Filtering-based graph neural networks (GNNs) constitute a distinct class of GNNs that employ graph filters to handle graph-structured data, achieving notable success in various graph-related tasks. Conventional methods adopt a graph-wise filtering paradigm, imposing a uniform filter across all nodes, yet recent findings suggest that this rigid paradigm struggles with heterophilic graphs. To overcome this, recent works have introduced node-wise filtering, which assigns distinct filters to individual nodes, offering enhanced adaptability. However, a fundamental gap remains: a comprehensive framework unifying these two strategies is still absent, limiting theoretical insights into the filtering paradigms. Moreover, through the lens of Contextual Stochastic Block Model, we reveal that a synthesis of graph-wise and node-wise filtering provides a sufficient solution for classification on graphs exhibiting both homophily and heterophily, suggesting the risk of excessive parameterization and potential overfitting with node-wise filtering. To address the limitations, this paper introduces Coarsening-guided Partition-wise Filtering (CPF). CPF innovates by performing filtering on node partitions. The method begins with structure-aware partition-wise filtering, which filters node partitions obtained via graph coarsening algorithms, and then performs feature-aware partition-wise filtering, refining node embeddings via filtering on clusters produced by $k$-means clustering over features. In-depth analysis is conducted for each phase of CPF, showing its superiority over other paradigms. Finally, benchmark node classification experiments, along with a real-world graph anomaly detection application, validate CPF's efficacy and practical utility.
Hypergraphs, capable of representing high-order interactions via hyperedges, have become a powerful tool for modeling real-world biological and social systems. Inherent relationships within these real-world systems, such as the encoding relationship between genes and their protein products, drive the establishment of interconnections between multiple hypergraphs. Here, we demonstrate how to utilize those interconnections between multiple hypergraphs to synthesize integrated information from multiple higher-order systems, thereby enhancing understanding of underlying structures. We propose a model based on the stochastic block model, which integrates information from multiple hypergraphs to reveal latent high-order structures. Real-world hyperedges exhibit preferential attachment, where certain nodes dominate hyperedge formation. To characterize this phenomenon, our model introduces hyperedge internal degree to quantify nodes' contributions to hyperedge formation. This model is capable of mining communities, predicting missing hyperedges of arbitrary sizes within hypergraphs, and inferring inter-hypergraph edges between hypergraphs. We apply our model to high-order datasets to evaluate its performance. Experimental results demonstrate strong performance of our model in community detection, hyperedge prediction, and inter-hypergraph edge prediction tasks. Moreover, we show that our model enables analysis of multiple hypergraphs of different types and supports the analysis of a single hypergraph in the absence of inter-hypergraph edges. Our work provides a practical and flexible tool for analyzing multiple hypergraphs, greatly advancing the understanding of the organization in real-world high-order systems.
The behavior of multivariate dynamical processes is often governed by underlying structural connections that relate the components of the system. For example, brain activity which is often measured via time series is determined by an underlying structural graph, where nodes represent neurons or brain regions and edges represent cortical connectivity. Existing methods for inferring structural connections from observed dynamics, such as correlation-based or spectral techniques, may fail to fully capture complex relationships in high-dimensional time series in an interpretable way. Here, we propose the use of path signatures a mathematical framework that encodes geometric and temporal properties of continuous paths to address this problem. Path signatures provide a reparametrization-invariant characterization of dynamical data and, in particular, can be used to compute the lead matrix which reveals lead-lag phenomena. We showcase our approach on time series from coupled oscillators in the Kuramoto model defined on a stochastic block model graph, termed the Kuramoto stochastic block model (KSBM). Using mean-field theory and Gaussian approximations, we analytically derive reduced models of KSBM dynamics in different temporal regimes and theoretically characterize the lead matrix in these settings. Leveraging these insights, we propose a novel signature-based community detection algorithm, achieving exact recovery of structural communities from observed time series in multiple KSBM instances. Our results demonstrate that path signatures provide a novel perspective on analyzing complex neural data and other high-dimensional systems, explicitly exploiting temporal functional relationships to infer underlying structure.
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.
