Graphs are growing rapidly, along with the number of distinct label categories associated with them. Applications like e-commerce, healthcare, recommendation systems, and various social media platforms are rapidly moving towards graph representation of data due to their ability to capture both structural and attribute information. One crucial task in graph analysis is node classification, where unlabeled nodes are categorized into predefined classes. In practice, novel classes appear incrementally sometimes with just a few labels (seen classes) or even without any labels (unseen classes), either because they are new or haven't been explored much. Traditional methods assume abundant labeled data for training, which isn't always feasible. We investigate a broader objective: \emph{Graph Class Incremental Learning under Weak Supervision (GCL)}, addressing this challenge by meta-training on base classes with limited labeled instances. During the incremental streams, novel classes can have few-shot or zero-shot representation. Our proposed framework GOTHAM efficiently accommodates these unlabeled nodes by finding the closest prototype representation, serving as class representatives in the attribute space. For Text-Attributed Graphs (TAGs), our framework additionally incorporates semantic information to enhance the representation. By employing teacher-student knowledge distillation to mitigate forgetting, GOTHAM achieves promising results across various tasks. Experiments on datasets such as Cora-ML, Amazon, and OBGN-Arxiv showcase the effectiveness of our approach in handling evolving graph data under limited supervision. The repository is available here: \href{https://github.com/adityashahane10/GOTHAM--Graph-based-Class-Incremental-Learning-Framework-under-Weak-Supervision}{\small \textcolor{blue}{Code}}
Graph Neural Networks (GNNs) have emerged as the de facto standard for modeling graph data, with attention mechanisms and transformers significantly enhancing their performance on graph-based tasks. Despite these advancements, the performance of GNNs on heterogeneous graphs often remains complex, with networks generally underperforming compared to their homogeneous counterparts. This work benchmarks various GNN architectures to identify the most effective methods for heterogeneous graphs, with a particular focus on node classification and link prediction. Our findings reveal that graph attention networks excel in these tasks. As a main contribution, we explore enhancements to these attention networks by integrating positional encodings for node embeddings. This involves utilizing the full Laplacian spectrum to accurately capture both the relative and absolute positions of each node within the graph, further enhancing performance on downstream tasks such as node classification and link prediction.
Node classification in graphs aims to predict the categories of unlabeled nodes by utilizing a small set of labeled nodes. However, weighted graphs often contain noisy edges and anomalous edge weights, which can distort fine-grained relationships between nodes and hinder accurate classification. We propose the Edge Weight-aware Graph Structure Learning (EWGSL) method, which combines weight learning and graph structure learning to address these issues. EWGSL improves node classification by redefining attention coefficients in graph attention networks to incorporate node features and edge weights. It also applies graph structure learning to sparsify attention coefficients and uses a modified InfoNCE loss function to enhance performance by adapting to denoised graph weights. Extensive experimental results show that EWGSL has an average Micro-F1 improvement of 17.8% compared with the best baseline.
Link prediction is crucial for uncovering hidden connections within complex networks, enabling applications such as identifying potential customers and products. However, this research faces significant challenges, including concerns about data privacy, as well as high computational and storage costs, especially when dealing with large-scale networks. Condensed graphs, which are much smaller than the original graphs while retaining essential information, has become an effective solution to both maintain data utility and preserve privacy. Existing methods, however, initialize synthetic graphs through random node selection without considering node connectivity, and are mainly designed for node classification tasks. As a result, their potential for privacy-preserving link prediction remains largely unexplored. We introduce HyDRO\textsuperscript{+}, a graph condensation method guided by algebraic Jaccard similarity, which leverages local connectivity information to optimize condensed graph structures. Extensive experiments on four real-world networks show that our method outperforms state-of-the-art methods and even the original networks in balancing link prediction accuracy and privacy preservation. Moreover, our method achieves nearly 20* faster training and reduces storage requirements by 452*, as demonstrated on the Computers dataset, compared to link prediction on the original networks. This work represents the first attempt to leverage condensed graphs for privacy-preserving link prediction information sharing in real-world complex networks. It offers a promising pathway for preserving link prediction information while safeguarding privacy, advancing the use of graph condensation in large-scale networks with privacy concerns.
