Three different inferential problems related to a two dimensional categorical data from a Bayesian perspective have been discussed in this article. Conjugate prior distribution with symmetric and asymmetric hyper parameters are considered. Newly conceived asymmetric prior is based on perceived preferences of categories. An extension of test of independence by introducing a notion of measuring association between the parameters has been shown using correlation matrix. Probabilities of different parametric combinations have been estimated from the posterior distribution using closed form integration, Monte-Carlo integration and MCMC methods to draw further inference from categorical data. Bayesian computation is done using R programming language and illustrated with appropriate data sets. Study has highlighted the application of Bayesian inference exploiting the distributional form of underlying parameters.
We develop a Bayesian approach for selecting the model which is the most supported by the data within a class of marginal models for categorical variables formulated through equality and/or inequality constraints on generalised logits (local, global, continuation or reverse continuation), generalised log-odds ratios and similar higher-order interactions. For each constrained model, the prior distribution of the model parameters is formulated following the encompassing prior approach. Then, model selection is performed by using Bayes factors which are estimated by an importance sampling method.…
Multivariate categorical data are common in many fields. We are motivated by election polls studies assessing evidence of changes in voters opinions with their candidates preferences in the 2016 United States Presidential primaries or caucuses. Similar goals arise routinely in several applications, but current literature lacks a general methodology which combines flexibility, efficiency, and tractability in testing for group differences in multivariate categorical data at different---potentially complex---scales. We address this goal by leveraging a Bayesian representation which factorizes the…
Efficient optimisation of black-box problems that comprise both continuous and categorical inputs is important, yet poses significant challenges. We propose a new approach, Continuous and Categorical Bayesian Optimisation (CoCaBO), which combines the strengths of multi-armed bandits and Bayesian optimisation to select values for both categorical and continuous inputs. We model this mixed-type space using a Gaussian Process kernel, designed to allow sharing of information across multiple categorical variables, each with multiple possible values; this allows CoCaBO to leverage all available data…
It has become commonplace to use complex computer models to predict outcomes in regions where data does not exist. Typically these models need to be calibrated and validated using some experimental data, which often consists of multiple correlated outcomes. In addition, some of the model parameters may be categorical in nature, such as a pointer variable to alternate models (or submodels) for some of the physics of the system. Here we present a general approach for calibration in such situations where an emulator of the computationally demanding models and a discrepancy term from the model to …
We propose a Bayesian inference approach for a class of latent Markov models. These models are widely used for the analysis of longitudinal categorical data, when the interest is in studying the evolution of an individual unobservable characteristic. We consider, in particular, the basic latent Markov, which does not account for individual covariates, and its version that includes such covariates in the measurement model. The proposed inferential approach is based on a system of priors formulated on a transformation of the initial and transition probabilities of the latent Markov chain. This s…
The Markov chain random field (MCRF) model/theory provides a non-linear spatial Bayesian updating solution at the neighborhood nearest data level for simulating categorical spatial variables. In the MCRF solution, the spatial dependencies among nearest data and the central random variable is a probabilistic directed acyclic graph that conforms to a neighborhood-based Bayesian network on spatial data. By selecting different neighborhood sizes and structures, applying the spatial conditional independence assumption to nearest neighbors, or incorporating ancillary information, one may construct s…
Neural networks utilize the softmax as a building block in classification tasks, which contains an overconfidence problem and lacks an uncertainty representation ability. As a Bayesian alternative to the softmax, we consider a random variable of a categorical probability over class labels. In this framework, the prior distribution explicitly models the presumed noise inherent in the observed label, which provides consistent gains in generalization performance in multiple challenging tasks. The proposed method inherits advantages of Bayesian approaches that achieve better uncertainty estimation…
University of Oxford（牛津大学）；Amazon（亚马逊）；RMIT University（皇家墨尔本理工大学）
High-dimensional black-box optimisation remains an important yet notoriously challenging problem. Despite the success of Bayesian optimisation methods on continuous domains, domains that are categorical, or that mix continuous and categorical variables, remain challenging. We propose a novel solution -- we combine local optimisation with a tailored kernel design, effectively handling high-dimensional categorical and mixed search spaces, whilst retaining sample efficiency. We further derive convergence guarantee for the proposed approach. Finally, we demonstrate empirically that our method outp…
