Node Classification

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Overview

Node classification predicts categories for entities such as users, papers, accounts, or neurons, using their attributes and relationships. Common approaches include graph neural networks with message passing, label propagation, graph transformers, and methods that separate homophilic from heterophilic connections; text-attributed graphs also use language models and graph foundation models. Work covers transductive and inductive prediction, as well as few-shot learning, class imbalance, noisy labels, distribution shift, and calibrated uncertainty. A central challenge is determining when added structure or pretrained models truly help: results can depend on graph type, data splits, and careful tuning, and strong conventional GNN baselines remain difficult to beat consistently.

Latest papers

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99 papers13 papers in the last four weeks, down 13% on the four weeks before. 0.1% of all new papers.

May 25, 2026

ARMA-C3: A Contrastive ARMA Convolutional Framework for Unsupervised and Semi-supervised Classification

In biomedical and neurodegenerative disorders, accurate and early disease identification remains challenging due to the scarcity of labeled data and the complexity of imaging patterns. To address these challenges, we introduce ARMA-C3, a unified unsupervised and semi-supervised graph learning framework for node classification based on contrastive learning and graph-cut regularization to learn structurally meaningful and discriminative representations. By modeling samples or images as graph nodes and exploiting inter-sample relationships, the proposed framework captures subject-level dependencies that conventional machine learning methods typically overlook. We conduct extensive binary classification experiments across five clinically relevant datasets: the Alzheimer's Disease Neuroimaging Initiative (ADNI), the Neuroimaging in Frontotemporal Dementia (NIFD) dataset, and three medical imaging benchmarks (BreastMNIST, PneumoniaMNIST, and a liver ultrasound dataset). Experimental results demonstrate that ARMA-C3 achieves competitive and frequently superior performance compared to classical clustering techniques, state-of-the-art machine learning models, and existing graph-based deep learning approaches across multiple evaluation settings, particularly under limited supervision and severe class imbalance. The proposed framework further demonstrates robust representation learning and strong cross-modal generalization across diverse biomedical imaging modalities.

VSS Tejaswi Abburi, Saurabh J. Shigwan, Nitin Kumar

Department of Computer Science and Engineering, Shiv Nadar Institute of Eminence Deemed to be University, Delhi NCR, India

Graph Neural NetworksUnsupervised Representation LearningMedical Image ClassificationGraph-Based Semi-Supervised LearningGraph Contrastive LearningSemi-Supervised Learning+1
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May 25, 2026

SiST-GNN: Simultaneous Spatial-Temporal Message Passing for Dynamic Graph Representation Learning

Dynamic graph neural networks (DGNNs) that operate on snapshot sequences typically fall into one of two categories. Temporal-first approaches build per-node temporal embeddings and only afterward perform spatial aggregation, whereas Spatial-first approaches invert this order, feeding the output of a graph convolution into a downstream temporal module. In either case, the rigid sequencing forces the second stage to consume an already-compressed summary produced by the first, ruling out joint reasoning over topology and evolution; effectively, the message-passing operator never gets to weight a neighbor's contribution by that neighbor's past trajectory. This paper introduces SiST-GNN (Simultaneous Spatial-Temporal GNN), which fuses the two signals inside a single message-passing operation rather than chaining them. At each snapshot, we maintain a recurrent hidden state per node that summarises its history, pairs it with the node's current feature vector, and treats the pair as two nodes joined by a cross-time edge; running a standard graph convolution on this temporally augmented graph yields the updated representation. We compare against fourteen link-prediction baselines under both the fixed-split and live-update evaluation regimes, and eleven baselines on node classification. Across the public benchmarks, SiST-GNN improves on the strongest prior method in link prediction by 1-18% in the fixed-split setting, and is the leading learned method on five of six datasets in the live-update setting, improving on the strongest prior method by 1-158% there. We additionally derive three dynamic node-classification tasks by discretizing the underlying continuous-time event streams; here SiST-GNN beats the leading discrete-time (DTDG) baseline by 7-23% and matches continuous-time (CTDG) methods that consume the raw events directly.

Shubhajit Roy, Anirban Dasgupta

Department of Computer Science and Engineering Indian Institute of Technology Gandhinagar

Graph Representation LearningTemporal Link PredictionDynamic Graph LearningNode ClassificationSpatiotemporal GNNs
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May 19, 2026

Fast and Featureless Node Representation Learning with Partial Pairwise Supervision

We introduce Contrastive FUSE, a fast and unified framework for scalable node representation learning in graphs with partially available pairwise node labels and no available node features. Unlike existing methods, we directly optimize a spectral contrastive objective that integrates community-aware structural signals with signed pairwise constraints. To support large-scale training, we replace the expensive modularity gradient with a lightweight approximation, which preserves the structure-seeking behavior of modularity while reducing the computational cost significantly. This yields an efficient optimization scheme with a natural gradient decomposition and adaptive learning-rate scaling, enabling fast iterative updates even on million-edge graphs. Extensive experiments on benchmark citation networks, large co-purchase graphs, and OGB datasets show that Contrastive FUSE achieves competitive or superior contrastive classification performance without relying on node features, while offering substantial runtime gains over existing baselines. These results highlight the effectiveness of coupling modularity-inspired structural learning with contrastive supervision for efficient and scalable contrastive node representation learning.

