Graph Neural Networks

Graph neural networks (GNNs) aim to learn well-trained representations in a lower-dimension space for downstream tasks while preserving the topological structures. In recent years, attention mechanism, which is brilliant in the fields of natural language processing and computer vision, is introduced to GNNs to adaptively select the discriminative features and automatically filter the noisy information. To the best of our knowledge, due to the fast-paced advances in this domain, a systematic overview of attention-based GNNs is still missing. To fill this gap, this paper aims to provide a comprehensive survey on recent advances in attention-based GNNs. Firstly, we propose a novel two-level taxonomy for attention-based GNNs from the perspective of development history and architectural perspectives. Specifically, the upper level reveals the three developmental stages of attention-based GNNs, including graph recurrent attention networks, graph attention networks, and graph transformers. The lower level focuses on various typical architectures of each stage. Secondly, we review these attention-based methods following the proposed taxonomy in detail and summarize the advantages and disadvantages of various models. A model characteristics table is also provided for a more comprehensive comparison. Thirdly, we share our thoughts on some open issues and future directions of attention-based GNNs. We hope this survey will provide researchers with an up-to-date reference regarding applications of attention-based GNNs. In addition, to cope with the rapid development in this field, we intend to share the relevant latest papers as an open resource at https://github.com/sunxiaobei/awesome-attention-based-gnns.

Graphs with heterophily, where adjacent nodes carry different labels, are prevalent in real-world applications, from social networks to molecular interactions. However, existing spectral Graph Neural Network (GNN) approaches tailored for heterophilous graph classification suffer from hub-dominated (node with large degree) aggregation and oversmoothing, as their suboptimal polynomial filters introduce approximation errors and blend distant signals. To address the degree-biased aggregation and suboptimal polynomial filtering, we introduce a Hierarchical Multi-view HAAR (HMH), a novel spectral graph-learning framework that scales in near-linear time . HMH first learns feature- and structure-aware signed affinities via a heterophily-aware encoder, then constructs a soft graph hierarchy guided by these embeddings. At each hierarchical level, HMH constructs a sparse, orthonormal, and locality-aware Haar basis to apply learnable spectral filters in the frequency domain. Finally, skip-connection unpooling layers combine outputs from all hierarchical levels back into the original graph, effectively preventing hub domination and long-range signal bottleneck (over-squashing). Experimentation shows that HMH outperforms state-of-the-art spectral baselines, achieving up to a 3% improvement on node classification and 7% points on graph classification datasets, all while maintaining linear scalability.

In recent years, the use of edge information provided by knowledge graphs together with the advantages of higher-order connectivity in graph neural networks for recommendation systems has become an important research direction. However, existing approaches are often limited by sparse labels, insufficient graph structure learning, and noisy entities in the knowledge graph, which reduce recommendation accuracy. To address these limitations, we propose a multi-view graph contrastive learning framework. The proposed method enhances user representations through multi-view knowledge graph distillation, enabling more accurate modeling of user preferences over entities and relations. The network aggregates neighborhood entity information to construct informative item representations. Furthermore, we design a multi-level self-supervised contrastive learning module that performs comparisons across three perspectives: Inter-Level, Intra-Level, and Interaction-Level. This design improves the model's ability to generalize across intra-class samples while increasing discrimination between inter-class samples, thereby enabling more effective multi-dimensional feature modeling. We conduct extensive experiments on three public datasets using both baseline and ablation settings. Experimental results demonstrate that the proposed framework consistently outperforms existing state-of-the-art methods. Ablation studies further verify the effectiveness of each module in the proposed model.

Conformal prediction (CP) provides a distribution-free approach to uncertainty quantification with finite-sample guarantees. However, applying CP to graph neural networks (GNNs) remains challenging as the combinatorial nature of graphs often leads to insufficiently certain predictions and indiscriminative embeddings. Existing methods primarily rely on embedding-space proximity for localization, which can be unreliable for graphs and yield inefficient prediction sets. We propose GRAPHLCP, a proximity-based localized CP framework that explicitly incorporates graph topology and inter-node dependencies into localization and weighting. Our approach introduces a feature-aware densification step to mitigate locality bias in sparse graphs, followed by a Personalized PageRank-based kernel computation to model structural proximity. This enables topology-dependent anchor sampling and calibration weighting that captures both local and long-range dependencies. Extensive experiments on several regression and classification datasets demonstrate that GRAPHLCP guarantees marginal coverage with finite samples while efficiently attaining favorable test conditional coverage across various conditioning scenarios.

Physics-based digital twins aim to predict the dynamics of real-world objects under interaction, enabling real-to-sim-to-real applications in robotics. Current approaches reconstruct such twins as explicit physical models (such as spring-mass systems) to predict the dynamics, but the resulting models often inherit the resolution of the visual reconstruction rather than being reduced to the physical complexity required to reproduce task-relevant dynamics. This mismatch introduces redundant topology, making repeated forward-dynamics rollouts unnecessarily expensive. To address this challenge, we present PhySPRING, an fully differentiable GNN-based method to reduce complexity in spring--mass digital twins. PhySPRING jointly learns a hierarchy of coarsened graph topologies and their mechanical parameters from observations. At each reduction level, PhySPRING merges nodes with similar learned dynamic responses to optimize the topology, while maintaining every reduced layer as an explicit spring--mass system. On the PhysTwin benchmark, PhySPRING improves dense reconstruction and prediction accuracy over PhysTwin, while reduced models retain stable physical and visual fidelity with up to a 2.30 times speed-up. We further demonstrate the effectiveness of PhySPRING in a Real2Sim robot policy-evaluation pipeline, where the reduced models are substituted zero-shot into ACT and $π_0$ evaluations, maintaining comparable manipulation success rates across downsampling levels while improving action-sampling effectiveness. Together, PhySPRING enables efficient and structure-preserving spring--mass reduction without sacrificing fidelity or robotic utility.

