graph clustering

Graphs are a standard representation for data in the social sciences, cybersecurity, computer infrastructure, bioinformatics, and more. Typical real-world graphs are sparse, meaning the average degree is small (in the tens, while the number of vertices is more than millions). When graph data is collected from a source, a major task is to perform data exploration. Thus, any region of ``density" is of interest, since it indicates special structure. An important goal is to cover a significant portion of the graph using dense subgraphs. Existing algorithms that find many dense subgraphs do not have overlapping output, and hence provide limited coverage. Other methods that produce overlapping clusters do not generate dense subgraphs. The main goal of this paper is to develop provable and practical methods that can provide overlapping dense subgraphs that can cover large portions of real-world networks. Our contribution is an algorithm CohortRecovery that achieves this goal. We first develop a mathematical framework of triadic cohorts that captures the notion of ``detectable dense subgraphs'' that potentially overlap. We prove that CohortRecovery can output a set of dense subgraphs, such that each triadic cohort is almost completely contained in some dense subgraph. We give a practical implementation of CohortRecovery and demonstrate it on a variety of datasets. It typically runs in under ten minutes on a commodity machine even on graphs with tens of millions of edges. For numerous datasets, CohortRecovery is able to cover more than 25\% of the vertices in non-trivial subgraphs of density more than 0.8, and is significantly better than a wide variety of scalable graph clustering/community detection algorithms. Moreover, we demonstrate that output of CohortRecovery captures ground truth clusters obtained by manual curation.

Networks are a fundamental tool for understanding and modeling complex systems in physics, biology, neuroscience, engineering, and social science. Many networks are known to exhibit rich, lower-order connectivity patterns that can be captured at the level of individual nodes and edges. However, higher-order organization of complex networks---at the level of small network subgraphs---remains largely unknown. Here we develop a generalized framework for clustering networks based on higher-order connectivity patterns. This framework provides mathematical guarantees on the optimality of obtained clusters and scales to networks with billions of edges. The framework reveals higher-order organization in a number of networks including information propagation units in neuronal networks and hub structure in transportation networks. Results show that networks exhibit rich higher-order organizational structures that are exposed by clustering based on higher-order connectivity patterns.

The stochastic block model (SBM) is a random graph model with different group of vertices connecting differently. It is widely employed as a canonical model to study clustering and community detection, and provides a fertile ground to study the information-theoretic and computational tradeoffs that arise in combinatorial statistics and more generally data science. This monograph surveys the recent developments that establish the fundamental limits for community detection in the SBM, both with respect to information-theoretic and computational tradeoffs, and for various recovery requirements such as exact, partial and weak recovery. The main results discussed are the phase transitions for exact recovery at the Chernoff-Hellinger threshold, the phase transition for weak recovery at the Kesten-Stigum threshold, the optimal SNR-mutual information tradeoff for partial recovery, and the gap between information-theoretic and computational thresholds. The monograph gives a principled derivation of the main algorithms developed in the quest of achieving the limits, in particular two-round algorithms via graph-splitting, semi-definite programming, (linearized) belief propagation, classical/nonbacktracking spectral methods and graph powering. Extensions to other block models, such as geometric block models, and a few open problems are also discussed.

Graphs, such as social networks, word co-occurrence networks, and communication networks, occur naturally in various real-world applications. Analyzing them yields insight into the structure of society, language, and different patterns of communication. Many approaches have been proposed to perform the analysis. Recently, methods which use the representation of graph nodes in vector space have gained traction from the research community. In this survey, we provide a comprehensive and structured analysis of various graph embedding techniques proposed in the literature. We first introduce the embedding task and its challenges such as scalability, choice of dimensionality, and features to be preserved, and their possible solutions. We then present three categories of approaches based on factorization methods, random walks, and deep learning, with examples of representative algorithms in each category and analysis of their performance on various tasks. We evaluate these state-of-the-art methods on a few common datasets and compare their performance against one another. Our analysis concludes by suggesting some potential applications and future directions. We finally present the open-source Python library we developed, named GEM (Graph Embedding Methods, available at this https URL), which provides all presented algorithms within a unified interface to foster and facilitate research on the topic.

