Attributed graph clustering, which aims to group the nodes of an attributed graph into disjoint clusters, has made promising advancements in recent years. However, most existing methods face challenges when applied to large graphs due to the expensive computational cost and high memory usage. In this paper, we introduce Scalable and Adaptive Spectral Embedding (SASE), a simple attributed graph clustering method devoid of parameter learning. SASE comprises three main components: node features smoothing via $k$-order simple graph convolution, scalable spectral clustering using random Fourier features, and adaptive order selection. With these designs, SASE not only effectively captures global cluster structures but also exhibits linear time and space complexity relative to the graph size. Empirical results demonstrate the superiority of SASE. For example, on the ArXiv dataset with 169K nodes and 1.17M edges, SASE achieves a 6.9\% improvement in ACC and a $5.87\times$ speedup compared to the runner-up, S3GC.
Single-cell RNA sequencing (scRNA-seq) data analysis is pivotal for understanding cellular heterogeneity. However, the high sparsity and complex noise patterns inherent in scRNA-seq data present significant challenges for traditional clustering methods. To address these issues, we propose a deep clustering method, Attention-Enhanced Structural Deep Embedding Graph Clustering (scASDC), which integrates multiple advanced modules to improve clustering accuracy and robustness.Our approach employs a multi-layer graph convolutional network (GCN) to capture high-order structural relationships between cells, termed as the graph autoencoder module. To mitigate the oversmoothing issue in GCNs, we introduce a ZINB-based autoencoder module that extracts content information from the data and learns latent representations of gene expression. These modules are further integrated through an attention fusion mechanism, ensuring effective combination of gene expression and structural information at each layer of the GCN. Additionally, a self-supervised learning module is incorporated to enhance the robustness of the learned embeddings. Extensive experiments demonstrate that scASDC outperforms existing state-of-the-art methods, providing a robust and effective solution for single-cell clustering tasks. Our method paves the way for more accurate and meaningful analysis of single-cell RNA sequencing data, contributing to better understanding of cellular heterogeneity and biological processes. All code and public datasets used in this paper are available at \url{https://github.com/wenwenmin/scASDC} and \url{https://zenodo.org/records/12814320}.
Attributed networks containing entity-specific information in node attributes are ubiquitous in modeling social networks, e-commerce, bioinformatics, etc. Their inherent network topology ranges from simple graphs to hypergraphs with high-order interactions and multiplex graphs with separate layers. An important graph mining task is node clustering, aiming to partition the nodes of an attributed network into k disjoint clusters such that intra-cluster nodes are closely connected and share similar attributes, while inter-cluster nodes are far apart and dissimilar. It is highly challenging to capture multi-hop connections via nodes or attributes for effective clustering on multiple types of attributed networks. In this paper, we first present AHCKA as an efficient approach to attributed hypergraph clustering (AHC). AHCKA includes a carefully-crafted K-nearest neighbor augmentation strategy for the optimized exploitation of attribute information on hypergraphs, a joint hypergraph random walk model to devise an effective AHC objective, and an efficient solver with speedup techniques for the objective optimization. The proposed techniques are extensible to various types of attributed networks, and thus, we develop ANCKA as a versatile attributed network clustering framework, capable of attributed graph clustering (AGC), attributed multiplex graph clustering (AMGC), and AHC. Moreover, we devise ANCKA with algorithmic designs tailored for GPU acceleration to boost efficiency. We have conducted extensive experiments to compare our methods with 19 competitors on 8 attributed hypergraphs, 16 competitors on 6 attributed graphs, and 16 competitors on 3 attributed multiplex graphs, all demonstrating the superb clustering quality and efficiency of our methods.
Graph clustering, a classical task in graph learning, involves partitioning the nodes of a graph into distinct clusters. This task has applications in various real-world scenarios, such as anomaly detection, social network analysis, and community discovery. Current graph clustering methods commonly rely on module pre-training to obtain a reliable prior distribution for the model, which is then used as the optimization objective. However, these methods often overlook deeper supervised signals, leading to sub-optimal reliability of the prior distribution. To address this issue, we propose a novel deep graph clustering method called CGCN. Our approach introduces contrastive signals and deep structural information into the pre-training process. Specifically, CGCN utilizes a contrastive learning mechanism to foster information interoperability among multiple modules and allows the model to adaptively adjust the degree of information aggregation for different order structures. Our CGCN method has been experimentally validated on multiple real-world graph datasets, showcasing its ability to boost the dependability of prior clustering distributions acquired through pre-training. As a result, we observed notable enhancements in the performance of the model.
