Torus principal component analysis with applications to RNA structure

DOI10.1214/17-AOAS1115zbMATH Open1405.62173arXiv1511.04993OpenAlexW2964281304WikidataQ59883073 ScholiaQ59883073MaRDI QIDQ1624855FDOQ1624855

Stephan F. Huckemann, Kanti V. Mardia, Benjamin Eltzner

Publication date: 16 November 2018

Published in: The Annals of Applied Statistics (Search for Journal in Brave)

Abstract: There are several cutting edge applications needing PCA methods for data on tori and we propose a novel torus-PCA method with important properties that can be generally applied. There are two existing general methods: tangent space PCA and geodesic PCA. However, unlike tangent space PCA, our torus-PCA honors the cyclic topology of the data space whereas, unlike geodesic PCA, our torus-PCA produces a variety of non-winding, non-dense descriptors. This is achieved by deforming tori into spheres and then using a variant of the recently developed principle nested spheres analysis. This PCA analysis involves a step of small sphere fitting and we provide an improved test to avoid overfitting. However, deforming tori into spheres creates singularities. We introduce a data-adaptive pre-clustering technique to keep the singularities away from the data. For the frequently encountered case that the residual variance around the PCA main component is small, we use a post-mode hunting technique for more fine-grained clustering. Thus in general, there are three successive interrelated key steps of torus-PCA in practice: pre-clustering, deformation, and post-mode hunting. We illustrate our method with two recently studied RNA structure (tori) data sets: one is a small RNA data set which is established as the benchmark for PCA and we validate our method through this data. Another is a large RNA data set (containing the small RNA data set) for which we show that our method provides interpretable principal components as well as giving further insight into its structure.

Full work available at URL: https://arxiv.org/abs/1511.04993

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zbMATH Keywords

dimension reductiondirectional statisticsdihedral anglesstatistics on manifoldsfitting small spheresprincipal nested spheres analysistori deformation

Mathematics Subject Classification ID

Factor analysis and principal components; correspondence analysis (62H25) Applications of statistics to biology and medical sciences; meta analysis (62P10) Applications of differential geometry to physics (53Z05)

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Cited In (21)

• Finite Mixtures of Multivariate Wrapped Normal Distributions for Model Based Clustering of p -Torus Data
• Comments on: ``Recent advances in directional statistics
• Rejoinder on: ``Recent advances in directional statistics
• An infinitesimal probabilistic model for principal component analysis of manifold valued data
• Estimation of parameters in multivariate wrapped models for data on a \(p\)-torus
• Principal Boundary on Riemannian Manifolds
• Recent advances in directional statistics
• Statistics for data with geometric structure. Abstracts from the workshop held January 21--27, 2018
• Principal component analysis and clustering on manifolds
• Scaled Torus Principal Component Analysis
• Rejoinder: Fitting a folded normal distribution without EM
• Random Fixed Boundary Flows
• Kurtosis test of modality for rotationally symmetric distributions on hyperspheres
• Density estimation for toroidal data using semiparametric mixtures
• Tukey’s Depth for Object Data
• Toroidal PCA via density ridges
• Statistical Methods Generalizing Principal Component Analysis to Non-Euclidean Spaces
• Clustering on the torus by conformal prediction
• Response to `Fitting a folded normal distribution without EM'
• Functional random effects modeling of brain shape and connectivity
• Data analysis on nonstandard spaces

Uses Software

• GeoPCA
• MolProbity

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