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.

May 19, 2026

Do Better Volatility Forecasts Lead to Better Portfolios? Evidence from Graph Neural Networks

This paper tests whether graph neural networks improve realized volatility forecasts and whether those forecasts improve portfolio performance. Using weekly realized volatility for 465 S&P 500 equities from 2015-2025, Heterogeneous Autoregressive and Long Short-Term Memory baselines are compared against GraphSAGE models built on rolling correlation, sector, and Granger-causal graphs, with and without macro regime features. The empirical finding is that the model with the lowest forecast MSE, the model with the highest cross-sectional ranking accuracy, and the model with the highest portfolio Sharpe ratio are three different models. Forecast accuracy, ranking quality, and portfolio performance are related but not interchangeable objectives. Graph volatility models add value only when the portfolio rule can exploit the cross-sectional structure they encode.

Rylan Wade

University of Southern California

Multivariate Time Series Forecasting Graph Neural Networks Quantitative Finance Time Series Forecasting Portfolio Optimization

May 18, 2026

Deep Neural Sheaf Diffusion

Deep Graph Neural Networks (GNNs) are essential for capturing complex dependencies in graph-structured data. However, scaling GNNs to depth remains challenging, as stacking layers leads to representation collapse and diminishing sensitivity due to repeated aggregation. While Neural Sheaf Diffusion (NSD) provides strong theoretical guarantees against such collapse, these guarantees do not translate to practice: as depth increases, the disagreement signal of the sheaf Laplacian vanishes, limiting the contribution of deeper layers. We identify mechanisms that hinder NSD effectiveness at depth and propose Deep Neural Sheaf Diffusion (DNSD), which replaces the sheaf Laplacian with a sheaf adjacency operator to maintain informative signals across layers. This is complemented by normalization, odd nonlinearities, and gating. To provide a principled explanation of the expected performance improvement, we contrast sheaf diffusion to graph attention mechanisms, highlighting that DNSD replaces scalar attention scores with matrix-valued edge functions and normalizes node representations rather than attention scores. We demonstrate empirically that DNSD effectively utilizes deep aggregation in graph tasks, outperforming GNN and NSD baselines with up to 30pp accuracy on synthetic long-range datasets, and consistently outperforming them on real-world benchmarks. These results position sheaf-based architectures as a promising building block for graph foundation models by supporting effective deep architectures.

Rémi Bourgerie, Šarūnas Girdzijauskas, Viktoria Fodor

School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, Stockholm, Sweden.

Graph Neural Networks Sheaf Neural Networks Graph Diffusion

May 18, 2026

Efficient Lookahead Encoding and Abstracted Width for Learning General Policies in Classical Planning

Generalized planning aims to learn policies that generalize across collections of instances within a classical planning domain. Recent Graph Neural Network (GNN) approaches have learned nearly perfect policies for several domains. This work improves on the recently published idea of Iterated Width (IW) policies. Therein, the policy broadens its successor scope through an IW-lookahead search that can "jump" over multiple transitions, simplifying the problem structure. Yet, each transition is evaluated individually, leading to unscalable compute costs and expressivity limitations. Furthermore, although IW(1) is attractive because it scales linearly with the number of atoms, it becomes inefficient once thousands of objects are considered, as in the International Planning Competition (IPC) 2023 benchmark. We address both limitations. First, we introduce a vastly more efficient holistic encoding of the entire search tree. It jointly represents IW(1)-reachable states only by their relational differences to the current state, enabling Relational GNNs (R-GNNs) to score all transitions in a single forward pass. Second, we define Abstracted IW(1) to improve scaling through relational abstraction during novelty checks. Rather than testing fully instantiated atoms, it abstracts each atom by replacing all but one argument with its type. The original atom is novel if any of its abstracted forms is novel. This structural compression shifts novelty search scaling from atoms to objects, while preserving meaningful subgoal structure. We evaluate our contributions on the hyperscaling IPC 2023 benchmark and across diverse domains, including domains requiring features beyond the

C_2

logic fragment. Our policies achieve new state-of-the-art performance, significantly surpassing prior work, including the classical planner LAMA.

Michael Aichmüller, Simon Ståhlberg, Martin Funkquist +1

RWTH Aachen University · Linköping University

Graph Neural Networks Tree Search Symbolic Planning

May 18, 2026

Graph Hierarchical Recurrence for Long-Range Generalization

Graph Neural Networks and Graph Transformers have become central to graph learning, combining expressive representation learning with sample-efficient inductive biases. Yet they remain fundamentally limited when predictions depend on correlations between distant graph regions. We address this limitation with Graph Hierarchical Recurrence (GHR), a novel framework that jointly operates on the input graph and a pooled hierarchical abstraction. We also show that existing models degrade more sharply under out-of-range generalization, where test instances require interactions across distances exceeding those observed during training. Despite its minimal design, GHR consistently strengthens every tested message-passing backbone, yielding robust performance on long-range dependencies and particularly pronounced gains in out-of-range regimes. Across a broad suite of long-range benchmarks, GHR achieves state-of-the-art or competitive results on multiple tasks, establishing hierarchical recurrence as an effective mechanism for extending graph models beyond their observed interaction range.

Stefano Carotti, Marco Pacini, Alessio Gravina +3

Department of Computer Science, University of Trento, Italy. · Fondazione Bruno Kessler, Italy. · Department of Computer Science, University of Pisa, Italy.

