Topological data analysis of collective and individual epithelial cells using persistent homology of loops
Bhaskar D, Zhang W, Wong I. Topological data analysis of collective and individual epithelial cells using persistent homology of loops. Soft Matter 2021, 17: 4653-4664. PMID: 33949592, PMCID: PMC8276269, DOI: 10.1039/d1sm00072a.Peer-Reviewed Original ResearchAnalyzing collective motion with machine learning and topology
Bhaskar D, Manhart A, Milzman J, Nardini JT, Storey KM, Topaz CM, Ziegelmeier L. Analyzing collective motion with machine learning and topology. Chaos An Interdisciplinary Journal Of Nonlinear Science 2019, 29: 123125. PMID: 31893635, PMCID: PMC7027427, DOI: 10.1063/1.5125493.Peer-Reviewed Original ResearchSupervised machine learning methodsMachine learning methodsTopological data analysisCollective motionMachine learningLearning methodsOrder parameterSimulation dataTopological approachPersistent homologyTraditional order parametersPrior knowledgeMachineCollective behaviorModel parametersData analysisLarge librariesNumerical simulationsTopologyMultiple scalesMotionTime seriesLearningDifferent typesParametersTopological data analysis of spatial patterning in heterogeneous cell populations: clustering and sorting with varying cell-cell adhesion
Bhaskar D, Zhang W, Volkening A, Sandstede B, Wong I. Topological data analysis of spatial patterning in heterogeneous cell populations: clustering and sorting with varying cell-cell adhesion. Npj Systems Biology And Applications 2023, 9: 43. PMID: 37709793, PMCID: PMC10502054, DOI: 10.1038/s41540-023-00302-8.Peer-Reviewed Original ResearchConceptsTopological data analysisPersistence imagesClassification accuracyHigh classification accuracyMachine learningRobust classificationDimensionality reductionUnsupervised classificationHierarchical architectureData analysisArchitectureHierarchical clusteringImagesTopological featuresClassificationDifferent topological featuresAutoencoderAccuracyClusteringLearningSimulationsInformationRecent developments