Accurate prediction of structural displacements under external loading is fundamental to structural health monitoring and seismic safety assessment. Although the finite element method (FEM) remains the prevailing approach because of its high accuracy, its considerable computational cost restricts its suitability for real-time monitoring applications. To address this limitation, this study proposes a data-driven framework based on Graph Neural Networks (GNNs), in which structural systems are represented as graphs with joints modeled as nodes and structural members as edges. By incorporating both geometric and mechanical properties into the graph representation, the proposed model learns the relationship between applied loads and structural responses directly from simulated data. A synthetic dataset was generated from a two-story frame structure using ANSYS, and both a conventional Neural Network (NN) and a GNN were trained for comparison. The results show that the proposed GNN framework predicts displacements and rotations with high accuracy and outperforms the NN model, demonstrating its potential as a fast and efficient alternative to traditional FEM-based analysis.

Recent work has observed that explanations produced by Self-Interpretable Graph Neural Networks (SI-GNNs) can be self-inconsistent: when the model is reapplied to its own explanatory graph subset, it may produce a different explanation. However, why self-inconsistency arises remains poorly understood. In this work, we first identify re-explanation-induced context perturbation as the direct cause of score variation. We then introduce a latent signal assignment hypothesis to explain why only some edges are sensitive to this perturbation, and analyze how conciseness regularization affects latent signal assignment. Given that self-inconsistent edges do not provide stable evidence for the model's prediction, we propose Self-Denoising (SD), a model-agnostic and training-free post-processing strategy that calibrates explanations with only one additional forward pass. Experiments across representative SI-GNN frameworks, backbone architectures, and benchmark datasets support our hypothesis and show that SD consistently improves explanation quality while adding only about 4--6% computational overhead in practice.

EDA problems are graph-structured, but not all graph-structured problems call for the same GNN computation. We argue that successful GNN-for-EDA methods are those whose propagation, aggregation, and supervision align with the native algebra of the target task. Concretely: static timing analysis is a max-plus/min-plus recurrence on a topologically ordered DAG, structurally aligned with asynchronous DAG-GNNs; placement is governed by hypergraph wirelength and density penalties and is exploited by differentiable placers rather than by message-passing GNNs alone; routing congestion is a sparse demand-supply field over a layout grid; switching-activity propagation is a probabilistic recurrence on a directed netlist; IR drop is a linear system on the power-delivery network; and analog symmetry extraction is a discrete constraint-prediction problem on schematic graphs. Through these task-by-task alignments we (i) review the GNN architectural toolkit relevant to circuits, (ii) formalize how circuit graphs differ from generic graphs (directed, heterogeneous, multi-scale, with sequential and clock structure), (iii) characterize where current methods succeed and where the algebra-architecture mismatch limits them, and (iv) identify failure modes--stage leakage, proxy-to-signoff gap, calibration, and design-distribution shift--that we believe are likely to dominate the next phase of work. We position the paper as a GNN-for-EDA, task-aligned analysis rather than a comprehensive AI-for-chip-design survey. Continuous SE(3)-equivariant geometric GNNs are usually mismatched to Manhattan digital layout, and LLM-for-RTL, HLS, and RL/diffusion-based topology generation are outside our scope.

GNNs have become a standard tool for learning on relational data, yet they remain highly vulnerable to backdoor attacks. Prior defenses often depend on inspecting specific subgraph patterns or node features, and thus can be circumvented by adaptive attackers. We propose PRAETORIAN, a new defense that targets intrinsic requirements of effective GNN backdoors rather than surface-level cues. Our key observation is that flipping a victim node's prediction requires substantial influence on the victim: attackers tend to either inject many trigger nodes or rely on a small set of highly influential ones. Building on this observation, PRAETORIAN (i) analyzes internal correlations within potential trigger subgraphs to detect abnormally large injected structures, and (ii) quantifies external node influence to identify triggers with disproportionate impact. Across our evaluations, PRAETORIAN reduces the average attack success rate (ASR) to 0.55% with only a 0.62% drop in clean accuracy (CA), whereas state-of-the-art defenses still yield an average ASR of >20% and a CA drop of >3% under the same conditions. Moreover, PRAETORIAN remains effective against a range of adaptive attacks, forcing adversaries to either inject many trigger nodes to achieve high ASR (>80%), which incurs a >10% CA drop, or preserve CA at the cost of limiting ASR to 18.1%. Overall, PRAETORIAN constrains attackers to an unfavorable trade-off between efficacy and detectability.

Exact solution of hard combinatorial optimization problems often relies on strong convex relaxations, but solving these relaxations repeatedly inside a branch-and-bound algorithm can be prohibitively expensive. Hence, we consider this challenge for Max-Cut, where branch and bound commonly uses semidefinite programming (SDP) relaxations to bound subproblems. We propose a Max-Cut-specific graph neural network that serves as a principled, lightweight neural proxy for these SDP solvers and can be plugged directly into an exact branch-and-bound framework. The proposed architecture has update steps of complexity $\mathcal{O}(n^2 + ne)$, and predicts both primal- and dual-feasible SDP solutions. The primal SDP solutions yield feasible Max-Cut solutions via the Goemans--Williamson algorithm. In addition, it is trained in a self-supervised fashion without requiring solved SDP relaxations as labels. Empirically, we show that our architecture can substantially reduce the cost of bounding in exact Max-Cut solving by up to $10.6 \times$ compared with using the state-of-the-art SDP solver Mosek. Our work highlights the potential of learned, validity-preserving surrogates for accelerating exact optimization over structured convex relaxations.

