Sparse Bayesian hierarchical modeling of high-dimensional clustering problems
From MaRDI portal
Publication:972898
DOI10.1016/J.JMVA.2010.03.009zbMATH Open1188.62137arXiv0904.2906OpenAlexW2077666315MaRDI QIDQ972898FDOQ972898
Publication date: 21 May 2010
Published in: Journal of Multivariate Analysis (Search for Journal in Brave)
Abstract: Clustering is one of the most widely used procedures in the analysis of microarray data, for example with the goal of discovering cancer subtypes based on observed heterogeneity of genetic marks between different tissues. It is well-known that in such high-dimensional settings, the existence of many noise variables can overwhelm the few signals embedded in the high-dimensional space. We propose a novel Bayesian approach based on Dirichlet process with a sparsity prior that simultaneous performs variable selection and clustering, and also discover variables that only distinguish a subset of the cluster components. Unlike previous Bayesian formulations, we use Dirichlet process (DP) for both clustering of samples as well as for regularizing the high-dimensional mean/variance structure. To solve the computational challenge brought by this double usage of DP, we propose to make use of a sequential sampling scheme embedded within Markov chain Monte Carlo (MCMC) updates to improve the naive implementation of existing algorithms for DP mixture models. Our method is demonstrated on a simulation study and illustrated with the leukemia gene expression dataset.
Full work available at URL: https://arxiv.org/abs/0904.2906
Recommendations
- Bayesian Variable Selection in Clustering High-Dimensional Data
- Variable selection in clustering via Dirichlet process mixture models
- Bayesian variable selection in clustering high-dimensional data with substructure
- Variable Selection for Model-Based High-Dimensional Clustering and Its Application to Microarray Data
- Penalized model-based clustering
Bayesian inference (62F15) Classification and discrimination; cluster analysis (statistical aspects) (62H30) Applications of statistics to biology and medical sciences; meta analysis (62P10) Monte Carlo methods (65C05) Medical applications (general) (92C50)
Cites Work
- Penalized Clustering of Large-Scale Functional Data With Multiple Covariates
- BART: Bayesian additive regression trees
- Title not available (Why is that?)
- Model-Based Clustering, Discriminant Analysis, and Density Estimation
- Clustering Objects on Subsets of Attributes (with Discussion)
- Bayesian Density Estimation and Inference Using Mixtures
- Title not available (Why is that?)
- Variable selection in clustering via Dirichlet process mixture models
- Model-Based Gaussian and Non-Gaussian Clustering
- Comparison of Discrimination Methods for the Classification of Tumors Using Gene Expression Data
- Dealing With Label Switching in Mixture Models
- Bayesian Variable Selection in Clustering High-Dimensional Data
- Mixtures of Dirichlet processes with applications to Bayesian nonparametric problems
- Class prediction by nearest shrunken centroids, with applications to DNA microarrays.
- Some theory for Fisher's linear discriminant function, `naive Bayes', and some alternatives when there are many more variables than observations
- Title not available (Why is that?)
- Partially Collapsed Gibbs Samplers
- High-Dimensional Sparse Factor Modeling: Applications in Gene Expression Genomics
- Bayesian Models for Gene Expression With DNA Microarray Data
- Model-based subspace clustering
- The Nested Dirichlet Process
- Of mice and men: sparse statistical modeling in cardiovascular genomics
- Predictive performance of Dirichlet process shrinkage methods in linear regression
Cited In (6)
- Bayesian curve fitting and clustering with Dirichlet process mixture models for microarray data
- On two‐way Bayesian agglomerative clustering of gene expression data
- Model-based clustering based on sparse finite Gaussian mixtures
- A hierarchical framework for state-space matrix inference and clustering
- Clustering sparse binary data with hierarchical Bayesian Bernoulli mixture model
- A Bayesian sparse finite mixture model for clustering data from a heterogeneous population
Uses Software
This page was built for publication: Sparse Bayesian hierarchical modeling of high-dimensional clustering problems
Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q972898)
