Dynamic load balancing for the distributed mining of molecular structures

In molecular biology, it is often desirable to find common properties in large numbers of drug candidates. One family of methods stems from the data mining community, where algorithms to find frequent graphs have received increasing attention over the past years. However, the computational complexity of the underlying problem and the large amount of data to be explored essentially render sequential algorithms useless. In this paper, we present a distributed approach to the frequent subgraph mining problem to discover interesting patterns in molecular compounds. This problem is characterized by a highly irregular search tree, whereby no reliable workload prediction is available. We describe the three main aspects of the proposed distributed algorithm, namely, a dynamic partitioning of the search space, a distribution process based on a peer-to-peer communication framework, and a novel receiverinitiated load balancing algorithm. The effectiveness of the distributed method has been evaluated on the well-known National Cancer Institute’s HIV-screening data set, where we were able to show close-to linear speedup in a network of workstations. The proposed approach also allows for dynamic resource aggregation in a non dedicated computational environment. These features make it suitable for large-scale, multi-domain, heterogeneous environments, such as computational grids

Fast Sequential and Parallel Algorithms for Association Rule Mining: A Comparison

The field of knowledge discovery in databases, or "Data Mining", has received increasing attention during recent years as large organizations have begun to realize the potential value of the information that is stored implicitly in their databases. One specific data mining task is the mining of Association Rules, particularly from retail data. The task is to determine patterns (or rules) that characterize the shopping behavior of customers from a large database of previous consumer transactions. The rules can then be used to focus marketing efforts such as product placement and sales promotions. Because early algorithms required an unpredictably large number of IO operations, reducing IO cost has been the primary target of the algorithms presented in the literature. One of the most recent proposed algorithms, called PARTITION, uses a new TID-list data representation and a new partitioning technique. The partitioning technique reduces IO cost to a constant amount by processing one database portion at a time in memory. We implemented an algorithm called SPTID that incorporates both TID-lists and partitioning to study their benefits. For comparison, a non-partitioning algorithm called SEAR, which is based on a new prefix-tree data structure, is used. Our experiments with SPTID and SEAR indicate that TID-lists have inherent inefficiencies; furthermore, because all of the algorithms tested tend to be CPU-boundn trading CPU-overhead against I/O operations by partitioning did not lead to better performance. In order to scale mining algorithms to the huge databases (e.g., multiple Terabytes) that large organizations will manage in the near future, we implemented parallel versions of SEAR and SPEAR (its partitioned counterpart). The performance results show that, while both algorithms parallelize easily and obtain good speedup and scale-up results, the parallel SEAR version performs better than parallel SPEAR, despite the fact that it uses more communication

Mrdbscan: An efficient parallel density-based clustering algorithm using mapreduce

Abstract-Data clustering is an important data mining technology that plays a crucial role in numerous scientific applications. However, it is challenging due to the size of datasets has been growing rapidly to extra-large scale in the real world. Meanwhile, MapReduce is a desirable parallel programming platform that is widely applied in kinds of data process fields. In this paper, we propose an efficient parallel density-based clustering algorithm and implement it by a 4-stages MapReduce paradigm. Furthermore, we adopt a quick partitioning strategy for large scale non-indexed data. We study the metric of merge among bordering partitions and make optimizations on it. At last, we evaluate our work on real large scale datasets using Hadoop platform. Results reveal that the speedup and scaleup of our work are very efficient

Structural Graph-based Metamodel Matching

Data integration has been, and still is, a challenge for applications processing multiple heterogeneous data sources. Across the domains of schemas, ontologies, and metamodels, this imposes the need for mapping specifications, i.e. the task of discovering semantic correspondences between elements. Support for the development of such mappings has been researched, producing matching systems that automatically propose mapping suggestions. However, especially in the context of metamodel matching the result quality of state of the art matching techniques leaves room for improvement. Although the traditional approach of pair-wise element comparison works on smaller data sets, its quadratic complexity leads to poor runtime and memory performance and eventually to the inability to match, when applied on real-world data. The work presented in this thesis seeks to address these shortcomings. Thereby, we take advantage of the graph structure of metamodels. Consequently, we derive a planar graph edit distance as metamodel similarity metric and mining-based matching to make use of redundant information. We also propose a planar graph-based partitioning to cope with large-scale matching. These techniques are then evaluated using real-world mappings from SAP business integration scenarios and the MDA community. The results demonstrate improvement in quality and managed runtime and memory consumption for large-scale metamodel matching

