Restricted Neighborhood Search Clustering Research Articles

TriRNSC: triclustering of gene expression microarray data using restricted neighbourhood search.

Computational analysis of microarray data is crucial for understanding the gene behaviours and deriving meaningful results. Clustering and biclustering of gene expression microarray data in the unsupervised domain are extremely important as their outcomes directly dominate healthcare research in many aspects. However, these approaches fail when the time factor is added as the third dimension to the microarray datasets. This three-dimensional data set can be analysed using triclustering that discovers similar gene sets that pursue identical behaviour under a subset of conditions at a specific time point. A novel triclustering algorithm (TriRNSC) is proposed in this manuscript to discover meaningful triclusters in gene expression profiles. TriRNSC is based on restricted neighbourhood search clustering (RNSC), a popular graph-based clustering approach considering the genes, the experimental conditions and the time points at an instance. The performance of the proposed algorithm is evaluated in terms of volume and some performance measures. Gene Ontology and KEGG pathway analysis are used to validate the TriRNSC results biologically. The efficiency of TriRNSC indicates its capability and reliability and also demonstrates its usability over other state-of-art schemes. The proposed framework initiates the application of the RNSC algorithm in the triclustering of gene expression profiles.

An evolutionary restricted neighborhood search clustering approach for PPI networks

Protein–protein interaction networks have been broadly studied in the last few years, in order to understand the behavior of proteins inside the cell. Proteins interacting with each other often share common biological functions or they participate in the same biological process. Thus, discovering protein complexes made of a group of proteins strictly related can be useful to predict protein functions. Clustering techniques have been widely employed to detect significant biological complexes. In this paper, we integrate one of the most popular network clustering techniques, namely the Restricted Neighborhood Search Clustering (RNSC), with evolutionary computation. The two cost functions introduced by RNSC, besides a new one that combines them, are used by a Genetic Algorithm as fitness functions to be optimized. Experimental evaluations performed on two different groups of interactions of the budding yeast Saccharomyces cerevisiae show that the clusters obtained by the genetic approach are a larger number of those found by RNSC, though this method predicts more true complexes.

Comparative Performance Analysis Of Rnsc And Mcl Algorithms On Power-Law Distribution

Cluster analysis of graph related problems is an important issue now-a-day. Different types of graph clustering techniques are appeared in the field but most of them are vulnerable in terms of effectiveness and fragmentation of output in case of real-world applications in diverse systems. In this paper, we will provide a comparative behavioural analysis of RNSC (Restricted Neighbourhood Search Clustering) and MCL (Markov Clustering) algorithms on Power-Law Distribution graphs. RNSC is a graph clustering technique using stochastic local search. RNSC algorithm tries to achieve optimal cost clustering by assigning some cost functions to the set of clusterings of a graph. This algorithm was implemented by A. D. King only for undirected and unweighted random graphs. Another popular graph clustering algorithm MCL is based on stochastic flow simulation model for weighted graphs. There are plentiful applications of power-law or scale-free graphs in nature and society. Scale-free topology is stochastic i.e. nodes are connected in a random manner. Complex network topologies like World Wide Web, the web of human sexual contacts, or the chemical network of a cell etc., are basically following power-law distribution to represent different real-life systems. This paper uses real large-scale power-law distribution graphs to conduct the performance analysis of RNSC behaviour compared with Markov clustering (MCL) algorithm. Extensive experimental results on several synthetic and real power-law distribution datasets reveal the effectiveness of our approach to comparative performance measure of these algorithms on the basis of cost of clustering, cluster size, modularity index of clustering results and normalized mutual information (NMI).

