This paper presents the Bayesian Hierarchical Words Representation (BHWR) learning algorithm. BHWR facilitates Variational Bayes word representation learning combined with semantic taxonomy modeling via hierarchical priors. By propagating relevant information between related words, BHWR utilizes the taxonomy to improve the quality of such representations. Evaluation of several linguistic datasets demonstrates the advantages of BHWR over suitable alternatives that facilitate Bayesian modeling with or without semantic priors. Finally, we further show that BHWR produces better representations for rare words.
The Australian National University（澳大利亚国立大学）；Data61/NICTA；Monash University（莫纳什大学）；Duke University（杜克大学）
The Dirichlet process and its extension, the Pitman-Yor process, are stochastic processes that take probability distributions as a parameter. These processes can be stacked up to form a hierarchical nonparametric Bayesian model. In this article, we present efficient methods for the use of these processes in this hierarchical context, and apply them to latent variable models for text analytics. In particular, we propose a general framework for designing these Bayesian models, which are called topic models in the computer science community. We then propose a specific nonparametric Bayesian topic…
Deployments of Bayesian Optimization (BO) for functions with stochastic evaluations, such as parameter tuning via cross validation and simulation optimization, typically optimize an average of a fixed set of noisy realizations of the objective function. However, disregarding the true objective function in this manner finds a high-precision optimum of the wrong function. To solve this problem, we propose Bayesian Optimization by Sampling Hierarchically (BOSH), a novel BO routine pairing a hierarchical Gaussian process with an information-theoretic framework to generate a growing pool of realiza…
Massachusetts Institute of Technology（麻省理工学院）；Harvard University（哈佛大学）
In this note we provide detailed derivations of two versions of small-variance asymptotics for hierarchical Dirichlet process (HDP) mixture models and the HDP hidden Markov model (HDP-HMM, a.k.a. the infinite HMM). We include derivations for the probabilities of certain CRP and CRF partitions, which are of more general interest.
Common statistical practice has shown that the full power of Bayesian methods is not realized until hierarchical priors are used, as these allow for greater "robustness" and the ability to "share statistical strength." Yet it is an ongoing challenge to provide a learning-theoretically sound formalism of such notions that: offers practical guidance concerning when and how best to utilize hierarchical models; provides insights into what makes for a good hierarchical prior; and, when the form of the prior has been chosen, can guide the choice of hyperparameter settings. We present a set of analyt…
We present a novel hierarchical distance-dependent Bayesian model for event coreference resolution. While existing generative models for event coreference resolution are completely unsupervised, our model allows for the incorporation of pairwise distances between event mentions -- information that is widely used in supervised coreference models to guide the generative clustering processing for better event clustering both within and across documents. We model the distances between event mentions using a feature-rich learnable distance function and encode them as Bayesian priors for nonparametr…
Columbia University（哥伦比亚大学）；University of Ljubljana（卢布尔雅那大学）；Aalto University（阿尔托大学）
Stacking is a widely used model averaging technique that asymptotically yields optimal predictions among linear averages. We show that stacking is most effective when model predictive performance is heterogeneous in inputs, and we can further improve the stacked mixture with a hierarchical model. We generalize stacking to Bayesian hierarchical stacking. The model weights are varying as a function of data, partially-pooled, and inferred using Bayesian inference. We further incorporate discrete and continuous inputs, other structured priors, and time series and longitudinal data. To verify the p…
Istituto Dalle Molle di studi sull’Intelligenza Artificiale (IDSIA)（达勒莫勒人工智能研究所 (IDSIA)）；University of Ljubljana（卢布尔雅那大学）
Usually one compares the accuracy of two competing classifiers via null hypothesis significance tests (nhst). Yet the nhst tests suffer from important shortcomings, which can be overcome by switching to Bayesian hypothesis testing. We propose a Bayesian hierarchical model which jointly analyzes the cross-validation results obtained by two classifiers on multiple data sets. It returns the posterior probability of the accuracies of the two classifiers being practically equivalent or significantly different. A further strength of the hierarchical model is that, by jointly analyzing the results ob…
Department of Technology, Management and Economics, Danish Technical University（丹麦技术大学技术、管理与经济系）；Max Planck Institute for Intelligent Systems（马克斯·普朗克智能系统研究所）
University of Torontoland（托伦托兰大学）；Googol ShallowMind；University of Edenborrow（伊登伯勒大学）
Making inferences from data streams is a pervasive problem in many modern data analysis applications. But it requires to address the problem of continuous model updating and adapt to changes or drifts in the underlying data generating distribution. In this paper, we approach these problems from a Bayesian perspective covering general conjugate exponential models. Our proposal makes use of non-conjugate hierarchical priors to explicitly model temporal changes of the model parameters. We also derive a novel variational inference scheme which overcomes the use of non-conjugate priors while mainta…
