Data for several applications in diverse fields can be represented as multiple matrices that are linked across rows or columns. This is particularly common in molecular biomedical research, in which multiple molecular "omics" technologies may capture different feature sets (e.g., corresponding to rows in a matrix) and/or different sample populations (corresponding to columns). This has motivated a large body of work on integrative matrix factorization approaches that identify and decompose low-dimensional signal that is shared across multiple matrices or specific to a given matrix. We propose an empirical variational Bayesian approach to this problem that has several advantages over existing techniques, including the flexibility to accommodate shared signal over any number of row or column sets (i.e., bidimensional integration), an intuitive model-based objective function that yields appropriate shrinkage for the inferred signals, and a relatively efficient estimation algorithm with no tuning parameters. A general result establishes conditions for the uniqueness of the underlying decomposition for a broad family of methods that includes the proposed approach. For scenarios with missing data, we describe an associated iterative imputation approach that is novel for the single-matrix context and a powerful approach for "blockwise" imputation (in which an entire row or column is missing) in various linked matrix contexts. Extensive simulations show that the method performs very well under different scenarios with respect to recovering underlying low-rank signal, accurately decomposing shared and specific signals, and accurately imputing missing data. The approach is applied to gene expression and miRNA data from breast cancer tissue and normal breast tissue, for which it gives an informative decomposition of variation and outperforms alternative strategies for missing data imputation.
The vast majority of current machine learning algorithms are designed to predict single responses or a vector of responses, yet many types of response are more naturally organized as matrices or higher-order tensor objects where characteristics are shared across modes. We present a new machine learning algorithm BaTFLED (Bayesian Tensor Factorization Linked to External Data) that predicts values in a three-dimensional response tensor using input features for each of the dimensions. BaTFLED uses a probabilistic Bayesian framework to learn projection matrices mapping input features for each mode…
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））
A Y-linked two-sex branching process with mutations and blind choice of males is a suitable model for analyzing the evolution of the number of carriers of an allele and its mutations of a Y-linked gene. Considering a two-sex monogamous population, in this model each female chooses her partner from among the male population without caring about his type (i.e., the allele he carries). In this work, we deal with the problem of estimating the main parameters of such model developing the Bayesian inference in a parametric framework. Firstly, we consider, as sample scheme, the observation of the tot…
Several modern applications require the integration of multiple large data matrices that have shared rows and/or columns. For example, cancer studies that integrate multiple omics platforms across multiple types of cancer, pan-omics pan-cancer analysis, have extended our knowledge of molecular heterogenity beyond what was observed in single tumor and single platform studies. However, these studies have been limited by available statistical methodology. We propose a flexible approach to the simultaneous factorization and decomposition of variation across such bidimensionally linked matrices, BI…
Colorado State University（科罗拉多州立大学）；University of Florida（佛罗里达大学）；Duke University（杜克大学）
Entity resolution (ER), comprising record linkage and de-duplication, is the process of merging noisy databases in the absence of unique identifiers to remove duplicate entities. One major challenge of analysis with linked data is identifying a representative record among determined matches to pass to an inferential or predictive task, referred to as the \emph{downstream task}. Additionally, incorporating uncertainty from ER in the downstream task is critical to ensure proper inference. To bridge the gap between ER and the downstream task in an analysis pipeline, we propose five methods to cho…
Siemens AG（西门子股份公司）；TU Munich（慕尼黑工业大学）；University of Cambridge（剑桥大学）；Harvard University（哈佛大学）
Bayesian neural networks with latent variables are scalable and flexible probabilistic models: They account for uncertainty in the estimation of the network weights and, by making use of latent variables, can capture complex noise patterns in the data. We show how to extract and decompose uncertainty into epistemic and aleatoric components for decision-making purposes. This allows us to successfully identify informative points for active learning of functions with heteroscedastic and bimodal noise. Using the decomposition we further define a novel risk-sensitive criterion for reinforcement lea…
