Improved community detection in weighted bipartite networks.
Ontology highlight
ABSTRACT:
SUBMITTER: Beckett SJ
PROVIDER: S-EPMC4736915 | biostudies-literature | 2016 Jan
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Networks are useful tools to represent and analyze interactions on a large, or genome-wide scale and have therefore been widely used in biology. Many biological networks-such as those that represent regulatory interactions, drug-gene, or gene-disease associations-are of a bipartite nature, meaning they consist of two different types of nodes, with connections only forming between the different node sets. Analysis of such networks requires methodologies that are specifically designed to handle their bipartite nature. Community structure detection is a method used to identify clusters of nodes in a network. This approach is especially helpful in large-scale biological network analysis, as it can find structure in networks that often resemble a "hairball" of interactions in visualizations. Often, the communities identified in biological networks are enriched for specific biological processes and thus allow one to assign drugs, regulatory molecules, or diseases to such processes. In addition, comparison of community structures between different biological conditions can help to identify how network rewiring may lead to tissue development or disease, for example. In this mini review, we give a theoretical basis of different methods that can be applied to detect communities in bipartite biological networks. We introduce and discuss different scores that can be used to assess the quality of these community structures. We then apply a wide range of methods to a drug-gene interaction network to highlight the strengths and weaknesses of these methods in their application to large-scale, bipartite biological networks.
| S-EPMC8099108 | biostudies-literature
Project description:Community detection is a ubiquitous problem in applied network analysis, however efficient techniques do not yet exist for all types of network data. Directed and weighted networks are an example, where the different information encoded by link weights and the possibly high graph density can cause difficulties for some approaches. Here we present an algorithm based on Voronoi partitioning generalized to deal with directed weighted networks. As an added benefit, this method can directly employ edge weights that represent lengths, in contrast to algorithms that operate with connection strengths, requiring ad-hoc transformations of length data. We demonstrate the method on inter-areal brain connectivity, air transportation networks, and several social networks. We compare the performance with several other well-known algorithms, applying them on a set of randomly generated benchmark networks. The algorithm can handle dense graphs where weights are the main factor determining communities. The hierarchical structure of networks can also be detected, as shown for the brain. Its time efficiency is comparable or even outperforms some of the state-of-the-art algorithms, the part with the highest time-complexity being Dijkstra's shortest paths algorithm ( O(|E|+|V|log|V|) ).
| S-EPMC10998900 | biostudies-literature
Project description:The human brain can be regarded as a complex network with interacting connections between brain regions. Complex brain network analyses have been widely applied to functional magnetic resonance imaging (fMRI) data and have revealed the existence of community structures in brain networks. The identification of communities may provide insight into understanding the topological functions of brain networks. Among various community detection methods, the modularity maximization (MM) method has the advantages of model conciseness, fast convergence and strong adaptability to large-scale networks and has been extended from single-layer networks to multilayer networks to investigate the community structure changes of brain networks. However, the problems of MM, suffering from instability and failing to detect hierarchical community structure in networks, largely limit the application of MM in the community detection of brain networks. In this study, we proposed the weighted modularity maximization (WMM) method by using the weight matrix to weight the adjacency matrix and improve the performance of MM. Moreover, we further proposed the two-step WMM method to detect the hierarchical community structures of networks by utilizing node attributes. The results of the synthetic networks without node attributes demonstrated that WMM showed better partition accuracy than both MM and robust MM and better stability than MM. The two-step WMM method showed better accuracy of community partitioning than WMM for synthetic networks with node attributes. Moreover, the results of resting state fMRI (rs-fMRI) data showed that two-step WMM had the advantage of detecting the hierarchical communities over WMM and was more insensitive to the density of the rs-fMRI networks than WMM.
