In this paper, we propose anew class of low-cardinality algorithm that generalizes the local update tomaximize asemidefinite relaxation derived from max-k-cut.

A Noise-Resilient Semi-Supervised Graph Autoencoder for Overlapping Semantic Community Detection Abdelfateh Bekkair, Slimane Bellaouar and Slimane Oulad-Naoui Laboratoire des Mathématiques et Sciences Appliquées (LMSA), Université de Ghardaia, Ghardaia, Algeria Faculty of Sciences and Technology, Université de Ghardaia, Ghardaia, AlgeriaA R T I C L E I N F OKeywords: Overlapping community detection Graph attention autoencoder Semi-supervised learning Attributed networks Attribute noise analysis A B S T R A C T Community detection in networks with overlapping structures remains a significant challenge, particularly in noisy real-world environments where integrating topology, node attributes, and prior information is critical. To address this, we propose a semi-supervised graph autoencoder that combines graph multi-head attention and modularity maximization to robustly detect overlapping communities. The model learns semantic representations by fusing structural, attribute, and prior knowledge while explicitly addressing noise in node features. Key innovations include a noise-resistant architecture and a semantic semi-supervised design optimized for community quality through modularity constraints. Experiments demonstrate superior performance the model outperforms state-of-the-art methods in overlapping community detection (improvements in NMI and F1-score) and exhibits exceptional robustness to attribute noise, maintaining stable performance under 60% feature corruption.

This Dissertation is comprised of two main projects, addressing questions in neuroscience through applications of generative modeling. Project #1 (Chapter 4) explores how neurons encode features of the external world. I combine Helmholtz's "Perception as Unconscious Inference" -- paralleled by modern generative models like variational autoencoders (VAE) -- with the hierarchical structure of the visual cortex. This combination leads to the development of a hierarchical VAE model, which I test for its ability to mimic neurons from the primate visual cortex in response to motion stimuli. Results show that the hierarchical VAE perceives motion similar to the primate brain. Additionally, the model identifies causal factors of retinal motion inputs, such as object- and self-motion, in a completely unsupervised manner. Collectively, these results suggest that hierarchical inference underlines the brain's understanding of the world, and hierarchical VAEs can effectively model this understanding. Project #2 (Chapter 5) investigates the spatiotemporal structure of spontaneous brain activity and its reflection of brain states like rest. Using simultaneous fMRI and wide-field Ca2+ imaging data, this project demonstrates that the mouse cortex can be decomposed into overlapping communities, with around half of the cortical regions belonging to multiple communities. Comparisons reveal similarities and differences between networks inferred from fMRI and Ca2+ signals. The introduction (Chapter 1) is divided similarly to this abstract: sections 1.1 to 1.8 provide background information about Project #1, and sections 1.9 to 1.13 are related to Project #2. Chapter 2 includes historical background, Chapter 3 provides the necessary mathematical background, and finally, Chapter 6 contains concluding remarks and future directions.

Graph clustering, a fundamental and challenging task in graph mining, aims to classify nodes in a graph into several disjoint clusters. In recent years, graph contrastive learning (GCL) has emerged as a dominant line of research in graph clustering and advances the new state-of-the-art. However, GCL-based methods heavily rely on graph augmentations and contrastive schemes, which may potentially introduce challenges such as semantic drift and scalability issues. Another promising line of research involves the adoption of modularity maximization, a popular and effective measure for community detection, as the guiding principle for clustering tasks. Despite the recent progress, the underlying mechanism of modularity maximization is still not well understood. In this work, we dig into the hidden success of modularity maximization for graph clustering. Our analysis reveals the strong connections between modularity maximization and graph contrastive learning, where positive and negative examples are naturally defined by modularity. In light of our results, we propose a community-aware graph clustering framework, coined MAGI, which leverages modularity maximization as a contrastive pretext task to effectively uncover the underlying information of communities in graphs, while avoiding the problem of semantic drift. Extensive experiments on multiple graph datasets verify the effectiveness of MAGI in terms of scalability and clustering performance compared to state-of-the-art graph clustering methods. Notably, MAGI easily scales a sufficiently large graph with 100M nodes while outperforming strong baselines.

Community detection, which involves partitioning nodes within a network, has widespread applications across computational sciences. Modularity-based algorithms identify communities by attempting to maximize the modularity function across network node partitions. Our study assesses the performance of various modularity-based algorithms in obtaining optimal partitions. Our analysis utilizes 104 networks, including both real-world instances from diverse contexts and modular graphs from two families of synthetic benchmarks. We analyze ten inexact modularity-based algorithms against the exact integer programming baseline that globally optimizes modularity. Our comparative analysis includes eight heuristics, two variants of a graph neural network algorithm, and nine variations of the Bayan approximation algorithm. Our findings reveal that the average modularity-based heuristic yields optimal partitions in only 43.9% of the 104 networks analyzed. Graph neural networks and approximate Bayan, on average, achieve optimality on 68.7% and 82.3% of the networks respectively. Additionally, our analysis of three partition similarity metrics exposes substantial dissimilarities between high-modularity sub-optimal partitions and any optimal partition of the networks. We observe that near-optimal partitions are often disproportionately dissimilar to any optimal partition. Taken together, our analysis points to a crucial limitation of the commonly used modularity-based methods: they rarely produce an optimal partition or a partition resembling an optimal partition even on networks with modular structures. If modularity is to be used for detecting communities, we recommend approximate optimization algorithms for a more methodologically sound usage of modularity within its applicability limits.

