Graph Neural Networks

Also known as GNN

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Latest papers 686

88 papers in the last four weeks, up 31% on the four weeks before. 0.5% of all new papers.

Mar 20, 2026

Modeling subgrid scale production rates on complex meshes using graph neural networks

Large-eddy simulations (LES) require closures for filtered production rates because the resolved fields do not contain all correlations that govern chemical source terms. We develop a graph neural network (GNN) that predicts filtered species production rates on non-uniform meshes from inputs of filtered mass fractions and temperature. Direct numerical simulations of turbulent premixed hydrogen-methane jet flames with hydrogen fractions of 10%, 50%, and 80% provide the dataset. All fields are Favre filtered with the filter width matched to the operating mesh, and learning is performed on subdomain graphs constructed from mesh-point connectivity. A compact set of reactants, intermediates, and products is used, and their filtered production rates form the targets. The model is trained on 10% and 80% blends and evaluated on the unseen 50% blend to test cross-composition generalization. The GNN is compared against an unclosed reference that evaluates rates at the filtered state, and a convolutional neural network baseline that requires remeshing. Across in-distribution and out-of-distribution cases, the GNN yields lower errors and closer statistical agreement with the reference data. Furthermore, the model demonstrates robust generalization across varying filter widths without retraining, maintaining bounded errors at coarser spatial resolutions. A backward facing step configuration further confirms prediction efficacy on a practically relevant geometry. These results highlight the capability of GNNs as robust data-driven closure models for LES on complex meshes.

Priyabrat Dash, Mathis Bode, Konduri Aditya

Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, 560012, KA, India · Jülich Supercomputing Centre, Forschungszentrum Jülich GmbH, Jülich, 52425, NRW, Germany

Computational Fluid Dynamics Graph Neural Networks

Mar 20, 2026

A graph neural network based chemical mechanism reduction method for combustion applications

Direct numerical simulations of turbulent reacting flows involving millions of grid points and detailed chemical mechanisms with hundreds of species and thousands of reactions are computationally prohibitive. To address this challenge, we present two data-driven chemical mechanism reduction formulations based on graph neural networks (GNNs) with message-passing transformer layers that learn nonlinear dependencies among species and reactions. The first formulation, GNN-SM, employs a pre-trained surrogate model to guide reduction across a broad range of reactor conditions. The second formulation, GNN-AE, uses an autoencoder formulation to obtain highly compact mechanisms that remain accurate within the thermochemical regimes used during training. The approaches are demonstrated on detailed mechanisms for methane (53 species, 325 reactions), ethylene (96 species, 1054 reactions), and iso-octane (1034 species, 8453 reactions). GNN-SM achieves reductions comparable to the established graph-based method DRGEP while maintaining accuracy across a wide range of thermochemical states. In contrast, GNN-AE achieves up to 95% reduction in species and reactions and outperforms DRGEP within its target conditions. Overall, the proposed framework provides an automated, machine-learning-based pathway for chemical mechanism reduction that can complement traditional expert-guided analytical approaches.

Manuru Nithin Padiyar, Priyabrat Dash, Konduri Aditya

Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, 560012, KA, India

Reduced-Order Modeling Graph Neural Networks

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 Networks Multi-View Learning Multi-View Consistency Node Classification Graph Structure Learning

Mar 19, 2026

WarPGNN: A Parametric Thermal Warpage Analysis Framework with Physics-aware Graph Neural Network

With the advent of system-in-package (SiP) chiplet-based design and heterogeneous 2.5D/3D integration, thermal-induced warpage has become a critical reliability concern. While conventional numerical approaches can deliver highly accurate results, they often incur prohibitively high computational costs, limiting their scalability for complex chiplet-package systems. In this paper, we present WarPGNN, an efficient and accurate parametric thermal warpage analysis framework powered by Graph Neural Networks (GNNs). By operating directly on graphs constructed from the floorplans, WarPGNN enables fast warpage-aware floorplan exploration and exhibits strong transferability across diverse package configurations. Our method first encodes multi-die floorplans into reduced Transitive Closure Graphs (rTCGs), then a Graph Convolution Network (GCN)-based encoder extracts hierarchical structural features, followed by a U-Net inspired decoder that reconstructs warpage maps from graph feature embeddings. Furthermore, to address the long-tailed pattern of warpage data distribution, we developed a physics-informed loss and revised a message-passing encoder based on Graph Isomorphic Network (GIN) that further enhance learning performance for extreme cases and expressiveness of graph embeddings. Numerical results show that WarPGNN achieves more than 205.91x speedup compared with the 2-D efficient FEM-based method and over 119766.64x acceleration with 3-D FEM method COMSOL, respectively, while maintaining comparable accuracy at only 1.26% full-scale normalized RMSE and 2.21% warpage value error. Compared with recent DeepONet-based model, our method achieved comparable prediction accuracy and inference speedup with 3.4x lower training time. In addition, WarPGNN demonstrates remarkable transferability on unseen datasets with up to 3.69% normalized RMSE and similar runtime.

