Identifying latent structure in large data matrices is essential for exploring biological processes. Here, we consider recovering gene co-expression networks from gene expression data, where each network encodes relationships between genes that are locally co-regulated by shared biological mechanisms. To do this, we develop a Bayesian statistical model for biclustering to infer subsets of co-regulated genes whose covariation may be observed in only a subset of the samples. Our biclustering method, BicMix, has desirable properties, including allowing overcomplete representations of the data, computational tractability, and jointly modeling unknown confounders and biological signals. Compared with related biclustering methods, BicMix recovers latent structure with higher precision across diverse simulation scenarios. Further, we develop a method to recover gene co-expression networks from the estimated sparse biclustering matrices. We apply BicMix to breast cancer gene expression data and recover a gene co-expression network that is differential across ER+ and ER- samples.
High-throughput sequencing technology provides unprecedented opportunities to quantitatively explore human gut microbiome and its relation to diseases. Microbiome data are compositional, sparse, noisy, and heterogeneous, which pose serious challenges for statistical modeling. We propose an identifiable Bayesian multinomial matrix factorization model to infer overlapping clusters on both microbes and hosts. The proposed method represents the observed over-dispersed zero-inflated count matrix as Dirichlet-multinomial mixtures on which latent cluster structures are built hierarchically. Under the…
Bi-clustering is a technique that allows for the simultaneous clustering of observations and features in a dataset. This technique is often used in bioinformatics, text mining, and time series analysis. An important advantage of biclustering algorithm is the ability to uncover multiple ``views'' (i.e., through rows and column groupings) in the data. Several Gaussian mixture model based biclustering approach currently exist in the literature. However, they impose severe restrictions on the structure of the covariance matrix. Here, we propose a Gaussian mixture model-based bi-clustering approach…
Biclustering is a powerful data mining technique that allows simultaneously clustering rows (observations) and columns (features) in a matrix-format data set, which can provide results in a checkerboard-like pattern for visualization and exploratory analysis in a wide array of domains. Multiple biclustering algorithms have been developed in the past two decades, among which the convex biclustering can guarantee a global optimum by formulating in as a convex optimization problem. On the other hand, the application of biclustering has not progressed in parallel with the algorithm techniques. For…
Biclustering algorithms partition data and covariates simultaneously, providing new insights in several domains, such as analyzing gene expression to discover new biological functions. This paper develops a new model-free biclustering algorithm in abstract spaces using the notions of energy distance (ED) and the maximum mean discrepancy (MMD) -- two distances between probability distributions capable of handling complex data such as curves or graphs. The proposed method can learn more general and complex cluster shapes than most existing literature approaches, which usually focus on detecting …
Bayesian Genome- and Epigenome-wide Association Studies with Gene Level Dependence
高通量遗传和表观遗传数据经常被筛选与观察到的表型的关联。例如，人们可能希望测试数十万个遗传变异或DNA甲基化位点与疾病状态的关联。这些基因组变量可以自然地根据它们编码的基因以及其他标准进行分组。然而，在这种应用中的标准实践是独立筛选，具有对多重性的普遍校正。我们提出了一种贝叶斯方法，其中一个给定的基因组变量的关联的先验概率取决于它的基因，和基因特异性的概率建模非参数。这种分层模型允许适当的基因和全基因组多重性调整，并可以被纳入到各种贝叶斯关联筛选方法中，计算复杂性的增加可以忽略不计。我们描述了一个应用程序，以筛选低级别胶质瘤和多形性胶质母细胞瘤肿瘤样本之间的DNA甲基化差异的癌症基因组图谱。软件可通过https://github.com/lockEF/BayesianScreening上的BayesianScreening for R软件包获得。
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…
Complex simulators have become a ubiquitous tool in many scientific disciplines, providing high-fidelity, implicit probabilistic models of natural and social phenomena. Unfortunately, they typically lack the tractability required for conventional statistical analysis. Approximate Bayesian computation (ABC) has emerged as a key method in simulation-based inference, wherein the true model likelihood and posterior are approximated using samples from the simulator. In this paper, we draw connections between ABC and generalized Bayesian inference (GBI). First, we re-interpret the accept/reject step…
