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81
The geometry of graphs and some of its algorithmic applications
 Combinatorica
, 1995
"... In this paper we explore some implications of viewing graphs as geometric objects. This approach offers a new perspective on a number of graphtheoretic and algorithmic problems. There are several ways to model graphs geometrically and our main concern here is with geometric representations that r ..."
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Cited by 457 (19 self)
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In this paper we explore some implications of viewing graphs as geometric objects. This approach offers a new perspective on a number of graphtheoretic and algorithmic problems. There are several ways to model graphs geometrically and our main concern here is with geometric representations that respect the metric of the (possibly weighted) graph. Given a graph G we map its vertices to a normed space in an attempt to (i) Keep down the dimension of the host space and (ii) Guarantee a small distortion, i.e., make sure that distances between vertices in G closely match the distances between their geometric images. In this paper we develop efficient algorithms for embedding graphs lowdimensionally with a small distortion. Further algorithmic applications include: 0 A simple, unified approach to a number of problems on multicommodity flows, including the LeightonRae Theorem [29] and some of its extensions. 0 For graphs embeddable in lowdimensional spaces with a small distortion, we can find lowdiameter decompositions (in the sense of [4] and [34]). The parameters of the decomposition depend only on the dimension and the distortion and not on the size of the graph. 0 In graphs embedded this way, small balanced separators can be found efficiently. Faithful lowdimensional representations of statistical data allow for meaningful and efficient clustering, which is one of the most basic tasks in patternrecognition. For the (mostly heuristic) methods used
Mesh Generation And Optimal Triangulation
, 1992
"... We survey the computational geometry relevant to finite element mesh generation. We especially focus on optimal triangulations of geometric domains in two and threedimensions. An optimal triangulation is a partition of the domain into triangles or tetrahedra, that is best according to some cri ..."
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Cited by 180 (8 self)
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We survey the computational geometry relevant to finite element mesh generation. We especially focus on optimal triangulations of geometric domains in two and threedimensions. An optimal triangulation is a partition of the domain into triangles or tetrahedra, that is best according to some criterion that measures the size, shape, or number of triangles. We discuss algorithms both for the optimization of triangulations on a fixed set of vertices and for the placement of new vertices (Steiner points). We briefly survey the heuristic algorithms used in some practical mesh generators.
A Survey of Combinatorial Gray Codes
 SIAM Review
, 1996
"... The term combinatorial Gray code was introduced in 1980 to refer to any method for generating combinatorial objects so that successive objects differ in some prespecified, small way. This notion generalizes the classical binary reflected Gray code scheme for listing nbit binary numbers so that ..."
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Cited by 81 (2 self)
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The term combinatorial Gray code was introduced in 1980 to refer to any method for generating combinatorial objects so that successive objects differ in some prespecified, small way. This notion generalizes the classical binary reflected Gray code scheme for listing nbit binary numbers so that successive numbers differ in exactly one bit position, as well as work in the 1960's and 70's on minimal change listings for other combinatorial families, including permutations and combinations. The area of combinatorial Gray codes was popularized by Herbert Wilf in his invited address at the SIAM Discrete Mathematics Conference in 1988 and his subsequent SIAM monograph in which he posed some open problems and variations on the theme. This resulted in much recent activity in the area and most of the problems posed by Wilf are now solved. In this paper, we survey the area of combinatorial Gray codes, describe recent results, variations, and trends, and highlight some open problems. ...
Geometry of the Space of Phylogenetic Trees
 Adv. in Appl. Math
, 1999
"... ields to graphically represent various types of hierarchical relationships, including evolutionary relationships between species, divergent patterns between subpopulations and evolutionary relationships between genes. These trees are generally rooted and semilabeled, i.e., they descend from a singl ..."
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Cited by 77 (1 self)
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ields to graphically represent various types of hierarchical relationships, including evolutionary relationships between species, divergent patterns between subpopulations and evolutionary relationships between genes. These trees are generally rooted and semilabeled, i.e., they descend from a single node called the root, bifurcate at lower nodes and end at terminal nodes, called tips or leaves; the leaves are labeled by the names of the species, subpopulations or genes being studied. In biological studies the latter are called operational taxonomic units (OTU's). Traditionally, trees were inferred form morphological similarities among the OTU's. To build an evolutionary species tree, or phylogenetic tree, two species which shared the most characteristics were classified as `siblings' and assumed to share a common ancestor which is not the ancestor of any other species. Such `siblings' are said to be homologous, and it is this basic homo
On the Dynamic Finger Conjecture for Splay Trees. Part II: The Proof
 SIAM Journal on Computing
"... The following result is shown: On an nnode splay tree, the amortized cost of an access at distance d from the preceding access is O(log(d + 1)). In addition, there is an O(n) initialization cost. The accesses include searches, insertions and deletions. 1 Introduction The reader is advised that ..."
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Cited by 45 (1 self)
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The following result is shown: On an nnode splay tree, the amortized cost of an access at distance d from the preceding access is O(log(d + 1)). In addition, there is an O(n) initialization cost. The accesses include searches, insertions and deletions. 1 Introduction The reader is advised that this paper quotes results from the companion Part I paper [CMSS93]; in addition, the Part I paper introduces a number of the techniques used here, but in a somewhat less involved way. The splay tree is a selfadjusting binary search tree devised by Sleator and Tarjan [ST85]. They showed that it is competitive with many of the balanced search tree schemes for maintaining a dictionary. Specifically, Sleator and Tarjan showed that a sequence of m accesses performed on a splay tree takes time O(m log n), where n is the maximum size attained by the tree (n m). They also showed that in an amortized sense, up to a constant factor, on sufficiently long sequences of searches, the splay tree has as ...