| S-EPMC10707683 | biostudies-literature
Project description:In this work we are interested in identifying clusters of "positional equivalent" actors, i.e. actors who play a similar role in a system. In particular, we analyze weighted bipartite networks that describes the relationships between actors on one side and features or traits on the other, together with the intensity level to which actors show their features. We develop a methodological approach that takes into account the underlying multivariate dependence among groups of actors. The idea is that positions in a network could be defined on the basis of the similar intensity levels that the actors exhibit in expressing some features, instead of just considering relationships that actors hold with each others. Moreover, we propose a new clustering procedure that exploits the potentiality of copula functions, a mathematical instrument for the modelization of the stochastic dependence structure. Our clustering algorithm can be applied both to binary and real-valued matrices. We validate it with simulations and applications to real-world data.
| S-EPMC4193785 | biostudies-literature
Project description:Graph theory provides a powerful framework to investigate brain functional connectivity networks and their modular organization. However, most graph-based methods suffer from a fundamental resolution limit that may have affected previous studies and prevented detection of modules, or "communities", that are smaller than a specific scale. Surprise, a resolution-limit-free function rooted in discrete probability theory, has been recently introduced and applied to brain networks, revealing a wide size-distribution of functional modules (Nicolini and Bifone, 2016), in contrast with many previous reports. However, the use of Surprise is limited to binary networks, while brain networks are intrinsically weighted, reflecting a continuous distribution of connectivity strengths between different brain regions. Here, we propose Asymptotical Surprise, a continuous version of Surprise, for the study of weighted brain connectivity networks, and validate this approach in synthetic networks endowed with a ground-truth modular structure. We compare Asymptotical Surprise with leading community detection methods currently in use and show its superior sensitivity in the detection of small modules even in the presence of noise and intersubject variability such as those observed in fMRI data. We apply our novel approach to functional connectivity networks from resting state fMRI experiments, and demonstrate a heterogeneous modular organization, with a wide distribution of clusters spanning multiple scales. Finally, we discuss the implications of these findings for the identification of connector hubs, the brain regions responsible for the integration of the different network elements, showing that the improved resolution afforded by Asymptotical Surprise leads to a different classification compared to current methods.
| S-EPMC5312822 | biostudies-literature
Project description:The past decade has been marked with a proliferation of community detection algorithms that aim to organize nodes (e.g., individuals, brain regions, variables) into modular structures that indicate subgroups, clusters, or communities. Motivated by the emergence of big data across many fields of inquiry, these methodological developments have primarily focused on the detection of communities of nodes from matrices that are very large. However, it remains unknown if the algorithms can reliably detect communities in smaller graph sizes (i.e., 1000 nodes and fewer) which are commonly used in brain research. More importantly, these algorithms have predominantly been tested only on binary or sparse count matrices and it remains unclear the degree to which the algorithms can recover community structure for different types of matrices, such as the often used cross-correlation matrices representing functional connectivity across predefined brain regions. Of the publicly available approaches for weighted graphs that can detect communities in graph sizes of at least 1000, prior research has demonstrated that Newman's spectral approach (i.e., Leading Eigenvalue), Walktrap, Fast Modularity, the Louvain method (i.e., multilevel community method), Label Propagation, and Infomap all recover communities exceptionally well in certain circumstances. The purpose of the present Monte Carlo simulation study is to test these methods across a large number of conditions, including varied graph sizes and types of matrix (sparse count, correlation, and reflected Euclidean distance), to identify which algorithm is optimal for specific types of data matrices. The results indicate that when the data are in the form of sparse count networks (such as those seen in diffusion tensor imaging), Label Propagation and Walktrap surfaced as the most reliable methods for community detection. For dense, weighted networks such as correlation matrices capturing functional connectivity, Walktrap consistently outperformed the other approaches for recovering communities.
