Bayesian matching of unlabeled marked point sets using random fields, with an application to molecular alignment

DOI10.1214/11-AOAS486zbMATH Open1234.62141arXiv1203.0098WikidataQ58419229 ScholiaQ58419229MaRDI QIDQ766002FDOQ766002

Authors: Irina Czogiel, Ian L. Dryden, Christopher J. Brignell 

Publication date: 22 March 2012

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

Abstract: Statistical methodology is proposed for comparing unlabeled marked point sets, with an application to aligning steroid molecules in chemoinformatics. Methods from statistical shape analysis are combined with techniques for predicting random fields in spatial statistics in order to define a suitable measure of similarity between two marked point sets. Bayesian modeling of the predicted field overlap between pairs of point sets is proposed, and posterior inference of the alignment is carried out using Markov chain Monte Carlo simulation. By representing the fields in reproducing kernel Hilbert spaces, the degree of overlap can be computed without expensive numerical integration. Superimposing entire fields rather than the configuration matrices of point coordinates thereby avoids the problem that there is usually no clear one-to-one correspondence between the points. In addition, mask parameters are introduced in the model, so that partial matching of the marked point sets can be carried out. We also propose an adaptation of the generalized Procrustes analysis algorithm for the simultaneous alignment of multiple point sets. The methodology is illustrated with a simulation study and then applied to a data set of 31 steroid molecules, where the relationship between shape and binding activity to the corticosteroid binding globulin receptor is explored.

Full work available at URL: https://arxiv.org/abs/1203.0098

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zbMATH Keywords

spatialMarkov chain Monte Carloreproducing kernel Hilbert spaceshapesizeKrigingbioinformaticschemoinformaticsProcrustessteroids

Mathematics Subject Classification ID

Bayesian inference (62F15) Inference from spatial processes (62M30) Random fields; image analysis (62M40) Applications of statistics to biology and medical sciences; meta analysis (62P10) Numerical analysis or methods applied to Markov chains (65C40) Biochemistry, molecular biology (92C40) Applications of functional analysis in probability theory and statistics (46N30)

Cites Work

• Optimization by simulated annealing
• Interpolation of spatial data. Some theory for kriging
• Title not available (Why is that?)
• Bayesian alignment using hierarchical models, with applications in protein bioinformatics
• Theory of Reproducing Kernels
• Title not available (Why is that?)
• Title not available (Why is that?)
• An Approach to Statistical Spatial-Temporal Modeling of Meteorological Fields
• Local Maxima and the Expected Euler Characteristic of Excursion Sets of χ ², F and t Fields
• Random fields of multivariate test statistics, with applications to shape analysis
• Statistical Analysis of Unlabeled Point Sets: Comparing Molecules in Chemoinformatics
• Bayesian matching of unlabeled marked point sets using random fields, with an application to molecular alignment
• Title not available (Why is that?)

Cited In (11)

• Matching markers and unlabeled configurations in protein gels
• Bayesian matching of unlabeled point sets using Procrustes and configuration models
• Bayesian size-and-shape regression modelling
• Spatial Matching of Multiple Configurations of Points with a Bioinformatics Application
• Bayesian alignment of proteins via Delaunay tetrahedralization
• Bayesian comparison of protein structures using partial Procrustes distance
• Statistical Analysis of Unlabeled Point Sets: Comparing Molecules in Chemoinformatics
• Bayesian registration of functions and curves
• Unlabelled landmark matching via Bayesian data selection, and application to cell matching across imaging modalities
• Multinomial principal component logistic regression on shape data
• Bayesian matching of unlabeled marked point sets using random fields, with an application to molecular alignment

Uses Software

• R

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