Graph homophily refers to the phenomenon that connected nodes tend to share similar characteristics. Understanding this concept and its related metrics is crucial for designing effective Graph Neural Networks (GNNs). The most widely used homophily metrics, such as edge or node homophily, quantify such "similarity" as label consistency across the graph topology. These metrics are believed to be able to reflect the performance of GNNs, especially on node-level tasks. However, many recent studies have empirically demonstrated that the performance of GNNs does not always align with homophily metrics, and how homophily influences GNNs still remains unclear and controversial. Then, a crucial question arises: What is missing in our current understanding of homophily? To figure out the missing part, in this paper, we disentangle the graph homophily into $3$ aspects: label, structural, and feature homophily, providing a more comprehensive understanding of GNN performance. To investigate their synergy, we propose a Contextual Stochastic Block Model with $3$ types of Homophily (CSBM-3H), where the topology and feature generation are controlled by the $3$ metrics. Based on the theoretical analysis of CSBM-3H, we derive a new composite metric, named Tri-Hom, that considers all $3$ aspects and overcomes the limitations of conventional homophily metrics. The theoretical conclusions and the effectiveness of Tri-Hom have been verified through synthetic experiments on CSBM-3H. In addition, we conduct experiments on $31$ real-world benchmark datasets and calculate the correlations between homophily metrics and model performance. Tri-Hom has significantly higher correlation values than $17$ existing metrics that only focus on a single homophily aspect, demonstrating its superiority and the importance of homophily synergy. Our code is available at \url{https://github.com/zylMozart/Disentangle_GraphHom}.
When applying the Transformer architecture to source code, designing a good self-attention mechanism is critical as it affects how node relationship is extracted from the Abstract Syntax Trees (ASTs) of the source code. We present Code Structure Aware Transformer (CSA-Trans), which uses Code Structure Embedder (CSE) to generate specific PE for each node in AST. CSE generates node Positional Encoding (PE) using disentangled attention. To further extend the self-attention capability, we adopt Stochastic Block Model (SBM) attention. Our evaluation shows that our PE captures the relationships between AST nodes better than other graph-related PE techniques. We also show through quantitative and qualitative analysis that SBM attention is able to generate more node specific attention coefficients. We demonstrate that CSA-Trans outperforms 14 baselines in code summarization tasks for both Python and Java, while being 41.92% faster and 25.31% memory efficient in Java dataset compared to AST-Trans and SG-Trans respectively.
Graph clustering is a fundamental task in unsupervised learning with broad real-world applications. While spectral clustering methods for undirected graphs are well-established and guided by a minimum cut optimization consensus, their extension to directed graphs remains relatively underexplored due to the additional complexity introduced by edge directions. In this paper, we leverage statistical inference on stochastic block models to guide the development of a spectral clustering algorithm for directed graphs. Specifically, we study the maximum likelihood estimation under a widely used directed stochastic block model, and derive a global objective function that aligns with the underlying community structure. We further establish a theoretical upper bound on the misclustering error of its spectral relaxation, and based on this relaxation, introduce a novel, self-adaptive spectral clustering method for directed graphs. Extensive experiments on synthetic and real-world datasets demonstrate significant performance gains over existing baselines.
Graph neural networks (GNNs) have become increasingly popular for classification tasks on graph-structured data. Yet, the interplay between graph topology and feature evolution in GNNs is not well understood. In this paper, we focus on node-wise classification, illustrated with community detection on stochastic block model graphs, and explore the feature evolution through the lens of the "Neural Collapse" (NC) phenomenon. When training instance-wise deep classifiers (e.g. for image classification) beyond the zero training error point, NC demonstrates a reduction in the deepest features' within-class variability and an increased alignment of their class means to certain symmetric structures. We start with an empirical study that shows that a decrease in within-class variability is also prevalent in the node-wise classification setting, however, not to the extent observed in the instance-wise case. Then, we theoretically study this distinction. Specifically, we show that even an "optimistic" mathematical model requires that the graphs obey a strict structural condition in order to possess a minimizer with exact collapse. Interestingly, this condition is viable also for heterophilic graphs and relates to recent empirical studies on settings with improved GNNs' generalization. Furthermore, by studying the gradient dynamics of the theoretical model, we provide reasoning for the partial collapse observed empirically. Finally, we present a study on the evolution of within- and between-class feature variability across layers of a well-trained GNN and contrast the behavior with spectral methods.
We present a new angle on the expressive power of graph neural networks (GNNs) by studying how the predictions of real-valued GNN classifiers, such as those classifying graphs probabilistically, evolve as we apply them on larger graphs drawn from some random graph model. We show that the output converges to a constant function, which upper-bounds what these classifiers can uniformly express. This strong convergence phenomenon applies to a very wide class of GNNs, including state of the art models, with aggregates including mean and the attention-based mechanism of graph transformers. Our results apply to a broad class of random graph models, including sparse and dense variants of the Erd\H{o}s-R\'enyi model, the stochastic block model, and the Barab\'asi-Albert model. We empirically validate these findings, observing that the convergence phenomenon appears not only on random graphs but also on some real-world graphs.
