Diffusion State Distances: Multitemporal Analysis, Fast Algorithms, and Applications to Biological Networks

DOI10.1137/20M1324089zbMath1470.60231arXiv2003.03616OpenAlexW3128448394MaRDI QIDQ4999351

Kapil Devkota, Kaiyi Wu, Xiaozhe Hu, James M. Murphy, Lenore J. Cowen

Publication date: 6 July 2021

Published in: SIAM Journal on Mathematics of Data Science (Search for Journal in Brave)

Full work available at URL: https://arxiv.org/abs/2003.03616

zbMATH Keywords

computational biologymachine learningspectral graph theorymanifold learningapplied harmonic analysisdiffusion geometry

Mathematics Subject Classification ID

Classification and discrimination; cluster analysis (statistical aspects) (62H30) Inference from stochastic processes and spectral analysis (62M15) Probabilistic models, generic numerical methods in probability and statistics (65C20) Applications of Brownian motions and diffusion theory (population genetics, absorption problems, etc.) (60J70) Systems biology, networks (92C42) Computational aspects of data analysis and big data (68T09)

Related Items (4)

Random-walk based approximate \(k\)-nearest neighbors algorithm for diffusion state distance ⋮ NetMix2: unifying network propagation and altered subnetworks ⋮ The noncommutative $\ell_1-\ell_2$ inequality for Hilbert C*-modules and the exact constant ⋮ A multiscale environment for learning by diffusion

Uses Software

• ARPACK
• LAMG
• STRING

Cites Work

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• Learning the geometry of common latent variables using alternating-diffusion
• Error estimates for spectral convergence of the graph Laplacian on random geometric graphs toward the Laplace-Beltrami operator
• Diffusion maps
• Diffusion maps, spectral clustering and reaction coordinates of dynamical systems
• Algebraic Multilevel Preconditioners for the Graph Laplacian Based on Matching in Graphs
• Hitting and commute times in large graphs are often misleading
• Computing Diffusion State Distance Using Green’s Function and Heat Kernel on Graphs
• Lean Algebraic Multigrid (LAMG): Fast Graph Laplacian Linear Solver
• Diffusion Maps, Reduction Coordinates, and Low Dimensional Representation of Stochastic Systems
• Stochastic Complementation, Uncoupling Markov Chains, and the Theory of Nearly Reducible Systems
• ARPACK Users' Guide
• Community Detection and Stochastic Block Models
• Networks
• Algebraic multigrid methods
• Geometric diffusions as a tool for harmonic analysis and structure definition of data: Diffusion maps
• Computing the diffusion state distance on graphs via algebraic multigrid and random projections
• Laplacian Eigenmaps for Dimensionality Reduction and Data Representation
• Recovering Hidden Components in Multimodal Data with Composite Diffusion Operators
• The exact constant for the ℓ_1-ℓ_2 norm inequality
• An Adaptive Multigrid Method Based on Path Cover
• A Hitting Time Formula for the Discrete Green's Function
• Hessian eigenmaps: Locally linear embedding techniques for high-dimensional data
• The elements of statistical learning. Data mining, inference, and prediction

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