Bayesian neural networks (BNNs) with latent variables are probabilistic models which can automatically identify complex stochastic patterns in the data. We describe and study in these models a decomposition of predictive uncertainty into its epistemic and aleatoric components. First, we show how such a decomposition arises naturally in a Bayesian active learning scenario by following an information theoretic approach. Second, we use a similar decomposition to develop a novel risk sensitive objective for safe reinforcement learning (RL). This objective minimizes the effect of model bias in envi…
Decomposition for Bayesian Networks: Local and Parallel Inference
School of Mathematics and Statistics and KLAS, Northeast Normal University（数学与统计学学院及KLAS，东北师范大学）；College of Mathematics and System Sciences, Xinjiang University（数学与系统科学学院，新疆大学）；Institute of Statistics and Data Science, Xinjiang University of Finance and Economics（统计与数据科学学院，新疆财经大学）
Academy of Mathematics and Systems Science, Chinese Academy of Sciences（中国科学院数学与系统科学研究院）；University of Chinese Academy of Sciences（中国科学院大学）
Matrix decomposition is a popular and fundamental approach in machine learning and data mining. It has been successfully applied into various fields. Most matrix decomposition methods focus on decomposing a data matrix from one single source. However, it is common that data are from different sources with heterogeneous noise. A few of matrix decomposition methods have been extended for such multi-view data integration and pattern discovery. While only few methods were designed to consider the heterogeneity of noise in such multi-view data for data integration explicitly. To this end, we propos…
Google（谷歌）；University of Wisconsin-Madison（威斯康星大学麦迪逊分校）；XaiPient
We consider representation learning (hypothesis class $\mathcal{H} = \mathcal{F}\circ\mathcal{G}$) where training and test distributions can be different. Recent studies provide hints and failure examples for domain invariant representation learning, a common approach for this problem, but the explanations provided are somewhat different and do not provide a unified picture. In this paper, we provide new decompositions of risk which give finer-grained explanations and clarify potential generalization issues. For Single-Source Domain Adaptation, we give an exact decomposition (an equality) of t…
We introduce Bayesian Poisson Tucker decomposition (BPTD) for modeling country--country interaction event data. These data consist of interaction events of the form "country $i$ took action $a$ toward country $j$ at time $t$." BPTD discovers overlapping country--community memberships, including the number of latent communities. In addition, it discovers directed community--community interaction networks that are specific to "topics" of action types and temporal "regimes." We show that BPTD yields an efficient MCMC inference algorithm and achieves better predictive performance than related mode…
Modeling with multidimensional arrays, or tensors, often presents a problem due to high dimensionality. In addition, these structures typically exhibit inherent sparsity, requiring the use of regularization methods to properly characterize an association between a tensor covariate and a scalar response. We propose a Bayesian method to efficiently model a scalar response with a tensor covariate using the Tucker tensor decomposition in order to retain the spatial relationship within a tensor coefficient, while reducing the number of parameters varying within the model and applying regularization…
Fert Beijing Research Institute（费尔特北京研究院）；BDBC（BDBC（北京大数据研究院））；Qingdao Research Institute, Beihang University（北京航空航天大学青岛研究院）；Beihang University（北京航空航天大学）；Delft University of Technology（代尔夫特理工大学）
Bayesian method is capable of capturing real world uncertainties/incompleteness and properly addressing the over-fitting issue faced by deep neural networks. In recent years, Bayesian Neural Networks (BNNs) have drawn tremendous attentions of AI researchers and proved to be successful in many applications. However, the required high computation complexity makes BNNs difficult to be deployed in computing systems with limited power budget. In this paper, an efficient BNN inference flow is proposed to reduce the computation cost then is evaluated by means of both software and hardware implementat…
