty quantification. Conditional density models f(y|x), where x represents potentially high-dimensional features, are an integral part of uncertainty quantification in prediction and Bayesian inference. However, it is challenging to assess conditional density estimates and gain insight into modes of failure. While existing diagnostic tools can determine whether an approximated conditional density is compatible overall with a data sample, they lack a principled framework for identifying, locating, and interpreting the nature…
We introduce a Bayesian approach for analyzing (possibly) high-dimensional dependent data that are distributed according to a member from the natural exponential family of distributions. This problem requires extensive methodological advancements, as jointly modeling high-dimensional dependent data leads to the so-called "big n problem." The computational complexity of the "big n problem" is further exacerbated when allowing for non-Gaussian data models, as is the case here. Thus, we develop new computationally efficient distribution theory for this setting. In particular, we introduce the "co…
We present a Bayesian mixture model for estimating the joint distribution of mixed ordinal, nominal, and continuous data conditional on a set of fixed variables. The model uses multivariate normal and categorical mixture kernels for the random variables. It induces dependence between the random and fixed variables through the means of the multivariate normal mixture kernels and via a truncated local Dirichlet process. The latter encourages observations with similar values of the fixed variables to share mixture components. Using a simulation of data fusion, we illustrate that the model can est…
Ensembles of decision trees are a useful tool for obtaining for obtaining flexible estimates of regression functions. Examples of these methods include gradient boosted decision trees, random forests, and Bayesian CART. Two potential shortcomings of tree ensembles are their lack of smoothness and vulnerability to the curse of dimensionality. We show that these issues can be overcome by instead considering sparsity inducing soft decision trees in which the decisions are treated as probabilistic. We implement this in the context of the Bayesian additive regression trees framework, and illustrate…
Estimation of the long-term health effects of air pollution is a challenging task, especially when modelling small-area disease incidence data in an ecological study design. The challenge comes from the unobserved underlying spatial correlation structure in these data, which is accounted for using random effects modelled by a globally smooth conditional autoregressive model. These smooth random effects confound the effects of air pollution, which are also globally smooth. To avoid this collinearity a Bayesian localised conditional autoregressive model is developed for the random effects. This …
Many organizations face critical decisions that rely on forecasts of binary events. In these situations, organizations often gather forecasts from multiple experts or models and average those forecasts to produce a single aggregate forecast. Because the average forecast is known to be underconfident, methods have been proposed that create an aggregate forecast more extreme than the average forecast. But is it always appropriate to extremize the average forecast? And if not, when is it appropriate to anti-extremize (i.e., to make the aggregate forecast less extreme)? To answer these questions, …
Penalized B-splines are routinely used in additive models to describe smooth changes in a response with quantitative covariates. It is typically done through the conditional mean in the exponential family using generalized additive models with an indirect impact on other conditional moments. Another common strategy consists in focussing on several low-order conditional moments, leaving the complete conditional distribution unspecified. Alternatively, a multi-parameter distribution could be assumed for the response with several of its parameters jointly regressed on covariates using additive ex…
This article introduces a Bayesian nonparametric method for quantifying the relative evidence in a dataset in favour of the dependence or independence of two variables conditional on a third. The approach uses Polya tree priors on spaces of conditional probability densities, accounting for uncertainty in the form of the underlying distributions in a nonparametric way. The Bayesian perspective provides an inherently symmetric probability measure of conditional dependence or independence, a feature particularly advantageous in causal discovery and not employed in existing procedures of this type…
We propose a novel Bayesian model framework for discrete ordinal and count data based on conditional transformations of the responses. The conditional transformation function is estimated from the data in conjunction with an a priori chosen reference distribution. For count responses, the resulting transformation model is novel in the sense that it is a Bayesian fully parametric yet distribution-free approach that can additionally account for excess zeros with additive transformation function specifications. For ordinal categoric responses, our cumulative link transformation model allows the i…
Several studies on heritability in twins aim at understanding the different contribution of environmental and genetic factors to specific traits. Considering the National Merit Twin Study, our purpose is to correctly analyse the influence of the socioeconomic status on the relationship between twins' cognitive abilities. Our methodology is based on conditional copulas, which allow us to model the effect of a covariate driving the strength of dependence between the main variables. We propose a flexible Bayesian nonparametric approach for the estimation of conditional copulas, which can model an…
Unblinded sample size re-estimation (SSR) is often planned in a clinical trial when there is large uncertainty about the true treatment effect. For Proof-of Concept (PoC) in a Phase II dose finding study, contrast test can be adopted to leverage information from all treatment groups. In this article, we propose two-stage SSR designs using frequentist conditional power and Bayesian posterior predictive power for both single and multiple contrast tests. The Bayesian SSR can be implemented under a wide range of prior settings to incorporate different prior knowledge. Taking the adaptivity into ac…
This paper proposes new methodology for sequential state and parameter estimation within the ensemble Kalman filter. The method is fully Bayesian and propagates the joint posterior density of states and parameters over time. In order to implement the method we consider two representations of the marginal posterior distribution of the parameters: a grid-based approach and a Gaussian approximation. Contrary to existing algorithms, the new method explicitly accounts for parameter uncertainty and provides a formal way to combine information about the parameters from data at different time periods.…