Graph Neural Networks Graph Representation Learning Hierarchical Representation Learning

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 Networks Graph-Based Semi-Supervised Learning Transductive Learning Classification Semi-Supervised Learning Node Classification+1

May 18, 2026

Expressive Power of Deep Homomorphism Networks over Relational Databases

The expressive limitations of message-passing Graph Neural Networks (GNNs) have motivated a wide range of more powerful graph learning architectures. We advocate Deep Homomorphism Networks (DHNs) as a model particularly well-suited for learning over relational databases, due to their close connection to important fragments of SQL such as conjunctive queries. We study the precise expressive power of DHNs by relating them to various natural fragments and extensions of first-order logic (FO). For DHNs with max, sum, and mean aggregations, we establish connections to the unary negation fragment (UNFO) and to the extensions of UNFO with counting quantifiers and with ratio quantifiers. We further relate sum-aggregation DHNs to the unary quantifier alternation fragment of FO and to an extension of FO with expressive counting. Through the classical correspondence between FO and SQL, these results also illuminate the relation between DHNs and SQL. They also enable us to study the decidability of two fundamental static analysis problems for DHNs, the emptiness problem and the subsumption problem. Finally, we confirm through experiments that the established differences in expressive power are reflected in the performance on suitable prediction tasks.

Moritz Schönherr, Balder ten Cate, Maurice Funk +3

Leipzig University · University of Amsterdam · Technion & RelationalAI

Logical Reasoning Graph Neural Networks GNN Expressivity Relational Reasoning Relational Databases

May 18, 2026

Learning over Positive and Negative Edges with Contrastive Message Passing

Conventional approaches to learning on graphs involve message passing along existing (i.e., positive) edges to update node features. However, these approaches often disregard the potentially valuable information contained in the absence (i.e., negative) of edges. Here, we theoretically analyze the value of negative edges in graph representations and prove that in settings of low label rates, high homophily, and high edge density, access to negative edges provides significant information gain over using only positive edges. Motivated by this insight, we introduce Contrastive Message Passing (CMP), a general message passing architecture that enable graph neural network layers to reason over positive and negative edges. By imposing soft positive semidefinite constraints on the learnable weights, our approach differentially applies similarity-preserving transformations to positively connected nodes and dissimilarity-inducing transformations to negatively connected nodes. Over simulated and real datasets in varying data regimes, CMP consistently outperforms baselines in low-label settings when negative edges are informative.

Peter Pao-Huang, Charilaos I. Kanatsoulis, Michael Bereket +1

Department of Computer Science Stanford University · Stanford University

Graph Neural Networks Graph Representation Learning Message Passing Neural Networks

May 17, 2026

GraphMAR: Geometry-Aware Graph Learning Framework for Spatially Adaptive CT Metal Artifact Reduction

Computed tomography (CT) metal artifact reduction (MAR) aims to reduce the severe streaking artifacts induced by metallic implants and other high-density objects. Effective MAR generally requires both accurate artifact localization and artifact removal. Sinogram-domain methods can exploit explicit geometric cues, such as metal traces, to identify metal-corrupted measurements, while requiring raw projection data, which is often unavailable in clinical and practical scenarios. Image-domain methods are more flexible and widely applicable, yet they usually lack comparable geometric guidance, limiting their ability to localize artifacts and leading to suboptimal results. To address this limitation, we propose GraphMAR, a geometry-aware learning framework for explicit artifact identification and spatially adaptive MAR in the image domain. The key idea is to introduce graph-based geometric modeling as an image-domain analogue of sinogram metal traces. Specifically, we first construct a geometric graph from the metal mask and derive a geometric density graph that coarsely localizes artifact-prone regions according to inter-implant geometry. We then design GraphMoE, a graph-routed mixture-of-experts module that builds a polar-coordinate artifact graph in feature space and adaptively routes different experts to different spatial regions for MAR. By aligning the learned routing maps with the geometric density graph, GraphMAR provides explicit and interpretable artifact localization while enabling region-adaptive artifact reduction. Experiments on both simulated and real-world datasets demonstrate that GraphMAR achieves superior MAR performance compared with existing methods. To the best of our knowledge, this is the first work to introduce graph-based modeling for CT MAR and to enable explicit artifact identification in the image domain, improving both restoration quality and interpretability.

Zilong Li, Chenglong Ma, Yiming Lei +7

Shanghai Key Lab of Intelligent Information Processing, College of Computer Science and Artificial Intelligence, Fudan University, Shanghai 200433, China · Institute of Science and Technology for Brain-inspired Intelligence, Fudan University, Shanghai 200433, China · College of Computer Science and Technology, Qingdao University, Qingdao 266071, China +2

Graph Neural Networks Image Restoration Computed Tomography

May 17, 2026

Position: Graph Condensation Needs a Reset -- Move Beyond Full-dataset Training and Model-Dependence

Graph Neural Networks (GNNs) are powerful tools for learning from graph-structured data, but their scalability is increasingly strained by the size of real-world graphs in domains like recommender systems, fraud detection, and molecular biology. Graph condensation -- the task of generating a smaller synthetic graph that retains the performance of models trained on the original -- has emerged as a promising solution. However, the dominant approach of gradient matching introduces a fundamental contradiction: it requires training on the full dataset to create the compressed version, thereby undermining the goal of efficiency. Worse still, these methods suffer from high computational overhead, poor generalization across GNN architectures, and brittle reliance on specific model configurations. Equally concerning is the community's reliance on misleading evaluation protocols such as node compression ratios, which fail to reflect true resource savings, condensation overhead, and illusory application to neural architecture search. These shortcomings are not incidental -- they are systemic, and they obstruct meaningful progress. In this position paper, we argue that graph condensation, in its current form, needs a reset. We call for moving beyond full-dataset training and model-dependent design, and instead advocate for methods that are lightweight, architecture-agnostic, and practically deployable. By identifying key methodological flaws and outlining concrete research directions, we aim to reorient the field toward approaches that deliver on the true promise of condensation: efficient, generalizable, and usable GNN training at scale.