Assigning a value to a power likelihood in a general Bayesian model
贝叶斯数据分析和机器学习方法是广泛和流行的，因为它们为从数据中学习提供了直观而严格的公理;参见Bernardo and Smith（2004）and Bishop（2006）。然而，这种严格性伴随着一个警告，即贝叶斯模型是自然的精确反映。最近的趋势是通过将似然函数提高到幂来解决潜在的模型误设定，主要是出于鲁棒性原因，但不完全是。在本文中，我们提供了一个连贯的规范的功率参数，一旦贝叶斯模型已指定在没有一个完美的模型。
Generalised Bayesian inference updates prior beliefs using a loss function, rather than a likelihood, and can therefore be used to confer robustness against possible mis-specification of the likelihood. Here we consider generalised Bayesian inference with a Stein discrepancy as a loss function, motivated by applications in which the likelihood contains an intractable normalisation constant. In this context, the Stein discrepancy circumvents evaluation of the normalisation constant and produces generalised posteriors that are either closed form or accessible using standard Markov chain Monte Ca…
RIKEN Center for Advanced Intelligence Project（理化学研究所先进智能项目中心）；Technische Universität Darmstadt（达姆施塔特工业大学）；The Hessian Center for Artificial Intelligence（黑森人工智能中心）
In model development, model calibration and validation play complementary roles toward learning reliable models. In this article, we expand the Bayesian Validation Metric framework to a general calibration and validation framework by inverting the validation mathematics into a generalized Bayesian method for model calibration and regression. We perform Bayesian regression based on a user's definition of model-data agreement. This allows for model selection on any type of data distribution, unlike Bayesian and standard regression techniques, that "fail" in some cases. We show that our tool is c…
Estimation of reliability and hazard rate is one of the most important problems raised in many applications especially in engineering studies as well as human lifetime. In this regard, different methods of estimation have been used. Each method exploits various tools and suffers from problems such as complexity of computations, low precision, and so forth. This study is employed the E-Bayesian method, for estimating the parameter and survival functions of the Weibull Generalized Exponential distribution. The estimators are obtained under squared error and LINEX loss functions under progressive…
This study aims to show the fundamental difference between logistic regression and Bayesian classifiers in the case of exponential and unexponential families of distributions, yielding the following findings. First, the logistic regression is a less general representation of a Bayesian classifier. Second, one should suppose distributions of classes for the correct specification of logistic regression equations. Third, in specific cases, there is no difference between predicted probabilities from correctly specified generative Bayesian classifier and discriminative logistic regression.
The key distinguishing property of a Bayesian approach is marginalization, rather than using a single setting of weights. Bayesian marginalization can particularly improve the accuracy and calibration of modern deep neural networks, which are typically underspecified by the data, and can represent many compelling but different solutions. We show that deep ensembles provide an effective mechanism for approximate Bayesian marginalization, and propose a related approach that further improves the predictive distribution by marginalizing within basins of attraction, without significant overhead. We…
The Bayesian Case Model: A Generative Approach for Case-Based Reasoning and Prototype Classification
Massachusetts Institute of Technology（麻省理工学院）
我们提出了贝叶斯案例模型（Bayesian Case Model，简称CBR），它是贝叶斯案例推理（Bayesian Case-Based Reasoning，简称CBR）和原型分类与聚类的一个通用框架。它将CBR的直观力量引入贝叶斯生成框架。通过对聚类标签、原型和重要特征进行联合推理，该算法学习原型，即最能代表数据集中聚类的“精华”观察。与此同时，ESTA通过学习子空间来追求稀疏性，子空间是在原型表征中起重要作用的特征集。原型和子空间表示在保持分类准确性的同时在可解释性方面提供了定量优势。人类受试者实验证实，与现有技术给出的解释相比，当使用由ESTA产生的解释时，参与者的理解在统计学上显著改善。
Department of Statistics（统计系）；INSPER；Chicago Booth（芝加哥布斯商学院）；University of Chicago（芝加哥大学）；Volgenau School of Engineering（沃尔格瑙工程学院）；George Mason University（乔治梅森大学）
The connection between Bayesian neural networks and Gaussian processes gained a lot of attention in the last few years. Hidden units are proven to follow a Gaussian process limit when the layer width tends to infinity. Recent work has suggested that finite Bayesian neural networks may outperform their infinite counterparts because they adapt their internal representations flexibly. To establish solid ground for future research on finite-width neural networks, our goal is to study the prior induced on hidden units. Our main result is an accurate description of hidden units tails which shows tha…
