Showing papers by "David Eppstein published in 2005"

Confluent drawings: visualizing non-planar diagrams in a planar way.

Abstract: We introduce a new approach for drawing diagrams. Our approach is to use a technique we call confluent drawing for visualizing non-planar graphs in a planar way. This approach allows us to draw, in a crossing-free manner, graphs—such as software interaction diagrams—that would normally have many crossings. The main idea of this approach is quite simple: we allow groups of edges to be merged together and drawn as “tracks” (similar to train tracks). Producing such confluent diagrams automatically from a graph with many crossings is quite challenging, however, so we offer two heuristic algorithms to test if a non-planar graph can be drawn efficiently in a confluent way. In addition, we identify several large classes of graphs that can be completely categorized as being either confluently drawable or confluently non-drawable.

The skip quadtree: a simple dynamic data structure for multidimensional data

Abstract: We present a new multi-dimensional data structure, which we call the skip quadtree (for point data in R2) or the skip octree (for point data in Rd, with constant d > 2). Our data structure combines the best features of two well-known data structures, in that it has the well-defined "box"-shaped regions of region quadtrees and the logarithmic-height search and update hierarchical structure of skip lists. Indeed, the bottom level of our structure is exactly a region quadtree (or octree for higher dimensional data). We describe efficient algorithms for inserting and deleting points in a skip quadtree, as well as fast methods for performing point location, approximate range, and approximate nearest neighbor queries.

Improved Combinatorial Group Testing Algorithms for Real-World Problem Sizes

Abstract: We study practically efficient methods for performing combinatorial group testing. We present efficient non-adaptive and two-stage combinatorial group testing algorithms, which identify the at most d items out of a given set of n items that are defective, using fewer tests for all practical set sizes. For example, our two-stage algorithm matches the information theoretic lower bound for the number of tests in a combinatorial group testing regimen.

The lattice dimension of a graph

Abstract: We describe a polynomial time algorithm for, given an undirected graph G, finding the minimum dimension d such that G may be isometrically embedded into the d-dimensional integer lattice Zd.

Skip-webs: efficient distributed data structures for multi-dimensional data sets

Abstract: We present a framework for designing efficient distributed data structures for multi-dimensional data. Our structures, which we call skip-webs, extend and improve previous randomized distributed data structures, including skipnets and skip graphs. Our framework applies to a general class of data querying scenarios, which include linear (one-dimensional) data, such as sorted sets, as well as multi-dimensional data, such as d-dimensional octrees and digital tries of character strings defined over a fixed alphabet.We show how to perform a query over such a set of n items spread among n hosts using O(log n/log log n) messages for one-dimensional data, or O(log n) messages for fixed-dimensional data, while using only O(log n) space per host. We also show how to make such structures dynamic so as to allow for insertions and deletions in O(log n) messages for quadtrees, octrees, and digital tries, and O(log n/log log n) messages for one-dimensional data. Finally, we show how to apply a blocking strategy to skip-webs to further improve message complexity for one-dimensional data when hosts can store more data.

Hinged dissection of polyominoes and polyforms

Abstract: A hinged dissection of a set of polygons S is a collection of polygonal pieces hinged together at vertices that can be rotated into any member of S. We present a hinged dissection of all edge-to-edge gluings of n congruent copies of a polygon P that join corresponding edges of P. This construction uses kn pieces, where k is the number of vertices of P. When P is a regular polygon, we show how to reduce the number of pieces to ⌈k/2⌉ (n - 1). In particular, we consider polyominoes (made up of unit squares), polyiamonds (made up of equilateral triangles), and polyhexes (made up of regular hexagons). We also give a hinged dissection of all polyabolos (made up of right isosceles triangles), which do not fall under the general result mentioned above. Finally, we show that if P can be hinged into Q, then any edge-to-edge gluing of n congruent copies of P can be hinged into any edge-to-edge gluing of n congruent copies of Q.

Delta-confluent drawings

Abstract: We generalize the tree-confluent graphs to a broader class of graphs called Δ-confluent graphs. This class of graphs and distance-hereditary graphs, a well-known class of graphs, coincide. Some results about the visualization of Δ-confluent graphs are also given.

All maximal independent sets and dynamic dominance for sparse graphs

Abstract: We describe algorithms, based on Avis and Fukuda's reverse search paradigm, for listing all maximal independent sets in a sparse graph in polynomial time and delay per output. For bounded degree graphs, our algorithms take constant time per set generated; for minor-closed graph families, the time is O(n) per set, and for more general sparse graph families we achieve subquadratic time per set. We also describe new data structures for maintaining a dynamic vertex set S in a sparse or minor-closed graph family, and querying the number of vertices not dominated by S; for minor-closed graph families the time per update is constant, while it is sublinear for any sparse graph family. We can also maintain a dynamic vertex set in an arbitrary m-edge graph and test the independence of the maintained set in time O(√m) per update. We use the domination data structures as part of our enumeration algorithms.

Improved combinatorial group testing for real-world problem sizes

Abstract: We study practically efficient methods for performing combinatorial group testing. We present efficient non-adaptive and two-stage combinatorial group testing algorithms, which identify the at most d items out of a given set of n items that are defective, using fewer tests for all practical set sizes. For example, our two-stage algorithm matches the information theoretic lower bound for the number of tests in a combinatorial group testing regimen.

Minimum dilation stars

Abstract: The dilation of a Euclidean graph is defined as the ratio of distance in the graph divided by distance in Rd. In this paper we consider the problem of positioning the root of a star such that the dilation of the resulting star is minimal. We present a deterministic O(n log n)-time algorithm for evaluating the dilation of a given star; a randomized O(n log n) expected-time algorithm for finding an optimal center in Rd; and for the case d = 2, a randomized O(n2α(n) log2n) expected-time algorithm for finding an optimal center among the input points.