Performance Testing of RNSC and MCL Algorithms on Random Geometric Graphs

The exploration of quality clusters in complex networks is an important issue in many disciplines, which still remains a challenging task. Many graph clustering algorithms came into the field in the recent past but they were not giving satisfactory performance on the basis of robustness, optimality, etc. So, it is most difficult task to decide which one is giving more beneficial clustering results compared to others in case of real–world problems. In this paper, performance of RNSC (Restricted Neighbourhood Search Clustering) and MCL (Markov Clustering) algorithms are evaluated on a random geometric graph (RGG). RNSC uses stochastic local search method for clustering of a graph. RNSC algorithm tries to achieve optimal cost clustering by assigning some cost functions to the set of clusterings of a graph. Another standard clustering algorithm MCL is based on stochastic flow simulation model. RGG has conventionally been associated with areas such as statistical physics and hypothesis testing but have achieved new relevance with the advent of wireless ad-hoc and sensor networks. In this study, the performance testing of these methods is conducted on the basis of cost of clustering, cluster size, modularity index of clustering results and normalized mutual information (NMI) using both real and synthetic RGG.

An Effective Comparison of Graph Clustering Algorithms via Random Graphs

graph clustering algorithms have been proposed in recent past researches, each algorithm having its own advantages and drawbacks. All these algorithms rely on a very different approach so it's really hard to say that which one is the most efficient and optimal if we talk in the sense of performance. It is really hard to decide that which algorithm is beneficial in case of highly complex networks like PPI networks which consist of thousands of nodes. The paper proposes an effective data comparison of RNSC (Restricted Neighbourhood Search Clustering) and MCL (Markov Clustering) algorithms based on Erdos-Renyi and Power-Law Distribution graphs. The basic parameters used for comparison are Edge Density, Run Time, Number of Nodes, Cluster Size and Singleton Cluster. Our approach is an effective one because firstly we have used two types of graph generators, Erdos-Renyi and Scaled-Free for generation of input graphs which are very much closer to the real input graphs and secondly we have generated input graphs having more than 1000 nodes, so in our approach we have used both the algorithms for clustering highly complex input graphs just like PPI networks. For comparison and analysis purpose we have collected data sets and generated some graphs based on these parameters. The proposed approach depicts which algorithm is best to be used for clustering such complex graphs and also some fields for extension if possible in both them. All graphs used in this thesis are unweighted and undirected.

Evaluation of clustering algorithms for protein-protein interaction networks

BackgroundProtein interactions are crucial components of all cellular processes. Recently, high-throughput methods have been developed to obtain a global description of the interactome (the whole network of protein interactions for a given organism). In 2002, the yeast interactome was estimated to contain up to 80,000 potential interactions. This estimate is based on the integration of data sets obtained by various methods (mass spectrometry, two-hybrid methods, genetic studies). High-throughput methods are known, however, to yield a non-negligible rate of false positives, and to miss a fraction of existing interactions.The interactome can be represented as a graph where nodes correspond with proteins and edges with pairwise interactions. In recent years clustering methods have been developed and applied in order to extract relevant modules from such graphs. These algorithms require the specification of parameters that may drastically affect the results. In this paper we present a comparative assessment of four algorithms: Markov Clustering (MCL), Restricted Neighborhood Search Clustering (RNSC), Super Paramagnetic Clustering (SPC), and Molecular Complex Detection (MCODE).ResultsA test graph was built on the basis of 220 complexes annotated in the MIPS database. To evaluate the robustness to false positives and false negatives, we derived 41 altered graphs by randomly removing edges from or adding edges to the test graph in various proportions.Each clustering algorithm was applied to these graphs with various parameter settings, and the clusters were compared with the annotated complexes.We analyzed the sensitivity of the algorithms to the parameters and determined their optimal parameter values.We also evaluated their robustness to alterations of the test graph.We then applied the four algorithms to six graphs obtained from high-throughput experiments and compared the resulting clusters with the annotated complexes.ConclusionThis analysis shows that MCL is remarkably robust to graph alterations. In the tests of robustness, RNSC is more sensitive to edge deletion but less sensitive to the use of suboptimal parameter values. The other two algorithms are clearly weaker under most conditions.The analysis of high-throughput data supports the superiority of MCL for the extraction of complexes from interaction networks.