Long-range dependencies are critical for effective graph representation learning, yet most existing datasets focus on small graphs tailored to inductive tasks, offering limited insight into long-range interactions. Current evaluations primarily compare models employing global attention (e.g., graph transformers) with those using local neighborhood aggregation (e.g., message-passing neural networks) without a direct measurement of long-range dependency. In this work, we introduce City-Networks, a novel large-scale transductive learning dataset derived from real-world city roads. This dataset features graphs with over $10^5$ nodes and significantly larger diameters than those in existing benchmarks, naturally embodying long-range information. We annotate the graphs using an eccentricity-based approach, ensuring that the classification task inherently requires information from distant nodes. Furthermore, we propose a model-agnostic measurement based on the Jacobians of neighbors from distant hops, offering a principled quantification of long-range dependencies. Finally, we provide theoretical justifications for both our dataset design and the proposed measurement - particularly by focusing on over-smoothing and influence score dilution - which establishes a robust foundation for further exploration of long-range interactions in graph neural networks.
Low-dimensional embeddings are essential for machine learning tasks involving graphs, such as node classification, link prediction, community detection, network visualization, and network compression. Although recent studies have identified exact low-dimensional embeddings, the limits of the required embedding dimensions remain unclear. We presently prove that lower dimensional embeddings are possible when using Euclidean metric embeddings as opposed to vector-based Logistic PCA (LPCA) embeddings. In particular, we provide an efficient logarithmic search procedure for identifying the exact embedding dimension and demonstrate how metric embeddings enable inference of the exact embedding dimensions of large-scale networks by exploiting that the metric properties can be used to provide linearithmic scaling. Empirically, we show that our approach extracts substantially lower dimensional representations of networks than previously reported for small-sized networks. For the first time, we demonstrate that even large-scale networks can be effectively embedded in very low-dimensional spaces, and provide examples of scalable, exact reconstruction for graphs with up to a million nodes. Our approach highlights that the intrinsic dimensionality of networks is substantially lower than previously reported and provides a computationally efficient assessment of the exact embedding dimension also of large-scale networks. The surprisingly low dimensional representations achieved demonstrate that networks in general can be losslessly represented using very low dimensional feature spaces, which can be used to guide existing network analysis tasks from community detection and node classification to structure revealing exact network visualizations.
Graph sampling based Graph Convolutional Networks (GCNs) decouple the sampling from the forward and backward propagation during minibatch training, which exhibit good scalability in terms of layer depth and graph size. We propose HIS_GCNs, a hierarchical importance graph sampling based learning method. By constructing minibatches using sampled subgraphs, HIS_GCNs gives attention to the importance of both core and periphery nodes/edges in a scale-free training graph. Specifically, it preserves the centrum of the core to most minibatches, which maintains connectivity between periphery nodes, and samples periphery edges without core node interference, in order to keep more long chains composed entirely of low-degree nodes in the same minibatch. HIS_GCNs can maximize the discrete Ricci curvature (i.e., Ollivier-Ricci curvatures) of the edges in a subgraph that enables the preservation of important chains for information propagation, and can achieve a low node embedding variance and a high convergence speed. Diverse experiments on Graph Neural Networks (GNNs) with node classification tasks confirm superior performance of HIS_GCNs in both accuracy and training time. Open sourced code (https://github.com/HuQiaCHN/HIS-GCN).
Graph-structured data has become increasingly prevalent across various domains, raising the demand for effective models to handle graph tasks like node classification and link prediction. Traditional graph learning models like Graph Neural Networks (GNNs) have made significant strides, but their capabilities in handling graph data remain limited in certain contexts. In recent years, large language models (LLMs) have emerged as promising candidates for graph tasks, yet most studies focus primarily on performance benchmarks and fail to address their broader potential, including their ability to handle limited data, their transferability across tasks, and their robustness. In this work, we provide a comprehensive exploration of LLMs applied to graph tasks. We evaluate the performance of pure LLMs, including those without parameter optimization and those fine-tuned with instructions, across various scenarios. Our analysis goes beyond accuracy, assessing LLM ability to perform in few-shot/zero-shot settings, transfer across domains, understand graph structures, and demonstrate robustness in challenging scenarios. We conduct extensive experiments with 16 graph learning models alongside 6 LLMs (e.g., Llama3B, GPT-4o, Qwen-plus), comparing their performance on datasets like Cora, PubMed, ArXiv, and Products. Our findings show that LLMs, particularly those with instruction tuning, outperform traditional models in few-shot settings, exhibit strong domain transferability, and demonstrate excellent generalization and robustness. This work offers valuable insights into the capabilities of LLMs for graph learning, highlighting their advantages and potential for real-world applications, and paving the way for future research in this area. Codes and datasets are released in https://github.com/myflashbarry/LLM-benchmarking.