Haotian Lu, Jincong Lu, Sachin Sachdeva +1

Department of Electrical and Computer Engineering · University of California, Riverside · Riverside, CA, USA

Graph Neural Networks Physics-Informed ML

Mar 19, 2026

Attack by Unlearning: Unlearning-Induced Adversarial Attacks on Graph Neural Networks

Graph neural networks (GNNs) are widely used for learning from graph-structured data in domains such as social networks, recommender systems, and financial platforms. To comply with privacy regulations like the GDPR, CCPA, and PIPEDA, approximate graph unlearning, which aims to remove the influence of specific data points from trained models without full retraining, has become an increasingly important component of trustworthy graph learning. However, approximate unlearning often incurs subtle performance degradation, which may incur negative and unintended side effects. In this work, we show that such degradations can be amplified into adversarial attacks. We introduce the notion of unlearning corruption attacks, where an adversary injects carefully chosen nodes into the training graph and later requests their deletion. Because deletion requests are legally mandated and cannot be denied, this attack surface is both unavoidable and stealthy: the model performs normally during training, but accuracy collapses only after unlearning is applied. Technically, we formulate this attack as a bi-level optimization problem: to overcome the challenges of black-box unlearning and label scarcity, we approximate the unlearning process via gradient-based updates and employ a surrogate model to generate pseudo-labels for the optimization. Extensive experiments across benchmarks and unlearning algorithms demonstrate that small, carefully designed unlearning requests can induce significant accuracy degradation, raising urgent concerns about the robustness of GNN unlearning under real-world regulatory demands. The source code will be released upon paper acceptance.

Jiahao Zhang, Yilong Wang, Suhang Wang

The Pennsylvania State University University Park, PA, USA

Adversarial Attacks Graph Neural Networks Machine Unlearning

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

Graph Neural Networks Graph Transformer Node Classification

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 Networks Hyperbolic Representation Learning Node Classification

Mar 16, 2026

CrossADR: enhancing adverse drug reactions prediction for combination pharmacotherapy with cross-layer feature integration and cross-level associative learning

Combination pharmacotherapy offers substantial therapeutic advantages but also poses substantial risks of adverse drug reactions (ADRs). The accurate prediction of ADRs with interpretable computational methods is crucial for clinical safety management, drug development, and precision medicine. However, managing ADRs remains a challenge due to the vast search space of drug combinations and the complexity of physiological responses. Current graph-based architectures often struggle to effectively integrate multi-scale biological information and frequently rely on fixed association matrices, which limits their ability to capture dynamic organ-level dependencies and generalize across diverse datasets. Here we propose CrossADR, a hierarchical framework for organ-level ADR prediction through cross-layer feature integration and cross-level associative learning. It incorporates a gated-residual-flow graph neural network to fuse multi-scale molecular features and utilizes a learnable ADR embedding space to dynamically capture latent biological correlations across 15 organ systems. Systematic evaluation on the newly constructed CrossADR-Dataset-covering 1,376 drugs and 946,000 unique combinations-demonstrates that CrossADR consistently achieves state-of-the-art performance across 80 distinct experimental scenarios and provides high-resolution insights into drug-related protein protein interactions and pathways. Overall, CrossADR represents a robust tool for cross-scale biomedical information integration, cross-layer feature integration as well as cross-level associative learning, and can be effectively utilized to prevent ADRs in clinical decision-making.

Y. Cheung

School of Mathematical Sciences and Shanghai Key Laboratory of PMMP, East China Normal University, 200241, Shanghai, China

Clinical Risk Prediction Graph Neural Networks Multi-Scale Feature Fusion

Mar 16, 2026

Tackling Over-smoothing on Hypergraphs: A Ricci Flow-guided Neural Diffusion Approach

Hypergraph neural networks (HGNNs) have demonstrated strong capabilities in modeling complex higher-order relationships. However, existing HGNNs often suffer from over-smoothing as the number of layers increases and lack effective control over message passing among nodes. Inspired by the theory of Ricci flow in differential geometry, we theoretically establish that introducing discrete Ricci flow into hypergraph structures can effectively regulate node feature evolution and thereby alleviate over-smoothing. Building on this insight, we propose Ricci Flow-guided Hypergraph Neural Diffusion(RFHND), a novel message passing paradigm for hypergraphs guided by discrete Ricci flow. Specifically, RFHND is based on a PDE system that describes the continuous evolution of node features on hypergraphs and adaptively regulates the rate of information diffusion at the geometric level, preventing feature homogenization and producing high-quality node representations. Experimental results show that RFHND significantly outperforms existing methods across multiple benchmark datasets and demonstrates strong robustness, while also effectively mitigating over-smoothing.

