Multiple Community Detection Research Articles

VOLTA: adVanced mOLecular neTwork Analysis.

MotivationNetwork analysis is a powerful approach to investigate biological systems. It is often applied to study gene co-expression patterns derived from transcriptomics experiments. Even though co-expression analysis is widely used, there is still a lack of tools that are open and customizable on the basis of different network types and analysis scenarios (e.g. through function accessibility), but are also suitable for novice users by providing complete analysis pipelines.ResultsWe developed VOLTA, a Python package suited for complex co-expression network analysis. VOLTA is designed to allow users direct access to the individual functions, while they are also provided with complete analysis pipelines. Moreover, VOLTA offers when possible multiple algorithms applicable to each analytical step (e.g. multiple community detection or clustering algorithms are provided), hence providing the user with the possibility to perform analysis tailored to their needs. This makes VOLTA highly suitable for experienced users who wish to build their own analysis pipelines for a wide range of networks as well as for novice users for which a ‘plug and play’ system is provided.Availability and implementationThe package and used data are available at GitHub: https://github.com/fhaive/VOLTA and 10.5281/zenodo.5171719.Supplementary information Supplementary data are available at Bioinformatics online.

C ommunity D iff

Community detection is an oft-used analytical function of network analysis but can be a black art to apply in practice. Grouping of related nodes is important for identifying patterns in network datasets but also notoriously sensitive to input data and algorithm selection. This is further complicated by the fact that, depending on domain and use case, the ground truth knowledge of the end-user can vary from none to complete. In this work, we present C ommunity D iff , an interactive visualization system that combines visualization and active learning (AL) to support the end-user’s analytical process. As the end-user interacts with the system, a continuous refinement process updates both the community labels and visualizations. C ommunity D iff features a mechanism for visualizing ensemble spaces , weighted combinations of algorithm output, that can identify patterns, commonalities, and differences among multiple community detection algorithms. Among other features, C ommunity D iff introduces an AL mechanism that visually indicates uncertainty about community labels to focus end-user attention and supporting end-user control that ranges from explicitly indicating the number of expected communities to merging and splitting communities. Based on this end-user input, C ommunity D iff dynamically recalculates communities. We demonstrate the viability of our through a study of speed of end-user convergence on satisfactory community labels. As part of building C ommunity D iff , we describe a design process that can be adapted to other Interactive Machine Learning applications.

Sockpuppet gang detection on social media sites

Users of social media sites can use more than one account. These identities have pseudo anonymous properties, and as such some users abuse multiple accounts to perform undesirable actions, such as posting false or misleading remarks comments that praise or defame the work of others. The detection of multiple user accounts that are controlled by an individual or organization is important. Herein, we define the problem as sockpuppet gang (SPG) detection. First, we analyze user sentiment orientation to topics based on emotional phrases extracted from their posted comments. Then we evaluate the similarity between sentiment orientations of user account pairs, and build a similar-orientation network (SON) where each vertex represents a user account on a social media site. In an SON, an edge exists only if the two user accounts have similar sentiment orientations to most topics. The boundary between detected SPGs may be indistinct, thus by analyzing account posting behavior features we propose a multiple random walk method to iteratively remeasure the weight of each edge. Finally, we adopt multiple community detection algorithms to detect SPGs in the network. User accounts in the same SPG are considered to be controlled by the same individual or organization. In our experiments on real world datasets, our method shows better performance than other contemporary methods.

A separability framework for analyzing community structure

Four major factors govern the intricacies of community extraction in networks: (1) the literature offers a multitude of disparate community detection algorithms whose output exhibits high structural variability across the collection, (2) communities identified by algorithms may differ structurally from real communities that arise in practice, (3) there is no consensus characterizing how to discriminate communities from noncommunities, and (4) the application domain includes a wide variety of networks of fundamentally different natures. In this article, we present a class separability framework to tackle these challenges through a comprehensive analysis of community properties. Our approach enables the assessment of the structural dissimilarity among the output of multiple community detection algorithms and between the output of algorithms and communities that arise in practice. In addition, our method provides us with a way to organize the vast collection of community detection algorithms by grouping those that behave similarly. Finally, we identify the most discriminative graph-theoretical properties of community signature and the small subset of properties that account for most of the biases of the different community detection algorithms. We illustrate our approach with an experimental analysis, which reveals nuances of the structure of real and extracted communities. In our experiments, we furnish our framework with the output of 10 different community detection procedures, representative of categories of popular algorithms available in the literature, applied to a diverse collection of large-scale real network datasets whose domains span biology, online shopping, and social systems. We also analyze communities identified by annotations that accompany the data, which reflect exemplar communities in various domain. We characterize these communities using a broad spectrum of community properties to produce the different structural classes. As our experiments show that community structure is not a universal concept, our framework enables an informed choice of the most suitable community detection method for identifying communities of a specific type in a given network and allows for a comparison of existing community detection algorithms while guiding the design of new ones.

Exploring the limits of community detection strategies in complex networks

The characterization of network community structure has profound implications in several scientific areas. Therefore, testing the algorithms developed to establish the optimal division of a network into communities is a fundamental problem in the field. We performed here a highly detailed evaluation of community detection algorithms, which has two main novelties: 1) using complex closed benchmarks, which provide precise ways to assess whether the solutions generated by the algorithms are optimal; and, 2) A novel type of analysis, based on hierarchically clustering the solutions suggested by multiple community detection algorithms, which allows to easily visualize how different are those solutions. Surprise, a global parameter that evaluates the quality of a partition, confirms the power of these analyses. We show that none of the community detection algorithms tested provide consistently optimal results in all networks and that Surprise maximization, obtained by combining multiple algorithms, obtains quasi-optimal performances in these difficult benchmarks.