Graph Clustering

Single-cell RNA sequencing (scRNA-seq) serves a pivotal role in characterizing gene expression at the cellular level, enabling the identification of cell types and advancing the understanding of cellular heterogeneity. Despite the significant progress in scRNA-seq data clustering, we argue that current methods always ignore the sparsity and noise, as well as the complex intercellular structural information inherent in scRNA-seq data. Toward this end, in this paper, we propose a novel single-cell RNA-seq clustering framework via deep Siamese Graph Transformer Network (termed scGTN), which explicitly integrates gene expression profile and intercellular structural dependencies for cell clustering. In particular, we formulate scRNA-seq data as a graph and construct two augmented graph views that serve as dual views to capture complementary intercellular information. Then, a Siamese graph transformer network is employed to explicitly incorporate shortest-path information and node-wise distances for capturing richer structural relationships between cells. Finally, we employ an optimal transport strategy to guide the cell clustering in a self-supervised manner. Extensive experiments on multiple benchmark scRNA-seq datasets demonstrate that our scGTN consistently outperforms existing methods. Our code is available at https://github.com/W-RMSL/scGTN.

Graph clustering - partitioning the node set of a graph into disjoint subsets that reflect some latent information - is a fundamental problem as it finds applications in a myriad of different scenarios. While this classic problem has been tackled for decades by different communities, a recent variation of the problem driven by real data considers the scenario where nodes have attributes that are also informative. This has triggered novel methods that simultaneously leverage network information (edges) and node information (attributed) in the design of novel clustering algorithms. This work proposes a novel framework that builds on prior works that have applied graph neural networks (GNN) to graph clustering. The proposed framework operates in rounds of self learning in a fully unsupervised setting. In each round, a GNN generates representations for nodes that are used to cluster the nodes. This clustering influences the graph used to generate the node representation in the next round. Moreover, a context graph built in each round using the original graph is used to generate the node representations. Empirical results show that the proposed methodology extracts information from both network edges and node attributes in synthetic data, outperforming algorithms focused solely on the network or attributes when neither are very informative. Multiple rounds of learning also improve the performance and always outperforms a long single round of training (i.e., classic GNN graph clustering). When considering real datasets, empirical results indicate that the proposed methodology is competitive to state-of-the-art methods when cluster sizes are balanced.

Unsupervised term discovery involves segmenting unlabelled speech into word- or syllable-like units and clustering these into a lexicon of candidate types. True lexicons follow a Zipfian distribution, yet the dominant centre-based clustering approach -- K-means -- produces a more uniform distribution due to an inductive bias toward spherical clusters. In this paper we revisit graph-based clustering as a bottom-up alternative, where segment embeddings are connected by pairwise similarity and partitioned using the Leiden algorithm. We show that graph clustering substantially outperforms centre-based approaches (K-means, GMM, BIRCH) in both word- and syllable-level lexicon discovery across three languages, producing more Zipf-like distributions. Another bottom-up approach, agglomerative clustering with average linkage, also performs well, although it is computationally less efficient and allows for less control over the resulting distribution. Our work calls into question the dominance of centre-based clustering for term discovery, and promotes graph clustering as an attractive alternative.

Local Hyper-Flow Diffusion (HFD) gives an edge-size-independent Cheeger-type guarantee for seeded clustering in general submodular hypergraphs, but existing HFD solvers do not keep intermediate computation local at every iteration. We introduce Thresholded Local HFD (TL-HFD), a first-order method that maintains an active region around the seeds, performs projected subgradient updates on that region and its immediate boundary, and expands via thresholded (top-k) boundary activation. We prove that the local update is exact: the degree-preconditioned projected subgradient step restricted to the active region and its boundary coincides with the unrestricted global update. We establish finite-time dual suboptimality for both exact and thresholded updates, treating the latter as inexact projected subgradient steps with explicit skipped-boundary error. We further derive an additive activated-volume bound controlled by realized local subgradient norms and the minimum boundary-push among newly activated vertices, and translate approximate dual optimality with localized support into a robust sweep-cut guarantee for early-stopped iterates. For general submodular cut-costs, each iteration is local in the scanned region and oracle-sensitive in the hyperedge primitive. Empirically, TL-HFD often matches or improves over HFD while activating less volume, with the largest gains on noisy instances where diffusion tends to absorb non-target vertices.