Tractability of Parameterized Completion Problems on Chordal, Strongly Chordal and Proper Interval Graphs
, 1994
"... We study the parameterized complexity of three NPhard graph completion problems. The MINIMUM FILLIN problem is to decide if a graph can be triangulated by adding at most k edges. We develop O(c m) and O(k mn + f(k)) algorithms for this problem on a graph with n vertices and m edges. Here f(k ..."
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Cited by 40 (5 self)
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We study the parameterized complexity of three NPhard graph completion problems. The MINIMUM FILLIN problem is to decide if a graph can be triangulated by adding at most k edges. We develop O(c m) and O(k mn + f(k)) algorithms for this problem on a graph with n vertices and m edges. Here f(k) is exponential in k and the constants hidden by the bigO notation are small and do not depend on k. In particular, this implies that the problem is fixedparameter tractable (FPT). The PROPER
Dynamic Ray Shooting and Shortest Paths in Planar Subdivisions via Balanced Geodesic Triangulations
 J. Algorithms
, 1997
"... We give new methods for maintaining a data structure that supports ray shooting and shortest path queries in a dynamicallychanging connected planar subdivision S. Our approach is based on a new dynamic method for maintaining a balanced decomposition of a simple polygon via geodesic triangles. We ma ..."
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Cited by 39 (4 self)
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We give new methods for maintaining a data structure that supports ray shooting and shortest path queries in a dynamicallychanging connected planar subdivision S. Our approach is based on a new dynamic method for maintaining a balanced decomposition of a simple polygon via geodesic triangles. We maintain such triangulations by viewing their dual trees as balanced trees. We show that rotations in these trees can be implemented via a simple "diagonal swapping" operation performed on the corresponding geodesic triangles, and that edge insertion and deletion can be implemented on these trees using operations akin to the standard split and splice operations. We also maintain a dynamic point location structure on the geodesic triangulation, so that we may implement ray shooting queries by first locating the ray's endpoint and then walking along the ray from geodesic triangle to geodesic triangle until we hit the boundary of some region of S. The shortest path between two points in the same ...
Flipping Edges on Triangulations
, 1996
"... In this paper we study the problem of flipping edges in triangulations of polygons and point sets. We prove that if a polygon Q n has k reflex vertices, then any triangulation of Q n can be transformed to another triangulation of Q n with at most O(n + k 2 ) flips. We produce examples of polygons ..."
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Cited by 39 (7 self)
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In this paper we study the problem of flipping edges in triangulations of polygons and point sets. We prove that if a polygon Q n has k reflex vertices, then any triangulation of Q n can be transformed to another triangulation of Q n with at most O(n + k 2 ) flips. We produce examples of polygons with two triangulations T and T such that to transform T to T requires O(n 2 ) flips. These results are then extended to triangulations of point sets. We also show that any triangulation of an n point set always has n  4 2 edges that can be flipped. 1. Introduction Let P n = {v 1 , ..., v n } be a collection of points on the plane. A triangulation of P n is a partitioning of the convex hull Conv(P n ) of P n into a set of triangles T = {t 1 , ..., t m } with disjoint interiors in such a way that the vertices of each triangle t of T are points of P n . The elements of P n will be called the vertices of T and the edges of the triangles t 1 , ..., t m of T will be called the edges...
Ribbon graphs, quadratic differentials on Riemann surfaces, and algebraic curves defined over Q, Asian
 Journal of Mathematics
, 1998
"... Abstract. It is well known that there is a bijective correspondence between metric ribbon graphs and compact Riemann surfaces with meromorphic Strebel differentials. In this article, we prove that Grothendieck’s correspondence between dessins d’enfants and Belyi morphisms is a special case of this c ..."
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Cited by 37 (9 self)
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Abstract. It is well known that there is a bijective correspondence between metric ribbon graphs and compact Riemann surfaces with meromorphic Strebel differentials. In this article, we prove that Grothendieck’s correspondence between dessins d’enfants and Belyi morphisms is a special case of this correspondence through an explicit construction of Strebel differentials. For a metric ribbon graph with edge length 1, an algebraic curve over Q and a Strebel differential on it is constructed. It is also shown that the critical trajectories of the measured foliation that is determined by the Strebel differential recover the original metric ribbon graph. Conversely, for every Belyi morphism, a unique Strebel differential is constructed such that the critical leaves of the measured foliation it determines form a metric ribbon graph of edge length 1,
On Distances between Phylogenetic Trees
, 1997
"... Different phylogenetic trees for the same group of species are often produced either by procedures that use diverse optimality criteria [18] or from different genes [12] in the study of molecular evolution. Comparing these trees to find their similarities (e.g. agreement or consensus) and dissimila ..."
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Cited by 36 (9 self)
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Different phylogenetic trees for the same group of species are often produced either by procedures that use diverse optimality criteria [18] or from different genes [12] in the study of molecular evolution. Comparing these trees to find their similarities (e.g. agreement or consensus) and dissimilarities, i.e. distance, is thus an important issue in computational molecular biology. The nearest neighbor interchange (nni) distance [26, 24, 32, 4, 5, 3, 16, 17, 19, 30, 20, 21, 23] and the subtreetransfer distance [12, 13, 15] are two major distance metrics that have been proposed and extensively studied for different reasons. Despite their many appealing aspects such as simplicity and sensitivity to tree topologies, computing these distances has remained very challenging. This article studies the complexity and efficient approximation algorithms for computing the nni distance and a natural extension of the subtreetransfer distance, called the linearcost subtreetransfer distance. The ...