2022
A Manifold Proximal Linear Method for Sparse Spectral Clustering with Application to Single-Cell RNA Sequencing Data Analysis
Wang Z, Liu B, Chen S, Ma S, Xue L, Zhao H. A Manifold Proximal Linear Method for Sparse Spectral Clustering with Application to Single-Cell RNA Sequencing Data Analysis. INFORMS Journal On Optimization 2022, 4: 200-214. DOI: 10.1287/ijoo.2021.0064.Peer-Reviewed Original ResearchSparse spectral clusteringOptimization problemSpectral clusteringLinear methodsIteration complexity resultsNonconvex objectiveNonsmooth objectiveConvex relaxationStiefel manifoldSingle-cell RNA sequencing data setsSSC problemComplexity resultsSmoothing techniquesRNA sequencing data analysisData setsOriginal formulationUnsupervised learning methodData analysisNonsmoothProblemAlgorithmFormulationManifoldClusteringConvergence
2017
Structured subcomposition selection in regression and its application to microbiome data analysis
Wang T, Zhao H. Structured subcomposition selection in regression and its application to microbiome data analysis. The Annals Of Applied Statistics 2017, 11: 771-791. DOI: 10.1214/16-aoas1017.Peer-Reviewed Original ResearchRegularization methodLinear log contrast modelGeneralized lasso problemLog-contrast modelNovel penalty functionMicrobiome data analysisCompositional covariatesOptimization problemLasso problemHigher dimensionsStatistical challengesPenalty functionPractical problemsSymmetric versionTree structure informationSubtree levelProblemPrior knowledgeTree structureSubcompositionsCompositional dataSuch dataStructure informationData analysisNodes
2000
Assessing reliability of gene clusters from gene expression data
Zhang K, Zhao H. Assessing reliability of gene clusters from gene expression data. Functional & Integrative Genomics 2000, 1: 156-173. PMID: 11793234, DOI: 10.1007/s101420000019.Peer-Reviewed Original ResearchConceptsStatistical resampling methodsHierarchical clustering methodCluster identification methodNumerical algorithmGene expression dataClustering methodClustering treesResampling methodHierarchical clustering algorithmExpression dataExperiment designClustering algorithmAlgorithmChallenging problemData setsMeasured gene expression levelsEffect of variationData analysisClustersUncertaintyProblemReliability