Sujan Chakraborty, Saptarshi Bej

School of Data Science, Indian Institute of Science Education and Research, Thiruvananthapuram, 695551, Kerala, India

Graph Representation LearningGraph Contrastive LearningNode Classification
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May 18, 2026

Graph Transductive Sharpening: Leveraging Unlabeled Predictions in Node Classification

In the transductive setting, where the full graph is observed but node labels are only partially available, progress in semi-supervised node classification has largely focused on architectural innovation. In this paper, we revisit an orthogonal axis: the training objective. We start from a simple observation: transductive models produce predictions for every node during training, including nodes without labels. These unlabeled-node predictions may contain useful training signal, but standard supervised objectives discard them because no ground-truth labels are available. Inspired by the decomposition of cross-entropy into a label-dependent alignment term and a label-independent entropy term, we propose prediction confidence as a natural way to extract this signal in the absence of labels. This motivates Transductive Sharpening (TS): a loss-level modification that minimizes prediction entropy on unlabeled nodes while counterbalancing this effect on labeled nodes. We evaluate Transductive Sharpening across a wide range of node-classification benchmarks and observe consistent performance improvements without requiring any changes to the backbone architecture. Code is available at https://github.com/transductive-sharpening/tunedGNN.

Brown Zaz, Mar Gonzàlez I Català, Ferran Hernandez Caralt +2

University of Cambridge

Graph Neural NetworksGraph-Based Semi-Supervised LearningTransductive LearningClassificationSemi-Supervised LearningNode Classification+1
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May 12, 2026

Modeling Heterophily in Multiplex Graphs: An Adaptive Approach for Node Classification

Existing multiplex graph models often assume homophily, where connected nodes tend to belong to the same class or share similar attributes. Consequently, these models may struggle with graphs exhibiting heterophily, where connected nodes typically belong to different classes and have dissimilar attributes. While recent methods have been developed to learn reliable node representations from unidimensional graphs with heterophily, they do not fully address the complexities of multiplex graphs. In a multiplex graph, nodes are linked through multiple types of edges (referred to as dimensions), which can simultaneously exhibit homophilic and heterophilic interactions. To address this gap, we propose \methodname, a novel method for node classification in multiplex graphs that adapts to both homophilic and heterophilic dimensions. \methodname introduces dimension-specific compatibility matrices to model varying degrees of homophily and heterophily across dimensions. A key innovation is its use of a product of trainable low-pass and high-pass filters, approximated via Chebyshev polynomials, to capture both smooth and abrupt changes in the graph signal. By composing these filters and optimizing label predictions using a proximal-gradient method, \methodname dynamically adjusts to the heterophilic characteristics of each dimension. Extensive experiments on synthetic and real-world datasets provide evidence that \methodname captures the complex interplay of homophilic and heterophilic interactions in multiplex graphs, and tends to yield improved node classification performance compared to state-of-the-art methods.

Kamel Abdous, Nairouz Mrabah, Mohamed Bouguessa

Department of Computer Science, University of Quebec at Montreal, Montreal, QC, Canada

Graph Representation LearningSpectral MethodsNode ClassificationGraph Heterophily
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May 6, 2026

A Unified Benchmark for Evaluating Knowledge Graph Construction Methods and Graph Neural Networks

Knowledge graphs automatically constructed from text are increasingly used in real-world applications. However, their inherent noise, fragmentation, and semantic inconsistencies significantly affect the performance of Graph Neural Networks (GNNs) on downstream tasks. Assessing their performance and robustness remains difficult, as it is often unclear whether observed results stem from the learning model or from the quality of the constructed graph itself. In this work, we introduce a dual-purpose benchmark designed to jointly evaluate (i) the performance of GNNs on noisy, text-derived graphs and (ii) the effectiveness of graph construction methods on a downstream task. The benchmark is built in the biomedical domain from a single textual corpus and includes two automatically constructed graphs generated using different extraction methods, alongside a high-quality reference graph curated by experts that serves as an upper performance bound. This design enables controlled comparison of construction methods and systematic evaluation of GNN robustness through semi-supervised node classification. We further provide a standardized, reproducible, and extensible evaluation framework, facilitating the integration of new graph extraction methods and learning models.

Othmane Kabal, Mounira Harzallah, Fabrice Guillet +2

Nantes University, LS2N, Nantes, 44300, France · National Institute of Informatics, Chiyoda-ku, Tokyo, 101-8430, Japan · Institute of Science Tokyo, Tokyo, 152-8550, Japan

KG ConstructionGraph Neural NetworksGraph RobustnessNode ClassificationBiomedical KGs
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May 6, 2026

HeterSEED: Semantics-Structure Decoupling for Heterogeneous Graph Learning under Heterophily

Many real-world heterogeneous graphs exhibit pronounced heterophily, where connected nodes often have dissimilar labels or play different semantic roles. In such settings, standard heterogeneous graph neural networks that aggregate messages along metapaths or meta-relations primarily based on feature similarity can propagate misleading information, since feature similarity may be misaligned with underlying relational semantics. In this paper, we propose HeterSEED, a semantics-structure decoupling framework for heterogeneous graph learning under heterophily. HeterSEED decouples representation learning into a heterogeneous semantic channel that captures type- and relation-aware local semantics and a structure-aware heterophily channel that separates homophilic and heterophilic neighborhoods via pseudo-label-guided partitioning and aggregates them using metapath-based structural weights. A node-level adaptive fusion mechanism then combines the two channels to produce context-dependent node representations. Theoretically, we establish that, on heterogeneous graphs under heterophily, HeterSEED is strictly more expressive than standard heterogeneous graph neural networks that rely primarily on feature similarity and provably reduces the prediction bias introduced by heterophilic neighbors. Experiments on five real-world heterogeneous graphs, including two large-scale networks at the million-node and hundred-million-edge scale, demonstrate that HeterSEED consistently outperforms representative heterogeneous graph neural networks and recent heterophily-aware baselines, especially in strongly heterophilic regimes.

Xinyi Li, Ming Li, Lu Bai +5

Zhejiang Normal University · Beijing Normal University · Central University of Finance and Economics +2

Heterogeneous GNNsNode ClassificationGraph Heterophily
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May 2, 2026

Rethinking Multi-Label Node Classification: Do Tuned Classic GNNs Suffice?