Learning-based approaches to NP-hard problems have shown increasing promise, but their progress is fundamentally constrained by the high cost of generating labeled training data. In domains such as Boolean satisfiability (SAT), standard pipelines rely on solver-in-the-loop labeling, which scales poorly with problem size and limits the amount of usable supervision. This bottleneck hinders the broader goal of leveraging machine learning to capture structure in hard combinatorial problems. In this work, we propose a target-aware, solver-free data generation framework for SAT that produces correctly labeled SAT and UNSAT instances by construction, eliminating the need for expensive solver calls. Our method aligns generated instances with the structural properties of a target benchmark, making synthetic data effective for downstream learning. We further develop a linear-programming-aware graph neural network (LPGNN) architecture that incorporates constraint-violation residuals into message passing, enabling the model to exploit underlying optimization structure. Together, these contributions support a data-centric paradigm for learning on NP-hard problems, where scalable, task-aligned data generation is as critical as model design. Our approach yields orders-of-magnitude speedups in data generation, demonstrating that benchmark-aligned synthetic data can effectively augment solver-labeled datasets for GNN-based SAT prediction.

Previous methods that predict system-wide travel time, predominantly grounded in graph neural networks, remain limited to typical and recurring demand patterns. While they successfully predict future congestion following daily commute, they inherently approximate a single demand realisation and fail to capture varying route choices. In this work, we propose a Generalised Travel Time Predictor (GenTTP) that successfully differentiates route choices and offers accurate flow and travel time predictions. Our framework learns to uncover complex spatiotemporal traffic patterns and microscopic relationships between route choices and the resulting travel times. This addresses a critical gap: the lack of travel time prediction models that generalise across varying route assignments, where the same demand can produce substantially different network-wide outcomes depending on how travellers are distributed over available paths.

Graph Neural Networks (GNNs) achieve high performance but can be opaque to humans, making it difficult to understand and compare the many proposed architectures. While existing explainability methods attribute individual predictions to nodes, edges, or features, they do not provide architectural transparency or explain the fundamental performance gap between simple and more complex models. To address this limitation, we introduce Model-to-Data (M2D) distillation, a new framework that increases transparency by transferring model complexity into the data space. M2D distills the teacher model into an augmented graph with enriched features and structure, enabling a simple student to match the teacher's performance. By materializing model behavior in the data, our approach allows humans to inspect architectural advantages directly. We show that M2D reveals underlying mechanisms such as fairness objectives and attention-based aggregation in an interpretable way, enhancing GNN transparency while preserving performance.

Graph Edit Distance (GED) is a fundamental, albeit NP-hard, metric for structural graph similarity. Recent neural graph matching architectures approximate GED by first encoding graphs with a Graph Neural Network (GNN) and then applying either a graph-level regression head or a matching-based alignment module. Despite substantial architectural progress, the role of encoder geometry in neural GED estimation remains poorly understood. In this paper, we develop a theoretical framework that connects encoder geometry to GED estimation quality for two broad classes of neural GED estimators: graph similarity predictors and alignment-based methods. On fixed graph collections, where the doubly-stochastic metric $d_{\mathrm{DS}}$ is comparable to GED, we show that graph-level bi-Lipschitz encoders yield controlled GED surrogates and improved ranking stability; for matching-based estimators, node-level bi-Lipschitz geometry propagates to encoder-induced alignment costs and the resulting optimized alignment objective. We instantiate this perspective using FSW-GNN, a bi-Lipschitz WL-equivalent encoder, as a drop-in replacement in representative neural GED architectures. Across representative baselines and benchmark datasets, the resulting geometry-aware variants significantly improve GED prediction and ranking metrics. A faithfulness case study of untrained encoders, together with ablations and transfer experiments, supports the view that these gains arise from improved representation geometry, positioning encoder geometry as a useful design principle for neural graph matching.

Graph representation learning (GRL) has evolved from topology-only graph embeddings to task-specific supervised GNNs, and more recently to reusable representations and graph foundation models (GFMs). However, existing evaluations mainly measure clean transfer, adaptation, and task coverage. It remains unclear whether GRL methods stay reliable when deployment stresses affect graph signals, graph contexts, label support, structural groups, or predictive evidence. We introduce GRL-Safety, a multi-axis safety evaluation benchmark for GRL. GRL-Safety evaluates twelve representative methods, spanning topology-only embedding methods, supervised GNNs, self-supervised graph models, and GFMs, on twenty-five graph datasets under standardized evaluation conditions while preserving method-native adaptation. The evaluation covers five safety axes: corruption robustness, OOD generalization, class imbalance, fairness, and interpretation, with per-axis and sub-condition reporting rather than a single aggregate score. Our analysis yields three cross-axis insights that can inspire future research. First, safety behavior is shaped by the interaction between representation design and the stressed graph factor, rather than by method family alone. Second, foundation-era methods show axis-specific strengths rather than broad safety dominance. Third, several deployment regimes remain difficult even for the best evaluated method, revealing capability gaps that require new robustness, adaptation, or training objectives beyond model selection. The benchmark, evaluation protocols, and code are available at: https://github.com/GXG-CS/GRL-Safety.

Progress on graph foundation models is hindered by benchmark practices that conflate the contributions of node features and graph structure, making it hard to tell whether a model actually learns from connectivity, or whether it even needs to. We propose addressing this using graph invariants, i.e., permutation-invariant, task-agnostic structural descriptors that serve as a diagnostic framework for graph benchmarks. We show that (i) invariants are more expressive than standard GNNs, (ii) invariants characterize structural heterogeneity within and across benchmark datasets, (iii) invariants predict multi-task performance, and (iv) simple invariant-based models are competitive with, and sometimes exceed, transformer and message-passing baselines across 26 datasets. Our results suggest that expressivity is not the main driver of predictive performance, and that on tasks where structure matters, a non-trainable structural proxy often matches trained message-passing models. We thus posit that invariant baselines should become a standard for evaluating whether structure is required for a task and whether a model picks up on it, serving as a stepping stone towards graph foundation models.