| S-EPMC5102890 | biostudies-literature
Project description:Genome Wide Association Studies (GWAS) and expression quantitative trait locus (eQTL) analyses have identified genetic associations with a wide range of human phenotypes. However, many of these variants have weak effects and understanding their combined effect remains a challenge. One hypothesis is that multiple SNPs interact in complex networks to influence functional processes that ultimately lead to complex phenotypes, including disease states. Here we present CONDOR, a method that represents both cis- and trans-acting SNPs and the genes with which they are associated as a bipartite graph and then uses the modular structure of that graph to place SNPs into a functional context. In applying CONDOR to eQTLs in chronic obstructive pulmonary disease (COPD), we found the global network "hub" SNPs were devoid of disease associations through GWAS. However, the network was organized into 52 communities of SNPs and genes, many of which were enriched for genes in specific functional classes. We identified local hubs within each community ("core SNPs") and these were enriched for GWAS SNPs for COPD and many other diseases. These results speak to our intuition: rather than single SNPs influencing single genes, we see groups of SNPs associated with the expression of families of functionally related genes and that disease SNPs are associated with the perturbation of those functions. These methods are not limited in their application to COPD and can be used in the analysis of a wide variety of disease processes and other phenotypic traits.
| S-EPMC5019382 | biostudies-literature
Project description:BACKGROUND:Recently, numerous biological experiments have indicated that microRNAs (miRNAs) play critical roles in exploring the pathogenesis of various human diseases. Since traditional experimental methods for miRNA-disease associations detection are costly and time-consuming, it becomes urgent to design efficient and robust computational techniques for identifying undiscovered interactions. METHODS:In this paper, we proposed a computation framework named weighted bipartite network projection for miRNA-disease association prediction (WBNPMD). In this method, transfer weights were constructed by combining the known miRNA and disease similarities, and the initial information was properly configured. Then the two-step bipartite network algorithm was implemented to infer potential miRNA-disease associations. RESULTS:The proposed WBNPMD was applied to the known miRNA-disease association data, and leave-one-out cross-validation (LOOCV) and fivefold cross-validation were implemented to evaluate the performance of WBNPMD. As a result, our method achieved the AUCs of 0.9321 and [Formula: see text] in LOOCV and fivefold cross-validation, and outperformed other four state-of-the-art methods. We also carried out two kinds of case studies on prostate neoplasm, colorectal neoplasm, and lung neoplasm, and most of the top 50 predicted miRNAs were confirmed to have an association with the corresponding diseases based on dbDeMC, miR2Disease, and HMDD V3.0 databases. CONCLUSIONS:The experimental results demonstrate that WBNPMD can accurately infer potential miRNA-disease associations. We anticipated that the proposed WBNPMD could serve as a powerful tool for potential miRNA-disease associations excavation.
| S-EPMC6757419 | biostudies-literature
Project description:We describe techniques for the robust detection of community structure in some classes of time-dependent networks. Specifically, we consider the use of statistical null models for facilitating the principled identification of structural modules in semi-decomposable systems. Null models play an important role both in the optimization of quality functions such as modularity and in the subsequent assessment of the statistical validity of identified community structure. We examine the sensitivity of such methods to model parameters and show how comparisons to null models can help identify system scales. By considering a large number of optimizations, we quantify the variance of network diagnostics over optimizations ("optimization variance") and over randomizations of network structure ("randomization variance"). Because the modularity quality function typically has a large number of nearly degenerate local optima for networks constructed using real data, we develop a method to construct representative partitions that uses a null model to correct for statistical noise in sets of partitions. To illustrate our results, we employ ensembles of time-dependent networks extracted from both nonlinear oscillators and empirical neuroscience data.
| S-EPMC3618100 | biostudies-other
Project description:The interactions between fundamental life molecules, people and social organisations build complex architectures that often result in undesired behaviours. Despite all of the advances made in our understanding of network structures over the past decade, similar progress has not been achieved in the controllability of real-world networks. In particular, an analytical framework to address the controllability of bipartite networks is still absent. Here, we present a dominating set (DS)-based approach to bipartite network controllability that identifies the topologies that are relatively easy to control with the minimum number of driver nodes. Our theoretical calculations, assisted by computer simulations and an evaluation of real-world networks offer a promising framework to control unidirectional bipartite networks. Our analysis should open a new approach to reverting the undesired behaviours in unidirectional bipartite networks at will.
| S-EPMC3622082 | biostudies-other