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.
We have previously @cite_33 @cite_4 studied geodesics between small tree-shapes in the same type of singular shape space as studied here, but most proofs have been left out. @cite_5 , we study different algorithms for computing average trees based on the QED metric. This paper extends and continues @cite_4 , giving proofs, in-depth explanations and more extensive examples illustrating the potential of the QED metric.
@cite_5 @cite_4 @cite_33
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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. 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. This paper presents a new geometric framework for analysis of planar treelike shapes for applications such as shape matching, recognition and morphology, using the geometry of the space of treelike shapes. Mathematically, the shape space is given the structure of a stratified set which is a quotient of a normed vector space with a metric inherited from the vector space norm. We give examples of geodesic paths in tree-space corresponding to fundamental deformations of small trees, and discuss how these deformations are key building blocks for understanding deformations between larger trees. We introduce a novel measure called e-four-pointscondition (e-4PC), which assigns a value e ∈ [0,1] to every metric space quantifying how close the metric is to a tree metric. Data-sets taken from real Internet measurements indicate remarkable closeness of Internet latencies to tree metrics based on this condition. We study embeddings of e-4PC metric spaces into trees and prove tight upper and lower bounds. Specifically, we show that there are constants c1 and c2 such that, (1) every metric (X,d) which satisfies the e-4PC can be embedded into a tree with distortion (1+e)c1log|X|, and (2) for every e ∈: [0,1] and any number of nodes, there is a metric space (X,d) satisfying the e-4PC that does not embed into a tree with distortion less than (1+e)c2log|X|. In addition, we prove a lower bound on approximate distance labelings of e-4PC metrics, and give tight bounds for tree embeddings with additive error guarantees. 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. This paper addresses the basic question of how well a tree can approximate distances of a metric space or a graph. Given a graph, the problem of constructing a spanning tree in a graph which strongly preserves distances in the graph is a fundamental problem in network design. We present scaling distortion embeddings where the distortion scales as a function of @math , with the guarantee that for each @math simultaneously, the distortion of a fraction @math of all pairs is bounded accordingly. Quantitatively, we prove that any finite metric space embeds into an ultrametric with scaling distortion @math . For the graph setting, we prove that any weighted graph contains a spanning tree with scaling distortion @math . These bounds are tight even for embedding into arbitrary trees. These results imply that the average distortion of the embedding is constant and that the @math distortion is @math . For probabilistic embedding into spanning trees we prove a scaling distortion of @math , which implies constant @math -distortion for every fixed @math . Y. Bartal (1996, 1998) gave a randomized polynomial time algorithm that given any n point metric G, constructs a tree T such that the expected stretch (distortion) of any edge is at most O (log n log log n). His result has found several applications and in particular has resulted in approximation algorithms for many graph optimization problems. However approximation algorithms based on his result are inherently randomized. In this paper we derandomize the use of Bartal's algorithm in the design of approximation algorithms. We give an efficient polynomial time algorithm that given a finite n point metric G, constructs O(n log n) trees and a probability distribution spl mu on them such that the expected stretch of any edge of G in a tree chosen according to spl mu is at most O(log n log log n). Our result establishes that finite metrics can be probabilistically approximated by a small number of tree metrics. We obtain the first deterministic approximation algorithms for buy-at-bulk network design and vehicle routing; in addition we subsume results from our earlier work on derandomization. Our main result is obtained by a novel view of probabilistic approximation of metric spaces as a deterministic optimization problem via linear programming. Let G= (V, E) be a connected graph endowed with the standard graph-metric dGand in which longest induced simple cycle has length? (G). We prove that there exists a tree T= (V,F ) such that| dG(u, v) ?dT(u, v)| ? ??(G)2? +?for all vertices u, v?V, where?= 1 if ?(G) ?= 4, 5 and ?= 2 otherwise. The case ?(G) = 3 (i.e., G is a chordal graph) has been considered in Brandstadt, Chepoi, and Dragan, (1999) J.Algorithms 30. The proof contains an efficient algorithm for determining such a treeT . A prominent tool in many problems involving metric spaces is a notion of randomized low-diameter decomposition. Loosely speaking, ( )-decomposition refers to a probability distribution over partitions of the metric into sets of low diameter, such that nearby points (parameterized by ( >0 )) are likely to be “clustered” together. Applying this notion to the shortest-path metric in edge-weighted graphs, it is known that n-vertex graphs admit an (O( n) )-padded decomposition (Bartal, 37th annual symposium on foundations of computer science. IEEE, pp 184–193, 1996), and that excluded-minor graphs admit O(1)-padded decomposition (, 25th annual ACM symposium on theory of computing, pp 682–690, 1993; Fakcharoenphol and Talwar, J Comput Syst Sci 69(3), 485–497, 2004; , Proceedings of the 46th annual ACM symposium on theory of computing. STOC ’14, pp 79–88. ACM, New York, NY, USA, 2014). We design decompositions to the family of p-path-separable graphs, which was defined by Abraham and Gavoille (Proceedings of the twenty-fifth annual acm symposium on principles of distributed computing, PODC ’06, pp 188–197, 2006) and refers to graphs that admit vertex-separators consisting of at most p shortest paths in the graph. Our main result is that every p-path-separable n-vertex graph admits an (O( (p n)) )-decomposition, which refines the (O( n) ) bound for general graphs, and provides new bounds for families like bounded-treewidth graphs. Technically, our clustering process differs from previous ones by working in (the shortest-path metric of) carefully chosen subgraphs. The metric Ramsey problem asks for the largest subset S of a metric space that can be embedded into an ultrametric (more generally into a Hilbert space) with a given distortion. Study of this problem was motivated as a non-linear version of Dvoretzky theorem. Mendel and Naor [MN07] devised the so called Ramsey Partitions to address this problem, and showed the algorithmic applications of their techniques to approximate distance oracles and ranking problems. In this paper we study the natural extension of the metric Ramsey problem to graphs, and introduce the notion of Ramsey Spanning Trees. We ask for the largest subset S ⊆ V of a given graph G = (V, E), such that there exists a spanning tree of G that has small stretch for S. Applied iteratively, this provides a small collection of spanning trees, such that each vertex has a tree providing low stretch paths to all other vertices. The union of these trees serves as a special type of spanner, a tree-padding spanner. We use this spanner to devise the first compact stateless routing scheme with O(1) routing decision time, and labels which are much shorter than in all currently existing schemes. We first revisit the metric Ramsey problem, and provide a new deterministic construction. We prove that for every k, any n-point metric space has a subset S of size at least n1--1 k which embeds into an ultrametric with distortion 8k. We use this result to obtain the state-of-the-art deterministic construction of a distance oracle. Building on this result, we prove that for every k, any n-vertex graph G = (V, E) has a subset S of size at least n1--1 k, and a spanning tree of G, that has stretch O(k log log n) between any point in S and any point in V. We consider the problem of embedding general metrics into trees. We give the first non-trivial approximation algorithm for minimizing the multiplicative distortion. Our algorithm produces an embedding with distortion (c log n)O(√log Δ), where c is the optimal distortion, and Δ is the spread of the metric (i.e. the ratio of the diameter over the minimum distance). We give an improved O(1)-approximation algorithm for the case where the input is the shortest path metric over an unweighted graph. Moreover, we show that by composing our approximation algorithm for embedding general metrics into trees, with the approximation algorithm of [BCIS05] for embedding trees into the line, we obtain an improved approximation algorithm for embedding general metrics into the line. We also provide almost tight bounds for the relation between embedding into trees and embedding into spanning subtrees. We show that for any unweighted graph G, the ratio of the distortion required to embed G into a spanning subtree, over the distortion of an optimal tree embedding of G, is at most O(log n). We complement this bound by exhibiting a family of graphs for which the ratio is Ω(log n log log n). 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. For similarity search in high-dimensional vector spaces (or ‘HDVSs’), researchers have proposed a number of new methods (or adaptations of existing methods) based, in the main, on data-space partitioning. However, the performance of these methods generally degrades as dimensionality increases. Although this phenomenon-known as the ‘dimensional curse’-is well known, little or no quantitative a.nalysis of the phenomenon is available. In this paper, we provide a detailed analysis of partitioning and clustering techniques for similarity search in HDVSs. We show formally that these methods exhibit linear complexity at high dimensionality, and that existing methods are outperformed on average by a simple sequential scan if the number of dimensions exceeds around 10. Consequently, we come up with an alternative organization based on approximations to make the unavoidable sequential scan as fast as possible. We describe a simple vector approximation scheme, called VA-file, and report on an experimental evaluation of this and of two tree-based index methods (an R*-tree and an X-tree). We consider the Erdős–Renyi random graph G(n, p) inside the critical window, that is when p = 1 n + λn −4 3, for some fixed ( R ) . We prove that the sequence of connected components of G(n, p), considered as metric spaces using the graph distance rescaled by n −1 3, converges towards a sequence of continuous compact metric spaces. The result relies on a bijection between graphs and certain marked random walks, and the theory of continuum random trees. Our result gives access to the answers to a great many questions about distances in critical random graphs. In particular, we deduce that the diameter of G(n, p) rescaled by n −1 3 converges in distribution to an absolutely continuous random variable with finite mean. This paper establishes information-theoretic limits for estimating a finite-field low-rank matrix given random linear measurements of it. These linear measurements are obtained by taking inner products of the low-rank matrix with random sensing matrices. Necessary and sufficient conditions on the number of measurements required are provided. It is shown that these conditions are sharp and the minimum-rank decoder is asymptotically optimal. The reliability function of this decoder is also derived by appealing to de Caen's lower bound on the probability of a union. The sufficient condition also holds when the sensing matrices are sparse-a scenario that may be amenable to efficient decoding. More precisely, it is shown that if the n × n-sensing matrices contain, on average, Ω(nlog n) entries, the number of measurements required is the same as that when the sensing matrices are dense and contain