Subgraph pattern detection aims to uncover complex interaction structures in graphs. However, state-of-the-art graph neural network (GNN)-based solutions assume centralized access to the entire graph. When graphs are instead distributed across multiple parties, client-local GNN computations diverge from those of a centralized model, resulting in a representation-equivalence gap. We formalize this as a structural observability problem, where subgraph patterns crossing partition boundaries become locally unidentifiable. To bridge this gap, we propose a per-step, layer-wise embedding exchange framework in which clients synchronize intermediate node representations at each layer of the forward pass, without exposing raw features or labels. Under an extended-subgraph assumption and shared model parameters across clients, this framework recovers the same node representations as a centralized GNN over the full graph. Experiments on synthetic directed multigraphs with cycles, bicliques, and scatter-gather patterns show that embedding exchange and federated parameter aggregation are complementary rather than interchangeable: their combination recovers most of the representation gap, provided exchanged embeddings are fresh per-step rather than stale per-epoch.

Graph pooling is commonly applied in graph classification, yet its empirical gains over standard WL-1 expressive GNNs are often marginal or inconsistent. We study this gap by analysing the interaction between node features and graph topology and their effect on pooling objectives. Our analysis reveals that pooling operators require node features that are well-aligned with the graph's topology -- a condition often overlooked and not guaranteed in empirical networks. We formalise fundamental requirements for node features to enable effective pooling, and introduce a quantitative measure of feature quality. Our empirical evaluation shows that, when these requirements are satisfied, pooling can be beneficial and improve performance on appropriate datasets.

It is well established that spectral graph neural networks (GNNs) can universally approximate node signals; however, their expressive power remains bounded by the 1-dimensional Weisfeiler-Lehman test, which is mirrored in their lack of universality for higher-order signals. To go beyond this bound, we propose the Full-Spectrum GNNs (FSpecGNNs), a second-order generalization of classical spectral GNNs. FSpecGNN advances spectral filtering from two perspectives: (1) it lifts signals from the node domain to the node-pair domain; and (2) it extends the univariate spectral filter over eigenvalues to a bivariate filter over eigenvalue pairs. We show that classical spectral GNNs arise as a diagonal special case of FSpecGNNs, and prove that FSpecGNNs can be at most as expressive as Local 2-GNN while universally approximating node-pair signals, the latter being particularly beneficial for heterophilic graph learning. Moreover, FSpecGNN admits scalable implementations that avoid explicit node-pair-level computations; combined with a low-rank approximation that reduces full-spectrum convolution to a combination of polynomial spectral filters, it enables learning on large graphs. Empirically, FSpecGNN validates the predicted expressivity and delivers strong performance on heterophilic benchmarks.

Adversarial learning and the robustness of Graph Neural Networks (GNNs) are topics of widespread interest in the machine learning community, as documented by the number of adversarial attacks and defenses designed for these purposes. While a rigorous evaluation of these adversarial methods is necessary to understand the robustness of GNNs in real-world applications, we posit that many works in the literature do not share the same experimental settings, leading to ambiguous and potentially contradictory scientific conclusions. In this benchmark, we demonstrate the importance of adopting fair, robust, and standardized evaluation protocols in adversarial GNN research. We perform a comprehensive re-evaluation of seven widely used attacks and eight recent defenses under both poisoning and evasion scenarios, across six popular graph datasets. Our study spans over 453,000 experiments conducted within a unified framework. We observe substantial differences in adversarial attack performance when evaluated under a fair and robust procedure. Our findings reveal that previously overlooked factors, such as target node selection and the training process of the attacked model, have a profound impact on attack effectiveness, to the extent of completely distorting performance insights. These results underscore the urgent need for standardized evaluations in adversarial graph machine learning.

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

Given two GNNs that output node embeddings, how can we determine if they were trained independently? An adversary could have trained one GNN specifically to mimic the other GNN's embeddings. To obscure this relationship between the GNNs, the adversarial GNN might then transform its output embeddings. The two GNNs could have different architectures, weights, and embedding dimensions, and the adversary can transform the embeddings. Despite these stringent conditions, our algorithm (named CopyCop) can identify such copycat GNNs, unlike existing watermarking and fingerprinting methods. We also provide theoretical guarantees for CopyCop. Finally, experiments on 14 datasets and 5 GNN architectures demonstrate that CopyCop is accurate and robust against a broad class of adversarial attacks and transformations. Code is available at: https://anonymous.4open.science/r/CopyCop-Graph-Ownership-Verification-8143/README.md

Uncertainty quantification (UQ) in graph neural networks (GNNs) is crucial in high-stakes domains but remains a significant challenge. In graph settings, message passing often relies on strong assumptions such as exchangeability, which are rarely satisfied in practice, and achieving reliable UQ typically requires costly resampling or post-hoc calibration. To address these issues, we introduce Quantile-free Prediction Interval GNN (QpiGNN), a framework that builds on quantile regression (QR) to enable GNN-based UQ by directly optimizing coverage and interval width without requiring quantile inputs or post-processing. QpiGNN employs a dual-head architecture that decouples prediction and uncertainty, and is trained with label-only supervision through a quantile-free joint loss. This design allows efficient training and yields robust prediction intervals, with theoretical guarantees of asymptotic coverage and near-optimal width under mild assumptions. Experiments on 19 synthetic and real-world benchmarks show QpiGNN achieves average 22% higher coverage and 50% narrower intervals than baselines, while ensuring efficiency and robustness to noise and structural shifts.

Graph neural networks have been widely used in Boolean satisfiability (SAT) tasks to learn structural information from SAT formulas. The goal of these studies is to solve SAT instances or to enhance SAT solvers, including tasks such as unsat-core prediction. However, most existing approaches model a SAT formula as a bipartite graph or a directed acyclic graph, which are less direct in capturing clause-level and higher-order interactions among literals and clauses. Moreover, these approaches are limited in modeling intrinsic polarity-related properties of SAT, such as the complementary relationship between the positive and negative literals of a variable. To address these limitations, we propose a polarity-aware representation learning framework over clause-literal hypergraphs. We model SAT formulas as clause-literal hypergraphs augmented with a clause incidence graph to capture higher-order structural interactions. We then introduce a polarity-aware decomposition mechanism that separates variable representations into polarity invariant and equivariant components, explicitly modeling the relationship between positive and negative literals, with the resulting literal representations propagated along the hypergraph structure. We further incorporate a polarity-inversion consistency regularization to reinforce polarity-consistent representations during training. Experimental results on multiple SAT datasets demonstrate the effectiveness of the proposed approach.