Multi-label node classification (MLNC) has recently been addressed by increasingly complex label-aware designs that explicitly model node-label interactions and inter-label dependencies.However, it remains unclear whether the advantages of these methods truly stem from their specialized designs, or simply from insufficiently optimized baselines. In this paper, we revisit MLNC from a strong-baseline perspective and investigate whether carefully tuned classic full-graph GNNs can already serve as strong solutions to this task. We systematically study several representative backbones, including GCN, SSGConv, and GCNII, and optimize them using standard yet effective techniques such as normalization, dropout, and residual connections. Experiments on five representative benchmark datasets show that our tuned baselines outperform representative specialized methods on four datasets and achieve state-of-the-art performance in multiple settings. These results indicate that careful tuning of classic backbones is a highly influential but often overlooked factor in MLNC, and highlight the need for more rigorous strong-baseline evaluation in future research on multi-label graph learning.

Yuxuan Xiao, Shengzhong Zhang

Nanjing University of Aeronautics and Astronautics

Multi-Label ClassificationGraph Neural NetworksNode Classification
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Apr 24, 2026

Operational Feature Fingerprints of Graph Datasets via a White-Box Signal-Subspace Probe

Graph neural networks achieve strong node-classification accuracy, but learned message passing entangles ego attributes, neighborhood smoothing, high-pass graph differences, class geometry, and classifier-boundary effects inside opaque representations. This obscures why nodes are classified as they are and which graph-learning mechanisms a dataset requires. We propose WG-SRC, a white-box signal-subspace probe for prediction and graph dataset diagnosis. WG-SRC replaces learned message passing with a fixed, named graph-signal dictionary containing raw features, row- and symmetric-normalized low-pass propagation, and high-pass graph differences. It combines Fisher coordinate selection, class-wise PCA subspaces, closed-form multi-alpha ridge classification, and validation-based score fusion, so prediction and analysis rely on explicit class subspaces, energy-controlled dimensions, and closed-form linear decisions. As a white-box graph-learning instrument, WG-SRC uses predictive performance to validate its diagnostics. Across six node-classification datasets, it remains competitive with reproduced baselines and achieves positive average gain under aligned splits. Its atlas decomposes behavior into raw-feature, low-pass, high-pass, class-geometric, and ridge-boundary components. The resulting fingerprints distinguish low-pass-dominated Amazon graphs, mixed high-pass and class-geometrically complex Chameleon behavior, and raw- or boundary-sensitive WebKB graphs. Aligned interventions show when high-pass blocks act as removable noise, when raw or graph-derived signals should be preserved, and when ridge correction matters. WG-SRC therefore serves both as a functioning white-box classifier and as a dataset-fingerprinting probe, enabling fingerprint-conditioned analysis of how black-box model components behave under different graph-signal conditions.

Yuchen Xiong, Swee Keong Yeap, Zhen Hong Ban

China-ASEAN College of Marine Sciences · Xiamen University Malaysia · Sepang 43900, Selangor, Malaysia +1

Graph Signal ProcessingNode ClassificationGNN Explainability
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Apr 22, 2026

F\textsuperscript{2}LP-AP: Fast & Flexible Label Propagation with Adaptive Propagation Kernel

Semi-supervised node classification is a foundational task in graph machine learning, yet state-of-the-art Graph Neural Networks (GNNs) are hindered by significant computational overhead and reliance on strong homophily assumptions. Traditional GNNs require expensive iterative training and multi-layer message passing, while existing training-free methods, such as Label Propagation, lack adaptability to heterophilo-us graph structures. This paper presents \textbf{F2^2LP-AP} (Fast and Flexible Label Propagation with Adaptive Propagation Kernel), a training-free, computationally efficient framework that adapts to local graph topology. Our method constructs robust class prototypes via the geometric median and dynamically adjusts propagation parameters based on the Local Clustering Coefficient (LCC), enabling effective modeling of both homophilous and heterophilous graphs without gradient-based training. Extensive experiments across diverse benchmark datasets demonstrate that \textbf{F2^2LP-AP} achieves competitive or superior accuracy compared to trained GNNs, while significantly outperforming existing baselines in computational efficiency.

Yutong Shen, Ruizhe Xia, Jingyi Liu +1

Beijing University of Technology

Graph-Based Semi-Supervised LearningSemi-Supervised LearningNode ClassificationGraph HeterophilyGraph-Based Label Propagation
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Apr 21, 2026

FOCAL-Attention for Heterogeneous Multi-Label Prediction

Heterogeneous graphs have attracted increasing attention for modeling multi-typed entities and relations in complex real-world systems. Multi-label node classification on heterogeneous graphs is challenging due to structural heterogeneity and the need to learn shared representations across multiple labels. Existing methods typically adopt either flexible attention mechanisms or meta-path constrained anchoring, but in heterogeneous multi-label prediction they often suffer from semantic dilution or coverage constraint. Both issues are further amplified under multi-label supervision. We present a theoretical analysis showing that as heterogeneous neighborhoods expand, the attention mass allocated to task-critical (primary) neighborhoods diminishes, and that meta-path constrained aggregation exhibits a dilemma: too few meta-paths intensify coverage constraint, while too many re-introduce dilution. To resolve this coverage-anchoring conflict, we propose FOCAL: Fusion Of Coverage and Anchoring Learning, with two components: coverage-oriented attention (COA) for flexible, unconstrained heterogeneous context aggregation, and anchoring-oriented attention (AOA) that restricts aggregation to meta-path-induced primary semantics. Our theoretical analysis and experimental results further indicates that FOCAL has a better performance than other state-of-the-art methods.

