Motivated by the fast‐growing need to compute centrality indices on large, yet very sparse, networks, new algorithms for betweenness are introduced in this paper. They require O(n + m) space and run in O(nm) and O(nm + n2 log n) time on unweighted and weighted networks, respectively, where m is the number of links. Experimental evidence is provided that this substantially increases the range of networks for which centrality analysis is feasible. The betweenness centrality index is essential in the analysis of social networks, but costly to compute. Currently, the fastest known algorithms require ?(n 3) time and ?(n 2) space, where n is the number of actors in the network.

/pdf/a-faster-algorithm-for-betweenness-centrality-2g52pt39q9.pdf

A faster algorithm for betweenness centrality

Many practical computing problems concern large graphs. Standard examples include the Web graph and various social networks. The scale of these graphs - in some cases billions of vertices, trillions of edges - poses challenges to their efficient processing. In this paper we present a computational model suitable for this task. Programs are expressed as a sequence of iterations, in each of which a vertex can receive messages sent in the previous iteration, send messages to other vertices, and modify its own state and that of its outgoing edges or mutate graph topology. This vertex-centric approach is flexible enough to express a broad set of algorithms. The model has been designed for efficient, scalable and fault-tolerant implementation on clusters of thousands of commodity computers, and its implied synchronicity makes reasoning about programs easier. Distribution-related details are hidden behind an abstract API. The result is a framework for processing large graphs that is expressive and easy to program.

/pdf/pregel-a-system-for-large-scale-graph-processing-30lgjenxxg.pdf

Pregel: a system for large-scale graph processing

We demonstrate an integrated approach to build, test, and refine a model of a cellular pathway, in which perturbations to critical pathway components are analyzed using DNA microarrays, quantitative proteomics, and databases of known physical interactions. Using this approach, we identify 997 messenger RNAs responding to 20 systematic perturbations of the yeast galactose-utilization pathway, provide evidence that approximately 15 of 289 detected proteins are regulated posttranscriptionally, and identify explicit physical interactions governing the cellular response to each perturbation. We refine the model through further iterations of perturbation and global measurements, suggesting hypotheses about the regulation of galactose utilization and physical interactions between this and a variety of other metabolic pathways.

/pdf/integrated-genomic-and-proteomic-analyses-of-a-3dp6ibi8g5.pdf

Integrated genomic and proteomic analyses of a systematically perturbed metabolic network.

Motion planning is one of the most important areas of robotics research. The complexity of the motion-planning problem has hindered the development of practical algorithms. This paper surveys the work on gross-motion planning, including motion planners for point robots, rigid robots, and manipulators in stationary, time-varying, constrained, and movable-object environments. The general issues in motion planning are explained. Recent approaches and their performances are briefly described, and possible future research directions are discussed.

Gross motion planning—a survey

https://www.linkgroup.hu/docs/13PharmTher.pdf

Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review

We give an overview of the LEDA platform for combinatorial and geometric computing and an account of its development. We discuss our motivation for building LEDA and to what extent we have reached our goals. We also discuss some recent theoretical developments. This paper contains no new technical material. It is intended as a guide to existing publications about the system. We refer the reader also to our web-pages for more information.

/pdf/the-leda-platform-of-combinatorial-and-geometric-computing-4r8e0w0sj0.pdf

The LEDA Platform of Combinatorial and Geometric Computing

We present a randomized and a deterministic data structure for maintaining a dynamic family of sequences under equality tests of pairs of sequences and creations of new sequences by joining or splitting existing sequences. Both data structures support equality tests inO(1) time. The randomized version supports new sequence creations inO(log2
 n) expected time wheren is the length of the sequence created. The deterministic solution supports sequence creations inO(logn(logmlog*
 m+logn)) time for themth operation.

/pdf/maintaining-dynamic-sequences-under-equality-tests-in-16ezh8y2w0.pdf

Maintaining dynamic sequences under equality tests in polylogarithmic time

Maintaining dynamic sequences under equality-tests in polylogarithmic time

Exact geometric computation in LEDA

A program checker verifies that a particular program execution is correct. We give simple and efficient program checkers for some basic geometric tasks. We report about our experiences with program checking in the context of the LEDA system. We discuss program checking for data structures that have to rely on user-provided functions.

/pdf/checking-geometric-programs-or-verification-of-geometric-2k8u3k5i1d.pdf

Christian Uhrig

Papers

The LEDA Platform of Combinatorial and Geometric Computing

Maintaining dynamic sequences under equality tests in polylogarithmic time

Maintaining dynamic sequences under equality-tests in polylogarithmic time

Exact geometric computation in LEDA

Checking geometric programs or verification of geometric structures