entries drawn uniformly at random from the field. Analogies are drawn between the aforementioned results and rank-metric codes in the coding theory literature. In fact, we are also strongly motivated by understanding when minimum rank distance decoding of random rank-metric codes succeeds. To this end, we derive minimum distance properties of equiprobable and sparse rank-metric codes. These distance properties provide a precise geometric interpretation of the fact that the sparse ensemble requires as few measurements as the dense one. This paper provides a novel technique for the analysis of randomized algorithms for optimization problems on metric spaces, by relating the randomized performance ratio for any, metric space to the randomized performance ratio for a set of "simple" metric spaces. We define a notion of a set of metric spaces that probabilistically-approximates another metric space. We prove that any metric space can be probabilistically-approximated by hierarchically well-separated trees (HST) with a polylogarithmic distortion. These metric spaces are "simple" as being: (1) tree metrics; (2) natural for applying a divide-and-conquer algorithmic approach. The technique presented is of particular interest in the context of on-line computation. A large number of on-line algorithmic problems, including metrical task systems, server problems, distributed paging, and dynamic storage rearrangement are defined in terms of some metric space. Typically for these problems, there are linear lower bounds on the competitive ratio of deterministic algorithms. Although randomization against an oblivious adversary has the potential of overcoming these high ratios, very little progress has been made in the analysis. We demonstrate the use of our technique by obtaining substantially improved results for two different on-line problems. Abstract A metric on general phylogenetic trees is presented. This extends the work of most previous authors, who constructed metrics for binary trees. The metric presented in this paper makes possible the comparison of the many nonbinary phylogenetic trees appearing in the literature. This provides an objective procedure for comparing the different methods for constructing phylogenetic trees. The metric is based on elementary operations which transform one tree into another. Various results obtained in applying these operations are given. They enable the distance between any pair of trees to be calculated efficiently. This generalizes previous work by Bourque to the case where interior vertices can be labeled, and labels may contain more than one element or may be empty. Let G = (V,E) be an undirected weighted graph with vVv = n and vEv = m. Let k ≥ 1 be an integer. We show that G = (V,E) can be preprocessed in O(kmn1 k) expected time, constructing a data structure of size O(kn1p1 k), such that any subsequent distance query can be answered, approximately, in O(k) time. The approximate distance returned is of stretch at most 2k−1, that is, the quotient obtained by dividing the estimated distance by the actual distance lies between 1 and 2k−1. A 1963 girth conjecture of Erdos, implies that Ω(n1p1 k) space is needed in the worst case for any real stretch strictly smaller than 2kp1. The space requirement of our algorithm is, therefore, essentially optimal. The most impressive feature of our data structure is its constant query time, hence the name "oracle". Previously, data structures that used only O(n1p1 k) space had a query time of Ω(n1 k).Our algorithms are extremely simple and easy to implement efficiently. They also provide faster constructions of sparse spanners of weighted graphs, and improved tree covers and distance labelings of weighted or unweighted graphs. We study the metric properties of finite subsets of L1. The analysis of such metrics is central to a number of important algorithmic problems involving the cut structure of weighted graphs, including the Sparsest Cut Problem, one of the most compelling open problems in the field of approximation algorithms. Additionally, many open questions in geometric non-linear functional analysis involve the properties of finite subsets of L1.We present some new observations concerning the relation of L1 to dimension, topology, and Euclidean distortion. We show that every n-point subset of L1 embeds into L2 with average distortion O(√log n), yielding the first evidence that the conjectured worst-case bound of O(√log n) is valid. We also address the issue of dimension reduction in Lp for p ∈ (1, 2). We resolve a question left open by M. Charikar and A. Sahai [Dimension reduction in the l1 norm, in: Proceedings of the 43rd Annual IEEE Conference on Foundations of Computer Science, ACM, 2002, pp. 251-260] concerning the impossibility of dimension reduction with a linear map in the above cases, and we show that a natural variant of the recent example of Brinkman and Charikar [On the impossibility of dimension reduction in l1, in: Proceedings of the 44th Annual IEEE Conference on Foundations of Computer Science, ACM, 2003, pp. 514-523], cannot be used to prove a lower bound for the non-linear case. This is acomplished by exhibiting constant-distortion embeddings of snowflaked planar metrics into Euclidean space. We consider the computational problem of finding nearest neighbors in general metric spaces. Of particular interest are spaces that may not be conveniently embedded or approximated in Euclidian space, or where the dimensionality of a Euclidian representation 1s very high. Also relevant are high-dimensional Euclidian settings in which the distribution of data is in some sense of lower dimension and embedded in the space. The up-tree (vantage point tree) is introduced in several forms, together‘ with &&ciated algorithms, as an improved method for these difficult search nroblems. Tree construcI tion executes in O(nlog(n i ) time, and search is under certain circumstances and in the imit, O(log(n)) expected time. The theoretical basis for this approach is developed and the results of several experiments are reported. In Euclidian cases, kd-tree performance is compared.