We introduce Attention Graphs, a new tool for mechanistic interpretability of Graph Neural Networks (GNNs) and Graph Transformers based on the mathematical equivalence between message passing in GNNs and the self-attention mechanism in Transformers. Attention Graphs aggregate attention matrices across Transformer layers and heads to describe how information flows among input nodes. Through experiments on homophilous and heterophilous node classification tasks, we analyze Attention Graphs from a network science perspective and find that: (1) When Graph Transformers are allowed to learn the optimal graph structure using all-to-all attention among input nodes, the Attention Graphs learned by the model do not tend to correlate with the input/original graph structure; and (2) For heterophilous graphs, different Graph Transformer variants can achieve similar performance while utilising distinct information flow patterns. Open source code: https://github.com/batu-el/understanding-inductive-biases-of-gnns
Graph Neural Networks (GNNs) have demonstrated remarkable proficiency in modeling data with graph structures, yet recent research reveals their susceptibility to adversarial attacks. Traditional attack methodologies, which rely on manipulating the original graph or adding links to artificially created nodes, often prove impractical in real-world settings. This paper introduces a novel adversarial scenario involving the injection of an isolated subgraph to deceive both the link recommender and the node classifier within a GNN system. Specifically, the link recommender is mislead to propose links between targeted victim nodes and the subgraph, encouraging users to unintentionally establish connections and that would degrade the node classification accuracy, thereby facilitating a successful attack. To address this, we present the LiSA framework, which employs a dual surrogate model and bi-level optimization to simultaneously meet two adversarial objectives. Extensive experiments on real-world datasets demonstrate the effectiveness of our method.
Message-passing Graph Neural Networks (GNNs) are often criticized for their limited expressiveness, issues like over-smoothing and over-squashing, and challenges in capturing long-range dependencies, while Graph Transformers (GTs) are considered superior due to their global attention mechanisms. Literature frequently suggests that GTs outperform GNNs, particularly in graph-level tasks such as graph classification and regression. In this study, we explore the untapped potential of GNNs through an enhanced framework, GNN+, which integrates six widely used techniques: edge feature integration, normalization, dropout, residual connections, feed-forward networks, and positional encoding, to effectively tackle graph-level tasks. We conduct a systematic evaluation of three classic GNNs, namely GCN, GIN, and GatedGCN, enhanced by the GNN+ framework across 14 well-known graph-level datasets. Our results show that, contrary to the prevailing belief, classic GNNs excel in graph-level tasks, securing top three rankings across all datasets and achieving first place in eight, while also demonstrating greater efficiency than GTs. This highlights the potential of simple GNN architectures, challenging the belief that complex mechanisms in GTs are essential for superior graph-level performance.
Maximizing the spectral gap through graph rewiring has been proposed to enhance the performance of message-passing graph neural networks (GNNs) by addressing over-squashing. However, as we show, minimizing the spectral gap can also improve generalization. To explain this, we analyze how rewiring can benefit GNNs within the context of stochastic block models. Since spectral gap optimization primarily influences community strength, it improves performance when the community structure aligns with node labels. Building on this insight, we propose three distinct rewiring strategies that explicitly target community structure, node labels, and their alignment: (a) community structure-based rewiring (ComMa), a more computationally efficient alternative to spectral gap optimization that achieves similar goals; (b) feature similarity-based rewiring (FeaSt), which focuses on maximizing global homophily; and (c) a hybrid approach (ComFy), which enhances local feature similarity while preserving community structure to optimize label-community alignment. Extensive experiments confirm the effectiveness of these strategies and support our theoretical insights.