Social networks are often associated with rich side information, such as texts and images. While numerous methods have been developed to identify communities from pairwise interactions, they usually ignore such side information. In this work, we study an extension of the Stochastic Block Model (SBM), a widely used statistical framework for community detection, that integrates vectorial edges covariates: the Vectorial Edges Covariates Stochastic Block Model (VEC-SBM). We propose a novel algorithm based on iterative refinement techniques and show that it optimally recovers the latent communities under the VEC-SBM. Furthermore, we rigorously assess the added value of leveraging edge's side information in the community detection process. We complement our theoretical results with numerical experiments on synthetic and semi-synthetic data.
Hypergraphs represent complex systems involving interactions among more than two entities and allow the investigation of higher-order structure and dynamics in complex systems. Node attribute data, which often accompanies network data, can enhance the inference of community structure in complex systems. While mixed-membership stochastic block models have been employed to infer community structure in hypergraphs, they complicate the visualization and interpretation of inferred community structure by assuming that nodes may possess soft community memberships. In this study, we propose a framework, HyperNEO, that combines mixed-membership stochastic block models for hypergraphs with dimensionality reduction methods. Our approach generates a node layout that largely preserves the community memberships of nodes. We evaluate our framework on both synthetic and empirical hypergraphs with node attributes. We expect our framework will broaden the investigation and understanding of higher-order community structure in complex systems.
The celebrated message-passing updates for graph neural networks allow representing large-scale graphs with local and computationally tractable updates. However, the updates suffer from backtracking, i.e., a message flowing through the same edge twice and revisiting the previously visited node. Since the number of message flows increases exponentially with the number of updates, the redundancy in local updates prevents the graph neural network from accurately recognizing a particular message flow relevant for downstream tasks. In this work, we propose to resolve such a redundancy issue via the non-backtracking graph neural network (NBA-GNN) that updates a message without incorporating the message from the previously visited node. We theoretically investigate how NBA-GNN alleviates the over-squashing of GNNs, and establish a connection between NBA-GNN and the impressive performance of non-backtracking updates for stochastic block model recovery. Furthermore, we empirically verify the effectiveness of our NBA-GNN on the long-range graph benchmark and transductive node classification problems.
The effect of underrepresentation on the performance of minority groups is known to be a serious problem in supervised learning settings; however, it has been underexplored so far in the context of self-supervised learning (SSL). In this paper, we demonstrate that contrastive learning (CL), a popular variant of SSL, tends to collapse representations of minority groups with certain majority groups. We refer to this phenomenon as representation harm and demonstrate it on image and text datasets using the corresponding popular CL methods. Furthermore, our causal mediation analysis of allocation harm on a downstream classification task reveals that representation harm is partly responsible for it, thus emphasizing the importance of studying and mitigating representation harm. Finally, we provide a theoretical explanation for representation harm using a stochastic block model that leads to a representational neural collapse in a contrastive learning setting.
We present DYMAG, a graph neural network based on a novel form of message aggregation. Standard message-passing neural networks, which often aggregate local neighbors via mean-aggregation, can be regarded as convolving with a simple rectangular waveform which is non-zero only on 1-hop neighbors of every vertex. Here, we go beyond such local averaging. We will convolve the node features with more sophisticated waveforms generated using dynamics such as the heat equation, wave equation, and the Sprott model (an example of chaotic dynamics). Furthermore, we use snapshots of these dynamics at different time points to create waveforms at many effective scales. Theoretically, we show that these dynamic waveforms can capture salient information about the graph including connected components, connectivity, and cycle structures even with no features. Empirically, we test DYMAG on both real and synthetic benchmarks to establish that DYMAG outperforms baseline models on recovery of graph persistence, generating parameters of random graphs, as well as property prediction for proteins, molecules and materials. Our code is available at https://github.com/KrishnaswamyLab/DYMAG.
Despite a surge in interest in GNN development, homogeneity in benchmarking datasets still presents a fundamental issue to GNN research. GraphWorld is a recent solution which uses the Stochastic Block Model (SBM) to generate diverse populations of synthetic graphs for benchmarking any GNN task. Despite its success, the SBM imposed fundamental limitations on the kinds of graph structure GraphWorld could create. In this work we examine how two additional synthetic graph generators can improve GraphWorld's evaluation; LFR, a well-established model in the graph clustering literature and CABAM, a recent adaptation of the Barabasi-Albert model tailored for GNN benchmarking. By integrating these generators, we significantly expand the coverage of graph space within the GraphWorld framework while preserving key graph properties observed in real-world networks. To demonstrate their effectiveness, we generate 300,000 graphs to benchmark 11 GNN models on a node classification task. We find GNN performance variations in response to homophily, degree distribution and feature signal. Based on these findings, we classify models by their sensitivity to the new generators under these properties. Additionally, we release the extensions made to GraphWorld on the GitHub repository, offering further evaluation of GNN performance on new graphs.