Mridul Gupta, Samyak Jain, Vansh Ramani +2

Yardi School of Artificial Intelligence, IIT Delhi, India · Department of Computer Science and Engineering, IIT Delhi, India · Department of Chemical Engineering, IIT Delhi, India

Graph Neural Networks Graph Representation Learning

May 16, 2026

Universal Graph Backdoor Defense: A Feature-based Homophily Perspective

Graph neural networks (GNNs) have achieved remarkable success in relational learning. However, their vulnerability to graph backdoor attacks (GBAs) poses a significant barrier to broader adoption in high-stakes applications. Despite recent advances in graph backdoor defense (GBD), existing methods primarily focus on subgraph-based GBAs, relying on the assumption that poisoned target nodes are explicitly connected to subgraph triggers. Our empirical results reveal that such structure-centric approaches fail to defend against emerging feature-based GBAs that preserve graph topology. Therefore, in this paper, we study a novel problem of universal graph backdoor defense. First, we investigate the shared effects of both attack types from a feature-based homophily perspective, which characterizes local feature consistency between nodes and their neighborhoods. Thorough theoretical and empirical analyses demonstrate that, regardless of trigger mechanisms, backdoors induced by GBAs exhibit lower feature-based homophily than clean nodes, indicating a discrepancy in local feature similarity. Motivated by this insight, we propose to leverage node-level local feature consistency, modeled by a neighbor-aware reconstruction loss, to distinguish backdoors from clean nodes. Then, a robust training strategy is developed to eliminate trigger effects while reducing noise induced by detection uncertainty. Extensive experiments demonstrate that our framework significantly degrades the attack success rate and maintains competitive clean accuracy under both subgraph-based and feature-based attacks.

Mengting Pan, Fan Li, Chen Chen +1

The University of New South Wales Sydney, Australia · University of Wollongong Wollongong, Australia

Graph Neural Networks Backdoor Detection

May 15, 2026

Towards Foundation Models for Relational Databases with Language Models and Graph Neural Networks

Relational databases store much of the world's structured information, and they are essential for driving complex predictive applications. However, deep learning progress on relational data remains limited, as conventional approaches flatten databases into single tables via manual feature engineering, discarding relational context. Relational deep learning (RDL) addresses this by modeling databases as relational entity graphs (REGs) for graph neural networks (GNNs), but remains task- and database-specific. To combine the strengths of both paradigms, we propose a hybrid architecture combining a fine-tuned BART encoder to capture intra-row semantics with a GraphSAGE-based GNN over REGs to inject relational context. Experiments on RelBench show that the GNN substantially enriches BART's row embeddings, achieving a ROC-AUC of 67.40 on the driver-dnf task from the rel-f1 dataset. This performance is competitive with supervised baselines such as LightGBM (68.86) and narrows the gap to RDL (72.62) to within 5.22 points, though a substantial gap remains to state-of-the-art foundation models such as KumoRFM (82.63). These results suggest that lightweight hybrid LM-GNN architectures offer a promising and resource-efficient path towards foundation models for relational databases.

Jingcheng Wu, Ratan Bahadur Thapa, Mojtaba Nayyeri +4

University of Stuttgart, Stuttgart, Germany · Web and Internet Science Research Group, University of Southampton, Southampton, United Kingdom

Relational Foundation Models Tabular Foundation Models Graph Neural Networks Graph Foundation Models Relational Deep Learning Relational Databases

May 15, 2026

OgBench: A Framework for Evaluating Graph Neural Networks on Omics Data

Graph Neural Networks (GNNs) have become the dominant framework for inductive graph-level learning. Yet most benchmarks focus on the regime

n \gg p

, where the number of graphs

n

greatly exceeds the number of nodes per graph

p

. This overlooks biological domains such as omics, which operate in the opposite

n \ll p

regime, characterized by large graphs of genes, transcripts, or proteins across few patient samples. This raises the question: how do GNNs perform in this low-sample, high-node omics setting? We introduce OgBench (Omics-Graph Bench), the first benchmarking platform for graph-level prediction in the

n \ll p

regime characteristic of omics data. We provide a standardized, end-to-end modular infrastructure from raw omics data to families of featured graphs with varied structural properties. We benchmark classical GNNs, as well as GNNs designed for large graphs and omics applications, alongside MLPs and machine learning baselines to establish reference performances. Our results show that widely used GNNs often do not outperform simple MLPs and classical baselines. These findings challenge the prevailing assumption that graph structure inherently adds value in this domain, fostering a critical reassessment of current learning paradigms. Ultimately, by exposing these limitations, OgBench provides the open-source ecosystem necessary for the community to develop and validate novel architectures explicitly tailored for biological graphs. The code is available at https://github.com/geometric-intelligence/ogbench.

