Structural Clustering Algorithm For Networks Research Articles

Drift Detection of Intelligent Sensor Networks Deployment Based on Graph Stream

The optimal deployment of sensor nodes can effectively improve the monitoring performance of the sensor network. The existing optimization deployment strategies focus on how to achieve the optimal coverage or the maximal monitoring efficiency of the sensor network deployment, and lack research on the issue of when a deployed sensor network need to update its deployment. Considering that the parameters of the monitored targets by sensor network will vary over time, making the deployment a certain degree of time drift characteristic. In this paper, we propose a deployment drift detection algorithm based on graph stream for intelligent sensor networks (ISNs) to investigate the optimization deployment update time of sensor nodes for more efficient targets monitoring. We utilize graph stream to represent the topology of sensor network at different timestamps, and propose a projection fusion clustering algorithm based on Structural Clustering Algorithm for Networks (SCAN) to construct the tensor graph summarization within a sliding time window. According to the contrast between the node-level and the graph-level queries of the summary graph in adjacent windows, we refer Hoeffding boundary and graph contrastive loss function as the criterion to judge the optimal update time of the sensor network deployment. Experiments on Intel_Lab_Data and CIMIS datasets demonstrate that our approach can effectively detect the update moment of the optimal deployment of sensor network.

Clustering Algorithm for Community Detection in Complex Network: A Comprehensive Review

Many real-world social networks exist in the form of a complex network, which includes very large scale networks with structured or unstructured data and a set of graphs. This complex network is available in the form of brain graph, protein structure, food web, transportation system, World Wide Web, and these networks are sparsely connected, and most of the subgraphs are densely connected. Due to the scaling of large scale graphs, efficient way for graph generation, complexity, the dynamic nature of graphs, and community detection are challenging tasks. From large scale graph to find the densely connected subgraph from the complex network, various community detection algorithms using clustering techniques are discussed here. In this paper, we discussed the taxonomy of various community detection algorithms like Structural Clustering Algorithm for Networks (SCAN), Structural-Attribute based Cluster (SA-cluster), Community Detection based on Hierarchical Clustering (CDHC), etc. In this comprehensive review, we provide a classification of community detection algorithm based on their approach, dataset used for the existing algorithm for experimental study and measure to evaluate them. In the end, insights into the future scope and research opportunities for community detection are discussed.

GPUSCAN: GPU-Based Parallel Structural Clustering Algorithm for Networks

This paper presents a massively parallel implementation of a prominent network clustering algorithm, the structural clustering algorithm for networks (SCAN), on a graphical processing unit (GPU). SCAN is a fast and efficient clustering technique for finding hidden communities and isolating hubs/outliers within a network. However, for very large networks, it still takes considerable amount of time. With the introduction of massively parallel Compute Unified Device Architecture (CUDA) by Nvidia, applications properly employing GPUs are demonstrating high speed up. In current study, GPUSCAN, a CUDA based parallel implementation of SCAN, is presented. SCAN's computation steps have been carefully redesigned to run very efficiently on the GPU by transforming SCAN into a series of highly regular and independent concurrent operations. All intermediate data structures are created in the GPU to efficiently benefit from GPU's memory hierarchy. How these structures reformed and represented in the GPU memory hierarchy are illustrated. Now, through GPUSCAN, a large network or a batch of disjoint networks can be offloaded to the GPU for very fast and equivalent structural clustering. The performance of the GPU accelerated structural clustering has been shown to be much faster than the sequential CPU implementation. Both GPUSCAN and SCAN are tested on different size artificial and real-world networks. Results indicate that network becomes larger GPUSCAN significantly over performs SCAN. In tested datasets, speed-up of over 500-fold is achieved. For instance, calculating structural similarity and clustering of 5.5 million edges of the California road network in GPUSCAN is 513-fold faster than the serial version of SCAN.

Community Detection in Dynamic Social Networks

There are many community detection algorithms for discovering communities in networks, but very few deal with networks that change structure. The SCAN (Structural Clustering Algorithm for Networks) algorithm is one of these algorithms that detect communities in static networks. To make SCAN more effective for the dynamic social networks that are continually changing their structure, we propose the algorithm DSCAN (Dynamic SCAN) which improves SCAN to allow it to update a local structure in less time than it would to run SCAN on the entire network. We also improve SCAN by removing the need for parameter tuning. DSCAN, tested on real world dynamic networks, performs faster and comparably to SCAN from one timestamp to another, relative to the size of the change. We also devised an approach to genetic algorithms for detecting communities in dynamic social networks, which performs well in speed and modularity.

Overlapping Community Detection in Dynamic Networks

Due to the increasingly large size and changing nature of social networks, algorithms for dynamic networks have become an important part of modern day community detection. In this paper, we use a well-known static community detection algorithm and modify it to discover communities in dynamic networks. We have developed a dynamic community detection algorithm based on Speaker-Listener Label Propagation Algorithm (SLPA) called SLPA Dynamic (SLPAD). This algorithm, tested on two real dynamic networks, cuts down on the time that it would take SLPA to run, as well as produces similar, and in some cases better, communities. We compared SLPAD to SLPA, LabelRankT, and another algorithm we developed, Dynamic Structural Clustering Algorithm for Networks Overlapping (DSCAN-O), to further test its validity and ability to detect overlapping communities when compared to other community detection algorithms. SLPAD proves to be faster than all of these algorithms, as well as produces communities with just as high modularity for each network.