Chenghao Zhang, Qingqing Long, Ludi Wang +3

Computer Network Information Center, Chinese Academy of Sciences, Beijing, China · University of Chinese Academy of Sciences, Beijing, China

Graph Attention NetworksMulti-Label ClassificationHeterogeneous GNNsNode Classification
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Apr 21, 2026

Learning Posterior Predictive Distributions for Node Classification from Synthetic Graph Priors

One of the most challenging problems in graph machine learning is generalizing across graphs with diverse properties. Graph neural networks (GNNs) face a fundamental limitation: they require separate training for each new graph, preventing universal generalization across diverse graph datasets. A critical challenge facing GNNs lies in their reliance on labeled training data for each individual graph, a requirement that hinders the capacity for universal node classification due to the heterogeneity inherent in graphs -- differences in homophily levels, community structures, and feature distributions across datasets. Inspired by the success of large language models (LLMs) that achieve in-context learning through massive-scale pre-training on diverse datasets, we introduce NodePFN. This universal node classification method generalizes to arbitrary graphs without graph-specific training. NodePFN learns posterior predictive distributions (PPDs) by training only on thousands of synthetic graphs generated from carefully designed priors. Our synthetic graph generation covers real-world graphs through the use of random networks with controllable homophily levels and structural causal models for complex feature-label relationships. We develop a dual-branch architecture combining context-query attention mechanisms with local message passing to enable graph-aware in-context learning. Extensive evaluation on 23 benchmarks demonstrates that a single pre-trained NodePFN achieves 71.27 average accuracy. These results validate that universal graph learning patterns can be effectively learned from synthetic priors, establishing a new paradigm for generalization in node classification.

Jeongwhan Choi, Jongwoo Kim, Woosung Kang +1

KAIST Daejeon, Republic of Korea

Synthetic Data PretrainingOOD GeneralizationIn-Context LearningGraph Foundation ModelsNode Classification
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Apr 20, 2026

Bridge-Centered Metapath Classification Using R-GCN-VGAE for Disaster-Resilient Maintenance Decisions

Daily infrastructure management in preparation for disasters is critical for urban resilience. When bridges remain resilient against disaster-induced external forces, access to hospitals, shops, and residences via metapaths can be sustained, maintaining essential urban functions. However, prioritizing bridge maintenance under limited budgets requires quantifying the multi-dimensional roles that bridges play in disaster scenarios -- a challenge that existing single-indicator approaches fail to address. We focus on metapaths from national highways through bridges to buildings (hospitals, shops, residences), constructing a heterogeneous graph with road, bridge, and building layers. A Relation-centric Graph Convolutional Network Variational Autoencoder (R-GCN-VGAE) learns metapath-based feature representations, enabling classification of bridges into disaster-preparedness categories: Supply Chain (commercial logistics), Medical Access (emergency healthcare), and Residential Protection (preventing isolation). Using OSMnx and open data, we validate our methodology on three diverse cities in Ibaraki Prefecture, Japan: Mito (697 bridges), Chikusei (258 bridges), and Moriya (148 bridges), totaling 1,103 bridges. The heterogeneous graph construction from open data enables redefining bridge roles for disaster scenarios, supporting maintenance budget decision-making. We contributed that (1) Open-data methodology for constructing urban heterogeneous graphs. (2) Redefinition of bridge roles for disaster scenarios via metapath-based classification. (3) Establishment of maintenance budget decision support methodology. (4) k-NN tuning strategy validated across diverse city scales. (5) Empirical demonstration of UMAP superiority over t-SNE/PCA for multi-role bridge visualization.

Takato Yasuno

Takato Yasuno

Node Classification
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Apr 19, 2026

HopRank: Self-Supervised LLM Preference-Tuning on Graphs for Few-Shot Node Classification

Node classification on text-attributed graphs (TAGs) is a fundamental task with broad applications in citation analysis, social networks, and recommendation systems. Current GNN-based approaches suffer from shallow text encoding and heavy dependence on labeled data, limiting their effectiveness in label-scarce settings. While large language models (LLMs) naturally address the text understanding gap with deep semantic reasoning, existing LLM-for-graph methods either still require abundant labels during training or fail to exploit the rich structural signals freely available in graph topology. Our key observation is that, in many real-world TAGs, edges predominantly connect similar nodes under the homophily principle, meaning graph topology inherently encodes class structure without any labels. Building on this insight, we reformulate node classification as a link prediction task and present HopRank, a fully self-supervised LLM-tuning framework for TAGs. HopRank constructs preference data via hierarchical hop-based sampling and employs adaptive preference learning to prioritize informative training signals without any class labels. At inference, nodes are classified by predicting their connection preferences to labeled anchors, with an adaptive early-exit voting scheme to improve efficiency. Experiments on three TAG benchmarks show that HopRank matches fully-supervised GNNs and substantially outperforms prior graph-LLM methods, despite using zero labeled training data.

Ziqing Wang, Kaize Ding

Northwestern University

LLM AlignmentGraph SSLText-Attributed Graph LearningNode ClassificationLLMs for Graph Learning
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Apr 13, 2026

Learning How Much to Think: Difficulty-Aware Dynamic MoEs for Graph Node Classification

Mixture-of-Experts (MoE) architectures offer a scalable path for Graph Neural Networks (GNNs) in node classification tasks but typically rely on static and rigid routing strategies that enforce a uniform expert budget or coarse-grained expert toggles on all nodes. This limitation overlooks the varying discriminative difficulty of nodes and leads to under-fitting for hard nodes and redundant computation for easy ones. To resolve this issue, we propose D2MoE, a novel framework that shifts the focus from static expert selection to node-wise expert resource allocation. By using predictive entropy as a real-time proxy for difficulty, D2MoE employs a difficulty-driven top-p routing mechanism to adaptively concentrate expert resources on hard nodes while reducing overhead for easy ones, achieving continuous and fine-grained expert budget scaling for node classification. Experiments on 13 benchmarks demonstrate that D2MoE achieves consistent state-of-the-art performance, surpassing leading baselines by up to 7.92% in accuracy on heterophilous graphs. Notably, on large-scale graphs, it reduces memory consumption by up to 73.07% and training time by 46.53% compared to the best-performing Graph MoE, thereby validating its superior efficiency.