Louisa Cornelis, Johan Mathe, Louis Van Langendonck +2

UC Santa Barbara · Atmo, Inc. · Universitat Politècnica de Catalunya

Graph Neural Networks Graph Representation Learning Graph Classification

May 14, 2026

Njord: A Probabilistic Graph Neural Network for Ensemble Ocean Forecasting

Ocean dynamics are inherently chaotic, yet existing machine learning ocean models produce only deterministic forecasts. We introduce Njord, a probabilistic data-driven model for ocean forecasting, applicable to both global and regional domains. Njord combines a deep latent variable framework with a graph neural network architecture, enabling sampling each forecast step in a single forward pass. We apply Njord globally at 0.25° resolution and regionally to the Baltic Sea at 2 km resolution. To scale to these large ocean grids we introduce K-means cluster meshes that adapt to irregular sea surface geometry. Experiments demonstrate strong performance on both domains compared to deterministic machine learning baselines, while also providing uncertainty estimates from the sampled ensemble forecasts. On the global OceanBench benchmark, Njord achieves the lowest errors on average across upper-ocean variables when evaluated against real-world observations, with the largest improvements in surface temperature prediction.

Daniel Holmberg, Joel Oskarsson, Erik Wikingsson +2

University of Helsinki · ETH AI Center · Linköping University

Graph Neural Networks Uncertainty Quantification Probabilistic Forecasting Spatiotemporal Forecasting

May 14, 2026

A finite-element-inspired bipartite graph learned simulator for manufacturability assessment in large-deformation sheet forming

Explicit dynamic finite element (FE) simulations are widely used for large-deformation analysis but remain expensive for design-space exploration. In explicit FE analysis, nodal kinematics and element-level deformation measures evolve through a coupled node-element update process. An FE-inspired learned simulator can preserve this structure and learn nodal kinematics and elemental deformation on their native domains. Nodal displacement describes geometry evolution, while elemental thinning identifies local deformation and critical regions. Feeding both outputs back during rollout allows each field to inform subsequent updates of the other. This work proposes CAtt-BiGNN, a cross-attention-based bipartite graph neural network for coupled nodal-elemental learning. The bipartite graph encodes FE-guided state organisation and information flow without imposing equilibrium or constitutive constraints. Mesh nodes and elements are represented as distinct graph entities connected by directed node-element edges, enabling prediction of nodal displacement increments and elemental deformation on their native domains. An edge-aware cross-attention processor dynamically updates edge representations and weights messages using the receiving state and evolving local relations. For larger graphs, CAtt-BiUGNN uses separate nodal and elemental downsampling and upsampling to enhance long-range propagation while preserving their interaction across graph levels. The method is evaluated on dome-shaped cold-forming and corner-shaped hot-forming benchmarks. Comparisons with node-centred baselines, an FE-inspired hypergraph model, a Physics-Attention-based neural operator, a graph Transformer, and attention ablations show improved joint accuracy in nodal displacement and elemental thinning prediction during autoregressive rollout.

Yingxue Zhao, Haoran Li, Haosu Zhou +2

Dyson School of Design Engineering, Imperial College London, London, UK · NVIDIA, UK

Neural Surrogate Modeling Graph Neural Networks Finite Element Method

May 14, 2026

Learned Suppression for 3D Keypoint Detection with a Graph-Transformer Backbone

Detecting 3D keypoints is a long-standing challenge in computer vision. Most detectors end with a heuristic post-processing step that is not learned. We propose a 3D keypoint detector that improves on this step with a learned suppression module, paired with a Point Transformer backbone that we extend with a directional graph neural network. The module is a graph network over candidates that learns which to keep, which to suppress, and how to relocate the remaining ones. Paired with three backbones, it improves over DBSCAN and greedy non-maximum suppression, and because it operates on candidate features rather than raw geometry, the same formulation applies to both structural and semantic keypoints. Our model surpasses the per-category trained KeypointDETR on 12 of 16 KeypointNet categories, attains the best Corner F1 on the Building3D Entry-Level benchmark, and remains competitive with BWFormer on the larger Tallinn split. GitHub implementation: https://github.com/cansdev/learned-suppression-3d.

Batuhan Arda Bekar, Can Sarı, Hüseyin Can Gülkan +1

Bahcesehir University Computer Engineering

3D ViTs Graph Neural Networks Point Cloud Learning

May 14, 2026

KGPFN: Unlocking the Potential of Knowledge Graph Foundation Model via In-Context Learning

Knowledge graph (KG) foundation models aim to generalize across graphs with unseen entities and relations by learning transferable relational structure. However, most existing methods primarily emphasize relation-level universality, while in-context learning, the other pillar of foundation models remains under-explored for KG reasoning. In KGs, context is inherently structured and heterogeneous: effective prediction requires conditioning on the local context around the query entities as well as the global context that summarizes how a relation behaves across many instances. We propose KGPFN, a KG foundation model using Prior-data Fitted Network that unifies transferable relational regularities with inference-time in-context learning from structured context. KGPFN first learns relation representations via message passing on relation graphs to capture cross-graph relational invariances. For query-specific reasoning, it encodes local neighborhoods using a multi-layer NBFNet as local context. To enable ICL at global scale, it constructs relation-specific global context by retrieving a large set of instances of the query relation together with their local neighborhoods, and aggregates them within a Prior-Data Fitted Network framework that combines feature-level and sample-level attention. Through multi-graph pretraining on diverse KGs, KGPFN learns when to instantiate reusable patterns and when to override them using contextual evidence. Experiments on 57 KG benchmarks demonstrate that KGPFN achieves strong adaptation to previously unseen graphs through in-context learning alone, consistently outperforming competitive fine-tuned KG foundation models. Our code is available at https://github.com/HKUST-KnowComp/KGPFN.

