Optimal Partition Trees

We revisit one of the most fundamental classes of data structure problems in computational geometry: range searching. Matoušek (Discrete Comput. Geom. 10:157–182, 1993) gave a partition tree method for d-dimensional simplex range searching achieving O(n) space and O(n ^1−1/d ) query time. Although this method is generally believed to be optimal, it is complicated and requires O(n ^1+ε ) preprocessing time for any fixed ε>0. An earlier method by Matoušek (Discrete Comput. Geom. 8:315–334, 1992) requires O(nlogn) preprocessing time but O(n ^1−1/d log ^O(1) n) query time. We give a new method that achieves simultaneously O(nlogn) preprocessing time, O(n) space, and O(n ^1−1/d ) query time with high probability. Our method has several advantages:

On the range maximum-sum segment query problem

The range minimum query problem, RMQ for short, is to preprocess a sequence of real numbers A[1…n] for subsequent queries of the form: “Given indices i, j, what is the index of the minimum value of A[i…j]?” This problem has been shown to be linearly equivalent to the LCA problem in which a tree is preprocessed for answering the lowest common ancestor of two nodes. It has also been shown that both the RMQ and LCA problems can be solved in linear preprocessing time and constant query time under the unit-cost RAM model. This paper studies a new query problem arising from the analysis of biological sequences. Specifically, we wish to answer queries of the form: “Given indices i and j, what is the maximum-sum segment of A[i…j]?” We establish the linear equivalence relation between RMQ and this new problem. As a consequence, we can solve the new query problem in linear preprocessing time and constant query time under the unit-cost RAM model. We then present alternative linear-time solutions for two other biological sequence analysis problems to demonstrate the utilities of the techniques developed in this paper.     

Preprocessing chains for fast dihedral rotations is hard or even impossible

We examine a computational geometric problem concerning the structure of polymers. We model a polymer as a polygonal chain in three dimensions. Each edge splits the polymer into two subchains, and a dihedral rotation rotates one of these subchains rigidly about the edge. The problem is to determine, given a chain, an edge, and an angle of rotation, if the motion can be performed without causing the chain to self-intersect. An Ω(nlogn) lower bound on the time complexity of this problem is known.We prove that preprocessing a chain of n edges and answering n dihedral rotation queries is 3 -hard, giving strong evidence that Ω(n²) preprocessing is required to achieve sublinear query time in the worst case. For dynamic queries, which also modify the chain if the requested dihedral rotation is feasible, we show that answering n queries is by itself 3 -hard, suggesting that sublinear query time is impossible after any amount of preprocessing.     

Extremal point queries with lines and line segments and related problems

We address a number of extremal point query problems when P is a set of n points in , d3 a constant, including the computation of the farthest point from a query line and the computation of the farthest point from each of the lines spanned by the points in P. In , we give a data structure of size O(n¹⁺), that can be constructed in O(n¹⁺) time and can report the farthest point of P from a query line segment in O(n^2/3+) time, where >0 is an arbitrarily small constant. Applications of our results also include: (1) Sub-cubic time algorithms for fitting a polygonal chain through an indexed set of points in , d3 a constant, and (2) A sub-quadratic time and space algorithm that, given P and an anchor point q, computes the minimum (maximum) area triangle defined by q with P{q}.     

Approximating the Pathway Axis and the Persistence Diagrams for a Collection of Balls in 3-Space

Given a collection ℬ of balls in a three-dimensional space, we wish to explore the cavities, voids, and tunnels in the complement space of ∪ℬ. We introduce the pathway axis of ℬ as a useful subset of the medial axis of the complement of ∪ℬ and prove that it satisfies several desirable geometric properties. We present an algorithm that constructs the pathway graph of ∪ℬ, a piecewise-linear approximation of the pathway axis. At the heart of our approach is an approximation scheme that constructs a collection K{\mathcal{K}} of same-size balls that approximate ℬ so that the Hausdorff distance between ∪ℬ and èK\bigcup{\mathcal{K}} is bounded by a prescribed parameter. We prove a bound on the ratio between the number of balls in K{\mathcal{K}} and the number of balls in ℬ. We employ this bound and the approximation scheme to show how to approximate the persistence diagrams for ∪ℬ, which can be used to extract major topological features such as the large voids and tunnels in the complement of ∪ℬ. We show that our approach is superior in terms of complexity to the standard point-sample approaches for the two problems that we address in this paper: approximating the pathway axis of ℬ and approximating the persistence diagrams for ∪ℬ. In a companion paper we introduce MolAxis, a tool for the identification of channels in macromolecules that demonstrates how the pathway graph and the persistence diagrams are used to identify plausible pathways in the complement of molecules.     