Mengyao Zhou, Zhiheng Zhou, Xiao Han +3

the Academy of Mathematics and Systems Science, Chinese Academy of Sciences and also with the University of Chinese Academy of Sciences, Beijing 100190, China · the School of Mathematics and Statistics, Shandong University, Weihai, Shandong 264209, China · School of Artificial Intelligence, Beihang University, Beijing 100191, China +1

Hypergraph Neural Networks Hypergraph Learning Graph Neural Networks Graph Diffusion

Mar 16, 2026

Lost in Aggregation: On a Fundamental Expressivity Limit of Message-Passing Graph Neural Networks

We define an information-complexity property for aggregation functions, capturing a vast range of practical aggregations, and prove that any Message-Passing Graph Neural Network (MP-GNN) model with such aggregations induces only a polynomial number of equivalence classes on all graphs - while the number of non-isomorphic graphs is super-exponential (in number of vertices). Adding a familiar perspective, we observe that merely 2 iterations of Color Refinement (CR) induce at least an exponential number of equivalence classes, making the aforementioned MP-GNNs relatively infinitely weaker. Previous studies state that sum-aggregation MP-GNNs match full CR however they consider a weak, 'non-uniform', notion of distinguishing-power where each graph size may require a different MP-GNN to distinguish graphs up to that size. Our results concern both distinguishing between non-equivariant vertices and distinguishing between non-isomorphic graphs.

Eran Rosenbluth

RWTH Aachen University

Graph Neural Networks GNN Expressivity Message Passing Neural Networks

Mar 15, 2026

Geometric and Topological Deep Learning for Predicting Thermo-mechanical Performance in Cold Spray Deposition Process Modeling

This study presents a geometric deep learning framework for predicting cold spray particle impact responses using finite element simulation data. A parametric dataset was generated through automated Abaqus simulations spanning a systematic range of particle velocity, particle temperature, and friction coefficient, yielding five output targets including maximum equivalent plastic strain, average contact plastic strain, maximum temperature, maximum von Mises stress, and deformation ratio. Four novel algorithms i.e. a GraphSAGE-style inductive graph neural network, a Chebyshev spectral graph convolution network, a topological data analysis augmented multilayer perceptron, and a geometric attention network were implemented and evaluated. Each input sample was treated as a node in a k-nearest-neighbour feature-space graph, enabling the models to exploit spatial similarity between process conditions during training. Three-dimensional feature space visualisations and two-dimensional contour projections confirmed the highly non-linear and velocity-dominated nature of the input-output relationships. Quantitative evaluation demonstrated that GraphSAGE and GAT consistently achieved R-square values exceeding 0.93 across most targets, with GAT attaining peak performance of R-square equal to 0.97 for maximum plastic strain. ChebSpectral and TDA-MLP performed considerably worse, yielding negative R-square values for several targets. These findings establish spatial graph-based neighbourhood aggregation as a robust and physically interpretable surrogate modelling strategy for cold spray process optimisation.

Akshansh Mishra

School of Industrial and Information Engineering, Politecnico di Milano, Milan, Italy

Surrogate Modeling Manufacturing Graph Neural Networks Geometric Representation Learning

Mar 15, 2026

Flood Risk Follows Valleys, Not Grids: Graph Neural Networks for Flash Flood Susceptibility Mapping in Himachal Pradesh with Conformal Uncertainty Quantification