Items in modern recommender systems are often organized in hierarchical structures. These hierarchical structures and the data within them provide valuable information for building personalized recommendation systems. In this paper, we propose a general hierarchical Bayesian learning framework, i.e., \emph{HBayes}, to learn both the structures and associated latent factors. Furthermore, we develop a variational inference algorithm that is able to learn model parameters with fast empirical convergence rate. The proposed HBayes is evaluated on two real-world datasets from different domains. The …
Insight Centre for Data Analytics（洞察数据分析中心）；University College Dublin（都柏林大学）；Maynooth University（梅努斯大学）
This paper focuses on the problem of hierarchical non-overlapping clustering of a dataset. In such a clustering, each data item is associated with exactly one leaf node and each internal node is associated with all the data items stored in the sub-tree beneath it, so that each level of the hierarchy corresponds to a partition of the dataset. We develop a novel Bayesian nonparametric method combining the nested Chinese Restaurant Process (nCRP) and the Hierarchical Dirichlet Process (HDP). Compared with other existing Bayesian approaches, our solution tackles data with complex latent mixture fe…
Tufts University（塔夫茨大学）；Tufts Medical Center（塔夫茨医学中心）
We consider the problem of forecasting the daily number of hospitalized COVID-19 patients at a single hospital site, in order to help administrators with logistics and planning. We develop several candidate hierarchical Bayesian models which directly capture the count nature of data via a generalized Poisson likelihood, model time-series dependencies via autoregressive and Gaussian process latent processes, and share statistical strength across related sites. We demonstrate our approach on public datasets for 8 hospitals in Massachusetts, U.S.A. and 10 hospitals in the United Kingdom. Further …
Population attributes are essential in health for understanding who the data represents and precision medicine efforts. Even within disease infection labels, patients can exhibit significant variability; "fever" may mean something different when reported in a doctor's office versus from an online app, precluding directly learning across different datasets for the same prediction task. This problem falls into the domain adaptation paradigm. However, research in this area has to-date not considered who generates the data; symptoms reported by a woman versus a man, for example, could also have di…
Istituto Dalle Molle di Studi sull’Intelligenza Artificiale (IDSIA)（达莱莫莱人工智能研究所（IDSIA））；USI（意大利语区大学）；SUPSI（瑞士南部应用科学与艺术大学）
Score functions for learning the structure of Bayesian networks in the literature assume that data are a homogeneous set of observations; whereas it is often the case that they comprise different related, but not homogeneous, data sets collected in different ways. In this paper we propose a new Bayesian Dirichlet score, which we call Bayesian Hierarchical Dirichlet (BHD). The proposed score is based on a hierarchical model that pools information across data sets to learn a single encompassing network structure, while taking into account the differences in their probabilistic structures. We der…
Analyzing and understanding the structure of complex relational data is important in many applications including analysis of the connectivity in the human brain. Such networks can have prominent patterns on different scales, calling for a hierarchically structured model. We propose two non-parametric Bayesian hierarchical network models based on Gibbs fragmentation tree priors, and demonstrate their ability to capture nested patterns in simulated networks. On real networks we demonstrate detection of hierarchical structure and show predictive performance on par with the state of the art. We en…
Pohang University of Science and Technology（浦项科技大学）
Bayesian hierarchical clustering (BHC) is an agglomerative clustering method, where a probabilistic model is defined and its marginal likelihoods are evaluated to decide which clusters to merge. While BHC provides a few advantages over traditional distance-based agglomerative clustering algorithms, successive evaluation of marginal likelihoods and careful hyperparameter tuning are cumbersome and limit the scalability. In this paper we relax BHC into a non-probabilistic formulation, exploring small-variance asymptotics in conjugate-exponential models. We develop a novel clustering algorithm, re…
The Hierarchical Mixture of Experts (HME) is a well-known tree-based model for regression and classification, based on soft probabilistic splits. In its original formulation it was trained by maximum likelihood, and is therefore prone to over-fitting. Furthermore the maximum likelihood framework offers no natural metric for optimizing the complexity and structure of the tree. Previous attempts to provide a Bayesian treatment of the HME model have relied either on ad-hoc local Gaussian approximations or have dealt with related models representing the joint distribution of both input and output …
We introduce a hierarchical Bayesian approach to tackle the challenging problem of size recommendation in e-commerce fashion. Our approach jointly models a size purchased by a customer, and its possible return event: 1. no return, 2. returned too small 3. returned too big. Those events are drawn following a multinomial distribution parameterized on the joint probability of each event, built following a hierarchy combining priors. Such a model allows us to incorporate extended domain expertise and article characteristics as prior knowledge, which in turn makes it possible for the underlying par…