Yisen Gao, Jiaxin Bai, Haoyu Huang +5

Department of Computer Science and Engineering, HKUST, Hong Kong, China · Department of Computer Science and Engineering, HKBU, Hong Kong, China

Graph Neural Networks In-Context Learning Graph Foundation Models KG Completion

May 14, 2026

AIMing for Standardised Explainability Evaluation in GNNs: A Framework and Case Study on Graph Kernel Networks

Graph Neural Networks (GNNs) have advanced significantly in handling graph-structured data, but a comprehensive framework for evaluating explainability remains lacking. Existing evaluation frameworks primarily involve post-hoc explanations, and operate in the setting where multiple methods generate a suite of explanations for a single model. This makes comparison of explanations across models difficult. Evaluation of inherently interpretable models often targets a specific aspect of interpretability relevant to the model, but remains underdeveloped in terms of generating insight across a suite of measures. We introduce AIM, a comprehensive framework that addresses these limitations by measuring Accuracy, Instance-level explanations, and Model-level explanations. AIM is formulated with minimal constraints to enhance flexibility and facilitate broad applicability. Here, we use AIM in a pipeline, extracting explanations from inherently interpretable GNNs such as graph kernel networks (GKNs) and prototype networks (PNs), evaluating these explanations with AIM, identifying their limitations and obtaining insights to their characteristics. Taking GKNs as a case study, we show how the insights obtained from AIM can be used to develop an updated model, xGKN, that maintains high accuracy while demonstrating improved explainability. Our approach aims to advance the field of Explainable AI (XAI) for GNNs, providing more robust and practical solutions for understanding and improving complex models.

Magdalena Proszewska, N. Siddharth

School of Informatics, University of Edinburgh

Graph Neural Networks Interpretable ML Explainability Evaluation GNN Explainability

May 14, 2026

Exploitation of Hidden Context in Dynamic Movement Forecasting: A Neural Network Journey from Recurrent to Graph Neural Networks and General Purpose Transformers

Forecasting within signal processing pipelines is crucial for mitigating delays, particularly in predicting the dynamic movements of objects such as NBA players. This task poses significant challenges due to the inherently interactive and unpredictable nature of sports, where abrupt changes in velocity and direction are prevalent. Traditional approaches, including (S)ARIMA(X), Kalman filters (KF), and Particle filters (PF), often struggle to model the non-linear dynamics present in such scenarios. Machine learning (ML) methods, such as long short-term memory (LSTM) networks, graph neural networks (GNNs), and Transformers, offer greater flexibility and accuracy but frequently fail to explicitly capture the interplay between temporal dependencies and contextual interactions, which are critical in chaotic sports environments. In this paper, we evaluate these models and assess their strengths and weaknesses. Experimental results reveal key performance trade-offs across input history length, generalizability, and the ability to incorporate contextual information. ML-based methods demonstrated substantial improvements over linear models across forecast horizons of up to 2s. Among the tested architectures, our hybrid LSTM augmented with contextual information achieved the lowest final displacement error (FDE) of 1.51m, outperforming temporal convolutional neural network (TCNN), graph attention network (GAT), and Transformers, while also requiring less data and training time compared to GAT and Transformers. Our findings indicate that no single architecture excels across all metrics, emphasizing the need for task-specific considerations in trajectory prediction for fast-paced, dynamic environments such as NBA gameplay.

Lukas Schelenz, Shobha Rajanna, Denis Gosalci +6

Fraunhofer Institute for Integrated Circuits IIS, 90411 Nürnberg, Germany · Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany

Graph Neural Networks Multi-Agent Trajectory Prediction Recurrent Neural Networks Trajectory Prediction

May 13, 2026

Mask-Morph Graph U-Net: A Generalisable Mesh-Based Surrogate for Crashworthiness Field Prediction under Large Geometric Variation

Nonlinear finite element crash simulations are accurate but computationally expensive, limiting their use in iterative design optimisation. Machine-learning surrogate models based on graph neural networks (GNNs) offer a faster alternative. Message-passing GNNs are widely used for mesh simulation, and their shared node and edge update functions are relatively generalisable across varying graph structures. By contrast, non-shareable edge-specific aggregation layers can capture nonlinear relationships more accurately but usually require fixed graph connectivity, which limits generalisability. This paper presents Mask-Morph Graph U-Net (MMGUNet), a practical approach to addressing the limitation of hierarchical Graph U-Net architectures that use edge-specific downsampling and upsampling layers. Fixed coarse graph connectivity is required for edge-specific layers. To retain this while improving spatial correspondence, the proposed method morphs the coarsened graph hierarchy to each input mesh using feature-aligned barycentric parameterisation before constructing cross-graph edges. It further applies node masking during supervised pretraining, followed by parameter-efficient fine-tuning in which high-parameter edge-specific layers are frozen. The proposed approach is evaluated in in-distribution, out-of-distribution, and cross-component transfer settings using mean Euclidean distance and maximum intrusion percentage error. Results show that coarse-graph morphing improves test accuracy relative to a fixed-coarse-graph baseline, while masked supervised pretraining reduces the train-test discrepancy and improves data efficiency during transfer. The proposed model also achieves lower prediction error compared with external baselines. These results demonstrate a practical route toward reusable, data-efficient mesh-based surrogate modelling for crashworthiness design exploration.

