Spanners for Geometric Intersection Graphs

Efficient algorithms are presented for constructing spanners in geometric intersection graphs. For a unit ball graph in R^k, a (1+\epsilon)-spanner is obtained using efficient partitioning of the space into hypercubes and solving bichromatic closest pair problems. The spanner construction has almost equivalent complexity to the construction of Euclidean minimum spanning trees. The results are extended to arbitrary ball graphs with a sub-quadratic running time. For unit ball graphs, the spanners have a small separator decomposition which can be used to obtain efficient algorithms for approximating proximity problems like diameter and distance queries. The results on compressed quadtrees, geometric graph separators, and diameter approximation might be of independent interest.Comment: 16 pages, 5 figures, Late

A Combinatorial Algorithm for All-Pairs Shortest Paths in Directed Vertex-Weighted Graphs with Applications to Disc Graphs

We consider the problem of computing all-pairs shortest paths in a directed graph with real weights assigned to vertices. For an $n\times n$ 0-1 matrix $C,$ let $K_{C}$ be the complete weighted graph on the rows of $C$ where the weight of an edge between two rows is equal to their Hamming distance. Let $MWT(C)$ be the weight of a minimum weight spanning tree of $K_{C}.$ We show that the all-pairs shortest path problem for a directed graph $G$ on $n$ vertices with nonnegative real weights and adjacency matrix $A_G$ can be solved by a combinatorial randomized algorithm in time $$\widetilde{O}(n^{2}\sqrt {n + \min\{MWT(A_G), MWT(A_G^t)\}})$$ As a corollary, we conclude that the transitive closure of a directed graph $G$ can be computed by a combinatorial randomized algorithm in the aforementioned time. $\widetilde{O}(n^{2}\sqrt {n + \min\{MWT(A_G), MWT(A_G^t)\}})$ We also conclude that the all-pairs shortest path problem for uniform disk graphs, with nonnegative real vertex weights, induced by point sets of bounded density within a unit square can be solved in time $\widetilde{O}(n^{2.75})$

Entropy-scaling search of massive biological data

Many datasets exhibit a well-defined structure that can be exploited to design faster search tools, but it is not always clear when such acceleration is possible. Here, we introduce a framework for similarity search based on characterizing a dataset's entropy and fractal dimension. We prove that searching scales in time with metric entropy (number of covering hyperspheres), if the fractal dimension of the dataset is low, and scales in space with the sum of metric entropy and information-theoretic entropy (randomness of the data). Using these ideas, we present accelerated versions of standard tools, with no loss in specificity and little loss in sensitivity, for use in three domains---high-throughput drug screening (Ammolite, 150x speedup), metagenomics (MICA, 3.5x speedup of DIAMOND [3,700x BLASTX]), and protein structure search (esFragBag, 10x speedup of FragBag). Our framework can be used to achieve "compressive omics," and the general theory can be readily applied to data science problems outside of biology.Comment: Including supplement: 41 pages, 6 figures, 4 tables, 1 bo

HD-Index: Pushing the Scalability-Accuracy Boundary for Approximate kNN Search in High-Dimensional Spaces

Nearest neighbor searching of large databases in high-dimensional spaces is inherently difficult due to the curse of dimensionality. A flavor of approximation is, therefore, necessary to practically solve the problem of nearest neighbor search. In this paper, we propose a novel yet simple indexing scheme, HD-Index, to solve the problem of approximate k-nearest neighbor queries in massive high-dimensional databases. HD-Index consists of a set of novel hierarchical structures called RDB-trees built on Hilbert keys of database objects. The leaves of the RDB-trees store distances of database objects to reference objects, thereby allowing efficient pruning using distance filters. In addition to triangular inequality, we also use Ptolemaic inequality to produce better lower bounds. Experiments on massive (up to billion scale) high-dimensional (up to 1000+) datasets show that HD-Index is effective, efficient, and scalable.Comment: PVLDB 11(8):906-919, 201

Fast Shortest Path Distance Estimation in Large Networks

We study the problem of preprocessing a large graph so that point-to-point shortest-path queries can be answered very fast. Computing shortest paths is a well studied problem, but exact algorithms do not scale to huge graphs encountered on the web, social networks, and other applications. In this paper we focus on approximate methods for distance estimation, in particular using landmark-based distance indexing. This approach involves selecting a subset of nodes as landmarks and computing (offline) the distances from each node in the graph to those landmarks. At runtime, when the distance between a pair of nodes is needed, we can estimate it quickly by combining the precomputed distances of the two nodes to the landmarks. We prove that selecting the optimal set of landmarks is an NP-hard problem, and thus heuristic solutions need to be employed. Given a budget of memory for the index, which translates directly into a budget of landmarks, different landmark selection strategies can yield dramatically different results in terms of accuracy. A number of simple methods that scale well to large graphs are therefore developed and experimentally compared. The simplest methods choose central nodes of the graph, while the more elaborate ones select central nodes that are also far away from one another. The efficiency of the suggested techniques is tested experimentally using five different real world graphs with millions of edges; for a given accuracy, they require as much as 250 times less space than the current approach in the literature which considers selecting landmarks at random. Finally, we study applications of our method in two problems arising naturally in large-scale networks, namely, social search and community detection.Yahoo! Research (internship

Indexing Metric Spaces for Exact Similarity Search

With the continued digitalization of societal processes, we are seeing an explosion in available data. This is referred to as big data. In a research setting, three aspects of the data are often viewed as the main sources of challenges when attempting to enable value creation from big data: volume, velocity and variety. Many studies address volume or velocity, while much fewer studies concern the variety. Metric space is ideal for addressing variety because it can accommodate any type of data as long as its associated distance notion satisfies the triangle inequality. To accelerate search in metric space, a collection of indexing techniques for metric data have been proposed. However, existing surveys each offers only a narrow coverage, and no comprehensive empirical study of those techniques exists. We offer a survey of all the existing metric indexes that can support exact similarity search, by i) summarizing all the existing partitioning, pruning and validation techniques used for metric indexes, ii) providing the time and storage complexity analysis on the index construction, and iii) report on a comprehensive empirical comparison of their similarity query processing performance. Here, empirical comparisons are used to evaluate the index performance during search as it is hard to see the complexity analysis differences on the similarity query processing and the query performance depends on the pruning and validation abilities related to the data distribution. This article aims at revealing different strengths and weaknesses of different indexing techniques in order to offer guidance on selecting an appropriate indexing technique for a given setting, and directing the future research for metric indexes