The integration of deep learning approaches in biomedical research has been transformative, enabling breakthroughs in various applications. Despite these strides, its application in protein inference is impeded by the scarcity of extensively labeled datasets, a challenge compounded by the high costs and complexities of accurate protein annotation. In this study, we introduce GraphPI, a novel framework that treats protein inference as a node classification problem. We treat proteins as interconnected nodes within a protein-peptide-PSM graph, utilizing a Graph Neural Network-based architecture to elucidate their interrelations. To address label scarcity, we train the model on a set of unlabeled public protein datasets with pseudo-labels derived from an existing protein inference algorithm, enhanced by self-training to iteratively refine labels based on confidence scores. Contrary to prevalent methodologies necessitating dataset-specific training, our research illustrates that GraphPI, due to the well normalized nature of Percolator features, exhibits universal applicability without dataset-specific fine-tuning, a feature that not only mitigates the risk of overfitting but also enhances computational efficiency. Our empirical experiments reveal notable performance on various test datasets and deliver significantly reduced computation times compared to common protein inference algorithms.

Nonstabilizerness, commonly referred to as magic, is a fundamental resource underpinning quantum advantage. In this paper, we propose a magic-informed quantum architecture search (QAS) technique that enables control over a quantum resource within the general framework of circuit design. Inspired by the AlphaGo approach, we tackle the problem with a Monte Carlo Tree Search technique equipped with a Graph Neural Network (GNN) that estimates the magic of candidate quantum circuits. The GNN model induces a magic-based bias that steers the search toward either high- or low-magic regimes, depending on the target objective. We benchmark the proposed magic-informed QAS technique on both the structured ground-state energy problem and on the more general quantum state approximation problem, spanning different sizes and target magic levels. Experimental results show that the proposed technique effectively influences the magic across the search tree and notably also on the resulting final circuit, even in regimes where the GNN operates on out-of-distribution instances. Although introducing a problem-agnostic magic bias could, in principle, constrain the search dynamics, we observe consistent improvements in solution quality across all problems tested.

Local gauge structures play a central role in a wide range of condensed matter systems and synthetic quantum platforms, where they emerge as effective descriptions of strongly correlated phases and engineered dynamics. We introduce a gauge-invariant graph neural network (GNN) architecture for Abelian lattice gauge models, in which symmetry is enforced explicitly through local gauge-invariant inputs, such as Wilson loops, and preserved throughout message passing, eliminating redundant gauge degrees of freedom while retaining expressive power. We benchmark the approach on both $\mathbb{Z}_2$ and $\mathrm{U}(1)$ lattice gauge models, achieving accurate predictions of global observables and spatially resolved quantities despite the nonlocal correlations induced by gauge-matter coupling. We further demonstrate that the learned model serves as an efficient surrogate for semiclassical dynamics in $\mathrm{U}(1)$ quantum link models, enabling stable and scalable time evolution without repeated fermionic diagonalization, while faithfully reproducing both local dynamics and statistical correlations. These results establish gauge-invariant message passing as a compact and physically grounded framework for learning and simulating Abelian lattice gauge systems.

We present a method for finding hierarchy-aware embeddings of knowledge graphs (KGs) using graph neural networks (GNNs) enriched with a semantic loss derived from underlying ontologies. This method yields embeddings that better reflect domain knowledge. To demonstrate their utility, we predict and interpret the effects of gene deletions in the yeast Saccharomyces cerevisiae and learn box embeddings for KGs in the absence of a prediction task. We further show how box embeddings can serve as the basis for evaluating KG revisions. Our yeast KG is constructed from community databases and ontology terms. Low-dimensional box embeddings combined with GNNs are used to predict cell growth for double gene knockouts. Over 10-fold cross validation, these predictions have a mean $R^2$scoreof~0.360, significantly higher than baseline comparisons, demonstrating that high-level qualitative knowledge is informative about experimental outcomes. Incorporating semantic loss terms in the training of the models improves their predictive performance ($R^2$=0.377) by aligning embeddings with ontology structure. This shows that class hierarchies from ontologies can be exploited for quantitative prediction. We also test the trained models on triple gene knockouts, showing they generalise to data beyond those seen in training. Additionally, by identifying co-occurring relations in the yeast KG important for the cell-growth predictions, we construct hypotheses about interacting traits in yeast. A biological experiment validates one such finding, revealing an association between inositol utilisation and osmotic stress resistance, highlighting the model's potential to guide biological discovery.

Regulatory frameworks such as GDPR increasingly require that ML predictions be accompanied by post-hoc explanations, even when raw data and trained models cannot be released. Differential privacy (DP) is the standard mitigation for the residual privacy risk of releasing these explanations. We show that DP is not sufficient: an adversary observing only DP-perturbed GNN explanations can reconstruct hidden graph structure with high accuracy. Our attack, PRIVX, exploits the fact that the Gaussian DP mechanism is a single DDPM forward step at known noise level σ(ε), recasting reconstruction as reverse diffusion conditioned on the corrupted signal, a principled Bayesian denoiser under known DP corruption. We formalise a stratified adversary model parameterised by (M, \hatε, \hatδ, S, ρ) that interpolates between oblivious and oracle attackers, and derive endpoint-matched two-sided bounds on reconstruction AUC. For practitioners, we provide regime-stratified guidance on explainer choice: on homophilic graphs, neighbourhood-aggregating explainers (GraphLIME, GNNExplainer) leak more structure than per-node gradient explainers under the same DP budget; on strongly heterophilic graphs the ordering reverses. We introduce PRIVF as an auxiliary diagnostic sharing the same diffusion backbone to decompose leakage into explainer-induced and intrinsic graph-distribution components. Experiments across seven benchmarks, three DP mechanisms, and three GNN backbones show PRIVX achieves AUC above 0.7 at ε = 5 on five of seven datasets, with the attack succeeding well within typically deployed privacy budgets.