AtBioNet– an integrated network analysis tool for genomics and biomarker discovery

BackgroundLarge amounts of mammalian protein-protein interaction (PPI) data have been generated and are available for public use. From a systems biology perspective, Proteins/genes interactions encode the key mechanisms distinguishing disease and health, and such mechanisms can be uncovered through network analysis. An effective network analysis tool should integrate different content-specific PPI databases into a comprehensive network format with a user-friendly platform to identify key functional modules/pathways and the underlying mechanisms of disease and toxicity.ResultsatBioNet integrates seven publicly available PPI databases into a network-specific knowledge base. Knowledge expansion is achieved by expanding a user supplied proteins/genes list with interactions from its integrated PPI network. The statistically significant functional modules are determined by applying a fast network-clustering algorithm (SCAN: a Structural Clustering Algorithm for Networks). The functional modules can be visualized either separately or together in the context of the whole network. Integration of pathway information enables enrichment analysis and assessment of the biological function of modules. Three case studies are presented using publicly available disease gene signatures as a basis to discover new biomarkers for acute leukemia, systemic lupus erythematosus, and breast cancer. The results demonstrated that atBioNet can not only identify functional modules and pathways related to the studied diseases, but this information can also be used to hypothesize novel biomarkers for future analysis.ConclusionatBioNet is a free web-based network analysis tool that provides a systematic insight into proteins/genes interactions through examining significant functional modules. The identified functional modules are useful for determining underlying mechanisms of disease and biomarker discovery. It can be accessed at: http://www.fda.gov/ScienceResearch/BioinformaticsTools/ucm285284.htm.

Constructing a robust protein-protein interaction network by integrating multiple public databases

BackgroundProtein-protein interactions (PPIs) are a critical component for many underlying biological processes. A PPI network can provide insight into the mechanisms of these processes, as well as the relationships among different proteins and toxicants that are potentially involved in the processes. There are many PPI databases publicly available, each with a specific focus. The challenge is how to effectively combine their contents to generate a robust and biologically relevant PPI network.MethodsIn this study, seven public PPI databases, BioGRID, DIP, HPRD, IntAct, MINT, REACTOME, and SPIKE, were used to explore a powerful approach to combine multiple PPI databases for an integrated PPI network. We developed a novel method called k-votes to create seven different integrated networks by using values of k ranging from 1-7. Functional modules were mined by using SCAN, a Structural Clustering Algorithm for Networks. Overall module qualities were evaluated for each integrated network using the following statistical and biological measures: (1) modularity, (2) similarity-based modularity, (3) clustering score, and (4) enrichment.ResultsEach integrated human PPI network was constructed based on the number of votes (k) for a particular interaction from the committee of the original seven PPI databases. The performance of functional modules obtained by SCAN from each integrated network was evaluated. The optimal value for k was determined by the functional module analysis. Our results demonstrate that the k-votes method outperforms the traditional union approach in terms of both statistical significance and biological meaning. The best network is achieved at k=2, which is composed of interactions that are confirmed in at least two PPI databases. In contrast, the traditional union approach yields an integrated network that consists of all interactions of seven PPI databases, which might be subject to high false positives.ConclusionsWe determined that the k-votes method for constructing a robust PPI network by integrating multiple public databases outperforms previously reported approaches and that a value of k=2 provides the best results. The developed strategies for combining databases show promise in the advancement of network construction and modeling.

A structural approach for finding functional modules from large biological networks

BackgroundBiological systems can be modeled as complex network systems with many interactions between the components. These interactions give rise to the function and behavior of that system. For example, the protein-protein interaction network is the physical basis of multiple cellular functions. One goal of emerging systems biology is to analyze very large complex biological networks such as protein-protein interaction networks, metabolic networks, and regulatory networks to identify functional modules and assign functions to certain components of the system. Network modules do not occur by chance, so identification of modules is likely to capture the biologically meaningful interactions in large-scale PPI data. Unfortunately, existing computer-based clustering methods developed to find those modules are either not so accurate or too slow.ResultsWe devised a new methodology called SCAN (Structural Clustering Algorithm for Networks) that can efficiently find clusters or functional modules in complex biological networks as well as hubs and outliers. More specifically, we demonstrated that we can find functional modules in complex networks and classify nodes into various roles based on their structures. In this study, we showed the effectiveness of our methodology using the budding yeast (Saccharomyces cerevisiae) protein-protein interaction network. To validate our clustering results, we compared our clusters with the known functions of each protein. Our predicted functional modules achieved very high purity comparing with state-of-the-art approaches. Additionally the theoretical and empirical analysis demonstrated a linear running-time of the algorithm, which is the fastest approach for networks.ConclusionWe compare our algorithm with well-known modularity based clustering algorithm CNM. We successfully detect functional groups that are annotated with putative GO terms. Top-10 clusters with minimum p-value theoretically prove that newly proposed algorithm partitions network more accurately then CNM. Furthermore, manual interpretations of functional groups found by SCAN show superior performance over CNM.