We present a new package in R implementing Bayesian additive regression trees (BART). The package introduces many new features for data analysis using BART such as variable selection, interaction detection, model diagnostic plots, incorporation of missing data and the ability to save trees for future prediction. It is significantly faster than the current R implementation, parallelized, and capable of handling both large sample sizes and high-dimensional data.
We incorporate heteroskedasticity into Bayesian Additive Regression Trees (BART) by modeling the log of the error variance parameter as a linear function of prespecified covariates. Under this scheme, the Gibbs sampling procedure for the original sum-of- trees model is easily modified, and the parameters for the variance model are updated via a Metropolis-Hastings step. We demonstrate the promise of our approach by providing more appropriate posterior predictive intervals than homoskedastic BART in heteroskedastic settings and demonstrating the model's resistance to overfitting. Our implementa…
Tree-based regression and classification has become a standard tool in modern data science. Bayesian Additive Regression Trees (BART) has in particular gained wide popularity due its flexibility in dealing with interactions and non-linear effects. BART is a Bayesian tree-based machine learning method that can be applied to both regression and classification problems and yields competitive or superior results when compared to other predictive models. As a Bayesian model, BART allows the practitioner to explore the uncertainty around predictions through the posterior distribution. In this paper,…
University of Chicago（芝加哥大学）；Arizona State University（亚利桑那州立大学）
Bayesian additive regression trees (BART) (Chipman et. al., 2010) is a powerful predictive model that often outperforms alternative models at out-of-sample prediction. BART is especially well-suited to settings with unstructured predictor variables and substantial sources of unmeasured variation as is typical in the social, behavioral and health sciences. This paper develops a modified version of BART that is amenable to fast posterior estimation. We present a stochastic hill climbing algorithm that matches the remarkable predictive accuracy of previous BART implementations, but is many times …
University of Pennsylvania（宾夕法尼亚大学）；Medical College of Wisconsin（威斯康星医学院）；Arizona State University（亚利桑那州立大学）
Bayesian Additive Regression Trees (BART) is a fully Bayesian approach to modeling with ensembles of trees. BART can uncover complex regression functions with high dimensional regressors in a fairly automatic way and provide Bayesian quantification of the uncertainty through the posterior. However, BART assumes IID normal errors. This strong parametric assumption can lead to misleading inference and uncertainty quantification. In this paper, we use the classic Dirichlet process mixture (DPM) mechanism to nonparametrically model the error distribution. A key strength of BART is that default pri…
The Wharton School of the University of Pennsylvania（宾夕法尼亚大学沃顿商学院）
We present a method for incorporating missing data in non-parametric statistical learning without the need for imputation. We focus on a tree-based method, Bayesian Additive Regression Trees (BART), enhanced with "Missingness Incorporated in Attributes," an approach recently proposed incorporating missingness into decision trees (Twala, 2008). This procedure takes advantage of the partitioning mechanisms found in tree-based models. Simulations on generated models and real data indicate that our proposed method can forecast well on complicated missing-at-random and not-missing-at-random models …
Hamilton Institute（汉密尔顿研究所）；Insight Centre for Data Analytics（洞察数据分析中心）；Maynooth University（梅努斯大学）
Bayesian Additive Regression Trees (BART) is a tree-based machine learning method that has been successfully applied to regression and classification problems. BART assumes regularisation priors on a set of trees that work as weak learners and is very flexible for predicting in the presence of non-linearity and high-order interactions. In this paper, we introduce an extension of BART, called Model Trees BART (MOTR-BART), that considers piecewise linear functions at node levels instead of piecewise constants. In MOTR-BART, rather than having a unique value at node level for the prediction, a li…
A primary goal of computer experiments is to reconstruct the function given by the computer code via scattered evaluations. Traditional isotropic Gaussian process models suffer from the curse of dimensionality, when the input dimension is relatively high given limited data points. Gaussian process models with additive correlation functions are scalable to dimensionality, but they are more restrictive as they only work for additive functions. In this work, we consider a projection pursuit model, in which the nonparametric part is driven by an additive Gaussian process regression. We choose the …
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…
Ensemble of regression trees have become popular statistical tools for the estimation of conditional mean given a set of predictors. However, quantile regression trees and their ensembles have not yet garnered much attention despite the increasing popularity of the linear quantile regression model. This work proposes a Bayesian quantile additive regression trees model that shows very good predictive performance illustrated using simulation studies and real data applications. Further extension to tackle binary classification problems is also considered.
