2020
Local conformal autoencoder for standardized data coordinates
Peterfreund E, Lindenbaum O, Dietrich F, Bertalan T, Gavish M, Kevrekidis IG, Coifman RR. Local conformal autoencoder for standardized data coordinates. Proceedings Of The National Academy Of Sciences Of The United States Of America 2020, 117: 30918-30927. PMID: 33229581, PMCID: PMC7733838, DOI: 10.1073/pnas.2014627117.Peer-Reviewed Original Research
2019
Visualizing structure and transitions in high-dimensional biological data
Moon KR, van Dijk D, Wang Z, Gigante S, Burkhardt DB, Chen WS, Yim K, Elzen AVD, Hirn MJ, Coifman RR, Ivanova NB, Wolf G, Krishnaswamy S. Visualizing structure and transitions in high-dimensional biological data. Nature Biotechnology 2019, 37: 1482-1492. PMID: 31796933, PMCID: PMC7073148, DOI: 10.1038/s41587-019-0336-3.Peer-Reviewed Original ResearchConceptsSingle-cell RNA sequencing datasetsSingle-cell RNA sequencingUnique biological insightsRNA sequencing datasetsGerm layer differentiationMain developmental branchesHigh-throughput technologiesGut microbiome dataRNA sequencingUndescribed subpopulationsHigh-dimensional biological dataSequencing datasetsBiological insightsDevelopmental branches
2014
Quantitative Arbor Analytics: Unsupervised Harmonic Co-Clustering of Populations of Brain Cell Arbors Based on L-Measure
Lu Y, Carin L, Coifman R, Shain W, Roysam B. Quantitative Arbor Analytics: Unsupervised Harmonic Co-Clustering of Populations of Brain Cell Arbors Based on L-Measure. Neuroinformatics 2014, 13: 47-63. PMID: 25086878, DOI: 10.1007/s12021-014-9237-2.Peer-Reviewed Original ResearchConceptsCo-clustering methodAnalytics systemSynthetic datasetsThree-dimensional visualizationAnalysis ToolkitHeterogeneous ensembleDistance measureAlgorithmMultivariate data pointsData smoothingData pointsWavelet basisData matrixHarmonic analysis theoryL-measureNeuroMorpho databaseDatasetAnalysis theoryToolkitVisualizationEnsembleRobustnessDatabaseSuperiorityMethodDiffusion methods for aligning medical datasets: Location prediction in CT scan images
Fernández Á, Rabin N, Coifman RR, Eckstein J. Diffusion methods for aligning medical datasets: Location prediction in CT scan images. Medical Image Analysis 2014, 18: 425-432. PMID: 24444669, DOI: 10.1016/j.media.2013.12.009.Peer-Reviewed Original Research
2013
Identifying preseizure state in intracranial EEG data using diffusion kernels
Duncan D, Talmon R, Zaveri HP, Coifman RR. Identifying preseizure state in intracranial EEG data using diffusion kernels. Mathematical Biosciences And Engineering 2013, 10: 579-590. PMID: 23906137, DOI: 10.3934/mbe.2013.10.579.Peer-Reviewed Original Research
2012
The automated malnutrition assessment
David G, Bernstein LH, Coifman RR. The automated malnutrition assessment. Nutrition 2012, 29: 113-121. PMID: 23116774, DOI: 10.1016/j.nut.2012.04.017.Peer-Reviewed Original Research
2009
Detecting consistent common lines in cryo-EM by voting
Singer A, Coifman RR, Sigworth FJ, Chester DW, Shkolnisky Y. Detecting consistent common lines in cryo-EM by voting. Journal Of Structural Biology 2009, 169: 312-322. PMID: 19925867, PMCID: PMC2826584, DOI: 10.1016/j.jsb.2009.11.003.Peer-Reviewed Original ResearchDetecting intrinsic slow variables in stochastic dynamical systems by anisotropic diffusion maps
Singer A, Erban R, Kevrekidis IG, Coifman RR. Detecting intrinsic slow variables in stochastic dynamical systems by anisotropic diffusion maps. Proceedings Of The National Academy Of Sciences Of The United States Of America 2009, 106: 16090-16095. PMID: 19706457, PMCID: PMC2752552, DOI: 10.1073/pnas.0905547106.Peer-Reviewed Original ResearchConceptsStochastic dynamical systemsModel reduction approachHigh dimensional dynamic dataDynamical systemsNonlinear independent component analysisLocal principal component analysisSlow variablesMarkov matrixGood observablesDiffusion mapsNetwork simulationAnisotropic diffusionReduction approachData analysis techniqueAnalysis techniquesEigenvectorsDynamic dataObservablesIndependent component analysisComponent analysisSimulationsMatrix
2008
Graph Laplacian Tomography from Unknown Random Projections
Coifman RR, Shkolnisky Y, Sigworth FJ, Singer A. Graph Laplacian Tomography from Unknown Random Projections. IEEE Transactions On Image Processing 2008, 17: 1891-1899. PMID: 18784036, DOI: 10.1109/tip.2008.2002305.Peer-Reviewed Original Research
2007
Variable-free exploration of stochastic models: A gene regulatory network example
Erban R, Frewen TA, Wang X, Elston TC, Coifman R, Nadler B, Kevrekidis IG. Variable-free exploration of stochastic models: A gene regulatory network example. The Journal Of Chemical Physics 2007, 126: 155103. PMID: 17461667, DOI: 10.1063/1.2718529.Peer-Reviewed Original ResearchConceptsStochastic modelEquation-free approachLow-dimensional descriptionLong-time behaviorNetwork exampleAppropriate observablesStochastic simulationGood observablesGene regulatory networksObservablesComplex systemsDiffusion mapsSimulation dataPhysical variablesPrevious paperLong-term dynamicsAppropriate valuesDynamicsEigenvectorsLaplacianComputationRegulatory networksGraphModelRestriction procedures
2006
Data Fusion and Multicue Data Matching by Diffusion Maps
Lafon S, Keller Y, Coifman RR. Data Fusion and Multicue Data Matching by Diffusion Maps. IEEE Transactions On Pattern Analysis And Machine Intelligence 2006, 28: 1784-1797. PMID: 17063683, DOI: 10.1109/tpami.2006.223.Peer-Reviewed Original ResearchConceptsData fusionData matchingImage sequence alignmentHigh-dimensional data analysisGraph alignmentFundamental taskMatching schemeExtension algorithmGeometric harmonicsDiffusion mapsTaskMatchingDiffusion frameworkSequence alignmentInvariant embeddingData analysisSchemeDifferent sourcesAlgorithmEmbeddingFusionLipreadingData assimilationFrameworkAlignment
2005
Geometric diffusions for the analysis of data from sensor networks
Coifman RR, Maggioni M, Zucker SW, Kevrekidis IG. Geometric diffusions for the analysis of data from sensor networks. Current Opinion In Neurobiology 2005, 15: 576-584. PMID: 16150587, DOI: 10.1016/j.conb.2005.08.012.Peer-Reviewed Original ResearchConceptsSensor networksGeometric diffusionMathematical developmentComplex data setsHarmonic analysisNeural information processingActivity datasetsCertain analogyComputer modelingData setsInformation processingManifoldNetworkModelingGraphData analysisAlgorithmNew toolDatasetAnalysis of dataAnalogyField