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…
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））
State University of New York at Buffalo（纽约州立大学布法罗分校）；University of California, Irvine（加州大学欧文分校）
Current state-of-the-art nonparametric Bayesian text clustering methods model documents through multinomial distribution on bags of words. Although these methods can effectively utilize the word burstiness representation of documents and achieve decent performance, they do not explore the sequential information of text and relationships among synonyms. In this paper, the documents are modeled as the joint of bags of words, sequential features and word embeddings. We proposed Sequential Embedding induced Dirichlet Process Mixture Model (SiDPMM) to effectively exploit this joint document represe…
Existing methods for sparse channel estimation typically provide an estimate computed as the solution maximizing an objective function defined as the sum of the log-likelihood function and a penalization term proportional to the l1-norm of the parameter of interest. However, other penalization terms have proven to have strong sparsity-inducing properties. In this work, we design pilot-assisted channel estimators for OFDM wireless receivers within the framework of sparse Bayesian learning by defining hierarchical Bayesian prior models that lead to sparsity-inducing penalization terms. The estim…
The Alan Turing Institute（艾伦·图灵研究所）；Imperial College London（帝国理工学院）；University of Warwick（华威大学）
Potential violent criminals will often need to go through a sequence of preparatory steps before they can execute their plans. During this escalation process police have the opportunity to evaluate the threat posed by such people through what they know, observe and learn from intelligence reports about their activities. In this paper we customise a three-level Bayesian hierarchical model to describe this process. This is able to propagate both routine and unexpected evidence in real time. We discuss how to set up such a model so that it calibrates to domain expert judgments. The model illustra…
University of Potsdam（波茨坦大学）；École Nationale de la Statistique et de l’administration économique（国家统计与经济管理学院）；CNRS（法国国家科学研究中心）；Université Paris-Dauphine（巴黎九大）；PSL Research University（巴黎文理研究大学）
We present a case-study demonstrating the usefulness of Bayesian hierarchical mixture modelling for investigating cognitive processes. In sentence comprehension, it is widely assumed that the distance between linguistic co-dependents affects the latency of dependency resolution: the longer the distance, the longer the retrieval time (the distance-based account). An alternative theory, direct-access, assumes that retrieval times are a mixture of two distributions: one distribution represents successful retrievals (these are independent of dependency distance) and the other represents an initial…
Samsung AI Center（三星人工智能中心）；Rutgers University（罗格斯大学）
We propose a family of novel hierarchical Bayesian deep auto-encoder models capable of identifying disentangled factors of variability in data. While many recent attempts at factor disentanglement have focused on sophisticated learning objectives within the VAE framework, their choice of a standard normal as the latent factor prior is both suboptimal and detrimental to performance. Our key observation is that the disentangled latent variables responsible for major sources of variability, the relevant factors, can be more appropriately modeled using long-tail distributions. The typical Gaussian…
Collected data, which is used for analysis or prediction tasks, often have a hierarchical structure, for example, data from various people performing the same task. Modeling the data's structure can improve the reliability of the derived results and prediction performance of newly unobserved data. Bayesian modeling provides a tool-kit for designing hierarchical models. However, Markov Chain Monte Carlo methods which are commonly used for parameter estimation are computationally expensive. This often renders its use for many applications not applicable. However, variational Bayesian methods all…
The level set approach has proven widely successful in the study of inverse problems for interfaces, since its systematic development in the 1990s. Recently it has been employed in the context of Bayesian inversion, allowing for the quantification of uncertainty within the reconstruction of interfaces. However the Bayesian approach is very sensitive to the length and amplitude scales in the prior probabilistic model. This paper demonstrates how the scale-sensitivity can be circumvented by means of a hierarchical approach, using a single scalar parameter. Together with careful consideration of …
We classify two types of Hierarchical Bayesian Model found in the literature as Hierarchical Prior Model (HPM) and Hierarchical Stochastic Model (HSM). Then, we focus on studying the theoretical implications of the HSM. Using examples of polynomial functions, we show that the HSM is capable of separating different types of uncertainties in a system and quantifying uncertainty of reduced order models under the Bayesian model class selection framework. To tackle the huge computational cost for analyzing HSM, we propose an efficient approximation scheme based on Importance Sampling and Empirical …