The task of community detection, which aims to partition a network into clusters of nodes to summarize its large-scale structure, has spawned the development of many competing algorithms with varying objectives. Some community detection methods are inferential, explicitly deriving the clustering objective through a probabilistic generative model, while other methods are descriptive, dividing a network according to an objective motivated by a particular application, making it challenging to compare these methods on the same scale. Here we present a solution to this problem that associates any community detection objective, inferential or descriptive, with its corresponding implicit network generative model. This allows us to compute the description length of a network and its partition under arbitrary objectives, providing a principled measure to compare the performance of different algorithms without the need for "ground truth" labels. Our approach also gives access to instances of the community detection problem that are optimal to any given algorithm, and in this way reveals intrinsic biases in popular descriptive methods, explaining their tendency to overfit. Using our framework, we compare a number of community detection methods on artificial networks, and on a corpus of over 500 structurally diverse empirical networks. We find that more expressive community detection methods exhibit consistently superior compression performance on structured data instances, without having degraded performance on a minority of situations where more specialized algorithms perform optimally. Our results undermine the implications of the "no free lunch" theorem for community detection, both conceptually and in practice, since it is confined to unstructured data instances, unlike relevant community detection problems which are structured by requirement.

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 modularity maximization problem to optimality or approximate it within a factor. We compare Bayan against 30 alternative community detection methods using structurally diverse synthetic and real networks. Our results demonstrate Bayan's distinctive accuracy and stability in retrieving ground-truth communities of standard benchmark graphs. 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 real networks with up to 3000 edges (in their largest connected component) and approximating maximum modularity in larger instances on ordinary computers. A Python implementation of the Bayan algorithm (the bayanpy library) is publicly available through the package installer for Python (pip).

Normalized mutual information is widely used as a similarity measure for evaluating the performance of clustering and classification algorithms. In this paper, we show that results returned by the normalized mutual information are biased for two reasons: first, because they ignore the information content of the contingency table and, second, because their symmetric normalization introduces spurious dependence on algorithm output. We introduce a modified version of the mutual information that remedies both of these shortcomings. As a practical demonstration of the importance of using an unbiased measure, we perform extensive numerical tests on a basket of popular algorithms for network community detection and show that one's conclusions about which algorithm is best are significantly affected by the biases in the traditional mutual information.

Community detection is a fundamental problem in computational sciences with extensive applications in various fields. The most commonly used methods are the algorithms designed to maximize modularity over different partitions of the network nodes. Using 80 real and random networks from a wide range of contexts, we investigate the extent to which current heuristic modularity maximization algorithms succeed in returning maximum-modularity (optimal) partitions. We evaluate (1) the ratio of the algorithms' output modularity to the maximum modularity for each input graph, and (2) the maximum similarity between their output partition and any optimal partition of that graph. We compare eight existing heuristic algorithms against an exact integer programming method that globally maximizes modularity. The average modularity-based heuristic algorithm returns optimal partitions for only 19.4% of the 80 graphs considered. Additionally, results on adjusted mutual information reveal substantial dissimilarity between the sub-optimal partitions and any optimal partition of the networks in our experiments. More importantly, our results show that near-optimal partitions are often disproportionately dissimilar to any optimal partition. Taken together, our analysis points to a crucial limitation of commonly used modularity-based heuristics for discovering communities: they rarely produce an optimal partition or a partition resembling an optimal partition. If modularity is to be used for detecting communities, exact or approximate optimization algorithms are recommendable for a more methodologically sound usage of modularity within its applicability limits.

The analysis of network structure is essential to many scientific areas, ranging from biology to sociology. As the computational task of clustering these networks into partitions, i.e., solving the community detection problem, is generally NP-hard, heuristic solutions are indispensable. The exploration of expedient heuristics has led to the development of particularly promising approaches in the emerging technology of quantum computing. Motivated by the substantial hardware demands for all established quantum community detection approaches, we introduce a novel QUBO based approach that only needs number-of-nodes many qubits and is represented by a QUBO-matrix as sparse as the input graph's adjacency matrix. The substantial improvement on the sparsity of the QUBO-matrix, which is typically very dense in related work, is achieved through the novel concept of separation-nodes. Instead of assigning every node to a community directly, this approach relies on the identification of a separation-node set, which -- upon its removal from the graph -- yields a set of connected components, representing the core components of the communities. Employing a greedy heuristic to assign the nodes from the separation-node sets to the identified community cores, subsequent experimental results yield a proof of concept. This work hence displays a promising approach to NISQ ready quantum community detection, catalyzing the application of quantum computers for the network structure analysis of large scale, real world problem instances.