Partitioning series-parallel multigraphs into ν *-excluding edge covers

We prove that, for any given vertex ν* in a series-parallel graph G, its edge set can be partitioned into κ = min{κ′(G) + 1, δ(G)} subsets such that each subset covers all the vertices of G possibly except for ν*, where δ(G) is the minimum degree of G and κ′(G) is the edge-connectivity of G. In addition, we show that the results in this paper are best possible and a polynomial time algorithm can be obtained for actually finding such a partition by our proof.     

Steiner trees for fixed orientation metrics

We consider the problem of constructing Steiner minimum trees for a metric defined by a polygonal unit circle (corresponding to σ ≥ 2 weighted legal orientations in the plane). A linear-time algorithm to enumerate all angle configurations for degree three Steiner points is given. We provide a simple proof that the angle configuration for a Steiner point extends to all Steiner points in a full Steiner minimum tree, such that at most six orientations suffice for edges in a full Steiner minimum tree. We show that the concept of canonical forms originally introduced for the uniform orientation metric generalises to the fixed orientation metric. Finally, we give an O(σ n) time algorithm to compute a Steiner minimum tree for a given full Steiner topology with n terminal leaves.     

An exact algorithm for minimum CDS with shortest path constraint in wireless networks

In this paper, we study a minimum connected dominating set problem (CDS) in wireless networks, which selects a minimum CDS with property that all intermediate nodes inside every pairwise shortest path should be included. Such a minimum CDS (we name this problem as SPCDS) is an important tache of some other algorithms for constructing a minimum CDS. We prove that finding such a minimum SPCDS can be achieved in polynomial time and design an exact algorithm with time complexity O(δ ² n), where δ is the maximum node degree in communication graph.     

On proper secrets, (<Emphasis Type="Italic">t</Emphasis>, <Emphasis Type="Italic">k</Emphasis>)-bases and linear codes

This paper contains three parts where each part triggered and motivated the subsequent one. In the first part (Proper Secrets) we study the Shamir’s “k-out-of-n” threshold secret sharing scheme. In that scheme, the dealer generates a random polynomial of degree k−1 whose free coefficient is the secret and the private shares are point values of that polynomial. We show that the secret may, equivalently, be chosen as any other point value of the polynomial (including the point at infinity), but, on the other hand, setting the secret to be any other linear combination of the polynomial coefficients may result in an imperfect scheme. In the second part ((t, k)-bases) we define, for every pair of integers t and k such that 1 ≤ t ≤ k−1, the concepts of (t, k)-spanning sets, (t, k)-independent sets and (t, k)-bases as generalizations of the usual concepts of spanning sets, independent sets and bases in a finite-dimensional vector space. We study the relations between those notions and derive upper and lower bounds for the size of such sets. In the third part (Linear Codes) we show the relations between those notions and linear codes. Our main notion of a (t, k)-base bridges between two well-known structures: (1, k)-bases are just projective geometries, while (k−1, k)-bases correspond to maximal MDS-codes. We show how the properties of (t, k)-independence and (t, k)-spanning relate to the notions of minimum distance and covering radius of linear codes and how our results regarding the size of such sets relate to known bounds in coding theory. We conclude by comparing between the notions that we introduce here and some well known objects from projective geometry.      

Dynamic Coresets

We give a dynamic data structure that can maintain an ε-coreset of n points, with respect to the extent measure, in O(log n) time per update for any constant ε>0 and any constant dimension. The previous method by Agarwal, Har-Peled, and Varadarajan requires polylogarithmic update time. For points with integer coordinates bounded by U, we alternatively get O(log log U) time. Numerous applications follow, for example, on dynamically approximating the width, smallest enclosing cylinder, minimum bounding box, or minimum-width annulus. We can also use the same approach to maintain approximate k-centers in time O(log n) (or O(log log U) if the spread is bounded by U) for any constant k and any constant dimension. For the smallest enclosing cylinder problem, we also show that a constant-factor approximation can be maintained in O(1) randomized amortized time on the word RAM. This work has been supported by NSERC. A preliminary version of this paper has appeared in Proc. 24th ACM Sympos Comput. Geom., 2008.     