Graph clustering, which involves the partitioning of nodes within a graph into disjoint clusters, holds significant importance for numerous subsequent applications. Recently, contrastive learning, known for utilizing supervisory information, has demonstrated encouraging results in deep graph clustering. This methodology facilitates the learning of favorable node representations for clustering by attracting positively correlated node pairs and distancing negatively correlated pairs within the representation space. Nevertheless, a significant limitation of existing methods is their inadequacy in thoroughly exploring node-wise similarity. For instance, some hypothesize that the node similarity matrix within the representation space is identical, ignoring the inherent semantic relationships among nodes. Given the fundamental role of instance similarity in clustering, our research investigates contrastive graph clustering from the perspective of the node similarity matrix. We argue that an ideal node similarity matrix within the representation space should accurately reflect the inherent semantic relationships among nodes, ensuring the preservation of semantic similarities in the learned representations. In response to this, we introduce a new framework, Reliable Node Similarity Matrix Guided Contrastive Graph Clustering (NS4GC), which estimates an approximately ideal node similarity matrix within the representation space to guide representation learning. Our method introduces node-neighbor alignment and semantic-aware sparsification, ensuring the node similarity matrix is both accurate and efficiently sparse. Comprehensive experiments conducted on $8$ real-world datasets affirm the efficacy of learning the node similarity matrix and the superior performance of NS4GC.
Multi-relational graph clustering has demonstrated remarkable success in uncovering underlying patterns in complex networks. Representative methods manage to align different views motivated by advances in contrastive learning. Our empirical study finds the pervasive presence of imbalance in real-world graphs, which is in principle contradictory to the motivation of alignment. In this paper, we first propose a novel metric, the Aggregation Class Distance, to empirically quantify structural disparities among different graphs. To address the challenge of view imbalance, we propose Balanced Multi-Relational Graph Clustering (BMGC), comprising unsupervised dominant view mining and dual signals guided representation learning. It dynamically mines the dominant view throughout the training process, synergistically improving clustering performance with representation learning. Theoretical analysis ensures the effectiveness of dominant view mining. Extensive experiments and in-depth analysis on real-world and synthetic datasets showcase that BMGC achieves state-of-the-art performance, underscoring its superiority in addressing the view imbalance inherent in multi-relational graphs. The source code and datasets are available at https://github.com/zxlearningdeep/BMGC.
Graph clustering, which aims to divide a graph into several homogeneous groups, is a critical area of study with applications that span various fields such as social network analysis, bioinformatics, and image segmentation. This paper explores both traditional and more recent approaches to graph clustering. Firstly, key concepts and definitions in graph theory are introduced. The background section covers essential topics, including graph Laplacians and the integration of Deep Learning in graph analysis. The paper then delves into traditional clustering methods, including Spectral Clustering and the Leiden algorithm. Following this, state-of-the-art clustering techniques that leverage deep learning are examined. A comprehensive comparison of these methods is made through experiments. The paper concludes with a discussion of the practical applications of graph clustering and potential future research directions.
In this work, we propose to use a local clustering approach based on the sparse solution technique to study the medical image, especially the lung cancer image classification task. We view images as the vertices in a weighted graph and the similarity between a pair of images as the edges in the graph. The vertices within the same cluster can be assumed to share similar features and properties, thus making the applications of graph clustering techniques very useful for image classification. Recently, the approach based on the sparse solutions of linear systems for graph clustering has been found to identify clusters more efficiently than traditional clustering methods such as spectral clustering. We propose to use the two newly developed local clustering methods based on sparse solution of linear system for image classification. In addition, we employ a box spline-based tight-wavelet-framelet method to clean these images and help build a better adjacency matrix before clustering. The performance of our methods is shown to be very effective in classifying images. Our approach is significantly more efficient and either favorable or equally effective compared with other state-of-the-art approaches. Finally, we shall make a remark by pointing out two image deformation methods to build up more artificial image data to increase the number of labeled images.