Flash floods are the most destructive natural hazard in Himachal Pradesh (HP), India, causing over 400 fatalities and $1.2 billion in losses in the 2023 monsoon season alone. Existing risk maps treat every pixel independently, ignoring the basic fact that flooding upstream raises risk downstream. We address this with a Graph Neural Network (GraphSAGE) trained on a watershed connectivity graph (460 sub-watersheds, 1,700 directed edges), built from a six-year Sentinel-1 SAR flood inventory (2018-2023, 3,000 events) and 12 environmental variables at 30 m resolution. Four pixel-based ML models (RF, XGBoost, LightGBM, stacking ensemble) serve as baselines. All models are evaluated with leave-one-basin-out spatial cross-validation to avoid the 5-15% AUC inflation of random splits. Conformal prediction produces the first HP susceptibility maps with statistically guaranteed 90% coverage intervals. The GNN achieved AUC = 0.978 +/- 0.017, outperforming the best baseline (AUC = 0.881) and the published HP benchmark (AUC = 0.88). The +0.097 gain confirms that river connectivity carries predictive signal that pixel-based models miss. High-susceptibility zones overlap 1,457 km of highways (including 217 km of the Manali-Leh corridor), 2,759 bridges, and 4 major hydroelectric installations. Conformal intervals achieved 82.9% empirical coverage on the held-out 2023 test set; lower coverage in high-risk zones (45-59%) points to SAR label noise as a target for future work.

Paras Sharma, Swastika Sharma

Independent Researcher · Dr. YSPUHF, Solan, H.P., India

Graph Neural Networks

Mar 13, 2026

MR-GNF: Multi-Resolution Graph Neural Forecasting on Ellipsoidal Meshes for Efficient Regional Weather Prediction

Weather forecasting offers an ideal testbed for artificial intelligence (AI) to learn complex, multi-scale physical systems. Traditional numerical weather prediction remains computationally costly for frequent regional updates, as high-resolution nests require intensive boundary coupling. We introduce Multi-Resolution Graph Neural Forecasting (MR-GNF), a lightweight, physics-aware model that performs short-term regional forecasts directly on an ellipsoidal, multi-scale graph of the Earth. The framework couples a 0.25° region of interest with a 0.5° context belt and 1.0° outer domain, enabling continuous cross-scale message passing without explicit nested boundaries. Its axial graph-attention network alternates vertical self-attention across pressure levels with horizontal graph attention across surface nodes, capturing implicit 3-D structure in just 1.6 M parameters. Trained on 40 years of ERA5 reanalysis (1980-2024), MR-GNF delivers stable +6 h to +24 h forecasts for near-surface temperature, wind, and precipitation over the UK-Ireland sector. Despite a total compute cost below 80 GPU-hours on a single RTX 6000 Ada, the model matches or exceeds heavier regional AI systems while preserving physical consistency across scales. These results demonstrate that graph-based neural operators can achieve trustworthy, high-resolution weather prediction at a fraction of NWP cost, opening a practical path toward AI-driven early-warning and renewable-energy forecasting systems. Project page and code: https://github.com/AndriiShchur/MR-GNF

Andrii Shchur, Inna Skarga-Bandurova

Kyiv School of Economics · Oxford Brookes University

Weather Forecasting Graph Neural Networks Spatiotemporal GNNs

Mar 13, 2026

Modality-free Graph In-context Alignment

In-context learning (ICL) converts static encoders into task-conditioned reasoners, enabling adaptation to new data from just a few examples without updating pretrained parameters. This capability is essential for graph foundation models (GFMs) to approach LLM-level generality. Yet current GFMs struggle with cross-domain alignment, typically relying on modality-specific encoders that fail when graphs are pre-vectorized or raw data is inaccessible. In this paper, we introduce Modality-Free Graph In-context Alignment (MF-GIA), a framework that makes a pretrained graph encoder promptable for few-shot prediction across heterogeneous domains without modality assumptions. MF-GIA captures domain characteristics through gradient fingerprints, which parameterize lightweight transformations that align pre-encoded features and indexed labels into unified semantic spaces. During pretraining, a dual prompt-aware attention mechanism with episodic objective learns to match queries against aligned support examples to establish prompt-based reasoning capabilities. At inference, MF-GIA performs parameter-update-free adaptation using only a few-shot support set to trigger cross-domain alignment and enable immediate prediction on unseen domains. Experiments demonstrate that MF-GIA achieves superior few-shot performance across diverse graph domains and strong generalization to unseen domains.

Wei Zhuo, Siqiang Luo

Nanyang Technological University

Graph Foundation Models In-Context Learning Graph Neural Networks Few-Shot Domain Adaptation

Mar 13, 2026

Graph In-Context Operator Networks for Generalizable Spatiotemporal Prediction

In-context operator learning enables neural networks to infer solution operators from contextual examples without weight updates. While prior work has demonstrated the effectiveness of this paradigm in leveraging vast datasets, a systematic comparison against single-operator learning using identical training data has been absent. We address this gap through controlled experiments comparing in-context operator learning against classical operator learning (single-operator models trained without contextual examples), under the same training steps and dataset. To enable this investigation on real-world spatiotemporal systems, we propose GICON (Graph In-Context Operator Network), combining graph message passing for geometric generalization with example-aware positional encoding for cardinality generalization. Experiments on air quality prediction across two Chinese regions show that in-context operator learning outperforms classical operator learning on complex tasks, generalizing across spatial domains and scaling robustly from few training examples to 100 at inference.