Jiajun Zhou, Yadong Li, Xuanze Chen +4

Jiajun Zhou, Yadong Li, Xuanze Chen, Chen Ma, Shanqing Yu and Qi Xuan are with the Institute of Cyberspace Security, Zhejiang University of Technology, Hangzhou 310023, China, with the Binjiang Cyberspace Security Institute of ZJUT, Hangzhou, 310056, China, and with the Soovar Technologies Co., Ltd., Hangzhou 310056, China. · Chuang Zhao is with the Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Hong Kong, China.

Graph Neural NetworksMixture-of-Experts ModelsNode Classification
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Apr 10, 2026

Neighbourhood Transformer: Switchable Attention for Monophily-Aware Graph Learning

Graph neural networks (GNNs) have been widely adopted in engineering applications such as social network analysis, chemical research and computer vision. However, their efficacy is severely compromised by the inherent homophily assumption, which fails to hold for heterophilic graphs where dissimilar nodes are frequently connected. To address this fundamental limitation in graph learning, we first draw inspiration from the recently discovered monophily property of real-world graphs, and propose Neighbourhood Transformers (NT), a novel paradigm that applies self-attention within every local neighbourhood instead of aggregating messages to the central node as in conventional message-passing GNNs. This design makes NT inherently monophily-aware and theoretically guarantees its expressiveness is no weaker than traditional message-passing frameworks. For practical engineering deployment, we further develop a neighbourhood partitioning strategy equipped with switchable attentions, which reduces the space consumption of NT by over 95% and time consumption by up to 92.67%, significantly expanding its applicability to larger graphs. Extensive experiments on 10 real-world datasets (5 heterophilic and 5 homophilic graphs) show that NT outperforms all current state-of-the-art methods on node classification tasks, demonstrating its superior performance and cross-domain adaptability. The full implementation code of this work is publicly available at https://github.com/cf020031308/MoNT to facilitate reproducibility and industrial adoption.

Yi Luo, Xu Sun, Guangchun Luo +1

Laboratory of Intelligent Collaborative Computing, University of Electronic Science and Technology of China · School of Computer Science and Engineering, University of Electronic Science and Technology of China · Ubiquitous Intelligence and Trusted Services Key Laboratory of Sichuan Province, China

Graph TransformerGraph HeterophilyGNN ExpressivityNode Classification
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Apr 7, 2026

AgentGL: Towards Agentic Graph Learning with LLMs via Reinforcement Learning

Large Language Models (LLMs) increasingly rely on agentic capabilities-iterative retrieval, tool use, and decision-making-to overcome the limits of static, parametric knowledge. Yet existing agentic frameworks treat external information as unstructured text and fail to leverage the topological dependencies inherent in real-world data. To bridge this gap, we introduce Agentic Graph Learning (AGL), a paradigm that reframes graph learning as an interleaved process of topology-aware navigation and LLM-based inference. Specifically, we propose AgentGL, the first reinforcement learning (RL)-driven framework for AGL. AgentGL equips an LLM agent with graph-native tools for multi-scale exploration, regulates tool usage via search-constrained thinking to balance accuracy and efficiency, and employs a graph-conditioned curriculum RL strategy to stabilize long-horizon policy learning without step-wise supervision. Across diverse Text-Attributed Graph (TAG) benchmarks and multiple LLM backbones, AgentGL substantially outperforms strong GraphLLMs and GraphRAG baselines, achieving absolute improvements of up to 17.5% in node classification and 28.4% in link prediction. These results demonstrate that AGL is a promising frontier for enabling LLMs to autonomously navigate and reason over complex relational environments. The code is publicly available at https://github.com/sunyuanfu/AgentGL.

Yuanfu Sun, Kang Li, Dongzhe Fan +2

New York University Shanghai · New York University · Tsinghua University

LLMs for Graph LearningText-Attributed Graph LearningRL for LLM AgentsNode Classification
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Mar 31, 2026

Efficient and Scalable Granular-ball Graph Coarsening Method for Large-scale Graph Node Classification

Graph Convolutional Network (GCN) is a model that can effectively handle graph data tasks and has been successfully applied. However, for large-scale graph datasets, GCN still faces the challenge of high computational overhead, especially when the number of convolutional layers in the graph is large. Currently, there are many advanced methods that use various sampling techniques or graph coarsening techniques to alleviate the inconvenience caused during training. However, among these methods, some ignore the multi-granularity information in the graph structure, and the time complexity of some coarsening methods is still relatively high. In response to these issues, based on our previous work, in this paper, we propose a new framework called Efficient and Scalable Granular-ball Graph Coarsening Method for Large-scale Graph Node Classification. Specifically, this method first uses a multi-granularity granular-ball graph coarsening algorithm to coarsen the original graph to obtain many subgraphs. The time complexity of this stage is linear and much lower than that of the exiting graph coarsening methods. Then, subgraphs composed of these granular-balls are randomly sampled to form minibatches for training GCN. Our algorithm can adaptively and significantly reduce the scale of the original graph, thereby enhancing the training efficiency and scalability of GCN. Ultimately, the experimental results of node classification on multiple datasets demonstrate that the method proposed in this paper exhibits superior performance. The code is available at https://anonymous.4open.science/r/1-141D/.

