Convex biclustering

DOI10.1111/BIOM.12540zbMATH Open1366.62208arXiv1408.0856OpenAlexW3037425903WikidataQ39779484 ScholiaQ39779484MaRDI QIDQ5347398FDOQ5347398

Eric C. Chi, Richard G. Baraniuk, Genevera I. Allen

Publication date: 23 May 2017

Published in: Biometrics (Search for Journal in Brave)

Abstract: In the biclustering problem, we seek to simultaneously group observations and features. While biclustering has applications in a wide array of domains, ranging from text mining to collaborative filtering, the problem of identifying structure in high dimensional genomic data motivates this work. In this context, biclustering enables us to identify subsets of genes that are co-expressed only within a subset of experimental conditions. We present a convex formulation of the biclustering problem that possesses a unique global minimizer and an iterative algorithm, COBRA, that is guaranteed to identify it. Our approach generates an entire solution path of possible biclusters as a single tuning parameter is varied. We also show how to reduce the problem of selecting this tuning parameter to solving a trivial modification of the convex biclustering problem. The key contributions of our work are its simplicity, interpretability, and algorithmic guarantees - features that arguably are lacking in the current alternative algorithms. We demonstrate the advantages of our approach, which includes stably and reproducibly identifying biclusterings, on simulated and real microarray data.

Full work available at URL: https://arxiv.org/abs/1408.0856

zbMATH Keywords

clusteringconvex optimizationbiclusteringgene expressionstructured sparsityreproducible researchfused Lasso

Mathematics Subject Classification ID

Classification and discrimination; cluster analysis (statistical aspects) (62H30) Applications of statistics to biology and medical sciences; meta analysis (62P10) Convex programming (90C25) Ridge regression; shrinkage estimators (Lasso) (62J07) Protein sequences, DNA sequences (92D20)

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Cited In (27)

• Generalized co-clustering analysis via regularized alternating least squares
• Dynamic Tensor Clustering
• Biconvex Clustering
• Selective inference for latent block models
• Distribution-Free, Size Adaptive Submatrix Detection with Acceleration
• Tensor clustering with planted structures: statistical optimality and computational limits
• Dynamic Visualization and Fast Computation for Convex Clustering via Algorithmic Regularization
• A Doubly Enhanced EM Algorithm for Model-Based Tensor Clustering
• On uniform concentration bounds for bi-clustering by using the Vapnik-Chervonenkis theory
• Cluster analysis: a modern statistical review
• Title not available (Why is that?)
• Biclustering via structured regularized matrix decomposition
• A dual reformulation and solution framework for regularized convex clustering problems
• Profile likelihood biclustering
• Statistical properties of convex clustering
• Regularized matrix data clustering and its application to image analysis
• Covariate-Dependent Clustering of Undirected Networks with Brain-Imaging Data
• Statistical Foundations Driving 21st Century Innovation
• Title not available (Why is that?)
• Convex clustering analysis for histogram‐valued data
• Title not available (Why is that?)
• Recovering Trees with Convex Clustering
• Computational lower bounds for graphon estimation via low-degree polynomials
• Going Off the Grid: Iterative Model Selection for Biclustered Matrix Completion
• Uncovering block structures in large rectangular matrices
• Multilevel Matrix-Variate Analysis and its Application to Accelerometry-Measured Physical Activity in Clinical Populations
• Sparse Convex Clustering

Uses Software

• seriation
• dynamicTreeCut
• ElemStatLearn
• softImpute
• LAS

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