Faster Fully Dynamic Transitive Closure in Practice

The fully dynamic transitive closure problem asks to maintain reachability information in a directed graph between arbitrary pairs of vertices, while the graph undergoes a sequence of edge insertions and deletions. The problem has been thoroughly investigated in theory and many specialized algorithms for solving it have been proposed in the last decades. In two large studies [Frigioni ea, 2001; Krommidas and Zaroliagis, 2008], a number of these algorithms have been evaluated experimentally against simple, static algorithms for graph traversal, showing the competitiveness and even superiority of the simple algorithms in practice, except for very dense random graphs or very high ratios of queries. A major drawback of those studies is that only small and mostly randomly generated graphs are considered. In this paper, we engineer new algorithms to maintain all-pairs reachability information which are simple and space-efficient. Moreover, we perform an extensive experimental evaluation on both generated and real-world instances that are several orders of magnitude larger than those in the previous studies. Our results indicate that our new algorithms outperform all state-of-the-art algorithms on all types of input considerably in practice

Efficient Multi-Robot Coverage of a Known Environment

This paper addresses the complete area coverage problem of a known environment by multiple-robots. Complete area coverage is the problem of moving an end-effector over all available space while avoiding existing obstacles. In such tasks, using multiple robots can increase the efficiency of the area coverage in terms of minimizing the operational time and increase the robustness in the face of robot attrition. Unfortunately, the problem of finding an optimal solution for such an area coverage problem with multiple robots is known to be NP-complete. In this paper we present two approximation heuristics for solving the multi-robot coverage problem. The first solution presented is a direct extension of an efficient single robot area coverage algorithm, based on an exact cellular decomposition. The second algorithm is a greedy approach that divides the area into equal regions and applies an efficient single-robot coverage algorithm to each region. We present experimental results for two algorithms. Results indicate that our approaches provide good coverage distribution between robots and minimize the workload per robot, meanwhile ensuring complete coverage of the area.Comment: In proceedings of IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS), 201

Extreme Scale De Novo Metagenome Assembly

Metagenome assembly is the process of transforming a set of short, overlapping, and potentially erroneous DNA segments from environmental samples into the accurate representation of the underlying microbiomes's genomes. State-of-the-art tools require big shared memory machines and cannot handle contemporary metagenome datasets that exceed Terabytes in size. In this paper, we introduce the MetaHipMer pipeline, a high-quality and high-performance metagenome assembler that employs an iterative de Bruijn graph approach. MetaHipMer leverages a specialized scaffolding algorithm that produces long scaffolds and accommodates the idiosyncrasies of metagenomes. MetaHipMer is end-to-end parallelized using the Unified Parallel C language and therefore can run seamlessly on shared and distributed-memory systems. Experimental results show that MetaHipMer matches or outperforms the state-of-the-art tools in terms of accuracy. Moreover, MetaHipMer scales efficiently to large concurrencies and is able to assemble previously intractable grand challenge metagenomes. We demonstrate the unprecedented capability of MetaHipMer by computing the first full assembly of the Twitchell Wetlands dataset, consisting of 7.5 billion reads - size 2.6 TBytes.Comment: Accepted to SC1

Fully Dynamic Single-Source Reachability in Practice: An Experimental Study

Given a directed graph and a source vertex, the fully dynamic single-source reachability problem is to maintain the set of vertices that are reachable from the given vertex, subject to edge deletions and insertions. It is one of the most fundamental problems on graphs and appears directly or indirectly in many and varied applications. While there has been theoretical work on this problem, showing both linear conditional lower bounds for the fully dynamic problem and insertions-only and deletions-only upper bounds beating these conditional lower bounds, there has been no experimental study that compares the performance of fully dynamic reachability algorithms in practice. Previous experimental studies in this area concentrated only on the more general all-pairs reachability or transitive closure problem and did not use real-world dynamic graphs. In this paper, we bridge this gap by empirically studying an extensive set of algorithms for the single-source reachability problem in the fully dynamic setting. In particular, we design several fully dynamic variants of well-known approaches to obtain and maintain reachability information with respect to a distinguished source. Moreover, we extend the existing insertions-only or deletions-only upper bounds into fully dynamic algorithms. Even though the worst-case time per operation of all the fully dynamic algorithms we evaluate is at least linear in the number of edges in the graph (as is to be expected given the conditional lower bounds) we show in our extensive experimental evaluation that their performance differs greatly, both on generated as well as on real-world instances

Temporal Graph Traversals: Definitions, Algorithms, and Applications

A temporal graph is a graph in which connections between vertices are active at specific times, and such temporal information leads to completely new patterns and knowledge that are not present in a non-temporal graph. In this paper, we study traversal problems in a temporal graph. Graph traversals, such as DFS and BFS, are basic operations for processing and studying a graph. While both DFS and BFS are well-known simple concepts, it is non-trivial to adopt the same notions from a non-temporal graph to a temporal graph. We analyze the difficulties of defining temporal graph traversals and propose new definitions of DFS and BFS for a temporal graph. We investigate the properties of temporal DFS and BFS, and propose efficient algorithms with optimal complexity. In particular, we also study important applications of temporal DFS and BFS. We verify the efficiency and importance of our graph traversal algorithms in real world temporal graphs

A Generic Framework for Engineering Graph Canonization Algorithms

The state-of-the-art tools for practical graph canonization are all based on the individualization-refinement paradigm, and their difference is primarily in the choice of heuristics they include and in the actual tool implementation. It is thus not possible to make a direct comparison of how individual algorithmic ideas affect the performance on different graph classes. We present an algorithmic software framework that facilitates implementation of heuristics as independent extensions to a common core algorithm. It therefore becomes easy to perform a detailed comparison of the performance and behaviour of different algorithmic ideas. Implementations are provided of a range of algorithms for tree traversal, target cell selection, and node invariant, including choices from the literature and new variations. The framework readily supports extraction and visualization of detailed data from separate algorithm executions for subsequent analysis and development of new heuristics. Using collections of different graph classes we investigate the effect of varying the selections of heuristics, often revealing exactly which individual algorithmic choice is responsible for particularly good or bad performance. On several benchmark collections, including a newly proposed class of difficult instances, we additionally find that our implementation performs better than the current state-of-the-art tools

A Fast Order-Based Approach for Core Maintenance

Graphs have been widely used in many applications such as social networks, collaboration networks, and biological networks. One important graph analytics is to explore cohesive subgraphs in a large graph. Among several cohesive subgraphs studied, k-core is one that can be computed in linear time for a static graph. Since graphs are evolving in real applications, in this paper, we study core maintenance which is to reduce the computational cost to compute k-cores for a graph when graphs are updated from time to time dynamically. We identify drawbacks of the existing efficient algorithm, which needs a large search space to find the vertices that need to be updated, and has high overhead to maintain the index built, when a graph is updated. We propose a new order-based approach to maintain an order, called k-order, among vertices, while a graph is updated. Our new algorithm can significantly outperform the state-of-the-art algorithm up to 3 orders of magnitude for the 11 large real graphs tested. We report our findings in this paper