Guan Wang, Shuyin Xia, Lei Qian +4

School of Computer Science and Technology, Chongqing Key Laboratory of Computational Intelligence, Key Laboratory of Cyberspace Big Data Intelligent Security, Ministry of Education, Sichuan-Chongqing Co-construction Key Laboratory of Digital Economy Intelligence and Key Laboratory of Big Data Intelligent Computing, Chongqing University of Posts and Telecommunications, 400065, Chongqing, China. · School of Computer Science and Technology, School of Cyber Security and Information Law, Chongqing University of Posts and Telecommunications, 400065, Chongqing, China. · Chongqing Key Laboratory of Brain-Inspired Cognitive Computing and Educational Rehabilitation for Children with Special Needs, Chongqing Normal University, Chongqing, 401331, China. +1

Graph CoarseningGraph Neural NetworksNode Classification
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Mar 25, 2026

CGRL: Causal-Guided Representation Learning for Node-Level Out-of-Distribution Generalization

Graph Neural Networks (GNNs) deliver strong performance on graph tasks, but their accuracy drops significantly under out-of-distribution (OOD) scenarios. Under distribution shifts, GNNs often fit environmental noise and spurious correlations instead of stable causal mechanisms, leading to weak OOD robustness and unstable predictive representations. Existing solutions based on environment invariance or causal reasoning are insufficient for node classification, as they do not explicitly model the fine-grained latent geometry required by the task. We further observe a training instability named Info-Jitter, where the mutual information between predictive representations and ground-truth labels fluctuates throughout training. To address these issues, we construct a node-classification-specific causal graph derived from the task's geometric objective. Using do-calculus to block non-causal paths caused by environmental noise, we derive a deconfounded interventional objective and a variational lower bound to disentangle representations into intra-class and inter-class components. We then propose Causal-Guided Representation Learning (CGRL), a framework with two core modules. First, a multi-branch re-weighted representation learning (RRL) module learns a causal modulation matrix to amplify causal signals and suppress environmental noise during message passing. Second, an optimization strategy combining intra-class aggregation, inter-class separation, energy-based reconstruction and supervised prediction regularizes the latent space for robust node-level generalization. Experiments on multiple benchmark datasets show that CGRL outperforms strong baselines across various distribution shifts and effectively mitigates the Info-Jitter phenomenon.

Bowen Lu, Lianqiang Yang, Teng Li +1

Anhui University, Hefei, China · Carnegie Mellon University, Pittsburgh, Commonwealth of Pennsylvania, USA

OOD GeneralizationGraph Neural NetworksCausal Representation LearningNode ClassificationDisentangled Representation Learning
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Mar 25, 2026

Cost-Sensitive Neighborhood Aggregation for Heterophilous Graphs: When Does Per-Edge Routing Help?

Recent work distinguishes two heterophily regimes: adversarial, where cross-class edges dilute class signal and harm classification, and informative, where the heterophilous structure itself carries useful signal. We ask: when does per-edge message routing help, and when is a uniform spectral channel sufficient? To operationalize this question we introduce Cost-Sensitive Neighborhood Aggregation (CSNA), a GNN layer that computes pairwise distance in a learned projection and uses it to soft-route each message through concordant and discordant channels with independent transformations. Under a contextual stochastic block model we show that mean aggregation can reverse the label-aligned signal direction under heterophily, and that cost-sensitive weighting with w+/w−>q/pw_+/w_- > q/p preserves the correct sign. On six benchmarks with uniform tuning, CSNA is competitive with state-of-the-art methods on adversarial-heterophily datasets (Texas, Wisconsin, Cornell, Actor) but underperforms on informative-heterophily datasets (Chameleon, Squirrel) -- precisely the regime where per-edge routing has no useful decomposition to exploit. The pattern is itself the finding: the cost function's ability to separate edge types serves as a diagnostic for the heterophily regime, revealing when fine-grained routing adds value over uniform channels and when it does not. Code is available at https://github.com/eyal-weiss/CSNA-public .

Eyal Weiss

Computer Science Faculty, Technion — Israel Institute of Technology

Graph Neural NetworksGraph HeterophilyNode ClassificationCost-Sensitive Learning
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Mar 20, 2026

Multi-view Graph Convolutional Network with Fully Leveraging Consistency via Granular-ball-based Topology Construction, Feature Enhancement and Interactive Fusion

The effective utilization of consistency is crucial for multi-view learning. GCNs leverage node connections to propagate information across the graph, facilitating the exploitation of consistency in multi-view data. However, most existing GCN-based multi-view methods suffer from several limitations. First, current approaches predominantly rely on KNN for topology construction, where the artificial selection of the k value significantly constrains the effective exploitation of inter-node consistency. Second, the inter-feature consistency within individual views is often overlooked, which adversely affects the quality of the final embedding representations. Moreover, these methods fail to fully utilize inter-view consistency as the fusion of embedded representations from multiple views is often implemented after the intra-view graph convolutional operation. Collectively, these issues limit the model's capacity to fully capture inter-node, inter-feature and inter-view consistency. To address these issues, this paper proposes the multi-view graph convolutional network with fully leveraging consistency via GB-based topology construction, feature enhancement and interactive fusion (MGCN-FLC). MGCN-FLC can fully utilize three types of consistency via the following three modules to enhance learning ability:The topology construction module based on the granular ball algorithm, which clusters nodes into granular balls with high internal similarity to capture inter-node consistency;The feature enhancement module that improves feature representations by capturing inter-feature consistency;The interactive fusion module that enables each view to deeply interact with all other views, thereby obtaining more comprehensive inter-view consistency. Experimental results on nine datasets show that the proposed MGCN-FLC outperforms state-of-the-art semi-supervised node classification methods.