Demographic studies of cosmic populations must contend with measurement errors and selection effects. We survey some of the key ideas astronomers have developed to deal with these complications, in the context of galaxy surveys and the literature on corrections for Malmquist and Eddington bias. From the perspective of modern statistics, such corrections arise naturally in the context of multilevel models, particularly in Bayesian treatments of such models: hierarchical Bayesian models. We survey some key lessons from hierarchical Bayesian modeling, including shrinkage estimation, which is clos…
Bayesian algorithmic perfumery: A Hierarchical Relevance Vector Machine for the Estimation of Personalized Fragrance Preferences based on Three Sensory Layers and Jungian Personality Archetypes
Hierarchical models are versatile tools for joint modeling of data sets arising from different, but related, sources. Fully Bayesian inference may, however, become computationally prohibitive if the source-specific data models are complex, or if the number of sources is very large. To facilitate computation, we propose an approach, where inference is first made independently for the parameters of each data set, whereupon the obtained posterior samples are used as observed data in a substitute hierarchical model, based on a scaled likelihood function. Compared to direct inference in a full hier…
In this study, we present a Bayesian hierarchical framework to model fluid-induced seismicity. The framework is based on a non-homogeneous Poisson process (NHPP) with a fluid-induced seismicity rate proportional to the rate of injected fluid. The fluid-induced seismicity rate model depends upon a set of physically meaningful parameters, and has been validated for six fluid-induced case studies. In line with the vision of hierarchical Bayesian modeling, the rate parameters are considered as random variables. We develop both the Bayesian inference and updating rules, which are used to develop a …
This paper introduces a hierarchical framework to incorporate Hellinger distance methods into Bayesian analysis. We propose to modify a prior over non-parametric densities with the exponential of twice the Hellinger distance between a candidate and a parametric density. By incorporating a prior over the parameters of the second density, we arrive at a hierarchical model in which a non-parametric model is placed between parameters and the data. The parameters of the family can then be estimated as hyperparameters in the model. In frequentist estimation, minimizing the Hellinger distance between…
We discuss the methods of Evans and Moshonov [Bayesian Analysis 1 (2006) 893--914, Bayesian Statistics and Its Applications (2007) 145--159] concerning checking for prior-data conflict and their relevance to the method proposed in this paper. [arXiv:0802.0743]
We study a two-level multiview learning with more than two views under the PAC-Bayesian framework. This approach, sometimes referred as late fusion, consists in learning sequentially multiple view-specific classifiers at the first level, and then combining these view-specific classifiers at the second level. Our main theoretical result is a generalization bound on the risk of the majority vote which exhibits a term of diversity in the predictions of the view-specific classifiers. From this result it comes out that controlling the trade-off between diversity and accuracy is a key element for mu…
This paper introduces a new sparse Bayesian learning (SBL) algorithm that jointly recovers a temporal sequence of edge maps from noisy and under-sampled Fourier data. The new method is cast in a Bayesian framework and uses a prior that simultaneously incorporates intra-image information to promote sparsity in each individual edge map with inter-image information to promote similarities in any unchanged regions. By treating both the edges as well as the similarity between adjacent images as random variables, there is no need to separately form regions of change. Thus we avoid both additional co…
This paper introduces the parallel hierarchical sampler (PHS), a Markov chain Monte Carlo algorithm using several chains simultaneously. The connections between PHS and the parallel tempering (PT) algorithm are illustrated, convergence of PHS joint transition kernel is proved and and its practical advantages are emphasized. We illustrate the inferences obtained using PHS, parallel tempering and the Metropolis-Hastings algorithm for three Bayesian model selection problems, namely Gaussian clustering, the selection of covariates for a linear regression model and the selection of the structure of…
Bayesian hierarchical modeling is a popular approach to capturing unobserved heterogeneity across individual units. However, standard estimation methods such as Markov chain Monte Carlo (MCMC) can be impracticable for modeling outcomes from a large number of units. We develop a new method to sample from posterior distributions of Bayesian models, without using MCMC. Samples are independent, so they can be collected in parallel, and we do not need to be concerned with issues like chain convergence and autocorrelation. The algorithm is scalable under the weak assumption that individual units are…
We develop a new method to sample from posterior distributions in hierarchical models without using Markov chain Monte Carlo. This method, which is a variant of importance sampling ideas, is generally applicable to high-dimensional models involving large data sets. Samples are independent, so they can be collected in parallel, and we do not need to be concerned with issues like chain convergence and autocorrelation. Additionally, the method can be used to compute marginal likelihoods.