Optimal Topological Simplification of Discrete Functions on Surfaces

Given a function f on a surface and a tolerance δ>0, we construct a function f _δ subject to ‖f _δ −f‖_∞≤δ such that f _δ has a minimum number of critical points. Our construction relies on a connection between discrete Morse theory and persistent homology and completely removes homological noise with persistence ≤2δ from the input function f. The number of critical points of the resulting simplified function f _δ achieves the lower bound dictated by the stability theorem of persistent homology. We show that the simplified function can be computed in linear time after persistence pairs have been computed.     

Derived Azumaya algebras and generators for twisted derived categories

We introduce a notion of derived Azumaya algebras over ring and schemes generalizing the notion of Azumaya algebras of Grothendieck (Le groupe de Brauer. I. Algèbres d’Azumaya et interprétations diverses. Dix Exposés sur la Cohomologie des Schémas, pp. 46–66, North-Holland, Amsterdam, 1968). We prove that any such algebra B on a scheme X provides a class ϕ(B) in . We prove that for X a quasi-compact and quasi-separated scheme ϕ defines a bijective correspondence, and in particular that any class in , torsion or not, can be represented by a derived Azumaya algebra on X. Our result is a consequence of a more general theorem about the existence of compact generators in twisted derived categories, with coefficients in any local system of reasonable dg-categories, generalizing the well known existence of compact generators in derived categories of quasi-coherent sheaves of Bondal and Van Den Bergh (Mosc. Math. J. 3(1):1–36, 2003). A huge part of this paper concerns the treatment of twisted derived categories, as well as the proof that the existence of compact generator locally for the fppf topology implies the existence of a global compact generator. We present explicit examples of derived Azumaya algebras that are not represented by classical Azumaya algebras, as well as applications of our main result to the localization for twisted algebraic K-theory and to the stability of saturated dg-categories by direct push-forwards along smooth and proper maps.     

An application of coding theory to estimating Davenport constants

We investigate a certain well-established generalization of the Davenport constant. For j a positive integer (the case j = 1, is the classical one) and a finite Abelian group (G, +, 0), the invariant D _j (G) is defined as the smallest ℓ such that each sequence over G of length at least ℓ has j disjoint non-empty zero-sum subsequences. We investigate these quantities for elementary 2-groups of large rank (relative to j). Using tools from coding theory, we give fairly precise estimates for these quantities. We use our results to give improved bounds for the classical Davenport constant of certain groups.     

Segment Intersection Searching Problems in General Settings

   Abstract. We consider segment intersection searching amidst (possibly intersecting) algebraic arcs in the plane. We show how to preprocess n arcs in time O(n ^2+ɛ ) into a data structure of size O(n ^2+ɛ ) , for any ɛ >0 , such that the k arcs intersecting a query segment can be counted in time O( log n) or reported in time O( log n+k) . This problem was extensively studied in restricted settings (e.g., amidst segments, circles, or circular arcs), but no solution with comparable performance was previously presented for the general case of possibly intersecting algebraic arcs. Our data structure for the general case matches or improves (sometimes by an order of magnitude) the size of the best previously presented solutions for the special cases. As an immediate application of this result, we obtain an efficient data structure for the triangular windowing problem, which is a generalization of triangular range searching. As another application, the first substantially subquadratic algorithm for a red—blue intersection counting problem is derived. We also describe simple data structures for segment intersection searching among disjoint arcs, and for ray shooting among possibly intersecting arcs.     

A Sublinear Bipartiteness Tester for Bounded Degree Graphs

d , and the testing algorithm can perform queries of the form: ``who is the ith neighbor of vertex v'. The tester should determine with high probability whether the graph is bipartite or ε-far from bipartite for any given distance parameter ε. Distance between graphs is defined to be the fraction of entries on which the graphs differ in their incidence-lists representation. Our testing algorithm has query complexity and running time where N is the number of graph vertices. It was shown before that queries are necessary (for constant ε), and hence the performance of our algorithm is tight (in its dependence on N), up to polylogarithmic factors. In our analysis we use techniques that were previously applied to prove fast convergence of random walks on expander graphs. Here we use the contrapositive statement by which slow convergence implies small cuts in the graph, and further show that these cuts have certain additional properties. This implication is applied in showing that for any graph, the graph vertices can be divided into disjoint subsets such that: (1) the total number of edges between the different subsets is small; and (2) each subset itself exhibits a certain mixing property that is useful in our analysis. Received: February 6, 1998     

Comments on Harn–Lin’s cheating detection scheme

Detection of cheating and identification of cheaters in threshold schemes has been well studied, and several solid solutions have been provided in the literature. This paper analyses Harn and Lin’s recent work on cheating detection and identification of cheaters in Shamir’s threshold scheme. We will show that, in a broad area, Harn–Lin’s scheme fails to detect cheating and even if the cheating is detected cannot identify the cheaters. In particular, in a typical Shamir (t, n)-threshold scheme, where n = 2t − 1 and up to t − 1 of participants are corrupted, their scheme neither can detect nor can identify the cheaters. Moreover, for moderate size of groups their proposed cheaters identification scheme is not practical.     