Community detection in networks is one of the most popular topics of modern network science. Communities, or clusters, are usually groups of vertices having higher probability of being connected to each other than to members of other groups, though other patterns are possible. Identifying communities is an ill-defined problem. There are no universal protocols on the fundamental ingredients, like the definition of community itself, nor on other crucial issues, like the validation of algorithms and the comparison of their performances. This has generated a number of confusions and misconceptions, which undermine the progress in the field. We offer a guided tour through the main aspects of the problem. We also point out strengths and weaknesses of popular methods, and give directions to their use.

The processes by which communities come together, attract new members, and develop over time is a central research issue in the social sciences — political movements, professional organizations, and religious denominations all provide fundamental examples of such communities. In the digital domain, on-line groups are becoming increasingly prominent due to the growth of community and social networking sites such as MySpace and LiveJournal. However, the challenge of collecting and analyzing large-scale time-resolved data on social groups and communities has left most basic questions about the evolution of such groups largely unresolved: what are the structural features that influence whether individuals will join communities, which communities will grow rapidly, and how do the overlaps among pairs of communities change over time? Here we address these questions using two large sources of data: friendship links and community membership on LiveJournal, and co-authorship and conference publications in DBLP. Both of these datasets provide explicit user-defined communities, where conferences serve as proxies for communities in DBLP. We study how the evolution of these communities relates to properties such as the structure of the underlying social networks. We find that the propensity of individuals to join communities, and of communities to grow rapidly, depends in subtle ways on the underlying network structure. For example, the tendency of an individual to join a community is influenced not just by the number of friends he or she has within the community, but also crucially by how those friends are connected to one another. We use decision-tree techniques to identify the most significant structural determinants of these properties. We also develop a novel methodology for measuring movement of individuals between communities, and show how such movements are closely aligned with changes in the topics of interest within the communities.

Nodes in real-world networks organize into densely linked communities where edges appear with high concentration among the members of the community. Identifying such communities of nodes has proven to be a challenging task mainly due to a plethora of definitions of a community, intractability of algorithms, issues with evaluation and the lack of a reliable gold-standard ground-truth. In this paper we study a set of 230 large real-world social, collaboration and information networks where nodes explicitly state their group memberships. For example, in social networks nodes explicitly join various interest based social groups. We use such groups to define a reliable and robust notion of ground-truth communities. We then propose a methodology which allows us to compare and quantitatively evaluate how different structural definitions of network communities correspond to ground-truth communities. We choose 13 commonly used structural definitions of network communities and examine their sensitivity, robustness and performance in identifying the ground-truth. We show that the 13 structural definitions are heavily correlated and naturally group into four classes. We find that two of these definitions, Conductance and Triad-participation-ratio, consistently give the best performance in identifying ground-truth communities. We also investigate a task of detecting communities given a single seed node. We extend the local spectral clustering algorithm into a heuristic parameter-free community detection method that easily scales to networks with more than hundred million nodes. The proposed method achieves 30% relative improvement over current local clustering methods.

The modern science of networks has brought significant advances to our understanding of complex systems. One of the most relevant features of graphs representing real systems is community structure, or clustering, i. e. the organization of vertices in clusters, with many edges joining vertices of the same cluster and comparatively few edges joining vertices of different clusters. Such clusters, or communities, can be considered as fairly independent compartments of a graph, playing a similar role like, e. g., the tissues or the organs in the human body. Detecting communities is of great importance in sociology, biology and computer science, disciplines where systems are often represented as graphs. This problem is very hard and not yet satisfactorily solved, despite the huge effort of a large interdisciplinary community of scientists working on it over the past few years. We will attempt a thorough exposition of the topic, from the definition of the main elements of the problem, to the presentation of most methods developed, with a special focus on techniques designed by statistical physicists, from the discussion of crucial issues like the significance of clustering and how methods should be tested and compared against each other, to the description of applications to real networks.