2025
SuperGLUE facilitates an explainable training framework for multi-modal data analysis
Liu T, Zhao J, Zhao H. SuperGLUE facilitates an explainable training framework for multi-modal data analysis. Cell Reports Methods 2025, 5: 101167. PMID: 40914154, DOI: 10.1016/j.crmeth.2025.101167.Peer-Reviewed Original ResearchConceptsData integrationProbabilistic deep learningMulti-modal data analysisInference of gene regulatory networksMulti-modal data integrationDeep learningGene regulatory networksTraining frameworkBaseline modelRegulatory networksComplex biological systemsRegulatory relationshipsSensing dataCell statesGlobal structureArea of active researchActive researchOmicsBiological featuresScalable methodFrameworkBiological systemsStatistical modelNetworkBiological linkages
2019
Prediction Analysis for Microbiome Sequencing Data
Wang T, Yang C, Zhao H. Prediction Analysis for Microbiome Sequencing Data. Biometrics 2019, 75: 875-884. PMID: 30994187, DOI: 10.1111/biom.13061.Peer-Reviewed Original ResearchConceptsMonte Carlo expectation-maximization algorithmInverse regression modelReal data exampleTypes of covariatesNew statistical frameworkMaximum likelihood estimationExpectation-maximization algorithmDimension reduction structureInverse regressionStatistical frameworkData examplesStatistical challengesLikelihood estimationMicrobiome sequencing dataHuman microbiome studiesHuman microbiome compositionDifferent library sizesZerosPredictive analysisModelEstimationAlgorithmSimulationsRegression modelsFramework
2005
Aligning Peaks Across Multiple Mass Spectrometry Data Sets Using A Scale-Space Based Approach
Yu W, Li X, Zhao H. Aligning Peaks Across Multiple Mass Spectrometry Data Sets Using A Scale-Space Based Approach. 2005, 126-127. DOI: 10.1109/csbw.2005.19.Peer-Reviewed Original ResearchHierarchical clustering methodScale-space approachAlignment frameworkBased ApproachClustering methodIntensity informationZ-informationAlignment of peaksCurrent approachesPeak alignmentMass spectrometry dataConcrete examplesInformationSpectrometry dataSpace limitationsExtra advantageFrameworkAlignmentParameter determinationSet
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