Chenghan Wu, Zongmin Yu, Boai Sun +1

National University of Singapore

Operator Learning Spatiotemporal Forecasting Graph Neural Networks

Mar 13, 2026

Lyapunov Stable Graph Neural Flow

Graph Neural Networks (GNNs) are highly vulnerable to adversarial perturbations in both topology and features, making the learning of robust representations a critical challenge. In this work, we bridge GNNs with control theory to introduce a novel defense framework grounded in integer- and fractional-order Lyapunov stability. Unlike conventional strategies that rely on resource-heavy adversarial training or data purification, our approach fundamentally constrains the underlying feature-update dynamics of the GNN. We propose an adaptive, learnable Lyapunov function paired with a novel projection mechanism that maps the network's state into a stable space, thereby offering theoretically provable stability guarantees. Notably, this mechanism is orthogonal to existing defenses, allowing for seamless integration with techniques like adversarial training to achieve cumulative robustness. Extensive experiments demonstrate that our Lyapunov-stable graph neural flows substantially outperform base neural flows and state-of-the-art baselines across standard benchmarks and various adversarial attack scenarios.

Haoyu Chu, Xiaotong Chen, Wei Zhou +4

School of Computer Science and Technology / School of Artificial Intelligence, China University of Mining and Technology, Xuzhou 221008, China · School of Information Science and Technology, University of Science and Technology of China, Hefei 230026, China

Graph Neural Networks Adversarial Robustness Lyapunov Stability

Mar 12, 2026

Effective Resistance Rewiring: A Simple Topological Correction for Over-Squashing

Graph Neural Networks struggle to capture long-range dependencies due to over-squashing, where information from exponentially growing neighborhoods must pass through a small number of structural bottlenecks. While recent rewiring methods attempt to alleviate this limitation, many rely on local criteria such as curvature, which can overlook global connectivity constraints that restrict information flow. We introduce Effective Resistance Rewiring (ERR), a simple topology correction strategy that uses effective resistance as a global signal to detect structural bottlenecks. ERR iteratively adds edges between node pairs with the largest resistance while removing edges with minimal resistance, strengthening weak communication pathways while controlling graph densification under a fixed edge budget. The procedure is parameter-free beyond the rewiring budget and relies on a single global measure aggregating all paths between node pairs. Beyond predictive performance with GCN models, we analyze how rewiring affects message propagation. By tracking cosine similarity between node embeddings across layers, we examine how the relationship between initial node features and learned representations evolves during message passing, comparing graphs with and without rewiring. This analysis helps determine whether improvements arise from better long-range communication rather than changes in embedding geometry. Experiments on homophilic and heterophilic graphs, including directed settings with DirGCN, reveal a trade-off between over-squashing and oversmoothing, where oversmoothing corresponds to the loss of representation diversity across layers. Resistance-guided rewiring improves connectivity and signal propagation but can accelerate representation mixing in deep models. Combining ERR with normalization techniques such as PairNorm stabilizes this trade-off and improves performance.

Bertran Miquel-Oliver, Manel Gil-Sorribes, Victor Guallar +1

Barcelona Supercomputing Center (BSC), Barcelona, Spain · Universitat Politècnica de Catalunya - BarcelonaTech (UPC), Barcelona, Spain · Nostrum Biodiscovery, Barcelona, 08029, Spain +1

Graph Neural Networks Graph Rewiring Over-Squashing

Mar 12, 2026

Contextual Graph Representations for Task-Driven 3D Perception and Planning

Recent advances in computer vision facilitate fully automatic extraction of object-centric relational representations from visual-inertial data. These state representations, dubbed 3D scene graphs, are a hierarchical decomposition of real-world scenes with a dense multiplex graph structure. While 3D scene graphs claim to promote efficient task planning for robot systems, they contain numerous objects and relations when only small subsets are required for a given task. This magnifies the state space that task planners must operate over and prohibits deployment in resource constrained settings. This thesis tests the suitability of existing embodied AI environments for research at the intersection of robot task planning and 3D scene graphs and constructs a benchmark for empirical comparison of state-of-the-art classical planners. Furthermore, we explore the use of graph neural networks to harness invariances in the relational structure of planning domains and learn representations that afford faster planning.