Graph representation learning has emerged as a cornerstone for tasks like node classification and link prediction, yet prevailing self-supervised learning (SSL) methods face challenges such as computational inefficiency, reliance on contrastive objectives, and representation collapse. Existing approaches often depend on feature reconstruction, negative sampling, or complex decoders, which introduce training overhead and hinder generalization. Further, current techniques which address such limitations fail to account for the contribution of node embeddings to a certain prediction in the absence of labeled nodes. To address these limitations, we propose a novel joint embedding predictive framework for graph SSL that eliminates contrastive objectives and negative sampling while preserving semantic and structural information. Additionally, we introduce a semantic-aware objective term that incorporates pseudo-labels derived from Gaussian Mixture Models (GMMs), enhancing node discriminability by evaluating latent feature contributions. Extensive experiments demonstrate that our framework outperforms state-of-the-art graph SSL methods across benchmarks, achieving superior performance without contrastive loss or complex decoders. Key innovations include (1) a non-contrastive, view-invariant joint embedding predictive architecture, (2) Leveraging single context and multiple targets relationship between subgraphs, and (3) GMM-based pseudo-label scoring to capture semantic contributions. This work advances graph SSL by offering a computationally efficient, collapse-resistant paradigm that bridges spatial and semantic graph features for downstream tasks. The code for our paper can be found at https://github.com/Deceptrax123/JPEB-GSSL
Graph learning tasks often hinge on identifying key substructure patterns -- such as triadic closures in social networks or benzene rings in molecular graphs -- that underpin downstream performance. However, most existing graph neural networks (GNNs) rely on message passing, which aggregates local neighborhood information iteratively and struggles to explicitly capture such fundamental motifs, like triangles, k-cliques, and rings. This limitation hinders both expressiveness and long-range dependency modeling. In this paper, we introduce the Neural Graph Pattern Machine (GPM), a novel framework that bypasses message passing by learning directly from graph substructures. GPM efficiently extracts, encodes, and prioritizes task-relevant graph patterns, offering greater expressivity and improved ability to capture long-range dependencies. Empirical evaluations across four standard tasks -- node classification, link prediction, graph classification, and graph regression -- demonstrate that GPM outperforms state-of-the-art baselines. Further analysis reveals that GPM exhibits strong out-of-distribution generalization, desirable scalability, and enhanced interpretability. Code and datasets are available at: https://github.com/Zehong-Wang/GPM.
Graph distillation (GD) is an effective approach to extract useful information from large-scale network structures. However, existing methods, which operate in Euclidean space to generate condensed graphs, struggle to capture the inherent tree-like geometry of real-world networks, resulting in distilled graphs with limited task-specific information for downstream tasks. Furthermore, these methods often fail to extract dynamic properties from graphs, which are crucial for understanding information flow and facilitating graph continual learning. This paper presents the Hyperbolic Graph Distillation with Random Walks Optimization (HyDRO), a novel graph distillation approach that leverages hyperbolic embeddings to capture complex geometric patterns and optimize the spectral gap in hyperbolic space. Experiments show that HyDRO demonstrates strong task generalization, consistently outperforming state-of-the-art methods in both node classification and link prediction tasks. HyDRO also effectively preserves graph random walk properties, producing condensed graphs that achieve enhanced performance in continual graph learning. Additionally, HyDRO achieves competitive results on mainstream graph distillation benchmarks, while maintaining a strong balance between privacy and utility, and exhibiting robust resistance to noises.
Dynamic graph augmentation is used to improve the performance of dynamic GNNs. Most methods assume temporal locality, meaning that recent edges are more influential than earlier edges. However, for temporal changes in edges caused by random noise, overemphasizing recent edges while neglecting earlier ones may lead to the model capturing noise. To address this issue, we propose STAA (SpatioTemporal Activity-Aware Random Walk Diffusion). STAA identifies nodes likely to have noisy edges in spatiotemporal dimensions. Spatially, it analyzes critical topological positions through graph wavelet coefficients. Temporally, it analyzes edge evolution through graph wavelet coefficient change rates. Then, random walks are used to reduce the weights of noisy edges, deriving a diffusion matrix containing spatiotemporal information as an augmented adjacency matrix for dynamic GNN learning. Experiments on multiple datasets show that STAA outperforms other dynamic graph augmentation methods in node classification and link prediction tasks.