Multigraphs with Δ ≥ 3 are Totally-(2Δ−1)-Choosable

The total graph T(G) of a multigraph G has as its vertices the set of edges and vertices of G and has an edge between two vertices if their corresponding elements are either adjacent or incident in G. We show that if G has maximum degree Δ(G), then T(G) is (2Δ(G) − 1)-choosable. We give a linear-time algorithm that produces such a coloring. The best previous general upper bound for Δ(G) > 3 was , by Borodin et al. When Δ(G) = 4, our algorithm gives a better upper bound. When Δ(G)∈{3,5,6}, our algorithm matches the best known bound. However, because our algorithm is significantly simpler, it runs in linear time (unlike the algorithm of Borodin et al.).     

Routing of single-source and multiple-source queries in static sensor networks

In this paper, we introduce new geometric ad-hoc routing algorithms to route queries in static sensor networks. For single-source-queries routing, we utilise a centralised mechanism to accomplish a query using an asymptotically optimal number of transmissions O(c), where c is the length of the shortest path between the source and the destination. For multiple-source-queries routing, the number of transmissions for each query is bounded by O(clogn), where n is the number of nodes in the network. For both single-source and multiple-source queries, the routing stage is preceded by preprocessing stages requiring O(nD) and O(n²D) transmissions, respectively, where D is the diameter of the network. Our algorithm improves the complexity of the currently best known algorithms in terms of the number of transmissions for each query. The preprocessing is worthwhile if it is followed by frequent queries. We could also imagine that there is an extra initial power (say, batteries) available during the preprocessing stage or alternatively the positions of the sensors are known in advance and the preprocessing can be done before the sensors are deployed in the field. It is also worth mentioning that a lower bound of Ω(c²) transmissions has been proved if preprocessing is not allowed [F. Kuhn, R. Wattenhofer, A. Zollinger, Asymptotically optimal geometric mobile ad-hoc routing, in: Proceedings of the Sixth International Workshop on Discrete Algorithm and Methods for Mobility, Atlanta, GA, September 2002, pp. 24–33].     

Error estimates of a linear decoupled Euler–FEM scheme for a mass diffusion model

We present error estimates of a linear fully discrete scheme for a three-dimensional mass diffusion model for incompressible fluids (also called Kazhikhov–Smagulov model). All unknowns of the model (velocity, pressure and density) are approximated in space by C ⁰-finite elements and in time an Euler type scheme is used decoupling the density from the velocity–pressure pair. If we assume that the velocity and pressure finite-element spaces satisfy the inf–sup condition and the density finite-element space contains the products of any two discrete velocities, we first obtain point-wise stability estimates for the density, under the constraint lim_(h,k)→0 h/k = 0 (h and k being the space and time discrete parameters, respectively), and error estimates for the velocity and density in energy type norms, at the same time. Afterwards, error estimates for the density in stronger norms are deduced. All these error estimates will be optimal (of order O(h+k){\mathcal{O}(h+k)}) for regular enough solutions without imposing nonlocal compatibility conditions at the initial time. Finally, we also study two convergent iterative methods for the two problems to solve at each time step, which hold constant matrices (independent of iterations).     

A polynomial method for the pos/neg weighted 3-median problem on a tree

Let a connected undirected graph G  =  (V, E) be given. In the classical p-median problem we want to find a set X containing p points in G such that the sum of weighted distances from X to all vertices in V is minimized. We consider the semi-obnoxious case where every vertex has either a positive or negative weight. In this case we have two different objective functions: the sum of the minimum weighted distances from X to all vertices and the sum of the weighted minimum distances. In this paper we show that for the case p = 3 an optimal solution for the second model in a tree can be found in O(n ⁵) time. If the 3-median is restricted to vertices or if the tree is a path then the complexity can be reduced to O(n ³). This research has partially been supported by the Spezialforschungsbereich F 003 “Optimierung und Kontrolle”, Projektbereich Diskrete Optimierung.