Haoran Li, Tobias Lehrer, Yingxue Zhao +5

Dyson School of Design Engineering, Imperial College London, London, UK · TUM School of Engineering and Design, Technical University of Munich, Munich, Germany · Faculty of Mechanical Engineering, OTH Regensburg, Regensburg, Germany +1

Neural Surrogate Modeling Graph Neural Networks

May 13, 2026

Graph Neural Networks with Triangle-Based Messages for the Multicut Problem

The multicut problem is an NP-hard combinatorial optimization problem with diverse applications in fields such as bioinformatics, data mining and computer vision. Graph neural networks have been defined for the multicut problem but can be adapted further to its specific objective function and constraints. In this article, we introduce such an adapted graph neural network architecture in which features are assigned only to edges, and the computation of messages is based on triangles in the underlying graph. Experiments with synthetic and real-world instances with up to 200 nodes show that our method outperforms state-of-the-art heuristic solvers in terms of solution quality while maintaining feasible runtimes. For some instances, our method finds optimal solutions in seconds whereas exact solvers need hours to find and certify optimal solutions.

Jannik Irmai, Lucas Fabian Naumann, Bjoern Andres

Faculty of Computer Science, TU Dresden · Center for Scalable Data Analytics and AI, Dresden/Leipzig

Graph Neural Networks Combinatorial Optimization Message Passing Neural Networks Neural Combinatorial Optimization

May 13, 2026

Rethinking Generalization in Graph Neural Networks: A Structural Complexity Perspective

Graph neural networks (GNNs) have emerged as a fundamental tool for learning from graph-structured data, achieving strong performance across a wide range of applications. However, understanding their generalization capabilities remains challenging due to the complex structural dependencies inherent in such data. Existing generalization analyses largely follow the classical machine learning paradigm, focusing primarily on model complexity while overlooking the fundamental role of graph structure. Therefore, in this work, we systematically investigate this role by asking: does the graph structure actually influence generalization, and if so, by how much? To answer the first question and validate our intuition, we theoretically prove that incorporating more edges into the prediction process transforms the input representations to be overly accommodating to the output model, thereby inducing overfitting. To address the second question, we formulate a structural complexity measure based on the number of effective edges and derive a Rademacher complexity-based generalization bound. In doing so, we demonstrate that GNN generalization depends explicitly on structural complexity, alongside traditional parameter-dependent factors. Motivated by these theoretical findings, we propose a structural entropy regularization method. This approach controls structural complexity by regulating effective edges to balance underfitting and overfitting, ultimately improving the generalization performance of GNNs.

Peiyao Wang, Liang Bai, Xian Yang +2

Institute of Intelligent Information Processing Shanxi University, Taiyuan, 030006, China · Alliance Manchester Business School University of Manchester, Manchester, M13 9PL, UK · Department of Mathematics Hong Kong Baptist University, Hong Kong SAR, China

Neural Network Generalization Graph Neural Networks Generalization Bounds

May 13, 2026

Beyond Oversquashing: Understanding Signal Propagation in GNNs Via Observables

Graph Neural Networks (GNNs) perform computations on graphs by routing the signal between graph regions using a graph shift operator or a message passing scheme. Often, the propagation of the signal leads to a loss of information, where the signal tends to diffuse across the graph instead of being deliberately routed between regions of interest. Two notions that depict this phenomenon are oversmoothing and oversquashing. In this paper, we propose an alternative approach for modeling signal propagation, inspired by quantum mechanics, using the notion of observables. Specifically, we model the place in the graph where the signal lies, how much the signal is concentrated there, and how much of the signal is propagated towards a location of interest when applying a GNN. Using these new concepts, we prove that standard spectral GNNs have poor signal propagation capabilities. We then propose a new type of spectral GNN, termed Schrödinger GNN, which we show has a superior capacity to route the signal across the graph.

Eden Nagar, Ya-Wei Eileen Lin, Ron Levie

Technion - Israel Institute of Technology, Faculty of Mathematics · Technical University of Munich, School of Computation, Information and Technology · Munich Center for Machine Learning

Graph Neural Networks Spectral Graph Convolution

May 13, 2026

A Neural Hierarchical-Matrix Preconditioner for Real-Time GPU Solves

Interactive simulation solves Ax=b for a sparse SPD A that changes every frame, inside an 8-16 ms budget. At a few thousand unknowns, the setup of algebraic multigrid alone exceeds that budget, while Jacobi and other local preconditioners have no setup but cannot move error across the domain. We learn a preconditioner for this gap: a graph-and-attention network predicts an SPD approximate inverse in H^2-matrix format. On a spatially ordered 3D mesh, blocks of the true inverse lose rank as the clusters they couple move apart; the nested bases of the format follow that decay, so inference and apply are dominated by leaf-block work linear in N, where a dense inverse costs N^2. Our main finding concerns training. Probe losses reach M only through a product with A, so their gradient vanishes on the near-null modes that set the conjugate-gradient iteration count. A truncated Kaporin condition number has no such factor; changing only the objective cuts iterations on a held-out frame from 116 to 33. On a ladder of stiff tetrahedral diffusion problems ours alone fits an 8.3 ms (120 fps) frame from N=572 to 3,647.