Here we develop a method for performing nonparametric Bayesian inference on quantiles. Relying on geometric measure theory and employing a Hausdorff base measure, we are able to specify meaningful priors for the quantile while treating the distribution of the data otherwise nonparametrically. We further extend the method to a hierarchical model for quantiles of subpopulations, linking subgroups together solely through their quantiles. Our approach is computationally straightforward, allowing for censored and noisy data. We demonstrate the proposed methodology on simulated data and an applied p…
This is a vignette for the R package eggCounts version 2.0. The package implements a suite of Bayesian hierarchical models dealing with faecal egg count reductions. The models are designed for a variety of practical situations, including individual treatment efficacy, zero inflation, small sample size (less than 10) and potential outliers. The functions are intuitive to use and their output are easy to interpret, such that users are protected from being exposed to complex Bayesian hierarchical modelling tasks. In addition, the package includes plotting functions to display data and results in …
Considering the flexibility and applicability of Bayesian modeling, in this work we revise the main characteristics of two hierarchical models in a regression setting. We study the full probabilistic structure of the models along with the full conditional distribution for each model parameter. Under our hierarchical extensions, we allow the mean of the second stage of the model to have a linear dependency on a set of covariates. The Gibbs sampling algorithms used to obtain samples when fitting the models are fully described and derived. In addition, we consider a case study in which the plant …
Quantitative Fitness Analysis (QFA) is a high-throughput experimental and computational methodology for measuring the growth of microbial populations. QFA screens can be used to compare the health of cell populations with and without a mutation in a query gene in order to infer genetic interaction strengths genome-wide, examining thousands of separate genotypes. We introduce Bayesian, hierarchical models of population growth rates and genetic interactions that better reflect QFA experimental design than current approaches. Our new approach models population dynamics and genetic interaction sim…
This paper presents a hierarchical Bayesian model to reconstruct sparse images when the observations are obtained from linear transformations and corrupted by an additive white Gaussian noise. Our hierarchical Bayes model is well suited to such naturally sparse image applications as it seamlessly accounts for properties such as sparsity and positivity of the image via appropriate Bayes priors. We propose a prior that is based on a weighted mixture of a positive exponential distribution and a mass at zero. The prior has hyperparameters that are tuned automatically by marginalization over the hi…
A common problem faced in statistical inference is drawing conclusions from paired comparisons, in which two objects compete and one is declared the victor. A probabilistic approach to such a problem is the Bradley-Terry model, first studied by Zermelo in 1929 and rediscovered by Bradley and Terry in 1952. One obvious area of application for such a model is sporting events, and in particular Major League Baseball. With this in mind, we describe a hierarchical Bayesian version of Bradley-Terry suitable for use in ranking and prediction problems, and compare results from these application domain…
Social scientists have recently turned to analyzing text using tools from natural language processing like word embeddings to measure concepts like ideology, bias, and affinity. However, word embeddings are difficult to use in the regression framework familiar to social scientists: embeddings are are neither identified, nor directly interpretable. I offer two advances on standard embedding models to remedy these problems. First, I develop Bayesian Word Embeddings with Automatic Relevance Determination priors, relaxing the assumption that all embedding dimensions have equal weight. Second, I ap…