Representation learning on graphs is a fundamental problem that can be crucial in various tasks. Graph neural networks, the dominant approach for graph representation learning, are limited in their representation power. Therefore, it can be beneficial to explicitly extract and incorporate high-order topological and geometric information into these models. In this paper, we propose a principled approach to extract the rich connectivity information of graphs based on the theory of persistent homology. Our method utilizes the topological features to enhance the representation learning of graph neural networks and achieve state-of-the-art performance on various node classification and link prediction benchmarks. We also explore the option of end-to-end learning of the topological features, i.e., treating topological computation as a differentiable operator during learning. Our theoretical analysis and empirical study provide insights and potential guidelines for employing topological features in graph learning tasks.
Graph Neural Networks (GNNs) have demonstrated remarkable ability in semi-supervised node classification. However, most existing GNNs rely heavily on a large amount of labeled data for training, which is labor-intensive and requires extensive domain knowledge. In this paper, we first analyze the restrictions of GNNs generalization from the perspective of supervision signals in the context of few-shot semi-supervised node classification. To address these challenges, we propose a novel algorithm named NormProp, which utilizes the homophily assumption of unlabeled nodes to generate additional supervision signals, thereby enhancing the generalization against label scarcity. The key idea is to efficiently capture both the class information and the consistency of aggregation during message passing, via decoupling the direction and Euclidean norm of node representations. Moreover, we conduct a theoretical analysis to determine the upper bound of Euclidean norm, and then propose homophilous regularization to constraint the consistency of unlabeled nodes. Extensive experiments demonstrate that NormProp achieve state-of-the-art performance under low-label rate scenarios with low computational complexity.
Graph Neural Networks (GNNs) are popular deep learning models designed to process graph-structured data through recursive neighborhood aggregations in the message passing process. When applied to semi-supervised node classification, the message-passing enables GNNs to understand short-range spatial interactions, but also causes them to suffer from over-smoothing and over-squashing. These challenges hinder model expressiveness and prevent the use of deeper models to capture long-range node interactions (LRIs) within the graph. Popular solutions for LRIs detection are either too expensive to process large graphs due to high time complexity or fail to generalize across diverse graph structures. To address these limitations, we propose a mechanism called \emph{information flow control}, which leverages a novel connectivity measure, called \emph{information flow score}, to address over-smoothing and over-squashing with linear computational overhead, supported by theoretical evidence. Finally, to prove the efficacy of our methodology we design DeltaGNN, the first scalable and generalizable approach for detecting long-range and short-range interactions. We benchmark our model across 10 real-world datasets, including graphs with varying sizes, topologies, densities, and homophilic ratios, showing superior performance with limited computational complexity. The implementation of the proposed methods are publicly available at https://github.com/basiralab/DeltaGNN.
Egocentric videos capture scenes from a wearer's viewpoint, resulting in dynamic backgrounds, frequent motion, and occlusions, posing challenges to accurate keystep recognition. We propose a flexible graph-learning framework for fine-grained keystep recognition that is able to effectively leverage long-term dependencies in egocentric videos, and leverage alignment between egocentric and exocentric videos during training for improved inference on egocentric videos. Our approach consists of constructing a graph where each video clip of the egocentric video corresponds to a node. During training, we consider each clip of each exocentric video (if available) as additional nodes. We examine several strategies to define connections across these nodes and pose keystep recognition as a node classification task on the constructed graphs. We perform extensive experiments on the Ego-Exo4D dataset and show that our proposed flexible graph-based framework notably outperforms existing methods by more than 12 points in accuracy. Furthermore, the constructed graphs are sparse and compute efficient. We also present a study examining on harnessing several multimodal features, including narrations, depth, and object class labels, on a heterogeneous graph and discuss their corresponding contribution to the keystep recognition performance.