Graph Neural Networks (GNNs) achieve strong performance on node classification tasks but remain difficult to interpret, particularly with respect to which input features drive their predictions. Existing global GNN explainers operate at the structural level identifying recurring subgraph motifs, but none explain model behaviour globally at the level of input node attributes. We propose GRAFT, a posthoc global explanation framework that identifies class-level feature importance profiles for GNNs. The method combines diversity-guided exemplar selection, Integrated Gradients-based attribution, and aggregation to construct a global view of feature influence for each class, which can be further expressed as concise natural language rules using a large language model with self-refinement. We evaluate GRAFT across multiple datasets, architectures, and experimental settings, demonstrating its effectiveness in capturing model-relevant features, supporting bias analysis, and enabling feature-efficient transfer learning. In addition, we introduce a structured human evaluation protocol to assess the interpretability of generated rules along dimensions such as accuracy and usefulness. Our results suggest that GRAFT provides a practical and interpretable approach for analysing feature-level behaviour in GNNs, bridging quantitative attribution with human-understandable explanations.

Traditional Simultaneous Localization and Mapping (SLAM) algorithms rely heavily on the static environment assumption, which severely limits their applicability in real-world spaces populated by moving entities, such as pedestrians. In this work, we propose DynoSLAM, a tightly-coupled Dynamic GraphSLAM architecture that integrates socially-aware Graph Neural Networks (GNNs) directly into the factor graph optimization. Unlike conventional approaches that use rigid constant-velocity heuristics or deterministic single-agent neural priors, our framework formulates pedestrian motion forecasting as a stochastic World Model. By utilizing Monte Carlo rollouts from a trained GNN, we capture the multimodal epistemic uncertainty of human interactions and embed it into the SLAM graph via a dynamic Mahalanobis distance factor. We demonstrate through extensive simulated experiments that this stochastic formulation not only maintains highly accurate retrospective tracking but also prevents the optimization failures caused by the deterministic "argmax problem". Ultimately, extracting the empirical mean and covariance matrices of future pedestrian states provides a mathematically rigorous, probabilistic safety envelope for downstream local planners, enabling anticipatory and collision-free robot navigation in densely crowded environments.

Learning data-efficient object dynamics models for robotic manipulation remains challenging, especially for deformable objects. A popular approach is to model objects as sets of 3D particles and learn their motion using graph neural networks. In practice, this is not enough to maintain physical feasibility over long horizons and may require large amounts of interaction data to learn. We introduce PIEGraph, a novel approach to combining analytical physics and data-driven models to capture object dynamics for both rigid and deformable bodies using limited real-world interaction data. PIEGraph consists of two components: (1) a \textbf{P}hysically \textbf{I}nformed particle-based analytical model (implemented as a spring--mass system) to enforce physically feasible motion, and (2) an \textbf{E}quivariant \textbf{Graph} Neural Network with a novel action representation that exploits symmetries in particle interactions to guide the analytical model. We evaluate PIEGraph in simulation and on robot hardware for reorientation and repositioning tasks with ropes, cloth, stuffed animals and rigid objects. We show that our method enables accurate dynamics prediction and reliable downstream robotic manipulation planning, which outperforms state of the art baselines.

Capturing semantic consistency among nodes is crucial for effective graph representation learning. Existing approaches typically rely on $k$-nearest neighbors ($k$NN) or other node-level full search algorithms (FSA) to mine semantic relationships via exhaustive pairwise similarity computation, which suffer from high computational complexity and rigid neighbor selection, limiting scalability and introducing noisy connections. In this paper, we propose the Semantic Consistency enhanced Graph Neural Network (SCGNN), a novel plug-and-play framework that leverages granular-ball computing (GBC) to efficiently capture semantic consistency in a scalable manner. Unlike node-level FSA methods, SCGNN models group-level semantic structure by adaptively partitioning nodes into granular balls, significantly reducing computational cost while improving robustness to noise. To effectively utilize the discovered group-level semantic consistency, we design a dual enhancement strategy. Specifically, (1) a structure enhancement module constructs an anchor-based graph structure, where each anchor is a virtual node representing the group-level semantic carried by a granular ball, then injecting group-level semantic information into the graph structure; and (2) a supervision enhancement module performs label consistency checking (LCC) by combining GBC predictions with model-generated pseudo-labels, thereby producing more reliable supervision signals. SCGNN is compatible with various GNN backbones. During the forward propagation of SCGNN, the vanilla graph and the augment graph are jointly encoded, and their predictions are fused; during the backpropagation, the supervision enhancement module provides enhanced supervision signals to guide parameter updates.