Carl Osborne, Minghao Guo, Crystal Owens +1

MIT CSAIL, Cambridge, USA

Graph Neural Networks High-Performance Computing Physics-Based Simulation

May 13, 2026

MLGIB: Multi-Label Graph Information Bottleneck for Expressive and Robust Message Passing

Graph Neural Networks (GNNs) suffer from over-squashing in deep message passing, where information from exponentially growing neighborhoods is compressed into fixed-dimensional representations. We show that this issue becomes a distinct failure mode in multi-label graphs: neighboring nodes often share only limited labels while differing across many irrelevant ones, causing predictive signals to be diluted by noisy label information. To address this challenge, we propose the Multi-Label Graph Information Bottleneck (MLGIB), which formulates multi-label message passing as constrained information transmission under irrelevant label noise. MLGIB balances expressiveness and robustness by preserving predictive label signals while suppressing irrelevant noise. Specifically, it constructs a Markovian dependence space and derives tractable variational bounds, where the lower bound maximizes mutual information with target labels and the upper bound constrains redundant source information. These bounds lead to an end-to-end label-aware message-passing architecture. Extensive experiments on multiple benchmarks demonstrate consistent improvements over existing methods, validating the effectiveness and generality of the proposed framework.

Chaokai Wu, Haofu Shi, Ningxuan Ma +2

Multi-Label Classification Graph Neural Networks Information Bottleneck GNN Expressivity Message Passing Neural Networks

May 13, 2026

What Information Matters? Graph Out-of-Distribution Detection via Tri-Component Information Decomposition

Graph neural networks are widely used for node classification, but they remain vulnerable to out-of-distribution (OOD) shifts in node features and graph structure. Prior work established that methods trained with standard supervised learning (SL) objectives tend to capture spurious signals from either features and/or structure, leaving the model fragile under distributional changes. To address this, we propose TIDE, a novel and effective Tri-Component Information Decomposition framework that explicitly decomposes information into feature-specific, structure-specific and joint components. TIDE aims to preserve only the label-relevant part of the joint information while filtering out spurious feature- and structure-specific information, thereby enhancing the separation between in-distribution (ID) and OOD nodes. Beyond the framework, we provide theoretical and empirical analyses showing that an information bottleneck objective is preferable to standard SL for graph OOD detection, with higher ID confidence and a greater entropy gap between ID and OOD data. Extensive experiments across seven datasets confirm the efficacy of TIDE, achieving up to a 34% improvement in FPR95 over strong baselines while maintaining competitive ID accuracy.

Danny Wang, Ruihong Qiu, Zi Huang

The University of Queensland, Australia.

Graph Neural Networks OOD Detection

May 12, 2026

GraphIP-Bench: How Hard Is It to Steal a Graph Neural Network, and Can We Stop It?

Graph neural networks (GNNs) deployed as cloud services can be stolen through model-extraction attacks, which train a surrogate from query responses to reproduce the target's behavior, and a growing line of ownership defenses tries to prevent or trace such theft. This paper asks two questions: how hard is it to steal a GNN, and can we stop it? Prior work cannot answer either, because experiments use inconsistent datasets, threat models, and metrics. We introduce GraphIP-Bench, a unified benchmark that evaluates both sides under a single black-box protocol. GraphIP-Bench integrates twelve extraction attacks, twelve defenses spanning watermarking, output perturbation, and query-pattern detection, ten public graphs covering homophilic, heterophilic, and large-scale regimes, three GNN backbones, and three graph-learning tasks. It reports fidelity, task utility, ownership verification, and computational cost on shared splits, queries, and budgets. We further add a joint attack-and-defense track that runs every attack on every defended target and measures watermark verification on the resulting surrogate, exposing how much protection a defense retains after extraction. The empirical picture is clear: stealing a GNN is easy at medium query budgets and most defenses do not change this; several watermarks verify reliably on the protected model but lose most of their verification signal on the extracted surrogate, exposing a gap that single-model evaluations miss; and heterophilic graphs are systematically harder to steal, while a cross-architecture mismatch between target and surrogate reduces but does not prevent extraction. We release GraphIP-Bench with reproducible scripts and configurations, and integrate the attacks and defenses into the PyGIP library. Code: https://github.com/LabRAI/GraphIP-Bench. Library: https://labrai.github.io/PyGIP/index.html.

