In recent years, models based on Graph Convolutional Networks (GCN) have made significant strides in the field of graph data analysis. However, challenges such as over-smoothing and over-compression remain when handling large-scale and complex graph datasets, leading to a decline in clustering quality. Although the Graph Transformer architecture has mitigated some of these issues, its performance is still limited when processing heterogeneous graph data. To address these challenges, this study proposes a novel deep clustering framework that comprising GCN, Autoencoder (AE), and Graph Transformer, termed the Tri-Learn Graph Fusion Network (Tri-GFN). This framework enhances the differentiation and consistency of global and local information through a unique tri-learning mechanism and feature fusion enhancement strategy. The framework integrates GCN, AE, and Graph Transformer modules. These components are meticulously fused by a triple-channel enhancement module, which maximizes the use of both node attributes and topological structures, ensuring robust clustering representation. The tri-learning mechanism allows mutual learning among these modules, while the feature fusion strategy enables the model to capture complex relationships, yielding highly discriminative representations for graph clustering. It surpasses many state-of-the-art methods, achieving an accuracy improvement of approximately 0.87% on the ACM dataset, 14.14 % on the Reuters dataset, and 7.58 % on the USPS dataset. Due to its outstanding performance on the Reuters dataset, Tri-GFN can be applied to automatic news classification, topic retrieval, and related fields.
Research on Graph Structure Learning (GSL) provides key insights for graph-based clustering, yet current methods like Graph Neural Networks (GNNs), Graph Attention Networks (GATs), and contrastive learning often rely heavily on the original graph structure. Their performance deteriorates when the original graph's adjacency matrix is too sparse or contains noisy edges unrelated to clustering. Moreover, these methods depend on learning node embeddings and using traditional techniques like k-means to form clusters, which may not fully capture the underlying graph structure between nodes. To address these limitations, this paper introduces DeSE, a novel unsupervised graph clustering framework incorporating Deep Structural Entropy. It enhances the original graph with quantified structural information and deep neural networks to form clusters. Specifically, we first propose a method for calculating structural entropy with soft assignment, which quantifies structure in a differentiable form. Next, we design a Structural Learning layer (SLL) to generate an attributed graph from the original feature data, serving as a target to enhance and optimize the original structural graph, thereby mitigating the issue of sparse connections between graph nodes. Finally, our clustering assignment method (ASS), based on GNNs, learns node embeddings and a soft assignment matrix to cluster on the enhanced graph. The ASS layer can be stacked to meet downstream task requirements, minimizing structural entropy for stable clustering and maximizing node consistency with edge-based cross-entropy loss. Extensive comparative experiments are conducted on four benchmark datasets against eight representative unsupervised graph clustering baselines, demonstrating the superiority of the DeSE in both effectiveness and interpretability.
The indicator matrix plays an important role in machine learning, but optimizing it is an NP-hard problem. We propose a new relaxation of the indicator matrix and prove that this relaxation forms a manifold, which we call the Relaxed Indicator Matrix Manifold (RIM manifold). Based on Riemannian geometry, we develop a Riemannian toolbox for optimization on the RIM manifold. Specifically, we provide several methods of Retraction, including a fast Retraction method to obtain geodesics. We point out that the RIM manifold is a generalization of the double stochastic manifold, and it is much faster than existing methods on the double stochastic manifold, which has a complexity of \( \mathcal{O}(n^3) \), while RIM manifold optimization is \( \mathcal{O}(n) \) and often yields better results. We conducted extensive experiments, including image denoising, with millions of variables to support our conclusion, and applied the RIM manifold to Ratio Cut, we provide a rigorous convergence proof and achieve clustering results that outperform the state-of-the-art methods. Our Code in \href{https://github.com/Yuan-Jinghui/Riemannian-Optimization-on-Relaxed-Indicator-Matrix-Manifold}{here}.
Given a graph $G$ and a seed node $v_s$, the objective of local graph clustering (LGC) is to identify a subgraph $C_s \in G$ (a.k.a. local cluster) surrounding $v_s$ in time roughly linear with the size of $C_s$. This approach yields personalized clusters without needing to access the entire graph, which makes it highly suitable for numerous applications involving large graphs. However, most existing solutions merely rely on the topological connectivity between nodes in $G$, rendering them vulnerable to missing or noisy links that are commonly present in real-world graphs. To address this issue, this paper resorts to leveraging the complementary nature of graph topology and node attributes to enhance local clustering quality. To effectively exploit the attribute information, we first formulate the LGC as an estimation of the bidirectional diffusion distribution (BDD), which is specialized for capturing the multi-hop affinity between nodes in the presence of attributes. Furthermore, we propose LACA, an efficient and effective approach for LGC that achieves superb empirical performance on multiple real datasets while maintaining strong locality. The core components of LACA include (i) a fast and theoretically-grounded preprocessing technique for node attributes, (ii) an adaptive algorithm for diffusing any vectors over $G$ with rigorous theoretical guarantees and expedited convergence, and (iii) an effective three-step scheme for BDD approximation. Extensive experiments, comparing 17 competitors on 8 real datasets, show that LACA outperforms all competitors in terms of result quality measured against ground truth local clusters, while also being up to orders of magnitude faster. The code is available at https://github.com/HaoranZ99/alac.