Recommender systems are essential components of modern online platforms which presents personalized content in various domain. The traditional collaborative filtering methods depends on static user-item interaction graphs and a limited subset of similarity measures which fail to capture the changing nature of preferences of an individual. Recent graph neural network (GNN) based approaches focus on user-item bipartite graphs which do not use explicit user-user relational modelling and dynamic graph evolution during training. To address these limitations, this paper proposes a Dynamic Graph SimilarityAware Attention Graph Neural Network (DG-SA-GNN) framework that integrates dynamic user similarity graph construction with multi-similarity propagation and attention-based aggregation. The proposed architecture constructs four parallel user similarity graphs using Cosine, Jaccard, Discounted Pearson Correlation Coefficient (Discount PCC), and IPIJ similarity functions, each processed by a dedicated UserGNN module. A Graph Transformer fuses the four graph views, and a CrossAttention module refines user embeddings through interaction with item embeddings. Crucially, the graphs are reconstructed at scheduled epochs during training, enabling the model to adapt to the learned embedding space constituting the dynamic graph component. Mini-batch training with hard negative sampling improves scalability and convergence. Experiments on the MovieLens100K benchmark demonstrate that DG-SA-GNN achieves a Recall@20 of 0.162 and NDCG@20 of 0.065 which is better than the LightGCN baseline in recall. The results validate that dynamic multi-similarity graph construction coupled with attention-based fusion which produce recommendation performance

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

This paper investigates coordinated downlink transmission in a multi-base station (multi-BS) multi-reconfigurable intelligent surface (multi-RIS)-assisted pinching-antenna (PA) system, where each user equipment (UE) is associated with a single BS and each BS is equipped with movable PAs deployed on parallel waveguides. We formulate sum rate (SR) and energy efficiency (EE) maximization problems by jointly optimizing PA placement, RIS phase shifts, transmit beamforming, and BS-UE association under constraints of inter-PA spacing, power budget, and unit-modulus phase shift. To address the resulting highly coupled mixed-variable problem, we propose a three-stage graph neural network (GNN) that integrates heterogeneous and homogeneous graph representations and is trained end-to-end in an unsupervised manner. Extensive numerical results demonstrate that the proposed three-stage GNN consistently outperforms representative system and learning baselines, generalizes well to unseen numbers of UEs, RISs, and BSs, and maintains millisecond-level inference time. Besides, the results validate the effectiveness of the proposed design from both system and architectural perspectives. Moreover, PAs are shown to enhance SR and EE, and the performance gain is enlarged with increasing number of PAs.

Spectral graph sparsification is a classical tool for reducing graph complexity while preserving Laplacian quadratic forms. In graph neural networks (GNNs), sparsification is often used to accelerate computation while maintaining predictive performance. In this work, we study a complementary representation-level question: does sparsification preserve the geometry of learned embeddings? For polynomial-filter GNNs, we prove that any $ε$-spectral sparsifier induces $O(ε)$ perturbations in polynomial graph filters, multilayer hidden representations, and their Gram matrices. These guarantees imply stability of squared pairwise distances, class means, and covariance structure in embedding space. We further establish finite-time training stability: under smoothness and boundedness assumptions, gradient descent on dense and sparsified graphs produces weight trajectories whose separation grows at most proportionally to the sparsification distortion. Empirically, effective-resistance sparsification validates the predicted perturbation chain on synthetic graphs and preserves hidden representation geometry on real datasets. In our experiments, the gram matrix and training dynamics show low divergence even under substantial sparsification, consistent with the predicted stability under spectral sparsification. Hidden Gram preservation strongly predicts neighborhood preservation and class-centroid stability across FashionMNIST, Cora, and Paul15. Together, these results show that spectral sparsification preserves not only graph operators, but also the representation geometry that supports downstream use of GNN embeddings for interpretability.

Graph neural tangent kernels give a principled infinite-width theory for graph neural networks, but inherit a basic limitation of graph models: they see only pairwise structure. Many relational systems contain higher-order interactions that are more naturally represented by simplicial complexes. We introduce the Topological Neural Tangent Kernel (TopoNTK), an infinite-width kernel for simplicial message passing on edge features. TopoNTK combines lower Hodge interactions, capturing graph-like coupling through shared vertices, with upper Hodge interactions, capturing coupling through filled simplices. This makes the kernel sensitive to topology invisible to graph kernels, allowing complexes with the same graph but different filled simplices to induce different kernels. Beyond expressivity, the Hodge structure gives the kernel an interpretable learning geometry. Edge signals decompose into gradient-like, harmonic, and local circulation components, and the spectrum of the TopoNTK determines how quickly each component is learned. This yields a topological form of spectral bias: components aligned with large-eigenvalue modes are learned quickly, while global harmonic modes, retained through the residual channel, often lie at smaller eigenvalues and are learned more slowly. We prove expressivity, Hodge-alignment, spectral learning, and stability properties, and validate them on synthetic simplicial tasks and DBLP higher-order link prediction. The results show that topology is not merely extra structure; it can provide coordinates that make relational learning more faithful, interpretable, and effective.

Graph Neural Networks are powerful models for learning from graph-structured data, yet their effectiveness is often limited by two critical challenges: over-squashing, where information from distant nodes is excessively compressed, and over-smoothing, where repeated propagation makes node representations indistinguishable. Both phenomena stem from the interaction between message passing and the input topology, ultimately degrading information flow and limiting the performance of GNNs. In this survey, we examine graph rewiring techniques, a class of methods designed to modify the graph topology to enhance information propagation in GNNs. We provide a comprehensive review of state-of-the-art rewiring approaches, delving into their theoretical underpinnings, practical implementations, and performance trade-offs.

Edge classification, a crucial task for graph applications, remains relatively under-explored compared to link prediction. Current methods often overlook the potential causal influences of node features on edge features, leading to a loss of relevant prior information. In this work, we present an empirical exploration using the Causal Edge Classification Framework (CECF). Unlike conventional causal inference methods, CECF is the first framework to apply causal inference principles to the edge classification task and to explore modeling edge features as a high-dimensional treatment within a causal framework. Based on the node embedding of Graph Neural Network (GNN), CECF seeks to learn a balanced representation of high-dimensional edge features by mitigating the potential influence of node features. Then, a cross-attention network captures the complex dependencies between node and edge features for final edge classification. Extensive experiments demonstrate that CECF not only achieves superior performance but also serves as a flexible, plug-and-play enhancement for existing methods. We also provide empirical analyses, offering insights into when and how this high-dimensional causal modeling framework works for the edge classification.

