Persistent Homology Analysis of Brain Artery Trees.
@article{Bendich2016PersistentHA, title={Persistent Homology Analysis of Brain Artery Trees.}, author={Paul Bendich and J. S. Marron and Ezra Miller and Alex Pieloch and Sean Skwerer}, journal={The annals of applied statistics}, year={2016}, volume={10 1}, pages={ 198-218 } }
New representations of tree-structured data objects, using ideas from topological data analysis, enable improved statistical analyses of a population of brain artery trees. A number of representations of each data tree arise from persistence diagrams that quantify branching and looping of vessels at multiple scales. Novel approaches to the statistical analysis, through various summaries of the persistence diagrams, lead to heightened correlations with covariates such as age and sex, relative to…
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References
SHOWING 1-10 OF 43 REFERENCES
Tree-Oriented Analysis of Brain Artery Structure
- BiologyJournal of Mathematical Imaging and Vision
- 2013
This analysis of MRA data shows a statistically significant effect of age and sex on brain artery structure, and variation in the proximity of brain arteries to the cortical surface results in strong statistical difference between sexes and statistically significant age effect.
Functional Data Analysis of Tree Data Objects
- Computer ScienceJournal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America
- 2014
This article establishment of a connection between tree-data spaces and the well-developed area of functional data analysis (FDA), where the data objects are curves, through two tree representation approaches, the Dyck path representation and the branch length representation.
A Principal Component Analysis for Trees
- Computer Science
- 2008
An analog of Principal Component Analysis for trees is developed, based on the notion of tree-lines, and numerically fast algorithms are proposed to solve the resulting optimization problems.
Homological scaffolds of brain functional networks
- Computer ScienceJournal of The Royal Society Interface
- 2014
The results show that the homological structure of the brain's functional patterns undergoes a dramatic change post-psilocybin, characterized by the appearance of many transient structures of low stability and of a small number of persistent ones that are not observed in the case of placebo.
A Nonparametric Regression Model With Tree-Structured Response
- Computer Science, Mathematics
- 2012
The notion of nonparametric regression is generalized to the case of a tree-structured response variable and the proposed method to analyze a dataset of human brain artery trees is implemented.
Exploring uses of persistent homology for statistical analysis of landmark-based shape data
- PhysicsJ. Multivar. Anal.
- 2010
Object oriented data analysis: Sets of trees
- Mathematics
- 2007
Object oriented data analysis is the statistical analysis of populations of complex objects. In the special case of functional data analysis, these data objects are curves, where standard Euclidean…
Statistical topological data analysis using persistence landscapes
- MathematicsJ. Mach. Learn. Res.
- 2015
A new topological summary for data that is easy to combine with tools from statistics and machine learning and obeys a strong law of large numbers and a central limit theorem is defined.
Digital reconstruction and morphometric analysis of human brain arterial vasculature from magnetic resonance angiography
- BiologyNeuroImage
- 2013
Principal components analysis in the space of phylogenetic trees
- Biology
- 2011
A novel geometrical approach to PCA in tree-space that constructs the first principal path in an analogous way to standard linear Euclidean PCA is described, illustrated by application to simulated sets of trees and to a set of gene trees from metazoan (animal) species.