Christopher Agia

Robot Task Planning Graph-Based Planning 3D Scene Representation Symbolic Planning Graph Neural Networks

Mar 11, 2026

GNN-as-Judge: Unleashing the Power of LLMs for Graph Learning with GNN Feedback

Large Language Models (LLMs) have shown strong performance on text-attributed graphs (TAGs) due to their superior semantic understanding ability on textual node features. However, their effectiveness as predictors in the low-resource setting, where labeled nodes are severely limited and scarce, remains constrained since fine-tuning LLMs usually requires sufficient labeled data, especially when the TAG shows complex structural patterns. In essence, this paper targets two key challenges: (i) the difficulty of generating and selecting reliable pseudo labels on TAGs for LLMs, and (ii) the need to mitigate potential label noise when fine-tuning LLMs with pseudo labels. To counter the challenges, we propose a new framework, GNN-as-Judge, which can unleash the power of LLMs for few-shot semi-supervised learning on TAGs by incorporating the structural inductive bias of Graph Neural Networks (GNNs). Specifically, GNN-as-Judge introduces a collaborative pseudo-labeling strategy that first identifies the most influenced unlabeled nodes from labeled nodes, then exploits both the agreement and disagreement patterns between LLMs and GNNs to generate reliable labels. Furthermore, we develop a weakly-supervised LLM fine-tuning algorithm that can distill the knowledge from informative pseudo labels while mitigating the potential label noise. Experiments on multiple TAG datasets demonstrate that GNN-as-Judge significantly outperforms existing methods, particularly in low-resource regimes where labeled data are scarce.

Ruiyao Xu, Kaize Ding

Department of Statistics and Data Science, Northwestern University

Text-Attributed Graph Learning LLMs for Graph Learning Graph-Based Semi-Supervised Learning Pseudo-Labeling Weakly Supervised Learning Graph Neural Networks

Mar 11, 2026

Towards Intelligent Spectrum Management: Spectrum Demand Estimation Using Graph Neural Networks

The growing demand for wireless connectivity, combined with limited spectrum resources, calls for more efficient spectrum management. Spectrum sharing is a promising approach; however, regulators need accurate methods to characterize demand dynamics and guide allocation decisions. This paper builds and validates a spectrum demand proxy from public deployment records and uses a graph attention network in a hierarchical, multi-resolution setup (HR-GAT) to estimate spectrum demand at fine spatial scales. The model captures both neighborhood effects and cross-scale patterns, reducing spatial autocorrelation and improving generalization. Evaluated across five Canadian cities and against eight competitive baselines, HR-GAT reduces median RMSE by roughly 21% relative to the best alternative and lowers residual spatial bias. The resulting demand maps are regulator-accessible and support spectrum sharing and spectrum allocation in wireless networks.

Mohamad Alkadamani, Amir Ghasemi, Halim Yanikomeroglu

Communications Research Centre Canada, Ottawa, ON, Canada · Carleton University, Ottawa, ON, Canada

Wireless Communications Wireless Resource Allocation Graph Neural Networks Graph Attention Networks

Mar 10, 2026

GNNs for Time Series Anomaly Detection: An Open-Source Framework and a Critical Evaluation

There is growing interest in applying graph-based methods to Time Series Anomaly Detection (TSAD), particularly Graph Neural Networks (GNNs), as they naturally model dependencies among multivariate signals. GNNs are typically used as backbones in score-based TSAD pipelines, where anomalies are identified through reconstruction or prediction errors followed by thresholding. However, and despite promising results, the field still lacks standardized frameworks for evaluation and suffers from persistent issues with metric design and interpretation. We thus present an open-source framework for TSAD using GNNs, designed to support reproducible experimentation across datasets, graph structures, and evaluation strategies. Built with flexibility and extensibility in mind, the framework facilitates systematic comparisons between TSAD models and enables in-depth analysis of performance and interpretability. Using this tool, we evaluate several GNN-based architectures alongside baseline models across two real-world datasets with contrasting structural characteristics. Our results show that GNNs not only improve detection performance but also offer significant gains in interpretability, an especially valuable feature for practical diagnosis. We also find that attention-based GNNs offer robustness when graph structure is uncertain or inferred. In addition, we reflect on common evaluation practices in TSAD, showing how certain metrics and thresholding strategies can obscure meaningful comparisons. Overall, this work contributes both practical tools and critical insights to advance the development and evaluation of graph-based TSAD systems.

