scholarly journals Topological and functional comparison of community detection algorithms in biological networks

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Sara Rahiminejad ◽  
Mano R. Maurya ◽  
Shankar Subramaniam
Data ◽  
2019 ◽  
Vol 4 (4) ◽  
pp. 149
Author(s):  
Amulyashree Sridhar ◽  
Sharvani GS ◽  
AH Manjunatha Reddy ◽  
Biplab Bhattacharjee ◽  
Kalyan Nagaraj

Exploring gene networks is crucial for identifying significant biological interactions occurring in a disease condition. These interactions can be acknowledged by modeling the tie structure of networks. Such tie orientations are often detected within embedded community structures. However, most of the prevailing community detection modules are intended to capture information from nodes and its attributes, usually ignoring the ties. In this study, a modularity maximization algorithm is proposed based on nonlinear representation of local tangent space alignment (LTSA). Initially, the tangent coordinates are computed locally to identify k-nearest neighbors across the genes. These local neighbors are further optimized by generating a nonlinear network embedding function for detecting gene communities based on eigenvector decomposition. Experimental results suggest that this algorithm detects gene modules with a better modularity index of 0.9256, compared to other traditional community detection algorithms. Furthermore, co-expressed genes across these communities are identified by discovering the characteristic tie structures. These detected ties are known to have substantial biological influence in the progression of schizophrenia, thereby signifying the influence of tie patterns in biological networks. This technique can be extended logically on other diseases networks for detecting substantial gene “hotspots”.


2009 ◽  
Vol 23 (17) ◽  
pp. 2089-2106 ◽  
Author(s):  
ZHONGMIN XIONG ◽  
WEI WANG

Many networks, including social and biological networks, are naturally divided into communities. Community detection is an important task when discovering the underlying structure in networks. GN algorithm is one of the most influential detection algorithms based on betweenness scores of edges, but it is computationally costly, as all betweenness scores need to be repeatedly computed once an edge is removed. This paper presents an algorithm which is also based on betweenness scores but more than one edge can be removed when all betweenness scores have been computed. This method is motivated by the following considerations: many components, divided from networks, are independent of each other in their recalculation of betweenness scores and their split into smaller components. It is shown that this method is fast and effective through theoretical analysis and experiments with several real data sets, which have acted as test beds in many related works. Moreover, the version of this method with the minor adjustments allows for the discovery of the communities surrounding a given node without having to compute the full community structure of a graph.


Author(s):  
S Rao Chintalapudi ◽  
H. M. Krishna Prasad M

Social network analysis is one of the emerging research areas in the modern world. Social networks can be adapted to all the sectors by using graph theory concepts such as transportation networks, collaboration networks, and biological networks and so on. The most important property of social networks is community, collection of nodes with dense connections inside and sparse connections at outside. Community detection is similar to clustering analysis and has many applications in the real-time world such as recommendation systems, target marketing and so on. Community detection algorithms are broadly classified into two categories. One is disjoint community detection algorithms and the other is overlapping community detection algorithms. This chapter reviews overlapping community detection algorithms with their strengths and limitations. To evaluate these algorithms, a popular synthetic network generator, i.e., LFR benchmark generator and the new extended quality measures are discussed in detail.


2019 ◽  
Vol 10 ◽  
Author(s):  
Beethika Tripathi ◽  
Srinivasan Parthasarathy ◽  
Himanshu Sinha ◽  
Karthik Raman ◽  
Balaraman Ravindran

2021 ◽  
Vol 54 (3) ◽  
pp. 1-35
Author(s):  
Matteo Magnani ◽  
Obaida Hanteer ◽  
Roberto Interdonato ◽  
Luca Rossi ◽  
Andrea Tagarelli

A multiplex network models different modes of interaction among same-type entities. In this article, we provide a taxonomy of community detection algorithms in multiplex networks. We characterize the different algorithms based on various properties and we discuss the type of communities detected by each method. We then provide an extensive experimental evaluation of the reviewed methods to answer three main questions: to what extent the evaluated methods are able to detect ground-truth communities, to what extent different methods produce similar community structures, and to what extent the evaluated methods are scalable. One goal of this survey is to help scholars and practitioners to choose the right methods for the data and the task at hand, while also emphasizing when such choice is problematic.


2021 ◽  
pp. 1-17
Author(s):  
Mohammed Al-Andoli ◽  
Wooi Ping Cheah ◽  
Shing Chiang Tan

Detecting communities is an important multidisciplinary research discipline and is considered vital to understand the structure of complex networks. Deep autoencoders have been successfully proposed to solve the problem of community detection. However, existing models in the literature are trained based on gradient descent optimization with the backpropagation algorithm, which is known to converge to local minima and prove inefficient, especially in big data scenarios. To tackle these drawbacks, this work proposed a novel deep autoencoder with Particle Swarm Optimization (PSO) and continuation algorithms to reveal community structures in complex networks. The PSO and continuation algorithms were utilized to avoid the local minimum and premature convergence, and to reduce overall training execution time. Two objective functions were also employed in the proposed model: minimizing the cost function of the autoencoder, and maximizing the modularity function, which refers to the quality of the detected communities. This work also proposed other methods to work in the absence of continuation, and to enable premature convergence. Extensive empirical experiments on 11 publically-available real-world datasets demonstrated that the proposed method is effective and promising for deriving communities in complex networks, as well as outperforming state-of-the-art deep learning community detection algorithms.


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