Kaixiang Zhao, Bolin Shen, Yuyang Dai +2

University of Notre Dame · Florida State University · University of California, Berkeley

Graph Neural Networks Model Extraction Attacks

May 12, 2026

Graph-Based Financial Fraud Detection with Calibrated Risk Scoring and Structural Regularization

Financial transaction fraud prevention faces challenges such as complex relationship structures, concealed behavioral patterns, and dynamically changing data distribution. Discrimination models relying solely on independent sample features are insufficient to fully characterize the risks of group collaboration and chain transfers within transaction networks. This paper proposes a graph neural network representation learning and risk discrimination framework for financial transaction fraud prevention. It integrates transaction records and identity information into node attributes and constructs a transaction graph based on shared attributes and interaction consistency to explicitly model inter-transaction relationships. In model design, a multi-layer message passing mechanism is employed to aggregate neighborhood information, learn node embedding representations containing structural context semantics, and output transaction-level fraud probability and risk scores through a lightweight risk discrimination head. A weighted supervision objective is introduced to mitigate training bias caused by class imbalance, and structural consistency regularization constraints are combined to suppress the impact of noisy edges on representation drift, thereby improving the stability and usability of risk characterization. Experiments are conducted on a publicly available financial transaction dataset, comparing various methods in the same direction and comprehensively evaluating them under a unified evaluation protocol. The results show that the proposed method outperforms other methods in risk ranking and probability calibration quality, validating the effectiveness of graph structure modeling and representation learning collaboration in financial transaction fraud prevention.

Yunfei Nie, Jiawei Wang, Ruobing Yan +3

Brandeis University, Waltham, USA · University of California, Los Angeles, USA · Georgetown University, Washington, D.C., USA +2

Graph Neural Networks Graph Representation Learning Financial Fraud Detection

May 12, 2026

Estimating Subgraph Importance with Structural Prior Domain Knowledge

We propose a subgraph importance estimation method for pretrained Graph Neural Networks (GNNs) on graph-level tasks, formulated as a linear Group Lasso regression problem in the embedding space. Our method effectively leverages prior domain knowledge of graph substructures, while remaining independent of the specific form of the output layer or readout function used in the GNN architecture, and it does not require access to ground-truth target labels. Experiments on real-world graph datasets demonstrate that our method consistently outperforms existing baselines in subgraph importance estimation. Furthermore, we extend our method to identify important nodes within the graph.

Changhyun Kim, Seunghwan An, Jong-June Jeon

University of Seoul, Seoul, South Korea · Incheon National University, Incheon, South Korea

Graph Neural Networks GNN Explainability

May 12, 2026

Random-Set Graph Neural Networks

Uncertainty quantification has become an important factor in understanding the data representations produced by Graph Neural Networks (GNNs). Despite their predictive capabilities being ever useful across industrial workspaces, the inherent uncertainty induced by the nature of the data is a huge mitigating factor to GNN performance. While aleatoric uncertainty is the result of noisy and incomplete stochastic data such as missing edges or over-smoothing, epistemic uncertainty arises from lack of knowledge about a system or model (e.g., a graph's topology or node feature representation), which can be reduced by gathering more data and information. In this paper, we propose an original new framework in which node-level epistemic uncertainty is modelled in a belief function (finite random set) formalism. The resulting Random-Set Graph Neural Networks have a belief-function head predicting a random set over the list of classes, from which both a precise probability prediction and a measure of epistemic uncertainty can be obtained. Extensive experiments on 9 different graph learning datasets, including real-world autonomous driving benchmarks as such Nuscene and ROAD, demonstrate RS-GNN's superior uncertainty quantification capabilities

Tommy Woodley, Shireen Kudukkil Manchingal, Matteo Tolloso +2

School of Engineering, Computing and Mathematics Oxford Brookes University · Department of Computer Science University of Pisa · Oxford Brookes Institute for Artificial Intelligence, Data Analysis and Systems (AIDAS)

Graph Neural Networks Uncertainty Quantification Epistemic Uncertainty

May 12, 2026

Crash Assessment via Mesh-Based Graph Neural Networks and Physics-Aware Attention

Full-vehicle crash simulations are computationally expensive, limiting their use in iterative design exploration. This work investigates learned hybrid surrogate models (MeshTransolver, MeshGeoTransolver, and MeshGeoFLARE) for predicting time-resolved structural deformation fields in an industrial lateral pole-impact benchmark. We evaluate whether neural surrogates can reproduce full-field crash kinematics with sufficient accuracy, spatial regularity, and structural plausibility for engineering interpretation. The proposed architectures combine local mesh message passing, geometry-aware global attention, and sparse contact-aware correction for autoregressive crash rollout. We compare mesh-based graph neural networks, attention-based geometric models, and hybrid architectures under a common training and hyperparameter configuration. The hybrid models capture both short-range structural interactions and long-range deformation patterns, while a sparse contact-aware variant assesses the effect of dynamic proximity interactions during rollout. On a 25-sample full-vehicle test set, the best hybrid model achieves a temporal mean root-mean-square error of 3.20 mm. While geometry-aware attention baselines are quantitatively competitive, qualitative side-view inspection shows they can introduce local spatial noise and deformation irregularities that complicate structural interpretation. In contrast, hybrid mesh-attention models provide the best balance between scalar accuracy, survival-space consistency, and physically interpretable displacement fields. These results suggest that crash surrogate assessment should combine global error metrics with downstream safety-relevant quantities and qualitative field inspection. The proposed methodology enables fast full-field predictions while preserving essential structural information for industrial crash-engineering analysis.

Gabriel Curtosi, Carlos Manuel Ruiz Ruiz, Fabiola Cavaliere +1

SEAT S.A., Barcelona, Spain · IDIADA Automotive Technology S.A., Santa Oliva, Spain

Neural Surrogate Modeling Graph Neural Networks Structural Mechanics Physics-Based Simulation