Multi-scale decomposition has been an invaluable tool for the processing of physiological signals. Much focus in multi-scale decomposition for processing such signals have been based on scale-space theory and wavelet transforms. In this study, we take a different perspective on multi-scale decomposition by investigating the feasibility of utilizing a Bayesian-based method for multi-scale signal decomposition called Bayesian Residual Transform (BRT) for the purpose of physiological signal processing. In BRT, a signal is modeled as the summation of residual signals, each characterizing informati…
Ultrasonic guided waves offer a convenient and practical approach to structural health monitoring and non-destructive evaluation, thanks to some distinct advantages. Guided waves, in particular Lamb waves, can be used to localise damage by utilising prior knowledge of propagation and reflection characteristics. Typical localisation methods make use of the time of arrival of waves emitted or reflected from the damage, the simplest of which involves triangulation. It is useful to decompose the measured signal into the expected waves propagating directly from the actuation source in the absence o…
We investigate the decline of infant mortality in 42 low and middle income countries (LMIC) using detailed micro data from 84 Demographic and Health Surveys. We estimate infant mortality risk for each infant in our data and develop a novel extension of Oaxaca decomposition to understand the sources of these changes. We find that the decline in infant mortality is due to a declining propensity for parents with given characteristics to experience the death of an infant rather than due to changes in the distributions of these characteristics over time. Our results suggest that technical progress …
We consider the problem of estimating high-dimensional covariance matrices of a particular structure, which is a summation of low rank and sparse matrices. This covariance structure has a wide range of applications including factor analysis and random effects models. We propose a Bayesian method of estimating the covariance matrices by representing the covariance model in the form of a factor model with unknown number of latent factors. We introduce binary indicators for factor selection and rank estimation for the low rank component combined with a Bayesian lasso method for the sparse compone…
We present a Bayesian nonparametric system reliability model which scales well and provides a great deal of flexibility in modeling. The Bayesian approach naturally handles the disparate amounts of component and subsystem data that may exist. However, traditional Bayesian reliability models are quite computationally complex, relying on MCMC techniques. Our approach utilizes the conjugate properties of the beta-Stacy process, which is the fundamental building block of our model. These individual models are linked together using a method of moments estimation approach. This model is computationa…
Google Research（谷歌研究院）；Harvard University（哈佛大学）；Columbia University（哥伦比亚大学）
Ensemble learning is a standard approach to building machine learning systems that capture complex phenomena in real-world data. An important aspect of these systems is the complete and valid quantification of model uncertainty. We introduce a Bayesian nonparametric ensemble (BNE) approach that augments an existing ensemble model to account for different sources of model uncertainty. BNE augments a model's prediction and distribution functions using Bayesian nonparametric machinery. It has a theoretical guarantee in that it robustly estimates the uncertainty patterns in the data distribution, …
Johns Hopkins University（约翰斯·霍普金斯大学）；National Observatory of Athens（雅典国家天文台）；University of Piraeus（比雷埃夫斯大学）；Computer Technology Institute & Press “Diophantus”（“丢番图”计算机技术研究所与出版社）
The so-called block-term decomposition (BTD) tensor model, especially in its rank-$(L_r,L_r,1)$ version, has been recently receiving increasing attention due to its enhanced ability of representing systems and signals that are composed of \emph{blocks} of rank higher than one, a scenario encountered in numerous and diverse applications. Uniqueness conditions and fitting methods have thus been thoroughly studied. Nevertheless, the challenging problem of estimating the BTD model structure, namely the number of block terms, $R$, and their individual ranks, $L_r$, has only recently started to attr…
We propose a novel unsupervised approach for linking records across arbitrarily many files, while simultaneously detecting duplicate records within files. Our key innovation is to represent the pattern of links between records as a {\em bipartite} graph, in which records are directly linked to latent true individuals, and only indirectly linked to other records. This flexible new representation of the linkage structure naturally allows us to estimate the attributes of the unique observable people in the population, calculate $k$-way posterior probabilities of matches across records, and propag…
