论文检索

图对齐随机分区模型（GARP）AI 解读

Bayesian nonparametric mixtures and random partition models are powerful tools for probabilistic clustering. However, standard independent mixture models can be restrictive in some applications such as inference on cell lineage due to the biological relations of the clusters. The increasing availability of large genomic data requires new statistical tools to perform model-based clustering and infer the relationship between homogeneous subgroups of units. Motivated by…

利用贝叶斯非参数共同原子回归构建临床试验合成对照AI 解读

The availability of electronic health records (EHR) has opened opportunities to supplement increasingly expensive and difficult to carry out randomized controlled trials (RCT) with evidence from readily available real world data. In this paper, we use EHR data to construct synthetic control arms for treatment-only single arm trials. We propose a novel nonparametric Bayesian common atoms mixture model that allows us to find equivalent population strata in the EHR and the…

用于电子健康记录表型识别的贝叶斯双重特征分配AI 解读

Electronic health records (EHR) provide opportunities for deeper understanding of human phenotypes - in our case, latent disease - based on statistical modeling. We propose a categorical matrix factorization method to infer latent diseases from EHR data. 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…

带序贯转移时间的动态治疗方案的贝叶斯非参数估计AI 解读

We analyze a dataset arising from a clinical trial involving multi-stage chemotherapy regimes for acute leukemia. The trial design was a 2 × 2 factorial for frontline therapies only. Motivated by the idea that subsequent salvage treatments affect survival time, we model therapy as a dynamic treatment regime (DTR), that is, an alternating sequence of adaptive treatments or other actions and transition times between disease states. These sequences may vary substantially…

We propose small-variance asymptotic approximations for inference on tumor heterogeneity (TH) using next-generation sequencing data. Understanding TH is an important and open research problem in biology. The lack of appropriate statistical inference is a critical gap in existing methods that the proposed approach aims to fill. We build on a hierarchical model with an exponential family likelihood and a feature allocation prior. The proposed implementation of posterior…

基于疗效与毒性联合效用的两周期贝叶斯剂量探索AI 解读

Juhee Lee, Peter F. Thall, Yuan Ji & Peter MüllerJuhee Lee, Department of Statistics, Ohio State University, Columbus, OH 43210 (E-mail: ).Peter F. Thall, Department of Biostatistics, University of Texas, M.D. Anderson Cancer Center, Houston, TX 77230-1402 (E-mail: ).Yuan Ji, Center for Clinical and Research Informatics, North Shore University Health System, Evanston, IL 60201 (E-mail: ).Peter Müller, Department of Mathematics, University of Texas, Austin, TX 78712 (E-mail:…

用于局部聚类的非参数贝叶斯模型及其蛋白质组学应用AI 解读

We propose a nonparametric Bayesian local clustering (NoB-LoC) approach for heterogeneous data. NoB-LoC implements inference for nested clusters as posterior inference under a Bayesian model. Using protein expression data as an example, the NoB-LoC model defines a protein (column) cluster as a set of proteins that give rise to the same partition of the samples (rows). In other words, the sample partitions are nested within protein clusters. The common clustering of the…

组蛋白修饰 ChIP-Seq 数据的贝叶斯图模型AI 解读

Histone modifications (HMs) are an important post-translational feature. Different types of HMs are believed to co-exist and co-regulate biological processes such as gene expression and, therefore, are intrinsically dependent on each other. We develop inference for this complex biological network of HMs based on a graphical model using ChIP-Seq data. A critical computational hurdle in the inference for the proposed graphical model is the evaluation of a normalization…

一种贝叶斯发现程序AI 解读

Summary We discuss a Bayesian discovery procedure for multiple-comparison problems. We show that, under a coherent decision theoretic framework, a loss function combining true positive and false positive counts leads to a decision rule that is based on a threshold of the posterior probability of the alternative. Under a semiparametric model for the data, we show that the Bayes rule can be approximated by the optimal discovery procedure, which was recently introduced by…

