Parallel Graph Partitioning for Complex Networks

Processing large complex networks like social networks or web graphs has recently attracted considerable interest. In order to do this in parallel, we need to partition them into pieces of about equal size. Unfortunately, previous parallel graph partitioners originally developed for more regular mesh-like networks do not work well for these networks. This paper addresses this problem by parallelizing and adapting the label propagation technique originally developed for graph clustering. By introducing size constraints, label propagation becomes applicable for both the coarsening and the refinement phase of multilevel graph partitioning. We obtain very high quality by applying a highly parallel evolutionary algorithm to the coarsened graph. The resulting system is both more scalable and achieves higher quality than state-of-the-art systems like ParMetis or PT-Scotch. For large complex networks the performance differences are very big. For example, our algorithm can partition a web graph with 3.3 billion edges in less than sixteen seconds using 512 cores of a high performance cluster while producing a high quality partition -- none of the competing systems can handle this graph on our system.Comment: Review article. Parallelization of our previous approach arXiv:1402.328

Automated Protein Structure Classification: A Survey

Classification of proteins based on their structure provides a valuable resource for studying protein structure, function and evolutionary relationships. With the rapidly increasing number of known protein structures, manual and semi-automatic classification is becoming ever more difficult and prohibitively slow. Therefore, there is a growing need for automated, accurate and efficient classification methods to generate classification databases or increase the speed and accuracy of semi-automatic techniques. Recognizing this need, several automated classification methods have been developed. In this survey, we overview recent developments in this area. We classify different methods based on their characteristics and compare their methodology, accuracy and efficiency. We then present a few open problems and explain future directions.Comment: 14 pages, Technical Report CSRG-589, University of Toront

LogBase: A Scalable Log-structured Database System in the Cloud

Numerous applications such as financial transactions (e.g., stock trading) are write-heavy in nature. The shift from reads to writes in web applications has also been accelerating in recent years. Write-ahead-logging is a common approach for providing recovery capability while improving performance in most storage systems. However, the separation of log and application data incurs write overheads observed in write-heavy environments and hence adversely affects the write throughput and recovery time in the system. In this paper, we introduce LogBase - a scalable log-structured database system that adopts log-only storage for removing the write bottleneck and supporting fast system recovery. LogBase is designed to be dynamically deployed on commodity clusters to take advantage of elastic scaling property of cloud environments. LogBase provides in-memory multiversion indexes for supporting efficient access to data maintained in the log. LogBase also supports transactions that bundle read and write operations spanning across multiple records. We implemented the proposed system and compared it with HBase and a disk-based log-structured record-oriented system modeled after RAMCloud. The experimental results show that LogBase is able to provide sustained write throughput, efficient data access out of the cache, and effective system recovery.Comment: VLDB201

Recent Advances in Graph Partitioning

We survey recent trends in practical algorithms for balanced graph partitioning together with applications and future research directions