Community detection is a fundamental problem in the analysis of complex networks. It has applications across social, biological, and financial domains. Traditional algorithms such as Louvain, LPA, and modularity optimization often require manual parameter tuning. They also suffer from inaccurate cluster center selection and struggle with scalability. To address these challenges, we propose Automatic Laplacian Centrality Means (ALCMeans), a novel community detection algorithm. ALCMeans combines Laplacian energy-based automatic center identification with DeepWalk embeddings for robust node representation. Unlike existing Laplacian-based and clustering methods, ALCMeans eliminates the need to predefine the number of communities, enhances cluster center selection using structural importance, and leverages representation learning for more accurate and stable assignments. Experimental results on benchmark datasets demonstrate 10 to 20 percent higher NMI and ARI scores compared to Louvain, Newman-Girvan, LPA, Fast-Greedy, and a recent GNN-based competitor (MAGI, KDD 2024). Additional evaluations with modularity and F1-scores confirm the superiority of ALCMeans. Ablation studies highlight the critical contributions of each component. Despite its reliance on DeepWalk parameters and increased runtime relative to lightweight heuristics, ALCMeans consistently outperforms state-of-the-art methods. This makes it a promising tool for real-world network analysis.

We study the symmetric multi-type orthogonal non-negative matrix tri-factorization problem, where several symmetric non-negative matrices are simultaneously approximated by factors of the form $GS_{i}G^{\top}$, with a shared non-negative and orthogonal factor $G$. This model is motivated by clustering and network analysis, where non-negativity improves interpretability and orthogonality gives a natural assignment-type structure to the latent factor. Since the resulting optimization problem is highly non-convex, we develop two heuristic algorithms for computing high-quality local solutions. The first one is a fixed point method derived from the Karush-Kuhn-Tucker conditions after adding a penalty term for the orthogonality constraint. The second one is a three-stage ADAM-based method that combines non-negativity-preserving optimization, orthogonalization, and restricted ADAM refinement on the feasible set. We evaluate both methods on synthetic data, including noisy instances, and on citation network benchmarks. The synthetic experiments show that both algorithms recover factorizations close to the optimum and remain stable under noise. On real networks, the learned embeddings are competitive with or better than standard baselines such as SVD, node2vec, and classical link prediction heuristics in link prediction, node clustering, and node classification tasks.

We establish the first sharp thresholds for low-degree polynomial tests in planted-vs-planted settings, where the goal is to determine with vanishing error which of two structured planted mechanisms generated the observed data. We prove matching low-degree upper and lower bounds for counting communities in the planted submatrix and planted dense subgraph models. The resulting testing threshold coincides, down to the sharp constant, with the known low-degree recovery threshold. In contrast, the task of weak testing, where the goal is to outperform random guessing, does not have a sharp threshold but rather a smooth transition, which we identify. To prove our results, we develop a framework for planted-vs-planted testing that builds on a latent-variable expansion originating in low-degree recovery and employs new methods to identify and prune non-signal contributions.

Symmetric nonnegative matrix factorization (Symmetric NMF) approximates a matrix as $WW^T$ with nonnegative rectangular factor $W$. It has broad applications in graph clustering and machine learning. In contrast to the NMF, projected gradient methods for the symmetric problem had been associated with slow convergence. To address this, we introduce SNMPBB, the first adaptation of nonmonotone projected Barzilai-Borwein methods to Symmetric NMF, demonstrating that gradient algorithms are significantly more effective than previously understood. We further extend SNMPBB to graph clustering using the graph Laplacian regularization (Graph-SNMPBB) and to large problems with low-rank approximations (LAI-SNMPBB). For all variants we prove global convergence to first-order stationary points and also that Barzilai-Borwein curvature information is preserved with randomized approximations. On synthetic data, SNMPBB achieves 6 times speedup over the alternative SymANLS for similar residuals, with advantages growing at higher ranks. Across six real-world clustering benchmarks, Graph-SNMPBB matches or exceeds SymANLS accuracy. Lastly, LAI-SNMPBB outperforms state-of-the-art LAI-SymPGNCG on 34 SuiteSparse matrices in both runtime and residual quality.