Deep recommender systems rely heavily on large embedding tables to handle high-cardinality categorical features such as user/item identifiers, and face significant memory constraints at scale. To tackle this challenge, hashing techniques are often employed to map multiple entities to the same embedding and thus reduce the size of the embedding tables. Concurrently, graph-based collaborative signals have emerged as powerful tools in recommender systems, yet their potential for optimizing embedding table reduction remains unexplored. This paper introduces GraphHash, the first graph-based approach that leverages modularity-based bipartite graph clustering on user-item interaction graphs to reduce embedding table sizes. We demonstrate that the modularity objective has a theoretical connection to message-passing, which provides a foundation for our method. By employing fast clustering algorithms, GraphHash serves as a computationally efficient proxy for message-passing during preprocessing and a plug-and-play graph-based alternative to traditional ID hashing. Extensive experiments show that GraphHash substantially outperforms diverse hashing baselines on both retrieval and click-through-rate prediction tasks. In particular, GraphHash achieves on average a 101.52% improvement in recall when reducing the embedding table size by more than 75%, highlighting the value of graph-based collaborative information for model reduction. Our code is available at https://github.com/snap-research/GraphHash.
Clustering the nodes of a graph is a cornerstone of graph analysis and has been extensively studied. However, some popular methods are not suitable for very large graphs: e.g., spectral clustering requires the computation of the spectral decomposition of the Laplacian matrix, which is not applicable for large graphs with a large number of communities. This work introduces PASCO, an overlay that accelerates clustering algorithms. Our method consists of three steps: 1-We compute several independent small graphs representing the input graph by applying an efficient and structure-preserving coarsening algorithm. 2-A clustering algorithm is run in parallel onto each small graph and provides several partitions of the initial graph. 3-These partitions are aligned and combined with an optimal transport method to output the final partition. The PASCO framework is based on two key contributions: a novel global algorithm structure designed to enable parallelization and a fast, empirically validated graph coarsening algorithm that preserves structural properties. We demonstrate the strong performance of 1 PASCO in terms of computational efficiency, structural preservation, and output partition quality, evaluated on both synthetic and real-world graph datasets.
Most existing graph clustering methods primarily focus on exploiting topological structure, often neglecting the ``missing-half" node feature information, especially how these features can enhance clustering performance. This issue is further compounded by the challenges associated with high-dimensional features. Feature selection in graph clustering is particularly difficult because it requires simultaneously discovering clusters and identifying the relevant features for these clusters. To address this gap, we introduce a novel paradigm called ``one node one model", which builds an exclusive model for each node and defines the node label as a combination of predictions for node groups. Specifically, the proposed ``Feature Personalized Graph Clustering (FPGC)" method identifies cluster-relevant features for each node using a squeeze-and-excitation block, integrating these features into each model to form the final representations. Additionally, the concept of feature cross is developed as a data augmentation technique to learn low-order feature interactions. Extensive experimental results demonstrate that FPGC outperforms state-of-the-art clustering methods. Moreover, the plug-and-play nature of our method provides a versatile solution to enhance GNN-based models from a feature perspective.
Local clustering aims to find a compact cluster near the given starting instances. This work focuses on graph local clustering, which has broad applications beyond graphs because of the internal connectivities within various modalities. While most existing studies on local graph clustering adopt the discrete graph setting (i.e., unweighted graphs without self-loops), real-world graphs can be more complex. In this paper, we extend the non-approximating Andersen-Chung-Lang ("ACL") algorithm beyond discrete graphs and generalize its quadratic optimality to a wider range of graphs, including weighted, directed, and self-looped graphs and hypergraphs. Specifically, leveraging PageRank, we propose two algorithms: GeneralACL for graphs and HyperACL for hypergraphs. We theoretically prove that, under two mild conditions, both algorithms can identify a quadratically optimal local cluster in terms of conductance with at least 1/2 probability. On the property of hypergraphs, we address a fundamental gap in the literature by defining conductance for hypergraphs from the perspective of hypergraph random walks. Additionally, we provide experiments to validate our theoretical findings.