Chengjie Cui, Taihua Xu, Shuyin Xia +3

School of Computer, Jiangsu University of Science and Technology, Zhenjiang, 212100, China · Chongqing Key Laboratory of Computational Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China · College of Computer and Data Science, Fuzhou University, Fuzhou 350116, China

Graph Neural NetworksMulti-View LearningMulti-View ConsistencyNode ClassificationGraph Structure Learning
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Mar 19, 2026

Position: Spectral GNNs Are Neither Spectral Nor Superior for Node Classification

Spectral Graph Neural Networks (Spectral GNNs) for node classification promise frequency-domain filtering on graphs, yet rest on flawed foundations. Recent work shows that graph Laplacian eigenvectors do not in general have the key properties of a true Fourier basis, but leaves the empirical success of Spectral GNNs unexplained. We identify two theoretical glitches: (1) commonly used "graph Fourier bases" are not classical Fourier bases for graph signals; (2) (n-1)-degree polynomials (n = number of nodes) can exactly interpolate any spectral response via a Vandermonde system, so the usual "polynomial approximation" narrative is not theoretically justified. The effectiveness of GCN is commonly attributed to spectral low-pass filtering, yet we prove that low- and high-pass behaviors arise solely from message-passing dynamics rather than Graph Fourier Transform-based spectral formulations. We then analyze two representative directed spectral models, MagNet and HoloNet. Their reported effectiveness is not spectral: it arises from implementation issues that reduce them to powerful MPNNs. When implemented consistently with the claimed spectral algorithms, performance becomes weak. This position paper argues that: for node classification, Spectral GNNs neither meaningfully capture the graph spectrum nor reliably improve performance; competitive results are better explained by their equivalence to MPNNs, sometimes aided by implementations inconsistent with their intended design.

Qin Jiang, Chengjia Wang, Michael Lones +2

Department of Computer Science, University of Heriot-Watt, Edinburgh, UK

Spectral Graph ConvolutionNode Classification
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Mar 18, 2026

Gaussian Process Limit Reveals Structural Benefits of Graph Transformers

Graph transformers are the state-of-the-art for learning from graph-structured data and are empirically known to avoid several pitfalls of message-passing architectures. However, there is limited theoretical analysis on why these models perform well in practice. In this work, we prove that attention-based architectures have structural benefits over graph convolutional networks in the context of node-level prediction tasks. Specifically, we study the neural network gaussian process limits of graph transformers (GAT, Graphormer, Specformer) with infinite width and infinite heads, and derive the node-level and edge-level kernels across the layers. Our results characterise how the node features and the graph structure propagate through the graph attention layers. As a specific example, we prove that graph transformers structurally preserve community information and maintain discriminative node representations even in deep layers, thereby preventing oversmoothing. We provide empirical evidence on synthetic and real-world graphs that validate our theoretical insights, such as integrating informative priors and positional encoding can improve performance of deep graph transformers.

Nil Ayday, Lingchu Yang, Debarghya Ghoshdastidar

School of Computation, Information and Technology, Technical University of Munich · Graduate School of Information Science and Technology, The University of Tokyo

GNN OversmoothingGraph Neural NetworksGraph TransformerNode Classification
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Mar 17, 2026

A Depth-Aware Comparative Study of Euclidean and Hyperbolic Graph Neural Networks on Bitcoin Transaction Systems

Bitcoin transaction networks are large scale socio- technical systems in which activities are represented through multi-hop interaction patterns. Graph Neural Networks(GNNs) have become a widely adopted tool for analyzing such systems, supporting tasks such as entity detection and transaction classification. Large-scale datasets like Elliptic have allowed for a rise in the analysis of these systems and in tasks such as fraud detection. In these settings, the amount of transactional context available to each node is determined by the neighborhood aggregation and sampling strategies, yet the interaction between these receptive fields and embedding geometry has received limited attention. In this work, we conduct a controlled comparison of Euclidean and tangent-space hyperbolic GNNs for node classification on a large Bitcoin transaction graph. By explicitly varying the neighborhood while keeping the model architecture and dimensionality fixed, we analyze the differences in two embedding spaces. We further examine optimization behavior and observe that joint selection of learning rate and curvature plays a critical role in stabilizing high-dimensional hyperbolic embeddings. Overall, our findings provide practical insights into the role of embedding geometry and neighborhood depth when modeling large-scale transaction networks, informing the deployment of hyperbolic GNNs for computational social systems.

Ankit Ghimire, Saydul Akbar Murad, Nick Rahimi

School of Computing Sciences and Computer Engineering University of Southern Mississippi Hattiesburg, MS, 39406, USA

Graph Neural NetworksHyperbolic Representation LearningNode Classification
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Mar 11, 2026

GaLoRA: Parameter-Efficient Graph-Aware LLMs for Node Classification

The rapid rise of large language models (LLMs) and their ability to capture semantic relationships has led to their adoption in a wide range of applications. Text-attributed graphs (TAGs) are a notable example where LLMs can be combined with Graph Neural Networks to improve the performance of node classification. In TAGs, each node is associated with textual content and such graphs are commonly seen in various domains such as social networks, citation graphs, recommendation systems, etc. Effectively learning from TAGs would enable better representations of both structural and textual representations of the graph and improve decision-making in relevant domains. We present GaLoRA, a parameter-efficient framework that integrates structural information into LLMs. GaLoRA demonstrates competitive performance on node classification tasks with TAGs, performing on par with state-of-the-art models with just 0.24% of the parameter count required by full LLM fine-tuning. We experiment with three real-world datasets to showcase GaLoRA's effectiveness in combining structural and semantical information on TAGs.

Mayur Choudhary, Saptarshi Sengupta, Katerina Potika

Department of Computer Science, San Jose State University

LLMs for Graph LearningText-Attributed Graph LearningNode ClassificationParameter-Efficient Fine-Tuning
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Mar 10, 2026

Transductive Generalization via Optimal Transport and Its Application to Graph Node Classification

Many existing transductive bounds rely on classical complexity measures that are computationally intractable and often misaligned with empirical behavior. In this work, we establish new representation-based generalization bounds in a distribution-free transductive setting, where learned representations are dependent, and test features are accessible during training. We derive global and class-wise bounds via optimal transport, expressed in terms of Wasserstein distances between encoded feature distributions. We demonstrate that our bounds are efficiently computable and strongly correlate with empirical generalization in graph node classification, improving upon classical complexity measures. Additionally, our analysis reveals how the GNN aggregation process transforms the representation distributions, inducing a trade-off between intra-class concentration and inter-class separation. This yields depth-dependent characterizations that capture the non-monotonic relationship between depth and generalization error observed in practice. The code is available at https://github.com/ml-postech/Transductive-OT-Gen-Bound.

