Evaluating Overfit and Underfit in Models of Network Community Structure

A common data mining task on networks is community detection, which seeks an unsupervised decomposition of a network into structural groups based on statistical regularities in the network's connectivity. Although many methods exist, the No Free Lunch theorem for community detection implies that each makes some kind of tradeoff, and no algorithm can be optimal on all inputs. Thus, different algorithms will over or underfit on different inputs, finding more, fewer, or just different communities than is optimal, and evaluation methods that use a metadata partition as a ground truth will produce misleading conclusions about general accuracy. Here, we present a broad evaluation of over and underfitting in community detection, comparing the behavior of 16 state-of-the-art community detection algorithms on a novel and structurally diverse corpus of 406 real-world networks. We find that (i) algorithms vary widely both in the number of communities they find and in their corresponding composition, given the same input, (ii) algorithms can be clustered into distinct high-level groups based on similarities of their outputs on real-world networks, and (iii) these differences induce wide variation in accuracy on link prediction and link description tasks. We introduce a new diagnostic for evaluating overfitting and underfitting in practice, and use it to roughly divide community detection methods into general and specialized learning algorithms. Across methods and inputs, Bayesian techniques based on the stochastic block model and a minimum description length approach to regularization represent the best general learning approach, but can be outperformed under specific circumstances. These results introduce both a theoretically principled approach to evaluate over and underfitting in models of network community structure and a realistic benchmark by which new methods may be evaluated and compared.Comment: 22 pages, 13 figures, 3 table

The Bayan Algorithm: Detecting Communities in Networks Through Exact and Approximate Optimization of Modularity

Community detection is a classic problem in network science with extensive applications in various fields. Among numerous approaches, the most common method is modularity maximization. Despite their design philosophy and wide adoption, heuristic modularity maximization algorithms rarely return an optimal partition or anything similar. We propose a specialized algorithm, Bayan, which returns partitions with a guarantee of either optimality or proximity to an optimal partition. At the core of the Bayan algorithm is a branch-and-cut scheme that solves an integer programming formulation of the problem to optimality or approximate it within a factor. We demonstrate Bayan's distinctive accuracy and stability over 21 other algorithms in retrieving ground-truth communities in synthetic benchmarks and node labels in real networks. Bayan is several times faster than open-source and commercial solvers for modularity maximization making it capable of finding optimal partitions for instances that cannot be optimized by any other existing method. Overall, our assessments point to Bayan as a suitable choice for exact maximization of modularity in networks with up to 3000 edges (in their largest connected component) and approximating maximum modularity in larger networks on ordinary computers.Comment: 6 pages, 2 figures, 1 tabl

Resolution of ranking hierarchies in directed networks

Identifying hierarchies and rankings of nodes in directed graphs is fundamental in many applications such as social network analysis, biology, economics, and finance. A recently proposed method identifies the hierarchy by finding the ordered partition of nodes which minimises a score function, termed agony. This function penalises the links violating the hierarchy in a way depending on the strength of the violation. To investigate the resolution of ranking hierarchies we introduce an ensemble of random graphs, the Ranked Stochastic Block Model. We find that agony may fail to identify hierarchies when the structure is not strong enough and the size of the classes is small with respect to the whole network. We analytically characterise the resolution threshold and we show that an iterated version of agony can partly overcome this resolution limit.Comment: 27 pages, 9 figure

A generalised significance test for individual communities in networks

Many empirical networks have community structure, in which nodes are densely interconnected within each community (i.e., a group of nodes) and sparsely across different communities. Like other local and meso-scale structure of networks, communities are generally heterogeneous in various aspects such as the size, density of edges, connectivity to other communities and significance. In the present study, we propose a method to statistically test the significance of individual communities in a given network. Compared to the previous methods, the present algorithm is unique in that it accepts different community-detection algorithms and the corresponding quality function for single communities. The present method requires that a quality of each community can be quantified and that community detection is performed as optimisation of such a quality function summed over the communities. Various community detection algorithms including modularity maximisation and graph partitioning meet this criterion. Our method estimates a distribution of the quality function for randomised networks to calculate a likelihood of each community in the given network. We illustrate our algorithm by synthetic and empirical networks.Comment: 20 pages, 4 figures and 4 table

A Comprehensive Review of Community Detection in Graphs

The study of complex networks has significantly advanced our understanding of community structures which serves as a crucial feature of real-world graphs. Detecting communities in graphs is a challenging problem with applications in sociology, biology, and computer science. Despite the efforts of an interdisciplinary community of scientists, a satisfactory solution to this problem has not yet been achieved. This review article delves into the topic of community detection in graphs, which serves as a crucial role in understanding the organization and functioning of complex systems. We begin by introducing the concept of community structure, which refers to the arrangement of vertices into clusters, with strong internal connections and weaker connections between clusters. Then, we provide a thorough exposition of various community detection methods, including a new method designed by us. Additionally, we explore real-world applications of community detection in diverse networks. In conclusion, this comprehensive review provides a deep understanding of community detection in graphs. It serves as a valuable resource for researchers and practitioners in multiple disciplines, offering insights into the challenges, methodologies, and applications of community detection in complex networks

Transformers for Capturing Multi-level Graph Structure using Hierarchical Distances

Graph transformers need strong inductive biases to derive meaningful attention scores. Yet, current proposals rarely address methods capturing longer ranges, hierarchical structures, or community structures, as they appear in various graphs such as molecules, social networks, and citation networks. In this paper, we propose a hierarchy-distance structural encoding (HDSE), which models a hierarchical distance between the nodes in a graph focusing on its multi-level, hierarchical nature. In particular, this yields a framework which can be flexibly integrated with existing graph transformers, allowing for simultaneous application with other positional representations. Through extensive experiments on 12 real-world datasets, we demonstrate that our HDSE method successfully enhances various types of baseline transformers, achieving state-of-the-art empirical performances on 10 benchmark datasets