Graph clustering is an important unsupervised learning technique for partitioning graphs with attributes and detecting communities. However, current methods struggle to accurately capture true community structures and intra-cluster relations, be computationally efficient, and identify smaller communities. We address these challenges by integrating coarsening and modularity maximization, effectively leveraging both adjacency and node features to enhance clustering accuracy. We propose a loss function incorporating log-determinant, smoothness, and modularity components using a block majorization-minimization technique, resulting in superior clustering outcomes. The method is theoretically consistent under the Degree-Corrected Stochastic Block Model (DC-SBM), ensuring asymptotic error-free performance and complete label recovery. Our provably convergent and time-efficient algorithm seamlessly integrates with graph neural networks (GNNs) and variational graph autoencoders (VGAEs) to learn enhanced node features and deliver exceptional clustering performance. Extensive experiments on benchmark datasets demonstrate its superiority over existing state-of-the-art methods for both attributed and non-attributed graphs.
This paper proposes a model reduction approach for simplifying the interconnection topology of Lur'e network systems. A class of reduced-order models are generated by the projection framework based on graph clustering, which not only preserve the network structure but also ensure absolute stability. Furthermore, we provide an upper bound on the input-output approximation error between the original and reduced-order Lur'e network systems, which is expressed as a function of the characteristic matrix of graph clustering. Finally, the results are illustrated via a numerical example.
Graph Neural Networks (GNNs) have emerged as a prominent framework for graph mining, leading to significant advances across various domains. Stemmed from the node-wise representations of GNNs, existing explanation studies have embraced the subgraph-specific viewpoint that attributes the decision results to the salient features and local structures of nodes. However, graph-level tasks necessitate long-range dependencies and global interactions for advanced GNNs, deviating significantly from subgraph-specific explanations. To bridge this gap, this paper proposes a novel intrinsically interpretable scheme for graph classification, termed as Global Interactive Pattern (GIP) learning, which introduces learnable global interactive patterns to explicitly interpret decisions. GIP first tackles the complexity of interpretation by clustering numerous nodes using a constrained graph clustering module. Then, it matches the coarsened global interactive instance with a batch of self-interpretable graph prototypes, thereby facilitating a transparent graph-level reasoning process. Extensive experiments conducted on both synthetic and real-world benchmarks demonstrate that the proposed GIP yields significantly superior interpretability and competitive performance to~the state-of-the-art counterparts. Our code will be made publicly available.
Employing graph neural networks (GNNs) to learn cohesive and discriminative node representations for clustering has shown promising results in deep graph clustering. However, existing methods disregard the reciprocal relationship between representation learning and structure augmentation. This study suggests that enhancing embedding and structure synergistically becomes imperative for GNNs to unleash their potential in deep graph clustering. A reliable structure promotes obtaining more cohesive node representations, while high-quality node representations can guide the augmentation of the structure, enhancing structural reliability in return. Moreover, the generalization ability of existing GNNs-based models is relatively poor. While they perform well on graphs with high homogeneity, they perform poorly on graphs with low homogeneity. To this end, we propose a graph clustering framework named Synergistic Deep Graph Clustering Network (SynC). In our approach, we design a Transform Input Graph Auto-Encoder (TIGAE) to obtain high-quality embeddings for guiding structure augmentation. Then, we re-capture neighborhood representations on the augmented graph to obtain clustering-friendly embeddings and conduct self-supervised clustering. Notably, representation learning and structure augmentation share weights, significantly reducing the number of model parameters. Additionally, we introduce a structure fine-tuning strategy to improve the model's generalization. Extensive experiments on benchmark datasets demonstrate the superiority and effectiveness of our method. The code is released on GitHub and Code Ocean.
Expander decompositions of graphs have significantly advanced the understanding of many classical graph problems and led to numerous fundamental theoretical results. However, their adoption in practice has been hindered due to their inherent intricacies and large hidden factors in their asymptotic running times. Here, we introduce the first practically efficient algorithm for computing expander decompositions and their hierarchies and demonstrate its effectiveness and utility by incorporating it as the core component in a novel solver for the normalized cut graph clustering objective. Our extensive experiments on a variety of large graphs show that our expander-based algorithm outperforms state-of-the-art solvers for normalized cut with respect to solution quality by a large margin on a variety of graph classes such as citation, e-mail, and social networks or web graphs while remaining competitive in running time.
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.
The study seeks to develop an effective strategy based on the novel framework of statistical arbitrage based on graph clustering algorithms. Amalgamation of quantitative and machine learning methods, including the Kelly criterion, and an ensemble of machine learning classifiers have been used to improve risk-adjusted returns and increase immunity to transaction costs over existing approaches. The study seeks to provide an integrated approach to optimal signal detection and risk management. As a part of this approach, innovative ways of optimizing take profit and stop loss functions for daily frequency trading strategies have been proposed and tested. All of the tested approaches outperformed appropriate benchmarks. The best combinations of the techniques and parameters demonstrated significantly better performance metrics than the relevant benchmarks. The results have been obtained under the assumption of realistic transaction costs, but are sensitive to changes in some key parameters.