Federico Bello, Gonzalo Chiarlone, Marcelo Fiori +2

Facultad de Ingeniería, Universidad de la República, Montevideo, Uruguay · Pento, Montevideo, Uruguay · Centro Interdisciplinario en Ciencia de Datos y Aprendizaje Automático (CICADA), Universidad de la República, Uruguay

Time-Series Anomaly Detection Graph Neural Networks Interpretable Anomaly Detection

Mar 10, 2026

GIIM: Graph-based Learning of Inter- and Intra-view Dependencies for Multi-view Medical Image Diagnosis

Computer-aided diagnosis (CADx) has become vital in medical imaging, but automated systems often struggle to replicate the nuanced process of clinical interpretation. Expert diagnosis requires a comprehensive analysis of how abnormalities relate to each other across various views and time points, but current multi-view CADx methods frequently overlook these complex dependencies. Specifically, they fail to model the crucial relationships within a single view and the dynamic changes lesions exhibit across different views. This limitation, combined with the common challenge of incomplete data, greatly reduces their predictive reliability. To address these gaps, we reframe the diagnostic task as one of relationship modeling and propose GIIM, a novel graph-based approach. Our framework is uniquely designed to simultaneously capture both critical intra-view dependencies between abnormalities and inter-view dynamics. Furthermore, it ensures diagnostic robustness by incorporating specific techniques to effectively handle missing data, a common clinical issue. We demonstrate the generality of this approach through extensive evaluations on diverse imaging modalities, including CT, MRI, and mammography. The results confirm that our GIIM model significantly enhances diagnostic accuracy and robustness over existing methods, establishing a more effective framework for future CADx systems.

Tran Bao Sam, Hung Vu, Dao Trung Kien +3

NVIDIA, Ho Chi Minh City, Vietnam

Medical Image Analysis Medical Image Classification Multi-View Learning Graph Neural Networks

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 Learning Generalization Bounds Graph Neural Networks Node Classification

Mar 10, 2026

$P^2$ GNN: 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

P^2

GNN, 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

P^2

GNN 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 Networks Message Passing Neural Networks Node Classification Recommender Systems

Mar 9, 2026

Local Message-Passing for Discrete Graph Generation

Discrete graph generation has emerged as a powerful paradigm for modeling graph-structured data, yet state of the art models often rely on Graph Transformers or higher order architectures. We revisit this design assumption by introducing GenGNN, a modular message passing backbone for graph generation. GenGNN enables powerful generation by persisting edge fields through latent refinement of coupled node edge graph states, all without requiring global attention. Diffusion models integrating GenGNN achieve over 90 percent validity on standard benchmark datasets, performing within margins of Graph Transformer backbones and achieving up to 2x or even 5x faster inference. Systematic ablations isolate how GenGNN is resilient to oversmoothing during generative denoising, indicating each GenGNN component is necessary for downstream generation quality. Finally, representation-space analysis suggests GenGNN learns functionally similar representations to more theoretically-expressive architectures; even at deeper layers. As such, GenGNN uplifts local message-passing to challenge prevailing assumptions that performant discrete graph generation requires global attention or higher-order representations. Source Code Available Here

Jay Revolinsky, Harry Shomer, Jiliang Tang

Michigan State University East Lansing, Michigan, USA · University of Texas - Arlington Arlington, Texas, USA

Graph Neural Networks Graph Generation Message Passing Neural Networks

Mar 9, 2026

PCFEx: Point Cloud Feature Extraction for Graph Neural Networks

Graph neural networks (GNNs) have gained significant attention for their effectiveness across various domains. This study focuses on applying GNN to process 3D point cloud data for human pose estimation (HPE) and human activity recognition (HAR). We propose novel point cloud feature extraction (PCFEx) techniques to capture meaningful information at the point, edge, and graph levels of the point cloud by considering point cloud as a graph. Moreover, we introduce a GNN architecture designed to efficiently process these features. Our approach is evaluated on four most popular publicly available millimeter wave radar datasets, three for HPE and one for HAR. The results show substantial improvements, with significantly reduced errors in all three HPE benchmarks, and an overall accuracy of 98.8% in mmWave-based HAR, outperforming the existing state of the art models. This work demonstrates the great potential of feature extraction incorporated with GNN modeling approach to enhance the precision of point cloud processing.