Bayesian dynamic mode decomposition for real-time ship motion digital twinning
National Research Council（国家研究委员会）；Defence Research and Development Canada（加拿大国防研究与发展局）；Naval Surface Warfare Center-Carderock Division（海军水面作战中心卡德罗克分部）
Tumor is heterogeneous - a tumor sample usually consists of a set of subclones with distinct transcriptional profiles and potentially different degrees of aggressiveness and responses to drugs. Understanding tumor heterogeneity is therefore critical to precise cancer prognosis and treatment. In this paper, we introduce BayCount, a Bayesian decomposition method to infer tumor heterogeneity with highly over-dispersed RNA sequencing count data. Using negative binomial factor analysis, BayCount takes into account both the between-sample and gene-specific random effects on raw counts of sequencing …
We propose an unsupervised approach for linking records across arbitrarily many files, while simultaneously detecting duplicate records within files. Our key innovation involves the representation of the pattern of links between records as a bipartite graph, in which records are directly linked to latent true individuals, and only indirectly linked to other records. This flexible representation of the linkage structure naturally allows us to estimate the attributes of the unique observable people in the population, calculate transitive linkage probabilities across records (and represent this v…
Existing file linkage methods may produce sub-optimal results because they consider neither the interactions between different pairs of matched records nor relationships between variables that are exclusive to one of the files. In addition, many of the current methods fail to address the uncertainty in the linkage, which may result in overly precise estimates of relationships between variables that are exclusive to one of the files. Bayesian methods for record linkage can reduce the bias in the estimation of scientific relationships of interest and provide interval estimates that account for t…
A Bayesian agent learns about the structure of a stationary process from ob- serving past outcomes. We prove that his predictions about the near future become ap- proximately those he would have made if he knew the long run empirical frequencies of the process.
We propose a regression model for non-central $χ$ (NC-$χ$) distributed functional magnetic resonance imaging (fMRI) and diffusion weighted imaging (DWI) data, with the heteroscedastic Rician regression model as a prominent special case. The model allows both parameters in the NC-$χ$ distribution to be linked to explanatory variables, with the relevant covariates automatically chosen by Bayesian variable selection. A highly efficient Markov chain Monte Carlo (MCMC) algorithm is proposed for simulating from the joint Bayesian posterior distribution of all model parameters and the binary covariat…
Traffic flow count data in networks arise in many applications, such as automobile or aviation transportation, certain directed social network contexts, and Internet studies. Using an example of Internet browser traffic flow through site-segments of an international news website, we present Bayesian analyses of two linked classes of models which, in tandem, allow fast, scalable and interpretable Bayesian inference. We first develop flexible state-space models for streaming count data, able to adaptively characterize and quantify network dynamics efficiently in real-time. We then use these mode…
Approximate Bayesian computation (ABC) methods have become increasingly prevalent of late, facilitating as they do the analysis of intractable, or challenging, statistical problems. With the initial focus being primarily on the practical import of ABC, exploration of its formal statistical properties has begun to attract more attention. The aim of this paper is to establish general conditions under which ABC methods are Bayesian consistent, in the sense of producing draws that yield a degenerate posterior distribution at the true parameter (vector) asymptotically (in the sample size). We deriv…
Spatiotemporal Dynamics of Conflict Occurrence and Fatalities in Ethiopia: A Bayesian Model and Predictive Insights Using Event-level Data (1997--2024)
Anomaly Detection has several important applications. In this paper, our focus is on detecting anomalies in seller-reviewer data using tensor decomposition. While tensor-decomposition is mostly unsupervised, we formulate Bayesian semi-supervised tensor decomposition to take advantage of sparse labeled data. In addition, we use Polya-Gamma data augmentation for the semi-supervised Bayesian tensor decomposition. Finally, we show that the Pólya-Gamma formulation simplifies calculation of the Fisher information matrix for partial natural gradient learning. Our experimental results show that our se…