A massive human co-expression-network and its medical applications

Network-based analysis is indispensable in analyzing high throughput biological data. Based on the assumption that the variation of gene interactions under given biological conditions could be better interpreted in the context of a large-scale and wide variety of developmental, tissue, and disease, we leverage the large quantity of publicly-available transcriptomic data \u3e 40,000 HG U133A Affymetrix microarray chips stored in ArrayExpress (http://www.ebi.ac.uk/arrayexpress/) using MetaOmGraph (http://metnet.vrac.iastate.edu/MetNet_MetaOmGraph.htm). From this data, 18,637 chips encompassing over 500 experiments containing high quality data (18637Hu-dataset) were used to create a globally stable gene co-expression network (18637Hu-co-expressionnetwork). Regulons, groups of highly and consistently co-expressed genes, were obtained by partitioning the 18637Hu-co-expression-network using an MCL clustering algorithm. The regulon were demonstrated to be statistically significant using a gene ontology (GO) term overrepresentation test combined with evaluation of the effects of gene permutations. The regulons include approximately 12% of human genes, interconnected by 31,471 correlations. All network data and metadata is publically available (http://metnet.vrac.iastate.edu/ MetNet_MetaOmGraph.htm). Text mining of these metadata, GO term overrepresentation analysis, and statistical analysis of transcriptomic experiments across multiple environmental, tissue, and disease conditions, has revealed novel fingerprints distinguishing central nervous system (CNS)-related conditions. This study demonstrates the value of mega-scale network-based analysis for biologists to further refine transcriptomic data derived from a particular condition, to study the global relationships between genes and diseases, and to develop hypotheses that can inform future research

Parallel Community Detection Based on Distance Dynamics for Large-Scale Network

© 2013 IEEE. Data mining task is a challenge on finding a high-quality community structure from large-scale networks. The distance dynamics model was proved to be active on regular-size network community, but it is difficult to discover the community structure effectively from the large-scale network (0.1-1 billion edges), due to the limit of machine hardware and high time complexity. In this paper, we proposed a parallel community detection algorithm based on the distance dynamics model called P-Attractor, which is capable of handling the detection problem of large networks community. Our algorithm first developed a graph partitioning method to divide large network into lots of sub-networks, yet maintaining the complete neighbor structure of the original network. Then, the traditional distance dynamics model was improved by the dynamic interaction process to simulate the distance evolution of each sub-network. Finally, we discovered the real community structure by removing all external edges after evolution process. In our extensive experiments on multiple synthetic networks and real-world networks, the results showed the effectiveness and efficiency of P-Attractor, and the execution time on 4 threads and 32 threads are around 10 and 2 h, respectively. Our proposed algorithm is potential to discover community from a billion-scale network, such as Uk-2007

Adaptive Partitioning for Large-Scale Dynamic Graphs

Abstract—In the last years, large-scale graph processing has gained increasing attention, with most recent systems placing particular emphasis on latency. One possible technique to improve runtime performance in a distributed graph processing system is to reduce network communication. The most notable way to achieve this goal is to partition the graph by minimizing the num-ber of edges that connect vertices assigned to different machines, while keeping the load balanced. However, real-world graphs are highly dynamic, with vertices and edges being constantly added and removed. Carefully updating the partitioning of the graph to reflect these changes is necessary to avoid the introduction of an extensive number of cut edges, which would gradually worsen computation performance. In this paper we show that performance degradation in dynamic graph processing systems can be avoided by adapting continuously the graph partitions as the graph changes. We present a novel highly scalable adaptive partitioning strategy, and show a number of refinements that make it work under the constraints of a large-scale distributed system. The partitioning strategy is based on iterative vertex migrations, relying only on local information. We have implemented the technique in a graph processing system, and we show through three real-world scenarios how adapting graph partitioning reduces execution time by over 50 % when compared to commonly used hash-partitioning. I