We develop a method to perform model averaging in two-stage linear regression systems subject to endogeneity. Our method extends an existing Gibbs sampler for instrumental variables to incorporate a component of model uncertainty. Direct evaluation of model probabilities is intractable in this setting. We show that by nesting model moves inside the Gibbs sampler, model comparison can be performed via conditional Bayes factors, leading to straightforward calculations. This new Gibbs sampler is only slightly more involved than the original algorithm and exhibits no evidence of mixing difficultie…
Bayesian additive regression trees have seen increased interest in recent years due to their ability to combine machine learning techniques with principled uncertainty quantification. The Bayesian backfitting algorithm used to fit BART models, however, limits their application to a small class of models for which conditional conjugacy exists. In this article, we greatly expand the domain of applicability of BART to arbitrary \emph{generalized BART} models by introducing a very simple, tuning-parameter-free, reversible jump Markov chain Monte Carlo algorithm. Our algorithm requires only that th…
Ensembles of networks arise in various fields where multiple independent networks are observed on the same set of nodes, for example, a collection of brain networks constructed on the same brain regions for different individuals. However, there are few models that describe both the variations and characteristics of networks in an ensemble at the same time. In this paper, we propose to model the ensemble of networks using a Dirichlet Process Mixture of Exponential Random Graph Models (DPM-ERGMs), which divides the ensemble into different clusters and models each cluster of networks using a sepa…
We present the Sequential Ensemble Transform (SET) method, an approach for generating approximate samples from a Bayesian posterior distribution. The method explores the posterior distribution by solving a sequence of discrete optimal transport problems to produce a series of transport plans which map prior samples to posterior samples. We prove that the sequence of Dirac mixture distributions produced by the SET method converges weakly to the true posterior as the sample size approaches infinity. Furthermore, our numerical results indicate that, when compared to standard Sequential Monte Carl…
We study the Bayesian approach to variable selection in the context of linear regression. Motivated by a recent work by Rockova and George (2014), we propose an EM algorithm that returns the MAP estimate of the set of relevant variables. Due to its particular updating scheme, our algorithm can be implemented efficiently without inverting a large matrix in each iteration and therefore can scale up with big data. We also show that the MAP estimate returned by our EM algorithm achieves variable selection consistency even when $p$ diverges with $n$. In practice, our algorithm could get stuck with …
Models for heteroskedastic data are relevant in a wide variety of applications ranging from financial time series to environmental statistics. However, the topic of modeling the variance function conditionally has not seen near as much attention as modeling the mean. Volatility models have been used in specific applications, but these models can be difficult to fit in a Bayesian setting due to posterior distributions that are challenging to sample from efficiently. In this work, we introduce a general model for heteroskedastic data. This approach models the conditional variance in a mixed mode…
Feature selection represents a measure to reduce the complexity of high-dimensional datasets and gain insights into the systematic variation in the data. This aspect is of specific importance in domains that rely on model interpretability, such as life sciences. We propose UBayFS, an ensemble feature selection technique embedded in a Bayesian statistical framework. Our approach considers two sources of information: data and domain knowledge. We build a meta-model from an ensemble of elementary feature selectors and aggregate this information in a multinomial likelihood. The user guides UBayFS …
Like mean, quantile and variance, mode is also an important measure of central tendency and data summary. Many practical questions often focus on "Which element (gene or file or signal) occurs most often or is the most typical among all elements in a network?". In such cases mode regression provides a convenient summary of how the regressors affect the conditional mode and is totally different from other regression models based on conditional mean or conditional quantile or conditional variance. Some inference methods have been used for mode regression but none of them from the Bayesian perspe…
Parameter ensembles or sets of point estimates constitute one of the cornerstones of modern statistical practice. This is especially the case in Bayesian hierarchical models, where different decision-theoretic frameworks can be deployed to summarize such parameter ensembles. The estimation of these parameter ensembles may thus substantially vary depending on which inferential goals are prioritised by the modeller. In this note, we consider the problem of classifying the elements of a parameter ensemble above or below a given threshold. Two threshold classification losses (TCLs) --weighted and …
Conditional Hierarchical Bayesian Tucker Decomposition for Genetic Data Analysis
Engineering Sciences and Applied Mathematics（应用数学与工程科学）；Industrial Engineering and Management Sciences（工业工程与管理科学）；Preventive Medicine (Health and Biomedical Informatics)（预防医学（健康与生物医学信息学））
Cointegration is an important topic for time-series, and describes a relationship between two series in which a linear combination is stationary. Classically, the test for cointegration is based on a two stage process in which first the linear relation between the series is estimated by Ordinary Least Squares. Subsequently a unit root test is performed on the residuals. A well-known deficiency of this classical approach is that it can lead to erroneous conclusions about the presence of cointegration. As an alternative, we present a framework for estimating whether cointegration exists using Ba…
Sampling of sharp posteriors in high dimensions is a challenging problem, especially when gradients of the likelihood are unavailable. In low to moderate dimensions, affine-invariant methods, a class of ensemble-based gradient-free methods, have found success in sampling concentrated posteriors. However, the number of ensemble members must exceed the dimension of the unknown state in order for the correct distribution to be targeted. Conversely, the preconditioned Crank-Nicolson (pCN) algorithm succeeds at sampling in high dimensions, but samples become highly correlated when the posterior dif…