We study exact community recovery in the two-community stochastic block model on $n$ vertices under limited and noisy access to network data. The learner may query a noisy neighborhood oracle that reveals each true neighbor of a queried vertex independently with fixed probability and never returns non-neighbors, subject to a finite query budget. We consider both oracle-only access and a combined model where the learner also observes a single subsampled copy of the underlying graph. For oracle-only access, balanced uniform querying gives a sharp non-adaptive benchmark: when each vertex is queried the same integer number of times, the observations reduce to an SBM with attenuated edge probabilities and the Abbe-Bandeira-Hall exact-recovery threshold applies. We show that this benchmark is not adaptively optimal: a two-stage adaptive strategy succeeds with $n+o(n)$ queries in a regime where balanced uniform querying requires $m n$ queries for some $m>1$. With an additional subsampled graph, we prove a sublinear-query adaptivity gap: balanced data-independent uniform querying with a sublinear budget does not improve over the subsampled graph alone, whereas adaptive querying can target a small set of uncertain vertices and achieve exact recovery. Thus adaptive data acquisition can strictly improve the information-theoretic limits of exact recovery.

We study inference in stochastic block models (SBMs) through the lens of optimal transport (OT). We first establish that maximum likelihood variational inference (MLVI) can be interpreted as a semi-relaxed Gromov-Wasserstein (srGW) projection with entropic regularization. While this formulation yields accurate clustering, the entropic regularization prevents transport plans to be sparse, hindering intrinsic model selection. Consequently, we investigate unregularized srGW estimators, and prove that they consistently recover both the SBM connectivity matrix and latent cluster assignments in the asymptotic regime. However, this asymptotic property does not translate into reliable model selection in finite samples, and calls for additional mechanisms to promote sparsity in the inferred cluster proportions. We empirically show that such a regularized formulation yields estimators that simultaneously recover model parameters and select the number of clusters in a single optimization problem, thereby avoiding costly grid search or heuristic model selection procedures.

Graph clustering is essential in graph analysis for revealing structural patterns and node communities. Despite recent advances in self-supervised contrastive learning that have improved clustering via structural and attribute signals, existing methods still struggle to flexibly capture high-order local structures and often overlook global semantics in complex graphs. These limitations lead to suboptimal node representations, especially in real-world graphs with fragmented structures and ambiguous cluster boundaries. To address these limitations, a contrastive graph clustering framework is proposed to jointly integrate multi-scale local structures with global semantics via attention mechanisms. At the local level, GNN-based topological signals extracted from multiple propagation depths are adaptively fused through attention-based weighting to capture multi-scale neighborhood features. At the global level, semantic prototypes derived from dynamically evolving cluster centers are adaptively aggregated through attention to guide node representations and enhance inter-cluster separability. The model is trained under a dual-view contrastive learning paradigm with a hybrid objective that combines instance-level and structure-aware losses to improve representation robustness and discrimination. Experiments on eight real-world graph datasets demonstrate that our method achieves competitive clustering performance. Code is available at https://github.com/vege12138/w2.

Graph Partitioning is a critical problem in numerous scientific and engineering domains including social network analysis, VLSI design, and many more. Spectral methods are known to produce quality partitions while minimizing edge cuts for a wide range of problems. However, the computational cost associated with the calculation of the Fiedler vector, an eigenvector associated with the second smallest eigenvalue of the graph Laplacian, remains a significant bottleneck due to memory issues and computational costs. In this paper, we present an accelerated approach to spectral bisection partitioning by replacing the traditional eigenvalue calculation with a simple artificial neural network model to approximate the Fiedler vector. We demonstrate that our approach achieves partitioning quality comparable to spectral bisection while significantly reducing the computational overhead, making it more scalable and efficient for large-scale problems