We study how to train personalized models for different tasks on decentralized devices with limited local data. We propose "Structured Cooperative Learning (SCooL)", in which a cooperation graph across devices is generated by a graphical model prior to automatically coordinate mutual learning between devices. By choosing graphical models enforcing different structures, we can derive a rich class of existing and novel decentralized learning algorithms via variational inference. In particular, we show three instantiations of SCooL that adopt Dirac distribution, stochastic block model (SBM), and attention as the prior generating cooperation graphs. These EM-type algorithms alternate between updating the cooperation graph and cooperative learning of local models. They can automatically capture the cross-task correlations among devices by only monitoring their model updating in order to optimize the cooperation graph. We evaluate SCooL and compare it with existing decentralized learning methods on an extensive set of benchmarks, on which SCooL always achieves the highest accuracy of personalized models and significantly outperforms other baselines on communication efficiency. Our code is available at https://github.com/ShuangtongLi/SCooL.
Homophily principle, i.e., nodes with the same labels are more likely to be connected, has been believed to be the main reason for the performance superiority of Graph Neural Networks (GNNs) over Neural Networks on node classification tasks. Recent research suggests that, even in the absence of homophily, the advantage of GNNs still exists as long as nodes from the same class share similar neighborhood patterns. However, this argument only considers intra-class Node Distinguishability (ND) but neglects inter-class ND, which provides incomplete understanding of homophily on GNNs. In this paper, we first demonstrate such deficiency with examples and argue that an ideal situation for ND is to have smaller intra-class ND than inter-class ND. To formulate this idea and study ND deeply, we propose Contextual Stochastic Block Model for Homophily (CSBM-H) and define two metrics, Probabilistic Bayes Error (PBE) and negative generalized Jeffreys divergence, to quantify ND. With the metrics, we visualize and analyze how graph filters, node degree distributions and class variances influence ND, and investigate the combined effect of intra- and inter-class ND. Besides, we discovered the mid-homophily pitfall, which occurs widely in graph datasets. Furthermore, we verified that, in real-work tasks, the superiority of GNNs is indeed closely related to both intra- and inter-class ND regardless of homophily levels. Grounded in this observation, we propose a new hypothesis-testing based performance metric beyond homophily, which is non-linear, feature-based and can provide statistical threshold value for GNNs' the superiority. Experiments indicate that it is significantly more effective than the existing homophily metrics on revealing the advantage and disadvantage of graph-aware modes on both synthetic and benchmark real-world datasets.
In this paper, we introduce a method called graph fusion embedding, designed for multi-graph embedding with shared vertex sets. Under the framework of supervised learning, our method exhibits a remarkable and highly desirable synergistic effect: for sufficiently large vertex size, the accuracy of vertex classification consistently benefits from the incorporation of additional graphs. We establish the mathematical foundation for the method, including the asymptotic convergence of the embedding, a sufficient condition for asymptotic optimal classification, and the proof of the synergistic effect for vertex classification. Our comprehensive simulations and real data experiments provide compelling evidence supporting the effectiveness of our proposed method, showcasing the pronounced synergistic effect for multiple graphs from disparate sources.
This paper develops an R package rMultiNet to analyze multilayer network data. We provide two general frameworks from recent literature, e.g. mixture multilayer stochastic block model(MMSBM) and mixture multilayer latent space model(MMLSM) to generate the multilayer network. We also provide several methods to reveal the embedding of both nodes and layers followed by further data analysis methods, such as clustering. Three real data examples are processed in the package. The source code of rMultiNet is available at https://github.com/ChenyuzZZ73/rMultiNet.
Hierarchical Clustering is a popular unsupervised machine learning method with decades of history and numerous applications. We initiate the study of differentially private approximation algorithms for hierarchical clustering under the rigorous framework introduced by (Dasgupta, 2016). We show strong lower bounds for the problem: that any $\epsilon$-DP algorithm must exhibit $O(|V|^2/ \epsilon)$-additive error for an input dataset $V$. Then, we exhibit a polynomial-time approximation algorithm with $O(|V|^{2.5}/ \epsilon)$-additive error, and an exponential-time algorithm that meets the lower bound. To overcome the lower bound, we focus on the stochastic block model, a popular model of graphs, and, with a separation assumption on the blocks, propose a private $1+o(1)$ approximation algorithm which also recovers the blocks exactly. Finally, we perform an empirical study of our algorithms and validate their performance.