scholarly journals The Eminence of Co-Expressed Ties in Schizophrenia Network Communities

Data ◽  
2019 ◽  
Vol 4 (4) ◽  
pp. 149
Author(s):  
Amulyashree Sridhar ◽  
Sharvani GS ◽  
AH Manjunatha Reddy ◽  
Biplab Bhattacharjee ◽  
Kalyan Nagaraj
Keyword(s):  
Community Detection ◽  
Biological Networks ◽  
Gene Networks ◽  
Biological Interactions ◽  
K Nearest Neighbors ◽  
Nonlinear Network ◽  
Detection Algorithms ◽  
Network Communities ◽  
Disease Condition ◽  
Modularity Maximization

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”.

Determining Network Communities Based on Modular Density Optimization

2020 ◽  
Vol 13 (2) ◽  
pp. 128-136 ◽  
Author(s):  
Seema Rani ◽  
Monica Mehrotra
Keyword(s):  
Community Detection ◽  
Bat Algorithm ◽  
Limit Problem ◽  
Resolution Limit ◽  
Community Discovery ◽  
Detection Algorithms ◽  
Network Communities ◽  
Optimization Function ◽  
Np Hard Problem ◽  
Real World Datasets

Background: In today’s world, complex systems are conceptually observed in the form of network structure. Communities inherently existing in the networks have a recognizable elucidation in understanding the organization of networks. Community discovery in networks has grabbed the attention of researchers from multi-discipline. Community detection problem has been modeled as an optimization problem. In broad-spectrum, existing community detection algorithms have adopted modularity as the optimizing function. However, the modularity is not able to identify communities of smaller size as compared to the size of the network. Methods: This paper addresses the problem of the resolution limit posed by modularity. Modular density measure succeeds in countering the resolution limit problem. Finding network communities with maximum modular density is an NP-hard problem In this work, the discrete bat algorithm with modular density as the optimization function is recommended. Results: Experiments are conducted on three real-world datasets. For determining the consistency, ten independent runs of the proposed algorithm has been carried out. The experimental results show that our proposed algorithm produces high-quality community structure along with small size communities. Conclusion: The results are compared with traditional and evolutionary community detection algorithms. The final outcome shows the superiority of discrete bat algorithm with modular density as the optimization function with respect to number of communities, maximum modularity, and average modularity.

COMMUNITY DETECTION IN SOCIAL NETWORKS EMPLOYING COMPONENT INDEPENDENCY

2009 ◽  
Vol 23 (17) ◽  
pp. 2089-2106 ◽  
Author(s):  
ZHONGMIN XIONG ◽  
WEI WANG
Keyword(s):  
Social Networks ◽  
Community Structure ◽  
Theoretical Analysis ◽  
Community Detection ◽  
Biological Networks ◽  
Real Data ◽  
Important Task ◽  
Underlying Structure ◽  
Data Sets ◽  
Detection Algorithms

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.

A Survey on Overlapping Communities in Large-Scale Social Networks

2018 ◽  
pp. 198-215
Author(s):  
S Rao Chintalapudi ◽  
H. M. Krishna Prasad M
Keyword(s):  
Social Networks ◽  
Community Detection ◽  
Biological Networks ◽  
Modern World ◽  
Overlapping Community Detection ◽  
Overlapping Communities ◽  
Detection Algorithms ◽  
Research Areas ◽  
Network Generator ◽  
Overlapping Community

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.

scholarly journals Adapting Community Detection Algorithms for Disease Module Identification in Heterogeneous Biological Networks

2019 ◽  
Vol 10 ◽  
Author(s):  
Beethika Tripathi ◽  
Srinivasan Parthasarathy ◽  
Himanshu Sinha ◽  
Karthik Raman ◽  
Balaraman Ravindran
Keyword(s):  
Community Detection ◽  
Biological Networks ◽  
Module Identification ◽  
Detection Algorithms ◽  
Disease Module

Extract the network communities based on fuzzy clustering theory

2021 ◽  
pp. 2150311
Author(s):  
Zhenzhou Lin ◽  
Huijia Li
Keyword(s):  
Community Detection ◽  
Traditional Method ◽  
Fuzzy Relation ◽  
Interaction Patterns ◽  
Detection Algorithms ◽  
Fuzzy Function ◽  
Network Communities ◽  
New Strategy ◽  
Fuzzy Clustering Theory ◽  
Specific Community

Community detection in complex networks is of great importance in analyzing the interaction patterns and group behaviors. However, the traditional method of community division divide each node in the network into a specific community, while may ignore its internal connection. In this paper, a new strategy that selects a fuzzy function and fuzzy threshold (FF-FT) was presented to discover community structure. Edge dense degree coefficient was introduced to calculate fuzzy relation between nodes, and Fast–Warshall algorithm was used to reduce the complexity of FF-FT. Through the theoretical analysis and the comparison of eight current well-known community detection algorithms on seven real networks and artificial networks with different parameters, the results show that the FF-FT algorithm has a good community detection performance.

scholarly journals Hierarchical Hidden Community Detection for Protein Complex Prediction

2020 ◽  
Author(s):  
Chao Li ◽  
Kun He ◽  
Guang shuai Liu ◽  
John E. Hopcroft
Keyword(s):  
Community Detection ◽  
Hierarchical Structure ◽  
Biological Networks ◽  
Protein Complexes ◽  
Detection Methods ◽  
Biological Interactions ◽  
Protein Protein Interaction ◽  
Protein Complex Prediction ◽  
Detection Approach ◽  
New Perspective