We introduce \textbf{Prism}, a framework for structural symmetry diagnosis in complex networks. Given a graph Laplacian $L$ and a duality operator $P$ (a symmetric involution), Prism computes the \emph{duality defect} $δ(L,P) = \|LP - PL\|_F / \|L\|_F$ -- a scalar measuring how far the network deviates from structural self-consistency. When $P$ encodes the network's true symmetry, $δ$ starts near zero and rises monotonically as structure degrades; an arbitrary $P$ gives noise. We prove that the optimal $L'$ satisfying $[L', P] = 0$ is given by a closed-form block-diagonal projection, and provide an unsupervised alternating optimization that learns $P$ from the graph's own Fiedler vector. Experiments on synthetic networks show the true-$P$ defect is $3.38\times$ more sensitive to structural degradation than an index-reversal baseline and more sensitive than modularity. On Zachary's Karate Club with edge noise, Prism achieves $94.5\%$ community detection accuracy at $5\%$ noise versus $76.6\%$ for the raw Laplacian baseline. Applied to live S&P~500 data (2026-05-17), Prism detects rising structural stress (defect $0.43 \to 0.73$ over 90 days) while surface correlations remain low -- a signal invisible to correlation-based methods. In a historical backtest spanning five major stress events (2011--2020), the duality defect exhibits a consistent pattern: it reaches elevated levels \emph{before} the correlation spike that accompanies each crisis, and sustains high readings during periods of structural fragility that conventional metrics classify as calm. The duality defect is a first-principles structural admissibility condition, requiring no training data and computable in milliseconds.

Citation graphs are fundamental tools for modeling scientific structure, but are often fragmented due to missing citations of scientifically connected articles. To address this issue, we propose a computationally efficient hybrid framework integrating citation topology with large language model (LLM)-based text similarity. Using 662,369 Web of Science publications in Mathematics and Operations Research & Management Science, we augment the original graph by adding semantic edges from small, disconnected components and weighting existing citations according to textual similarity. Semantic augmentation substantially reduces fragmentation while preserving disciplinary homogeneity. Compared to embedding-only clustering, cluster detection on augmented graphs using the Leiden algorithm retains structural interpretability while offering multi-scale organization. The method scales efficiently to large datasets and offers a practical strategy for strengthening citation-based indicators without collapsing disciplinary boundaries.

We present AdaGraph, a graph-native clustering algorithm born from the Structure-Centric Machine Learning (SC-ML) paradigm -- a new field of unsupervised learning that replaces geometry-centric (distance-based) computation with structure-centric (topology-based) computation, fundamentally dissolving the curse of dimensionality. AdaGraph operates entirely within the kNN graph topology, a representation that retains meaningful relational structure in arbitrarily high dimensions where Euclidean distance metrics become uninformative. AdaGraph requires no a priori specification of the number of clusters k, handles noise natively, and scales via the SLCD (Sample-Learn-Calibrate-Deploy) prototype-deployment framework. As its unsupervised tuning objective, AdaGraph pairs with Graph-SCOPE, the topology-based cluster validity index introduced as a separate SC-ML contribution. On 10 synthetic benchmarks spanning d=10 to d=5000, Graph-SCOPE achieves mean ARI=0.900 and correctly selects k on 9/10 datasets -- outperforming Silhouette, Davies-Bouldin, and Calinski-Harabasz -- while maintaining Kendall tau >= 0.92 with ground-truth cluster quality across all dimensionalities (Silhouette: tau ~= 0.46). We validate AdaGraph across three scientific domains: (1) gene co-expression discovery in hepatocellular carcinoma (GSE14520, 10,000 genes, 488 patients, no dimensionality reduction), where AdaGraph identifies condition-specific gene modules that WGCNA, ICA, NMF, and Spectral Biclustering fail to resolve; (2) natural language text clustering, where AdaGraph achieves ARI=0.751 on 20NG-6cat versus HDBSCAN's 0.464 (62% relative improvement); (3) materials science clustering of superconductors (145-dimensional Magpie features), perovskites, and JARVIS-DFT materials, where AdaGraph achieves the highest Graph-SCOPE on all three datasets.

