Tropical Sufficient Statistics for Persistent Homology

DOI10.1137/17M1148037zbMATH Open1443.62018arXiv1709.02647OpenAlexW2753130960MaRDI QIDQ5234530FDOQ5234530

Anthea Monod, Lorin Crawford, Juan Ángel Patiño-Galindo, Sara Kališnik Verovšek

Publication date: 27 September 2019

Published in: SIAM Journal on Applied Algebra and Geometry (Search for Journal in Brave)

Abstract: We show that an embedding in Euclidean space based on tropical geometry generates stable sufficient statistics for barcodes. In topological data analysis, barcodes are multiscale summaries of algebraic topological characteristics that capture the `shape' of data; however, in practice, they have complex structures that make them difficult to use in statistical settings. The sufficiency result presented in this work allows for classical probability distributions to be assumed on the tropical geometric representation of barcodes. This makes a variety of parametric statistical inference methods amenable to barcodes, all while maintaining their initial interpretations. More specifically, we show that exponential family distributions may be assumed, and that likelihood functions for persistent homology may be constructed. We conceptually demonstrate sufficiency and illustrate its utility in persistent homology dimensions 0 and 1 with concrete parametric applications to human immunodeficiency virus and avian influenza data.

Full work available at URL: https://arxiv.org/abs/1709.02647

zbMATH Keywords

persistent homologytropical geometrysufficient statisticsinfectious viral disease

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Epidemiology (92D30) Persistent homology and applications, topological data analysis (55N31) Sufficient statistics and fields (62B05) Applications of tropical geometry (14T90) Topological data analysis (62R40)

Cites Work

• Title not available (Why is that?)
• Title not available (Why is that?)
• Title not available (Why is that?)
• Title not available (Why is that?)
• Title not available (Why is that?)
• Title not available (Why is that?)
• Confidence sets for persistence diagrams
• Hypothesis testing for topological data analysis
• Clique topology reveals intrinsic geometric structure in neural correlations
• Probability measures on the space of persistence diagrams
• Robust statistics, hypothesis testing, and confidence intervals for persistent homology on metric measure spaces
• Barcodes: The persistent topology of data
• Properties of sufficiency and statistical tests
• On Information and Sufficiency
• Fréchet means for distributions of persistence diagrams
• Stability of persistence diagrams
• Geometry of the space of phylogenetic trees
• Algebraic Statistics for Computational Biology
• Computing persistent homology
• Topological persistence and simplification
• Persistent homology transform for modeling shapes and surfaces
• Statistical topological data analysis using persistence landscapes
• Application of the Radon-Nikodym Theorem to the Theory of Sufficient Statistics
• Coordinate-free Coverage in Sensor Networks with Controlled Boundaries via Homology
• Topological complexity of smooth random functions. École d'Été de Probabilités de Saint-Flour XXXIX-2009.
• Topology of viral evolution
• Symmetric and \(r\)-symmetric tropical polynomials and rational functions
• Topological pattern recognition for point cloud data
• The ring of algebraic functions on persistence bar codes
• Stochastic Convergence of Persistence Landscapes and Silhouettes
• The neural ring: an algebraic tool for analyzing the intrinsic structure of neural codes
• Sufficiency and Approximate Sufficiency
• A Klein-bottle-based dictionary for texture representation
• Persistence Images: A Stable Vector Representation of Persistent Homology
• Geometry Helps to Compare Persistence Diagrams
• Modeling and replicating statistical topology and evidence for CMB nonhomogeneity

Cited In (10)

• Wavelet-based density estimation for persistent homology
• Title not available (Why is that?)
• Tropical diagrams of probability spaces
• Tropical geometry of statistical models
• ToFU: topology functional units for deep learning
• Bayesian topological signal processing
• Statistical topology via Morse theory, persistence and nonparametric estimation
• Symmetric polynomials in upper-bound semirings
• Convolutional persistence transforms
• Functional summaries of persistence diagrams

Uses Software

• ape
• MrBayes
• PAUP*
• MAFFT
• DEseq
• PhyML
• Cd-hit
• trimAl
• Ripser
• CliqueTop
• GitHub
• PersistenceImages

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