This paper presents an experiment conducted during a hackathon, focusing on using large language models (LLMs) and knowledge graph clustering to extract entities and relationships from astronomical text. The study demonstrates an approach to disambiguate entities that can appear in various contexts within the astronomical domain. By collecting excerpts around specific entities and leveraging the GPT-4 language model, relevant entities and relationships are extracted. The extracted information is then used to construct a knowledge graph, which is clustered using the Leiden algorithm. The resulting Leiden communities are utilized to identify the percentage of association of unknown excerpts to each community, thereby enabling disambiguation. The experiment showcases the potential of combining LLMs and knowledge graph clustering techniques for information extraction in astronomical research. The results highlight the effectiveness of the approach in identifying and disambiguating entities, as well as grouping them into meaningful clusters based on their relationships.
Effective resistance is a distance between vertices of a graph that is both theoretically interesting and useful in applications. We study a variant of effective resistance called the biharmonic distance. While the effective resistance measures how well-connected two vertices are, we prove several theoretical results supporting the idea that the biharmonic distance measures how important an edge is to the global topology of the graph. Our theoretical results connect the biharmonic distance to well-known measures of connectivity of a graph like its total resistance and sparsity. Based on these results, we introduce two clustering algorithms using the biharmonic distance. Finally, we introduce a further generalization of the biharmonic distance that we call the $k$-harmonic distance. We empirically study the utility of biharmonic and $k$-harmonic distance for edge centrality and graph clustering.
We consider the semi-random graph model of [Makarychev, Makarychev and Vijayaraghavan, STOC'12], where, given a random bipartite graph with $\alpha$ edges and an unknown bipartition $(A, B)$ of the vertex set, an adversary can add arbitrary edges inside each community and remove arbitrary edges from the cut $(A, B)$ (i.e. all adversarial changes are \textit{monotone} with respect to the bipartition). For this model, a polynomial time algorithm is known to approximate the Balanced Cut problem up to value $O(\alpha)$ [MMV'12] as long as the cut $(A, B)$ has size $\Omega(\alpha)$. However, it consists of slow subroutines requiring optimal solutions for logarithmically many semidefinite programs. We study the fine-grained complexity of the problem and present the first near-linear time algorithm that achieves similar performances to that of [MMV'12]. Our algorithm runs in time $O(|V(G)|^{1+o(1)} + |E(G)|^{1+o(1)})$ and finds a balanced cut of value $O(\alpha)$. Our approach appears easily extendible to related problem, such as Sparsest Cut, and also yields an near-linear time $O(1)$-approximation to Dagupta's objective function for hierarchical clustering [Dasgupta, STOC'16] for the semi-random hierarchical stochastic block model inputs of [Cohen-Addad, Kanade, Mallmann-Trenn, Mathieu, JACM'19].
Graph clustering is a central topic in unsupervised learning with a multitude of practical applications. In recent years, multi-view graph clustering has gained a lot of attention for its applicability to real-world instances where one has access to multiple data sources. In this paper we formalize a new family of models, called \textit{multi-view stochastic block models} that captures this setting. For this model, we first study efficient algorithms that naively work on the union of multiple graphs. Then, we introduce a new efficient algorithm that provably outperforms previous approaches by analyzing the structure of each graph separately. Furthermore, we complement our results with an information-theoretic lower bound studying the limits of what can be done in this model. Finally, we corroborate our results with experimental evaluations.
We present a novel end-to-end framework that generates highly compact (typically 6-15 dimensions), discrete (int4 type), and interpretable node representations, termed node identifiers (node IDs), to tackle inference challenges on large-scale graphs. By employing vector quantization, we compress continuous node embeddings from multiple layers of a Graph Neural Network (GNN) into discrete codes, applicable under both self-supervised and supervised learning paradigms. These node IDs capture high-level abstractions of graph data and offer interpretability that traditional GNN embeddings lack. Extensive experiments on 34 datasets, encompassing node classification, graph classification, link prediction, and attributed graph clustering tasks, demonstrate that the generated node IDs significantly enhance speed and memory efficiency while achieving competitive performance compared to current state-of-the-art methods.