We propose a streamlined spectral algorithm for community detection in the two-community stochastic block model (SBM) under constant edge density assumptions. By reducing algorithmic complexity through the elimination of non-essential preprocessing steps, our method directly leverages the spectral properties of the adjacency matrix. We demonstrate that our algorithm exploits specific characteristics of the second eigenvector to achieve improved error bounds that approach information-theoretic limits, representing a significant improvement over existing methods. Theoretical analysis establishes that our error rates are tighter than previously reported bounds in the literature. Comprehensive experimental validation confirms our theoretical findings and demonstrates the practical effectiveness of the simplified approach. Our results suggest that algorithmic simplification, rather than increasing complexity, can lead to both computational efficiency and enhanced performance in spectral community detection.

Given a weighted undirected graph, a number of clusters $k$, and an exponent $z$, the goal in the $(k, z)$-clustering problem on graphs is to select $k$ vertices as centers that minimize the sum of the distances raised to the power $z$ of each vertex to its closest center. In the dynamic setting, the graph is subject to adversarial edge updates, and the goal is to maintain explicitly an exact $(k, z)$-clustering solution in the induced shortest-path metric. While efficient dynamic $k$-center approximation algorithms on graphs exist [Cruciani et al. SODA 2024], to the best of our knowledge, no prior work provides similar results for the dynamic $(k,z)$-clustering problem. As the main result of this paper, we develop a randomized incremental $(k, z)$-clustering algorithm that maintains with high probability a constant-factor approximation in a graph undergoing edge insertions with a total update time of $\tilde O(k m^{1+o(1)}+ k^{1+\frac{1}λ} m)$, where $λ\geq 1$ is an arbitrary fixed constant. Our incremental algorithm consists of two stages. In the first stage, we maintain a constant-factor bicriteria approximate solution of size $\tilde{O}(k)$ with a total update time of $m^{1+o(1)}$ over all adversarial edge insertions. This first stage is an intricate adaptation of the bicriteria approximation algorithm by Mettu and Plaxton [Machine Learning 2004] to incremental graphs. One of our key technical results is that the radii in their algorithm can be assumed to be non-decreasing while the approximation ratio remains constant, a property that may be of independent interest. In the second stage, we maintain a constant-factor approximate $(k,z)$-clustering solution on a dynamic weighted instance induced by the bicriteria approximate solution. For this subproblem, we employ a dynamic spanner algorithm together with a static $(k,z)$-clustering algorithm.

Min cut is an important graph partitioning method. However, current solutions to the min cut problem suffer from slow speeds, difficulty in solving, and often converge to simple solutions. To address these issues, we relax the min cut problem into a double-bounded constraint and, for the first time, treat the min cut problem as a double-bounded nonlinear optimal transport problem. Additionally, we develop a method for solving double bounded nonlinear optimal transport based on the Frank-Wolfe method (abbreviated as DNF). We prove that for convex problems satisfying Lipschitz smoothness, the DNF method can achieve a convergence rate of $\mathcal{O}(\frac{1}{t})$. We apply DNF to size-constrained min-cut clustering and evaluate it on eight benchmark datasets. DNF achieves competitive clustering performance and matches or outperforms the compared baselines on several datasets and metrics.

Clustering is a fundamental task in machine learning and data science, and similarity graph-based clustering is an important approach within this domain. Doubly stochastic symmetric similarity graphs provide numerous benefits for clustering problems and downstream tasks, yet learning such graphs remains a significant challenge. Marcus theorem states that a strictly positive symmetric matrix can be transformed into a doubly stochastic symmetric matrix by diagonal matrices. However, in clustering, learning sparse matrices is crucial for computational efficiency. We extend Marcus theorem by proposing the Marcus mapping, which indicates that certain sparse matrices can also be transformed into doubly stochastic symmetric matrices via diagonal matrices. Additionally, we introduce rank constraints into the clustering problem and propose the Doubly Stochastic Adaptive Neighbors Clustering algorithm based on the Marcus Mapping (ANCMM). This ensures that the learned graph naturally divides into the desired number of clusters. We validate the effectiveness of our algorithm through extensive comparisons with state-of-the-art algorithms. Finally, we explore the relationship between the Marcus mapping and optimal transport. We prove that the Marcus mapping solves a specific type of optimal transport problem.

