Bayesian topological learning for classifying the structure of biological networks

DOI10.1214/21-BA1270MaRDI QIDQ6121774zbMATH OpenOpenAlexFDO

Authors Vasileios Maroulas, Cassie Putman Micucci, Farzana Nasrin

Publication date 27 February 2024

Published in Bayesian Analysis (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/2009.11974, https://projecteuclid.org/journals/bayesian-analysis/volume-17/issue-3/Bayesian-Topological-Learning-for-Classifying-the-Structure-of-Biological-Networks/10.1214/21-BA1270.full

zbMATH Keywords

Bayesian inference and classificationcardinalityintensitymarked point processestopological data analysis

Mathematics Subject Classification ID

Point processes (e.g., Poisson, Cox, Hawkes processes) (60G55) Bayesian inference (62F15) Applications of statistics to biology and medical sciences; meta analysis (62P10) Topological data analysis (62R40)

Abstract: Actin cytoskeleton networks generate local topological signatures due to the natural variations in the number, size, and shape of holes of the networks. Persistent homology is a method that explores these topological properties of data and summarizes them as persistence diagrams. In this work, we analyze and classify these filament networks by transforming them into persistence diagrams whose variability is quantified via a Bayesian framework on the space of persistence diagrams. The proposed generalized Bayesian framework adopts an independent and identically distributed cluster point process characterization of persistence diagrams and relies on a substitution likelihood argument. This framework provides the flexibility to estimate the posterior cardinality distribution of points in a persistence diagram and the posterior spatial distribution simultaneously. We present a closed form of the posteriors under the assumption of Gaussian mixtures and binomials for prior intensity and cardinality respectively. Using this posterior calculation, we implement a Bayes factor algorithm to classify the actin filament networks and benchmark it against several state-of-the-art classification methods.

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Cites work

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