Abstract BackgroundDiscovering functional modules in protein-protein interaction networks through optimization remains a longstanding challenge in Biology. Traditional algorithms simply consider strong protein complexes found in the original network by optimizing some metric, which may cause obstacles for discovering weak and hidden complexes that are overshadowed by strong complexes. Additionally, protein complexes have not only different densities but also various ranges of scales, making them extremely difficult to be detected. We address these issues and propose a hierarchical hidden community detection approach to predict protein complexes of various strengths and scales accurately. ResultsWe propose a meta-method called HirHide (Hierarchical Hidden Community Detection). It is the first combination of hierarchical structure with hidden structure, which provides a new perspective for finding protein complexes of various strengths and scales. We compare the performance of several standard community detection methods with their HirHide versions. Experimental results show that the HirHide versions achieve better performance and sometimes even significantly outperform the baselines. ConclusionsHirHide can adopt any standard community detection method as the base algorithm and enable it to discover hidden hierarchical communities as well as boosting the detection of strong hierarchical communities. Some biological networks are too complex for standard community detection algorithms to produce a positive performance. Most of the time, a better choice is to choose a corresponding algorithm based on the characteristics of a specific biological network. Under these circumstances, HirHide has clear advantages because of its flexibility. At the same time, according to the natural hierarchy of cells, organelle, intracellular compound etc., hierarchical structure with hidden structure is in line with the characteristics of the data itself, thus helping researchers to study biological interactions more deeply.

scholarly journals Embedding-based Silhouette community detection

2020 ◽  
Vol 109 (11) ◽  
pp. 2161-2193 ◽  
Author(s):  
Blaž Škrlj ◽  
Jan Kralj ◽  
Nada Lavrač
Keyword(s):  
Community Detection ◽  
Real Life ◽  
Interaction Network ◽  
Subgroup Discovery ◽  
Complex Data ◽  
Detection Algorithms ◽  
Scientific Disciplines ◽  
Network Communities ◽  
Art Community ◽  
Node Embeddings

AbstractMining complex data in the form of networks is of increasing interest in many scientific disciplines. Network communities correspond to densely connected subnetworks, and often represent key functional parts of real-world systems. This paper proposes the embedding-based Silhouette community detection (SCD), an approach for detecting communities, based on clustering of network node embeddings, i.e. real valued representations of nodes derived from their neighborhoods. We investigate the performance of the proposed SCD approach on 234 synthetic networks, as well as on a real-life social network. Even though SCD is not based on any form of modularity optimization, it performs comparably or better than state-of-the-art community detection algorithms, such as the InfoMap and Louvain. Further, we demonstrate that SCD’s outputs can be used along with domain ontologies in semantic subgroup discovery, yielding human-understandable explanations of communities detected in a real-life protein interaction network. Being embedding-based, SCD is widely applicable and can be tested out-of-the-box as part of many existing network learning and exploration pipelines.

scholarly journals Reduction of the molecular hamiltonian matrix using quantum community detection

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Susan M. Mniszewski ◽  
Pavel A. Dub ◽  
Sergei Tretiak ◽  
Petr M. Anisimov ◽  
Yu Zhang ◽  
...  
Keyword(s):  
Community Detection ◽  
Slater Determinant ◽  
Hamiltonian Matrix ◽  
Approximate Methods ◽  
Molecular Systems ◽  
Hartree Fock ◽  
Molecular Hamiltonian ◽  
Structure Problem ◽  
Modularity Maximization ◽  
Chemical Knowledge

AbstractQuantum chemistry is interested in calculating ground and excited states of molecular systems by solving the electronic Schrödinger equation. The exact numerical solution of this equation, frequently represented as an eigenvalue problem, remains unfeasible for most molecules and requires approximate methods. In this paper we introduce the use of Quantum Community Detection performed using the D-Wave quantum annealer to reduce the molecular Hamiltonian matrix in Slater determinant basis without chemical knowledge. Given a molecule represented by a matrix of Slater determinants, the connectivity between Slater determinants (as off-diagonal elements) is viewed as a graph adjacency matrix for determining multiple communities based on modularity maximization. A gauge metric based on perturbation theory is used to determine the lowest energy cluster. This cluster or sub-matrix of Slater determinants is used to calculate approximate ground state and excited state energies within chemical accuracy. The details of this method are described along with demonstrating its performance across multiple molecules of interest and bond dissociation cases. These examples provide proof-of-principle results for approximate solution of the electronic structure problem using quantum computing. This approach is general and shows potential to reduce the computational complexity of post-Hartree–Fock methods as future advances in quantum hardware become available.

scholarly journals Community Detection in Multiplex Networks

2021 ◽  
Vol 54 (3) ◽  
pp. 1-35
Author(s):  
Matteo Magnani ◽  
Obaida Hanteer ◽  
Roberto Interdonato ◽  
Luca Rossi ◽  
Andrea Tagarelli
Keyword(s):  
Community Detection ◽  
Experimental Evaluation ◽  
Network Models ◽  
Ground Truth ◽  
Community Structures ◽  
Multiplex Networks ◽  
Detection Algorithms ◽  
Multiplex Network ◽  
The Right ◽  
Modes Of Interaction

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.

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