We present a nonparametric Bayesian joint model for multivariate continuous and categorical variables, with the intention of developing a flexible engine for multiple imputation of missing values. The model fuses Dirichlet process mixtures of multinomial distributions for categorical variables with Dirichlet process mixtures of multivariate normal distributions for continuous variables. We incorporate dependence between the continuous and categorical variables by (i) modeling the means of the normal distributions as component-specific functions of the categorical variables and (ii) forming dis…
Applied Data Scientists throughout various industries are commonly faced with the challenging task of encoding high-cardinality categorical features into digestible inputs for machine learning algorithms. This paper describes a Bayesian encoding technique developed for WeWork's lead scoring engine which outputs the probability of a person touring one of our office spaces based on interaction, enrichment, and geospatial data. We present a paradigm for ensemble modeling which mitigates the need to build complicated preprocessing and encoding schemes for categorical variables. In particular, doma…
In this paper, we propose a Bayesian approach to obtain a sparse representation of the effect of a categorical predictor in regression type models. As the effect of a categorical predictor is captured by a group of level effects, sparsity cannot only be achieved by excluding single irrelevant level effects but also by excluding the whole group of effects associated to a predictor or by fusing levels which have essentially the same effect on the response. To achieve this goal, we propose a prior which allows for almost perfect as well as almost zero dependence between level effects a priori. We…
Multiple imputation is a common approach for dealing with missing values in statistical databases. The imputer fills in missing values with draws from predictive models estimated from the observed data, resulting in multiple, completed versions of the database. Researchers have developed a variety of default routines to implement multiple imputation; however, there has been limited research comparing the performance of these methods, particularly for categorical data. We use simulation studies to compare repeated sampling properties of three default multiple imputation methods for categorical …
The paper proposes a novel model assessment paradigm aiming to address shortcoming of posterior predictive $p-$values, which provide the default metric of fit for Bayesian structural equation modelling (BSEM). The model framework of the paper focuses on the approximate zero approach, according to which parameters that would before set to zero (e.g. factor loadings) are now formulated to be approximate zero via informative priors (Muthen and Asparouhov, 2012). The introduced model assessment procedure monitors the out-of-sample predictive performance of the fitted model, and together with a lis…
Bayesian Optimization (BO) methods are useful for optimizing functions that are expen- sive to evaluate, lack an analytical expression and whose evaluations can be contaminated by noise. These methods rely on a probabilistic model of the objective function, typically a Gaussian process (GP), upon which an acquisition function is built. The acquisition function guides the optimization process and measures the expected utility of performing an evaluation of the objective at a new point. GPs assume continous input variables. When this is not the case, for example when some of the input variables …
Factor analysis is a flexible technique for assessment of multivariate dependence and codependence. Besides being an exploratory tool used to reduce the dimensionality of multivariate data, it allows estimation of common factors that often have an interesting theoretical interpretation in real problems. However, standard factor analysis is only applicable when the variables are scaled, which is often inappropriate, for example, in data obtained from questionnaires in the field of psychology,where the variables are often categorical. In this framework, we propose a factor model for the analysis…
Target encoding is an effective encoding technique of categorical variables and is often used in machine learning systems for processing tabular data sets with mixed numeric and categorical variables. Recently en enhanced version of this encoding technique was proposed by using conjugate Bayesian modeling. This paper presents a further development of Bayesian encoding method by using sampling techniques, which helps in extracting information from intra-category distribution of the target variable, improves generalization and reduces target leakage.
A Bayesian joint model of multiple longitudinal and categorical outcomes with application to multiple myeloma using permutation-based variable importance
Standard linear modeling approaches make potentially simplistic assumptions regarding the structure of categorical effects that may obfuscate more complex relationships governing data. For example, recent work focused on the two-way unreplicated layout has shown that hidden groupings among the levels of one categorical predictor frequently interact with the ungrouped factor. We extend the notion of a "latent grouping factor" to linear models in general. The proposed work allows researchers to determine whether an apparent grouping of the levels of a categorical predictor reveals a plausible hi…
We introduce new estimation methods for a sub-class of the Gaussian scale mixture models for wavelet trees by Wainwright, Simoncelli & Willsky that rely on modern results for composite likelihoods and approximate Bayesian inference. Our methodology is illustrated for denoising and edge detection problems in two-dimensional images.