This study investigates the robustness of shallow graph embedding methods for community detection in the face of network perturbations, specifically node deletions. Graph embedding techniques, which represent nodes as low-dimensional vectors, are widely used for various graph machine learning tasks due to their ability to capture structural properties of networks effectively. However, the impact of perturbations on the performance of these methods remains relatively understudied. The research considers state-of-the-art shallow graph embedding methods from two families: matrix factorization (e.g., LE, LLE, HOPE, M-NMF) and random walk-based (e.g., DeepWalk, LINE, node2vec). Through experiments conducted on both synthetic and real-world networks, the study reveals varying degrees of robustness within each family of shallow graph embedding methods. The robustness is found to be influenced by factors such as network size, initial community partition strength, and the type of perturbation. Notably, node2vec and LLE consistently demonstrate higher robustness for community detection across different scenarios, including networks with degree and community size heterogeneity. These findings highlight the importance of selecting an appropriate shallow graph embedding method based on the specific characteristics of the network and the task at hand, particularly in scenarios where robustness to perturbations is crucial.

Graph clustering, an important unsupervised problem, has been shown to be more resistant to advances in Graph Neural Networks (GNNs). In addition, almost all clustering methods focus on homophilic graphs and ignore heterophily. This significantly limits their applicability in practice, since real-world graphs exhibit a structural disparity and cannot simply be classified as homophily and heterophily. Thus, a principled way to handle practical graphs is urgently needed. To fill this gap, we provide a novel solution with theoretical support. Interestingly, we find that most homophilic and heterophilic edges can be correctly identified on the basis of neighbor information. Motivated by this finding, we construct two graphs that are highly homophilic and heterophilic, respectively. They are used to build low-pass and high-pass filters to capture holistic information. Important features are further enhanced by the squeeze-and-excitation block. We validate our approach through extensive experiments on both homophilic and heterophilic graphs. Empirical results demonstrate the superiority of our method compared to state-of-the-art clustering methods.

In this paper, we consider the problem of partitioning a small data sample of size $n$ drawn from a mixture of $2$ sub-gaussian distributions in $\mathbb{R}^p$. We consider semidefinite programming relaxations of an integer quadratic program that is formulated essentially as finding the maximum cut on a graph, where edge weights in the cut represent dissimilarity scores between two nodes based on their $p$ features. We define the signal-to-noise ratio (SNR) as $s^2 := \min\{n p γ^2, Δ^2\}$, where $Δ^2 := p γ$ denotes the $\ell_2^2$ distance between the two cluster centers. Our contributions are twofold. First, we provide a unified framework for analyzing three computationally efficient algorithms: SDP1, BalancedSDP, and Spectral clustering, yielding universal polynomial-rate misclassification guarantees for all three algorithms. Moreover, our theory allows for partial recovery (success rate $< 100\%$) as long as $s^2$ is lower bounded by a constant. Second, we prove that the misclassification errors for SDP1 and BalancedSDP decay exponentially with respect to the SNR $s^2$ and the BalancedSDP requires no explicit debiasing when the two clusters have equal sizes. To our knowledge, this is the first time such results are obtained for semidefinite relaxations of MAX CUT in population clustering. We provide simulation evidence illuminating the theoretical predictions.

Vertex-level clustering for directed graphs (digraphs) remains challenging as edge directionality breaks the key assumptions underlying popular spectral methods, which also incur the overhead of eigen-decomposition. This paper proposes Parametrized Power-Iteration Clustering (ParPIC), a random-walk-based clustering method for weakly connected digraphs. This builds over the Power-Iteration Clustering paradigm, which uses the rows of the iterated diffusion operator as a data embedding. ParPIC has three important features: the use of parametrized reversible random walk operators, the automatic tuning of the diffusion time, and the efficient truncation of the final embedding, which produces low-dimensional data representations and reduces complexity. Empirical results on synthetic and real-world graphs demonstrate that ParPIC achieves competitive clustering accuracy with improved scalability relative to spectral and teleportation-based methods.