Cornell University（康奈尔大学）；New York University（纽约大学）
Gaussian processes (GPs) provide flexible distributions over functions, with inductive biases controlled by a kernel. However, in many applications Gaussian processes can struggle with even moderate input dimensionality. Learning a low dimensional projection can help alleviate this curse of dimensionality, but introduces many trainable hyperparameters, which can be cumbersome, especially in the small data regime. We use additive sums of kernels for GP regression, where each kernel operates on a different random projection of its inputs. Surprisingly, we find that as the number of random projec…
This article proposes Multinomial Probit Bayesian Additive Regression Trees (MPBART) as a multinomial probit extension of BART - Bayesian Additive Regression Trees (Chipman et al (2010)). MPBART is flexible to allow inclusion of predictors that describe the observed units as well as the available choice alternatives. Through two simulation studies and four real data examples, we show that MPBART exhibits very good predictive performance in comparison to other discrete choice and multiclass classification methods. To implement MPBART, we have developed an R package mpbart available freely from …
University College London（伦敦大学学院）；University of Toronto（多伦多大学）；University of Oxford（牛津大学）
Additive regression trees are flexible non-parametric models and popular off-the-shelf tools for real-world non-linear regression. In application domains, such as bioinformatics, where there is also demand for probabilistic predictions with measures of uncertainty, the Bayesian additive regression trees (BART) model, introduced by Chipman et al. (2010), is increasingly popular. As data sets have grown in size, however, the standard Metropolis-Hastings algorithms used to perform inference in BART are proving inadequate. In particular, these Markov chains make local changes to the trees and suff…
Bayesian Additive Main Effects and Multiplicative Interaction Models using Tensor Regression for Multi-environmental Trials
Hamilton Institute, Department of Mathematics（哈里顿研究所，数学系）；Statistics, Maynooth University, Ireland（统计学，梅诺特大学，爱尔兰）；School of Mathematics（数学学院）；Statistics, Insight Centre for Data Analytics, University College Dublin, Ireland（统计学，洞察数据分析师中心，都柏林大学学院，爱尔兰）
Additive nonparametric regression models provide an attractive tool for variable selection in high dimensions when the relationship between the response and predictors is complex. They offer greater flexibility compared to parametric non-linear regression models and better interpretability and scalability than the non-parametric regression models. However, achieving sparsity simultaneously in the number of nonparametric components as well as in the variables within each nonparametric component poses a stiff computational challenge. In this article, we develop a novel Bayesian additive regressi…
School of Mathematics；School of Statistics University of Minnesota, Minneapolis, MN 55455, USA
Using ensemble methods for regression has been a large success in obtaining high-accuracy prediction. Examples are Bagging, Random forest, Boosting, BART (Bayesian additive regression tree), and their variants. In this paper, we propose a new perspective named variable grouping to enhance the predictive performance. The main idea is to seek for potential grouping of variables in such way that there is no nonlinear interaction term between variables of different groups. Given a sum-of-learner model, each learner will only be responsible for one group of variables, which would be more efficient …
Bayesian additive regression tree (BART) models have seen increased attention in recent years as a general-purpose nonparametric modeling technique. BART combines the flexibility of modern machine learning techniques with the principled uncertainty quantification of Bayesian inference, and it has been shown to be uniquely appropriate for addressing the high-noise problems that occur commonly in many areas of science, including medicine and the social sciences. This paper introduces the SoftBart package for fitting the Soft BART algorithm of Linero and Yang (2018). In addition to improving upon…
Additive-interactive regression has recently been shown to offer attractive minimax error rates over traditional nonparametric multivariate regression in a wide variety of settings, including cases where the predictor count is much larger than the sample size and many of the predictors have important effects on the response, potentially through complex interactions. We present a Bayesian implementation of additive-interactive regression using an additive Gaussian process (AGP) prior and develop an efficient Markov chain sampler that extends stochastic search variable selection in this setting.…
In many longitudinal studies, the covariate and response are often intermittently observed at irregular, mismatched and subject-specific times. How to deal with such data when covariate and response are observed asynchronously is an often raised problem. Bayesian Additive Regression Trees(BART) is a Bayesian non-Parametric approach which has been shown to be competitive with the best modern predictive methods such as random forest and boosted decision trees. The sum of trees structure combined with a Bayesian inferential framework provide a accurate and robust statistic method. BART variant so…
We introduce Bayesian additive regression trees (BART) for log-linear models including multinomial logistic regression and count regression with zero-inflation and overdispersion. BART has been applied to nonparametric mean regression and binary classification problems in a range of settings. However, existing applications of BART have been limited to models for Gaussian "data", either observed or latent. This is primarily because efficient MCMC algorithms are available for Gaussian likelihoods. But while many useful models are naturally cast in terms of latent Gaussian variables, many others …
In this article, we develop a semiparametric Bayesian estimation and model selection approach for partially linear additive models in conditional quantile regression. The asymmetric Laplace distribution provides a mechanism for Bayesian inferences of quantile regression models based on the check loss. The advantage of this new method is that nonlinear, linear and zero function components can be separated automatically and simultaneously during model fitting without the need of pre-specification or parameter tuning. This is achieved by spike-and-slab priors using two sets of indicator variables…