Gaussian processes (GP) are widely used as a metamodel for emulating time-consuming computer codes. We focus on problems involving categorical inputs, with a potentially large number L of levels (typically several tens), partitioned in G << L groups of various sizes. Parsimonious covariance functions, or kernels, can then be defined by block covariance matrices T with constant covariances between pairs of blocks and within blocks. We study the positive definiteness of such matrices to encourage their practical use. The hierarchical group/level structure, equivalent to a nested Bayesian linear …
Harvard University（哈佛大学）；Vector Institute for Artificial Intelligence（矢量人工智能研究所）；University of Toronto（多伦多大学）；Atinary Technologies Sàrl（Atinary技术有限公司）
Designing functional molecules and advanced materials requires complex design choices: tuning continuous process parameters such as temperatures or flow rates, while simultaneously selecting catalysts or solvents. To date, the development of data-driven experiment planning strategies for autonomous experimentation has largely focused on continuous process parameters despite the urge to devise efficient strategies for the selection of categorical variables. Here, we introduce Gryffin, a general purpose optimization framework for the autonomous selection of categorical variables driven by expert…
Many real-world functions are defined over both categorical and category-specific continuous variables and thus cannot be optimized by traditional Bayesian optimization (BO) methods. To optimize such functions, we propose a new method that formulates the problem as a multi-armed bandit problem, wherein each category corresponds to an arm with its reward distribution centered around the optimum of the objective function in continuous variables. Our goal is to identify the best arm and the maximizer of the corresponding continuous function simultaneously. Our algorithm uses a Thompson sampling s…
Many real-world optimisation problems are defined over both categorical and continuous variables, yet efficient optimisation methods such asBayesian Optimisation (BO) are not designed tohandle such mixed-variable search spaces. Recent approaches to this problem cast the selection of the categorical variables as a bandit problem, operating independently alongside a BO component which optimises the continuous variables. In this paper, we adopt a holistic view and aim to consolidate optimisation of the categorical and continuous sub-spaces under a single acquisition metric. We derive candidates f…
In this paper, we present a Weibull link (skewed) model for categorical response data arising from binomial as well as multinomial model. We show that, for such types of categorical data, the most commonly used models (logit, probit and complementary log-log) can be obtained as limiting cases. We further compare the proposed model with some other asymmetrical models. The Bayesian as well as frequentist estimation procedures for binomial and multinomial data responses are presented in details. The analysis of two data sets to show the efficiency of the proposed model is performed.
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…
We pursue tractable Bayesian analysis of generalized linear models (GLMs) for categorical data. Thus far, GLMs are difficult to scale to more than a few dozen categories due to non-conjugacy or strong posterior dependencies when using conjugate auxiliary variable methods. We define a new class of GLMs for categorical data called categorical-from-binary (CB) models. Each CB model has a likelihood that is bounded by the product of binary likelihoods, suggesting a natural posterior approximation. This approximation makes inference straightforward and fast; using well-known auxiliary variables for…
Cumulative link models have been widely used for ordered categorical responses. Uniform allocation of experimental units is commonly used in practice, but often suffers from a lack of efficiency. We consider D-optimal designs with ordered categorical responses and cumulative link models. For a predetermined set of design points, we derive the necessary and sufficient conditions for an allocation to be locally D-optimal and develop efficient algorithms for obtaining approximate and exact designs. We prove that the number of support points in a minimally supported design only depends on the numb…
This paper studies posterior contraction rates in multi-category logit models with priors incorporating group sparse structures. We consider a general class of logit models that includes the well-known multinomial logit models as a special case. Group sparsity is useful when predictor variables are naturally clustered and particularly useful for variable selection in the multinomial logit models. We provide a unified platform for posterior contraction rates of group-sparse logit models that include binary logistic regression under individual sparsity. No size restriction is directly imposed on…
We propose a general formalism of iterated random functions with semigroup property, under which exact and approximate Bayesian posterior updates can be viewed as specific instances. A convergence theory for iterated random functions is presented. As an application of the general theory we analyze convergence behaviors of exact and approximate message-passing algorithms that arise in a sequential change point detection problem formulated via a latent variable directed graphical model. The sequential inference algorithm and its supporting theory are illustrated by simulated examples.
Pamminger and Fruwirth-Schnatter (2010) considered a Bayesian approach to model-based clustering of categorical time series assuming a fixed number of clusters. But the popular methods for selecting the number of clusters, for example, the Bayes Information Criterion (BIC), turned out to have severe problems in the categorical time series context. In this paper, we circumvent the difficulties of choosing the number of clusters by adopting the Bayesian semiparametric mixture model approach introduced by Bhattacharya (2008), who assume that the number of clusters is a random quantity, but is bou…
We discuss Bayesian inference for parameters selected using the data. First, we provide a critical analysis of the existing positions in the literature regarding the correct Bayesian approach under selection. Second, we propose two types of non-informative priors for selection models. These priors may be employed to produce a posterior distribution in the absence of prior information as well as to provide well-calibrated frequentist inference for the selected parameter. We test the proposed priors empirically in several scenarios.