MoonJeong Park, Seungbeom Lee, Kyungmin Kim +5

Graduate School of Artificial Intelligence, POSTECH, South Korea · CSIRO’s Data61, Canberra, Australia · Department of Computer Science & Engineering, POSTECH, South Korea

Transductive LearningGeneralization BoundsGraph Neural NetworksNode Classification
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Mar 10, 2026

P2P^2GNN: Two Prototype Sets to boost GNN Performance

Message Passing Graph Neural Networks (MP-GNNs) have garnered attention for addressing various industry challenges, such as user recommendation and fraud detection. However, they face two major hurdles: (1) heavy reliance on local context, often lacking information about the global context or graph-level features, and (2) assumption of strong homophily among connected nodes, struggling with noisy local neighborhoods. To tackle these, we introduce P2P^2GNN, a plug-and-play technique leveraging prototypes to optimize message passing, enhancing the performance of the base GNN model. Our approach views the prototypes in two ways: (1) as universally accessible neighbors for all nodes, enriching global context, and (2) aligning messages to clustered prototypes, offering a denoising effect. We demonstrate the extensibility of our proposed method to all message-passing GNNs and conduct extensive experiments across 18 datasets, including proprietary e-commerce datasets and open-source datasets, on node recommendation and node classification tasks. Results show that P2P^2GNN outperforms production models in e-commerce and achieves the top average rank on open-source datasets, establishing it as a leading approach. Qualitative analysis supports the value of global context and noise mitigation in the local neighborhood in enhancing performance.

Arihant Jain, Gundeep Arora, Anoop Saladi +1

Amazon, India

Graph Neural NetworksMessage Passing Neural NetworksNode ClassificationRecommender Systems
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Mar 9, 2026

Rel-MOSS: Towards Imbalanced Relational Deep Learning on Relational Databases

In recent advances, to enable a fully data-driven learning paradigm on relational databases (RDB), relational deep learning (RDL) is proposed to structure the RDB as a heterogeneous entity graph and adopt the graph neural network (GNN) as the predictive model. However, existing RDL methods neglect the imbalance problem of relational data in RDBs and risk under-representing the minority entities, leading to an unusable model in practice. In this work, we investigate, for the first time, class imbalance problem in RDB entity classification and design the relation-centric minority synthetic over-sampling GNN (Rel-MOSS), in order to fill a critical void in the current literature. Specifically, to mitigate the issue of minority-related information being submerged by majority counterparts, we design the relation-wise gating controller to modulate neighborhood messages from each individual relation type. Based on the relational-gated representations, we further propose the relation-guided minority synthesizer for over-sampling, which integrates the entity relational signatures to maintain relational consistency. Extensive experiments on 12 entity classification datasets provide compelling evidence for the superiority of Rel-MOSS, yielding an average improvement of up to 2.46% and 4.00% in terms of Balanced Accuracy and G-Mean, compared with SOTA RDL methods and classic methods for handling class imbalance.

Jun Yin, Peng Huo, Bangguo Zhu +4

Department of Data Science and Artificial Intelligence, Hong Kong Polytechnic University, Hong Kong SAR, China · National Super Computing Center, Tianjin, China · School of Computer Science and Engineering, Central South University, Hunan, China +1

Relational Deep LearningClass-Imbalanced LearningRelational DatabasesNode ClassificationGraph Neural Networks
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Mar 3, 2026

Graph Hopfield Networks: Energy-Based Node Classification with Associative Memory

We introduce Graph Hopfield Networks, whose energy function couples associative memory retrieval with graph Laplacian smoothing for node classification. Gradient descent on this joint energy yields an iterative update interleaving Hopfield retrieval with Laplacian propagation. Memory retrieval provides regime-dependent benefits: up to 2.0~pp on sparse citation networks and up to 5 pp additional robustness under feature masking; the iterative energy-descent architecture itself is a strong inductive bias, with all variants (including the memory-disabled NoMem ablation) outperforming standard baselines on Amazon co-purchase graphs. Tuning enables graph sharpening for heterophilous benchmarks without architectural changes.

Abinav Rao, Alex Wa, Rishi Athavale

Node ClassificationHopfield NetworksEnergy-Based Models
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Feb 23, 2026

VecFormer: Towards Efficient and Generalizable Graph Transformer with Graph Token Attention

Graph Transformer has demonstrated impressive capabilities in the field of graph representation learning. However, existing approaches face two critical challenges: (1) most models suffer from exponentially increasing computational complexity, making it difficult to scale to large graphs; (2) attention mechanisms based on node-level operations limit the flexibility of the model and result in poor generalization performance in out-of-distribution (OOD) scenarios. To address these issues, we propose VecFormer (the Vector Quantized Graph Transformer), an efficient and highly generalizable model for node classification, particularly under OOD settings. VecFormer adopts a two-stage training paradigm. In the first stage, two codebooks are used to reconstruct the node features and the graph structure, aiming to learn the rich semantic Graph Codes. In the second stage, attention mechanisms are performed at the Graph Token level based on the transformed cross codebook, reducing computational complexity while enhancing the model's generalization capability. Extensive experiments on datasets of various sizes demonstrate that VecFormer outperforms the existing Graph Transformer in both performance and speed.

Jingbo Zhou, Jun Xia, Siyuan Li +11

Zhejiang University Hangzhou, Zhejiang, China · Westlake University Hangzhou, Zhejiang, China · Hong Kong University of Science and Technology (Guangzhou) Guangzhou, Guangdong, China +4

Graph TransformerNode ClassificationOOD Generalization
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