We present a method for graph clustering that is analogous with gradient ascent methods previously proposed for clustering points in space. We show that, when applied to a random geometric graph with data iid from some density with Morse regularity, the method is asymptotically consistent. Here, consistency is understood with respect to a density-level clustering defined by the partition of the support of the density induced by the basins of attraction of the density modes.
Graph clustering is an essential aspect of network analysis that involves grouping nodes into separate clusters. Recent developments in deep learning have resulted in graph clustering, which has proven effective in many applications. Nonetheless, these methods often encounter difficulties when dealing with real-world graphs, particularly in the presence of noisy edges. Additionally, many denoising graph clustering methods tend to suffer from lower performance, training instability, and challenges in scaling to large datasets compared to non-denoised models. To tackle these issues, we introduce a new framework called the Robust Deep Graph Clustering Framework via Dual Soft Assignment (RDSA). RDSA consists of three key components: (i) a node embedding module that effectively integrates the graph's topological features and node attributes; (ii) a structure-based soft assignment module that improves graph modularity by utilizing an affinity matrix for node assignments; and (iii) a node-based soft assignment module that identifies community landmarks and refines node assignments to enhance the model's robustness. We assess RDSA on various real-world datasets, demonstrating its superior performance relative to existing state-of-the-art methods. Our findings indicate that RDSA provides robust clustering across different graph types, excelling in clustering effectiveness and robustness, including adaptability to noise, stability, and scalability.
Network analysis is increasingly important across various fields, including the fragrance industry, where perfumes are represented as nodes and shared user preferences as edges in perfume networks. Community detection can uncover clusters of similar perfumes, providing insights into consumer preferences, enhancing recommendation systems, and informing targeted marketing strategies. This study aims to apply community detection techniques to group perfumes favored by users into relevant clusters for better recommendations. We constructed a bipartite network from user reviews on the Persian retail platform "Atrafshan," with nodes representing users and perfumes, and edges formed by positive comments. This network was transformed into a Perfume Co-Preference Network, connecting perfumes liked by the same users. By applying community detection algorithms, we identified clusters based on shared preferences, enhancing our understanding of user sentiment in the fragrance market. To improve sentiment analysis, we integrated emojis and a user voting system for greater accuracy. Emojis, aligned with their Persian counterparts, captured the emotional tone of reviews, while user ratings for scent, longevity, and sillage refined sentiment classification. Edge weights were adjusted by combining adjacency values with user ratings in a 60:40 ratio, reflecting both connection strength and user preferences. These enhancements led to improved modularity of detected communities, resulting in more accurate perfume groupings. This research pioneers the use of community detection in perfume networks, offering new insights into consumer preferences. Our advancements in sentiment analysis and edge weight refinement provide actionable insights for optimizing product recommendations and marketing strategies in the fragrance industry.
Fair graph clustering is crucial for ensuring equitable representation and treatment of diverse communities in network analysis. Traditional methods often ignore disparities among social, economic, and demographic groups, perpetuating biased outcomes and reinforcing inequalities. This study introduces fair graph clustering within the framework of the disparate impact doctrine, treating it as a joint optimization problem integrating clustering quality and fairness constraints. Given the NP-hard nature of this problem, we employ a semidefinite relaxation approach to approximate the underlying optimization problem. For up to medium-sized graphs, we utilize a singular value decomposition-based algorithm, while for larger graphs, we propose a novel algorithm based on the alternative direction method of multipliers. Unlike existing methods, our formulation allows for tuning the trade-off between clustering quality and fairness. Experimental results on graphs generated from the standard stochastic block model demonstrate the superiority of our approach in achieving an optimal accuracy-fairness trade-off compared to state-of-the-art methods.
Cross-camera data association is one of the cornerstones of the multi-camera computer vision field. Although often integrated into detection and tracking tasks through architecture design and loss definition, it is also recognized as an independent challenge. The ultimate goal is to connect appearances of one item from all cameras, wherever it is visible. Therefore, one possible perspective on this task involves supervised clustering of the affinity graph, where nodes are instances captured by all cameras. They are represented by appropriate visual features and positional attributes. We leverage the advantages of GNN (Graph Neural Network) architecture to examine nodes' relations and generate representative edge embeddings. These embeddings are then classified to determine the existence or non-existence of connections in node pairs. Therefore, the core of this approach is graph connectivity prediction. Experimental validation was conducted on multicamera pedestrian datasets across diverse environments such as the laboratory, basketball court, and terrace. Our proposed method, named SGC-CCA, outperformed the state-of-the-art method named GNN-CCA across all clustering metrics, offering an end-to-end clustering solution without the need for graph post-processing. The code is available at https://github.com/djordjened92/cca-gnnclust.
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, 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 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.