Many time-to-event studies are complicated by the presence of competing risks. Such data are often analyzed using Cox models for the cause specific hazard function or Fine-Gray models for the subdistribution hazard. In practice regression relationships in competing risks data with either strategy are often complex and may include nonlinear functions of covariates, interactions, high-dimensional parameter spaces and nonproportional cause specific or subdistribution hazards. Model misspecification can lead to poor predictive performance. To address these issues, we propose a novel approach to fl…
Flexibly modeling how an entire density changes with covariates is an important but challenging generalization of mean and quantile regression. While existing methods for density regression primarily consist of covariate-dependent discrete mixture models, we consider a continuous latent variable model in general covariate spaces, which we call DR-BART. The prior mapping the latent variable to the observed data is constructed via a novel application of Bayesian Additive Regression Trees (BART). We prove that the posterior induced by our model concentrates quickly around true generative function…
We develop a Bayesian "sum-of-trees" model where each tree is constrained by a regularization prior to be a weak learner, and fitting and inference are accomplished via an iterative Bayesian backfitting MCMC algorithm that generates samples from a posterior. Effectively, BART is a nonparametric Bayesian regression approach which uses dimensionally adaptive random basis elements. Motivated by ensemble methods in general, and boosting algorithms in particular, BART is defined by a statistical model: a prior and a likelihood. This approach enables full posterior inference including point and inte…
In this paper we introduce a novel model for Gaussian process (GP) regression in the fully Bayesian setting. Motivated by the ideas of sparsification, localization and Bayesian additive modeling, our model is built around a recursive partitioning (RP) scheme. Within each RP partition, a sparse GP (SGP) regression model is fitted. A Bayesian additive framework then combines multiple layers of partitioned SGPs, capturing both global trends and local refinements with efficient computations. The model addresses both the problem of efficiency in fitting a full Gaussian process regression model and …
Quantile regression models are a powerful tool for studying different points of the conditional distribution of univariate response variables. Their multivariate counterpart extension though is not straightforward, starting with the definition of multivariate quantiles. We propose here a flexible Bayesian quantile regression model when the response variable is multivariate, where we are able to define a structured additive framework for all predictor variables. We build on previous ideas considering a directional approach to define the quantiles of a response variable with multiple-outputs and…
Large scale study of primary school student performance relative to their LMS activity and socioeconomic demographics using a Bayesian Additive Regression Trees containing random effects
Bayesian Additive Regression Trees (BART) is a flexible machine learning algorithm capable of capturing nonlinearities between an outcome and covariates and interaction among covariates. We extend BART to a semiparametric regression framework in which the conditional expectation of an outcome is a function of treatment, its effect modifiers, and confounders. The confounders, not of scientific interest, are allowed to have unspecified functional form, while treatment and other covariates that do have scientific importance are given the usual linear form from parametric regression. The result is…
We propose a novel spike and slab prior specification with scaled beta prime marginals for the importance parameters of regression coefficients to allow for general effect selection within the class of structured additive distributional regression. This enables us to model effects on all distributional parameters for arbitrary parametric distributions, and to consider various effect types such as non-linear or spatial effects as well as hierarchical regression structures. Our spike and slab prior relies on a parameter expansion that separates blocks of regression coefficients into overall scal…
To achieve the goal of providing the best possible care to each patient, physicians need to customize treatments for patients with the same diagnosis, especially when treating diseases that can progress further and require additional treatments, such as cancer. Making decisions at multiple stages as a disease progresses can be formalized as a dynamic treatment regime (DTR). Most of the existing optimization approaches for estimating dynamic treatment regimes including the popular method of Q-learning were developed in a frequentist context. Recently, a general Bayesian machine learning framewo…
The flexibility of the Bayesian approach to account for covariates with measurement error is combined with semiparametric regression models for a class of continuous, discrete and mixed univariate response distributions with potentially all parameters depending on a structured additive predictor. Markov chain Monte Carlo enables a modular and numerically efficient implementation of Bayesian measurement error correction based on the imputation of unobserved error-free covariate values. We allow for very general measurement errors, including correlated replicates with heterogeneous variances. Th…
Bayesian Additive Regression Trees (BART) is a Bayesian approach to flexible non-linear regression which has been shown to be competitive with the best modern predictive methods such as those based on bagging and boosting. BART offers some advantages. For example, the stochastic search Markov Chain Monte Carlo (MCMC) algorithm can provide a more complete search of the model space and variation across MCMC draws can capture the level of uncertainty in the usual Bayesian way. The BART prior is robust in that reasonable results are typically obtained with a default prior specification. However, t…
Generalized additive models (GAMs) are a well-established statistical tool for modeling complex nonlinear relationships between covariates and a response assumed to have a conditional distribution in the exponential family. In this article, P-splines and the Laplace approximation are coupled for flexible and fast approximate Bayesian inference in GAMs. The proposed Laplace-P-spline model contributes to the development of a new methodology to explore the posterior penalty space by considering a deterministic grid-based strategy or a Markov chain sampler, depending on the number of smooth additi…