Massachusetts Institute of Technology（麻省理工学院）；Woods Hole Oceanographic Institution（伍兹霍尔海洋研究所）
We propose a generative model for the spatio-temporal distribution of high dimensional categorical observations. These are commonly produced by robots equipped with an imaging sensor such as a camera, paired with an image classifier, potentially producing observations over thousands of categories. The proposed approach combines the use of Dirichlet distributions to model sparse co-occurrence relations between the observed categories using a latent variable, and Gaussian processes to model the latent variable's spatio-temporal distribution. Experiments in this paper show that the resulting mode…
Multi-objective Bayesian Optimization With Mixed-categorical Design Variables for Expensive-to-evaluate Aeronautical Applications
ONERA（法国航空航天研究院）；Université de Toulouse（图卢兹大学）；ISAE–SUPAERO（法国高等航空航天学院）；INSA（法国国立应用科学学院）；CNRS（法国国家科学研究中心）；MINES ALBI（阿尔比矿业学校）；UPS Université de Toulouse（图卢兹第三大学）；Polytechnique Montréal（蒙特利尔理工学院）；German Aerospace Center (DLR)（德国航空航天中心）；EMBRAER S.A.（巴西航空工业公司）；University di Napoli Federico II（那不勒斯费德里科二世大学）
We formulate Bayesian updates in Markov processes by means of path integral techniques and derive the imaginary-time Schrödinger equation with likelihood to direct the inference incorporated as a potential for the posterior probability distribution
Size-constrained clustering (SCC) refers to the dual problem of using observations to determine latent cluster structure while at the same time assigning observations to the unknown clusters subject to an analyst defined constraint on cluster sizes. While several approaches have been proposed, SCC remains a difficult problem due to the combinatorial dependency between observations introduced by the size-constraints. Here we reformulate SCC as a decision problem and introduce a novel loss function to capture various types of size constraints. As opposed to prior work, our approach is uniquely s…
We introduce the concepts of Bayesian lens, characterizing the bidirectional structure of exact Bayesian inference, and statistical game, formalizing the optimization objectives of approximate inference problems. We prove that Bayesian inversions compose according to the compositional lens pattern, and exemplify statistical games with a number of classic statistical concepts, from maximum likelihood estimation to generalized variational Bayesian methods. This paper is the first in a series laying the foundations for a compositional account of the theory of active inference, and we therefore pa…
Recognizing the successes of treed Gaussian process (TGP) models as an interpretable and thrifty model for nonparametric regression, we seek to extend the model to classification. Both treed models and Gaussian processes (GPs) have, separately, enjoyed great success in application to classification problems. An example of the former is Bayesian CART. In the latter, real-valued GP output may be utilized for classification via latent variables, which provide classification rules by means of a softmax function. We formulate a Bayesian model averaging scheme to combine these two models and describ…
Learning the structure of dependence relations between variables is a pervasive issue in the statistical literature. A directed acyclic graph (DAG) can represent a set of conditional independences, but different DAGs may encode the same set of relations and are indistinguishable using observational data. Equivalent DAGs can be collected into classes, each represented by a partially directed graph known as essential graph (EG). Structure learning directly conducted on the EG space, rather than on the allied space of DAGs, leads to theoretical and computational benefits. Still, the majority of e…
We propose a categorical matrix factorization method to infer latent diseases from electronic health records (EHR) data in an unsupervised manner. A latent disease is defined as an unknown biological aberration that causes a set of common symptoms for a group of patients. The proposed approach is based on a novel double feature allocation model which simultaneously allocates features to the rows and the columns of a categorical matrix. Using a Bayesian approach, available prior information on known diseases greatly improves identifiability and interpretability of latent diseases. This includes…
Fitting models to data using Bayesian inference is quite common, but when each point in parameter space gives a curve, fitting the curve to a data set requires new nuisance parameters, which specify the metric embedding the one-dimensional curve into the higher-dimensional space occupied by the data. A generic formalism for curve fitting in the context of Bayesian inference is developed which shows how the aforementioned metric arises. The result is a natural generalization of previous works, and is compared to oft-used frequentist approaches and similar Bayesian techniques.
Multivariate categorical data occur in many applications of machine learning. One of the main difficulties with these vectors of categorical variables is sparsity. The number of possible observations grows exponentially with vector length, but dataset diversity might be poor in comparison. Recent models have gained significant improvement in supervised tasks with this data. These models embed observations in a continuous space to capture similarities between them. Building on these ideas we propose a Bayesian model for the unsupervised task of distribution estimation of multivariate categorica…