Abdullah Al Masud, Shi Xintong, Mondher Bouazizi +1

Graduate School of Science and Technology, Keio University, Kanagawa, 223-8522, Japan · Faculty of Science and Technology, Keio University Kanagawa, 223-8522, Japan

Point Cloud Learning 3D Human Pose Estimation Human Activity Recognition Graph Neural Networks mmWave Radar Sensing

Mar 9, 2026

Graph-Instructed Neural Networks for parametric problems with varying boundary conditions

This work addresses the accurate and efficient simulation of physical phenomena governed by parametric Partial Differential Equations (PDEs) characterized by varying boundary conditions, where parametric instances modify not only the physics of the problem but also the imposition of boundary constraints on the computational domain. In such scenarios, classical Galerkin projection-based reduced order techniques encounter a fundamental bottleneck. Parametric boundaries typically necessitate a re-formulation of the discrete problem for each new configuration, and often, these approaches are unsuitable for real-time applications. To overcome these limitations, we propose a novel methodology based on Graph-Instructed Neural Networks (GINNs). The GINN framework effectively learns the mapping between the parametric description of the computational domain and the corresponding PDE solution. Our results demonstrate that the proposed GINN-based models, can efficiently represent highly complex parametric PDEs, serving as a robust and scalable asset for several applied-oriented settings when compared with fully connected architectures.

Francesco Della Santa, Sandra Pieraccini, Maria Strazzullo

Department of Mathematical Sciences, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129, Turin, Italy · Gruppo Nazionale per il Calcolo Scientifico INdAM, Piazzale Aldo Moro 5, 00185, Rome, Italy

PDE Surrogate Modeling Neural PDE Solvers Graph Neural Networks

Mar 9, 2026

SCL-GNN: Towards Generalizable Graph Neural Networks via Spurious Correlation Learning

Graph Neural Networks (GNNs) have demonstrated remarkable success across diverse tasks. However, their generalization capability is often hindered by spurious correlations between node features and labels in the graph. Our analysis reveals that GNNs tend to exploit imperceptible statistical correlations in training data, even when such correlations are unreliable for prediction. To address this challenge, we propose the Spurious Correlation Learning Graph Neural Network (SCL-GNN), a novel framework designed to enhance generalization on both Independent and Identically Distributed (IID) and Out-of-Distribution (OOD) graphs. SCL-GNN incorporates a principled spurious correlation learning mechanism, leveraging the Hilbert-Schmidt Independence Criterion (HSIC) to quantify correlations between node representations and class scores. This enables the model to identify and mitigate irrelevant but influential spurious correlations effectively. Additionally, we introduce an efficient bi-level optimization strategy to jointly optimize modules and GNN parameters, preventing overfitting. Extensive experiments on real-world and synthetic datasets demonstrate that SCL-GNN consistently outperforms state-of-the-art baselines under various distribution shifts, highlighting its robustness and generalization capabilities.

Yuxiang Zhang, Enyan Dai

The Hong Kong University of Science and Technology (Guangzhou)

Graph Neural Networks Spurious Correlation Robustness OOD Generalization

Mar 9, 2026

Mitigating Homophily Disparity in Graph Anomaly Detection: A Scalable and Adaptive Approach

Graph anomaly detection (GAD) aims to identify nodes that deviate from normal patterns in structure or features. While recent GNN-based approaches have advanced this task, they struggle with two major challenges: 1) homophily disparity, where nodes exhibit varying homophily at both class and node levels; and 2) limited scalability, as many methods rely on costly whole-graph operations. To address them, we propose SAGAD, a Scalable and Adaptive framework for GAD. SAGAD precomputes multi-hop embeddings and applies reparameterized Chebyshev filters to extract low- and high-frequency information, enabling efficient training and capturing both homophilic and heterophilic patterns. To mitigate node-level homophily disparity, we introduce an Anomaly Context-Aware Adaptive Fusion, which adaptively fuses low- and high-pass embeddings using fusion coefficients conditioned on Rayleigh Quotient-guided anomalous subgraph structures for each node. To alleviate class-level disparity, we design a Frequency Preference Guidance Loss, which encourages anomalies to preserve more high-frequency information than normal nodes. SAGAD supports mini-batch training, achieves linear time and space complexity, and drastically reduces memory usage on large-scale graphs. Theoretically, SAGAD ensures asymptotic linear separability between normal and abnormal nodes under mild conditions. Extensive experiments on 10 benchmarks confirm SAGAD's superior accuracy and scalability over state-of-the-art methods.

Yunhui Liu, Qizhuo Xie, Yinfeng Chen +4

State Key Laboratory for Novel Software Technology, Nanjing University, Nanjing, China · National Engineering Laboratory for Big Data Analysis and Applications, Peking University, Beijing, China

Anomaly Detection Graph Neural Networks

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 Learning Class-Imbalanced Learning Relational Databases Node Classification Graph Neural Networks