In order to develop statistical methods for shapes with a tree-structure, we construct a shape space framework for tree-like shapes and study metrics on the shape space. This shape space has singularities, corresponding to topological transitions in the represented trees. We study two closely related metrics on the shape space, TED and QED. QED is a quotient Euclidean distance arising naturally from the shape space formulation, while TED is the classical tree edit distance. Using Gromov's metric geometry we gain new insight into the geometries defined by TED and QED. We show that the new metric QED has nice geometric properties which facilitate statistical analysis, such as existence and local uniqueness of geodesics and averages. TED, on the other hand, does not share the geometric advantages of QED, but has nice algorithmic properties. We provide a theoretical framework and experimental results on synthetic data trees as well as airway trees from pulmonary CT scans. This way, we effectively illustrate that our framework has both the theoretical and qualitative properties necessary to build a theory of statistical tree-shape analysis.
Statistics on tree-shaped objects receive growing interest in the statistical community. Wang and Marron @cite_18 study metric spaces of trees and define a notion of average tree called the median-mean as well as a version of PCA, which finds modes of variation in terms of , encoding the maximum amount of structural and attributal variation. @cite_6 extend this work by finding efficient algorithms for PCA. This is applied to analysis of brain blood vessels. The metric defined by Wang and Marron does not give a natural geodesic structure on the space of trees, as it places a large emphasis on the tree-topological structure of the trees. The metric has discontinuities in the sense that a sequence of trees with a shrinking branch will not converge to a tree that does not have that branch. Such a metric is not suitable for studying trees with continuous topological variations and noise, such as anatomical tree-structures extracted from medical images, since the emphasis on topology makes the metric sensitive to structural noise.
@cite_18 @cite_6
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In order to develop statistical methods for shapes with a tree-structure, we construct a shape space framework for treelike shapes and study metrics on the shape space. The shape space has singularities, which correspond to topological transitions in the represented trees. We study two closely related metrics, TED and QED. The QED is a quotient euclidean distance arising from the new shape space formulation, while TED is essentially the classical tree edit distance. Using Gromov's metric geometry we gain new insight into the geometries defined by TED and QED. In particular, we show that the new metric QED has nice geometric properties which facilitate statistical analysis, such as existence and local uniqueness of geodesics and averages. TED, on the other hand, has algorithmic advantages, while it does not share the geometric strongpoints of QED. We provide a theoretical framework as well as computational results such as matching of airway trees from pulmonary CT scans and geodesics between synthetic data trees illustrating the dynamic and geometric properties of the QED metric. We study distorted metrics on binary trees in the context of phylogenetic reconstruction. Given a binary tree T on n leaves with a path metric d, consider the pairwise distances d(u,v) between leaves. It is well known that these determine the tree and the d length of all edges. Here, we consider distortions @math of d such that, for all leaves u and v, it holds that @math if either d(u,v)< M + f 2 or @math , where d satisfies f ≤ d(e) ≤ g for all edges e. Given such distortions, we show how to reconstruct in polynomial time a forest T1, ... ,Tα such that the true tree T may be obtained from that forest by adding α-1 edges and α-1 ≤ 2-Ω(M g) n. Our distorted metric result implies a reconstruction algorithm of phylogenetic forests with a small number of trees from sequences of length logarithmic in the number of species. The reconstruction algorithm is applicable for the general Markov model. Both the distorted metric result and its applications to phylogeny are almost tight. Given dissimilarity data on pairs of objects in a set, we study the problem of fitting a tree metric to this data so as to minimize additive error (i.e. some measure of the difference between the tree metric and the given data). This problem arises in constructing an M-level hierarchical clustering of objects (or an ultrametric on objects) so as to match the given dissimilarity data - a basic problem in statistics. Viewed in this way, the problem is a generalization of the correlation clustering problem (which corresponds to M = 1). We give a very simple randomized combinatorial algorithm for the M-level hierarchical clustering problem that achieves an approximation ratio of M+2. This is a generalization of a previous factor 3 algorithm for correlation clustering on complete graphs. The problem of fitting tree metrics also arises in phylogeny where the objective is to learn the evolution tree by fitting a tree to dissimilarity data on taxa. The quality of the fit is measured by taking the l sub p norm of the difference between the tree metric constructed and the given data. Previous results obtained a factor 3 approximation for finding the closest tree tree metric under the l spl infin norm. No nontrivial approximation for general l sub p norms was known before. We present a novel LP formulation for this problem and obtain an O((log n log log n) sup 1 p ) approximation using this. Enroute, we obtain an O((log n log log n) sup 1 p ) approximation for the closest ultrametric under the l sub p norm. Our techniques are based on representing and viewing an ultrametric as a hierarchy of clusterings, and may be useful in other contexts. In this paper, we show that any n point metric space can be embedded into a distribution over dominating tree metrics such that the expected stretch of any edge is O(log n). This improves upon the result of Bartal who gave a bound of O(log n log log n). Moreover, our result is existentially tight; there exist metric spaces where any tree embedding must have distortion Ω(log n)-distortion. This problem lies at the heart of numerous approximation and online algorithms including ones for group Steiner tree, metric labeling, buy-at-bulk network design and metrical task system. Our result improves the performance guarantees for all of these problems.