Nonrepetitive Paths and Cycles in Graphs with Application to Sudoku

Abstract: We provide a simple linear time transformation from a directed or undirected graph with labeled edges to an unlabeled digraph, such that paths in the input graph in which no two consecutive edges have the same label correspond to paths in the transformed graph and vice versa. Using this transformation, we provide efficient algorithms for finding paths and cycles with no two consecutive equal labels. We also consider related problems where the paths and cycles are required to be simple; we find efficient algorithms for the undirected case of these problems but show the directed case to be NP-complete. We apply our path and cycle finding algorithms in a program for generating and solving Sudoku puzzles, and show experimentally that they lead to effective puzzle-solving rules that may also be of interest to human Sudoku puzzle solvers.

The Skip Quadtree: A Simple Dynamic Data Structure for Multidimensional Data

Abstract: We present a new multi-dimensional data structure, which we call the skip quadtree (for point data in R^2) or the skip octree (for point data in R^d, with constant d>2). Our data structure combines the best features of two well-known data structures, in that it has the well-defined "box"-shaped regions of region quadtrees and the logarithmic-height search and update hierarchical structure of skip lists. Indeed, the bottom level of our structure is exactly a region quadtree (or octree for higher dimensional data). We describe efficient algorithms for inserting and deleting points in a skip quadtree, as well as fast methods for performing point location and approximate range queries.

The Weighted Maximum-Mean Subtree and Other Bicriterion Subtree Problems

Abstract: We consider problems in which we are given a rooted tree as input, and must find a subtree with the same root, optimizing some objective function of the nodes in the subtree. When this function is the sum of constant node weights, the problem is trivially solved in linear time. When the objective is the sum of weights that are linear functions of a parameter, we show how to list all optima for all possible parameter values in O(n log n) time; this parametric optimization problem can be used to solve many bicriterion optimizations problems, in which each node has two values xi and yi associated with it, and the objective function is a bivariate function f(SUM(xi),SUM(yi)) of the sums of these two values. A special case, when f is the ratio of the two sums, is the Weighted Maximum-Mean Subtree Problem, or equivalently the Fractional Prize-Collecting Steiner Tree Problem on Trees; for this special case, we provide a linear time algorithm for this problem when all weights are positive, improving a previous O(n log n) solution, and prove that the problem is NP-complete when negative weights are allowed.

Confluent Layered Drawings

Abstract: We combine the idea of confluent drawings with Sugiyama style drawings, in order to reduce the edge crossings in the resultant drawings. Furthermore, it is easier to understand the structures of graphs from the mixed style drawings. The basic idea is to cover a layered graph by complete bipartite subgraphs (bicliques), then replace bicliques with tree-like structures. The biclique cover problem is reduced to a special edge coloring problem and solved by heuristic coloring algorithms. Our method can be extended to obtain multi-depth confluent layered drawings.

Skip-Webs: Efficient Distributed Data Structures for Multi-Dimensional Data Sets

Abstract: We present a framework for designing efficient distributed data structures for multi-dimensional data. Our structures, which we call skip-webs, extend and improve previous randomized distributed data structures, including skipnets and skip graphs. Our framework applies to a general class of data querying scenarios, which include linear (one-dimensional) data, such as sorted sets, as well as multi-dimensional data, such as d-dimensional octrees and digital tries of character strings defined over a fixed alphabet. We show how to perform a query over such a set of n items spread among n hosts using O(log n / log log n) messages for one-dimensional data, or O(log n) messages for fixed-dimensional data, while using only O(log n) space per host. We also show how to make such structures dynamic so as to allow for insertions and deletions in O(log n) messages for quadtrees, octrees, and digital tries, and O(log n / log log n) messages for one-dimensional data. Finally, we show how to apply a blocking strategy to skip-webs to further improve message complexity for one-dimensional data when hosts can store more data.

The Maximum-Mean Subtree

Abstract: In this paper, we define the Maximum-Mean Subtree problem on trees, an equivalent reformulation of the Fractional Prize-Collecting Steiner Tree Problem on Trees. We describe an algorithm that solves the Maximum-Mean Subtree problem, and prove that our algorithm runs in O(n) time in the worst case, improving a previous O(n log n) algorithm. 1 The Maximum-Mean Subtree Problem Given a rooted tree of nodes such that each node has a real valued profit, we are to produce a pruning of the tree that maximizes the average profit of the remaining nodes. Note that pruning a node also prunes all of its descendants. A generalization of this problem gives each node a positive real valued cost, with the original problem assigning each node a cost of 1. The overall average of a tree is the sum of the profits divided by the sum of the costs, including only unpruned nodes. In this paper we present an algorithm that solves the generalization with both profits and costs per node in time O(n). We strictly restrict costs to be positive due to the fact that negative costs result in some instances of the problem being computationally equivalent to Subset-Sum on real numbers. While profits may be negative without affecting the correctness of the result produced by our algorithm (as long as the root has positive profit), it is not clear as to what a negative profit would represent conceptually.

Cubic Partial Cubes from Simplicial Arrangements

Abstract: We show how to construct a cubic partial cube from any simplicial arrangement of lines or pseudolines in the projective plane. As a consequence, we find nine new infinite families of cubic partial cubes as well as many sporadic examples.

Delta-confluent Drawings

Abstract: We generalize the tree-confluent graphs to a broader class of graphs called Delta-confluent graphs. This class of graphs and distance-hereditary graphs, a well-known class of graphs, coincide. Some results about the visualization of Delta-confluent graphs are also given.