带序贯参数学习的实用滤波方法AI 解读

Summary The paper develops a simulation-based approach to sequential parameter learning and filtering in general state space models. Our approach is based on approximating the target posterior by a mixture of fixed lag smoothing distributions. Parameter inference exploits a sufficient statistic structure and the methodology can be easily implemented by modifying state space smoothing algorithms. We avoid reweighting particles and hence sample degeneracy problems that plague…

利用纵向标志物建模疾病进展AI 解读

In this paper we propose a Bayesian natural history model for disease progression based on the joint modeling of longitudinal biomarker levels, age at clinical detection of disease and disease status at diagnosis. We establish a link between the longitudinal responses and the natural history of the disease by using an underlying latent disease process which describes the onset of the disease and models the transition to an advanced stage of the disease as dependent on the…

通过非齐次马尔可夫链模拟实现最优贝叶斯设计AI 解读

We consider decision problems defined by a utility function and an underlying probability model for all unknowns. The utility function quantifies the decision maker's preferences over consequences. The optimal decision maximizes the expected utility function where the expectation is taken with respect to all unknowns, that is, future data and parameters. In many problems, the solution is not analytically tractable. For example, the utility function might involve moments that…

相关非参数贝叶斯模型之间的联合推断方法AI 解读

Summary We consider the problem of combining inference in related nonparametric Bayes models. Analogous to parametric hierarchical models, the hierarchical extension formalizes borrowing strength across the related submodels. In the nonparametric context, modelling is complicated by the fact that the random quantities over which we define the hierarchy are infinite dimensional. We discuss a formal definition of such a hierarchical model. The approach includes a regression at…

依赖随机测度的 ANOVA 模型AI 解读

We consider dependent nonparametric models for related random probability distributions. For example, the random distributions might be indexed by a categorical covariate indicating the treatment levels in a clinical trial and might represent random effects distributions under the respective treatment combinations. We propose a model that describes dependence across random distributions in an analysis of variance (ANOVA)-type fashion. We define a probability model in such a…

具有状态依赖方差的非线性状态空间模型AI 解读

Nonlinear state-space models with state-dependent variances (SDVs) are commonly used in financial time series. Important examples include stochastic volatility (SV) and affine term structure models. We propose a methodology for state smoothing in this class of models. Our smoothing technique is simulation based and uses an auxiliary mixture model. Key features of the auxiliary mixture model are the use of state-dependent weights and efficient block sampling algorithms to…

检测非线性个体曲线急剧变化的贝叶斯模型AI 解读

We propose a model for longitudinal data with random effects that includes model-based smoothing of measurements over time. This research is motivated by experiments evaluating the hemodynamic effects of various agents in tumor-bearing rats. In one set of experiments, the rats breathed room air, followed by carbogen (a mixture of pure oxygen and carbon dioxide). The experimental responses are longitudinal measurements of oxygen pressure measured in tissue, tumor blood flow,…

采用层次混合先验的贝叶斯总体模型及其血细胞计数应用AI 解读

Population pharmacokinetic and pharmacodynamic studies require analyzing nonlinear growth curves fit to multiple measurements from study subjects. We propose a class of nonlinear population models with nonparametric second-stage priors for analyzing such data. The proposed models apply a flexible class of mixtures to implement the nonparametric second stage. The discussion is based on a pharmacodynamic study involving longitudinal data consisting of hematologic profiles…

通过条件高斯动态模型进行多项时间序列的贝叶斯预测AI 解读

We consider inference in the class of conditionally Gaussian dynamic models for nonnormal multivariate time series. In such models, data are represented as drawn from nonnormal sampling distributions whose parameters are related both through time and hierarchically across several multivariate series. A key example—the main focus here—is time series of multinomial observations, a common occurrence in sociological and demographic studies involving categorical count data.…

通过蒙特卡洛实验的曲线拟合实现最优设计AI 解读

This article explores numerical methods for stochastic optimization, with special attention to Bayesian design problems. A common and challenging situation occurs when the objective function (in Bayesian applications, the expected utility) is very expensive to evaluate, perhaps because it requires integration over a space of very large dimensionality. Our goal is to explore a class of optimization algorithms designed to gain efficiency in such situations, by exploiting…