We propose an arbitrary Lagrangian-Eulerian (ALE)-consistent machine learning framework for long-term fluid-structure interaction (FSI) prediction on deforming unstructured meshes. Specifically, the fluid dynamics are modeled by a surrogate that combines a graph neural operator (GNO) with a vision Transformer (ViT) for spatiotemporal prediction, while a lightweight long short-term memory (LSTM) network predicts structural kinematics at the interface. The two surrogates are coupled through a standard partitioned procedure. Most importantly, kinematic compatibility at the moving interface is enforced via an ALE-consistent boundary-correction step that updates the fluid-side interface velocity with the predicted structural velocity at each coupling update, thereby improving near-interface accuracy and long-term rollout stability. To mitigate autoregressive error accumulation, a two-stage training strategy is adopted, consisting of single-step supervised pretraining followed by long-term autoregressive fine-tuning. The proposed framework is validated on the benchmark problem of a flexible beam vibration in the wake of a cylinder. Results demonstrate accurate phase-consistent predictions over long rollouts and robust generalization under inlet-profile variations in both interpolation and extrapolation settings. Systematic ablation studies further assess the respective contributions of the ViT module, ALE-consistent boundary correction, and long-term training to predictive accuracy and rollout robustness.

Semidefinite programs (SDPs) are a powerful framework for convex optimization and for constructing strong relaxations of hard combinatorial problems. However, solving large SDPs can be computationally expensive, motivating the use of machine learning models as fast computational surrogates. Graph neural networks (GNNs) are a natural candidate in this setting due to their sparsity-awareness and ability to model variable-constraint interactions. In this work, we study what expressive power is sufficient to recover optimal SDP solutions. We first prove negative results showing that standard GNN architectures fail on recovering linear SDP solutions. We then identify a more expressive architecture that captures the key structure of SDPs and can, in particular, emulate the updates of a standard first-order solver. Empirically, on both synthetic and \textsc{SdpLib} benchmarks of various classes of SDPs, this more expressive architecture achieves consistently lower prediction error and objective gap than theoretically weaker baselines. Finally, using the learned high-quality predictions to warm-start the first-order solver yields practical speedups of up to 80%.

Heterogeneous graphs are widely used to model multi-relational systems, but missing node attributes remain a major bottleneck for downstream learning. In this paper, we identify and formalize type-dependent information asymmetry: the phenomenon that different node types provide substantially different levels of useful signal for attribute completion. Motivated by this observation, we propose TypeBandit, a lightweight, model-agnostic methodology for heterogeneous attribute completion. TypeBandit combines topology-aware initialization, type-level bandit sampling, and joint representation learning. It allocates a finite global sampling budget across node types, samples representative nodes within each type, and uses the resulting sampled type summaries as shared contextual signals during representation construction. By operating at the type level rather than over each target node's local neighborhood, TypeBandit keeps the adaptive state compact and practical for large heterogeneous graphs. A key advantage of TypeBandit is architectural flexibility. Rather than requiring a new heterogeneous graph neural network architecture, TypeBandit acts as a type-aware front end for representative heterogeneous GNN backbones, including R-GCN, HetGNN, HGT, and SimpleHGN. We further introduce a hybrid pretraining scheme that combines structural degree priors with feature propagation, yielding a more reliable initializer than degree-only pretraining. Under a fixed-split protocol on DBLP, IMDB, and ACM, TypeBandit provides dataset-dependent but practically meaningful gains. Additional ablation, stability, efficiency, semantic-propagation, and sampled OGBN-MAG experiments support TypeBandit as a practical strategy for heterogeneous attribute completion when type-specific information is unevenly distributed and sampling resources are limited.

Anticipating traffic accidents is a critical yet unresolved problem for autonomous driving, hindered by the inherent complexity of modeling interactions between road users and the limited availability of diverse, large-scale datasets. To address these issues, we propose a dual-path framework. On the one hand, we employ a video synthesis pipeline that, guided by structured prompts, derives feature distributions from existing corpora and produces high-fidelity synthetic driving scenes consistent with the statistical patterns of real data. On the other hand, we design a graph neural network enriched with semantic cues, enabling dynamic reasoning over both spatial and semantic relations among participants. To validate the effectiveness of our approach, we release a new benchmark dataset containing standardized, finely annotated video sequences that cover a broad spectrum of regions, weather, and traffic conditions. Evaluations across existing datasets and our new benchmark confirm notable gains in both accuracy and anticipation lead time, highlighting the capacity of the proposed framework to mitigate current data bottlenecks and enhance the reliability of autonomous driving systems.

Deploying a neuro-symbolic task planner on a new domain today requires significant manual effort: a domain expert must author relaxation and complementary rules, and hundreds of training problems must be solved to supervise a Graph Neural Network (GNN) object scorer. We propose LLM-Flax, a three-stage framework that eliminates all three sources of manual effort using a locally hosted LLM given only a PDDL domain file. Stage 1 automatically generates relaxation and complementary rules via structured prompting with format validation and self-correction. Stage 2 introduces LLM-guided failure recovery with a feasibility-gated budget policy that explicitly reserves API latency cost before each LLM call, preventing the downstream relaxation fallback from being starved. Stage 3 replaces the domain-trained GNN entirely with zero-shot LLM object importance scoring, requiring no training data. We evaluate all three stages on the MazeNamo benchmark across 10x10, 12x12, and 15x15 grids (8 benchmarks total). LLM-Flax achieves average SR 0.945 versus the manual baseline's 0.828 (+0.117), matching or outperforming manual rules on every one of the eight benchmarks. On 12x12 Expert, LLM-Flax attains SR 0.733 where the manual planner fails entirely (SR 0.000); on 15x15 Hard, it achieves SR 1.000 versus Manual's 0.900. Stage 3 demonstrates feasibility (SR 0.720 on 12x12 Hard with no training data) but faces a context-window bottleneck at scale, pointing to the primary open challenge for future work.

Graph-based text classification models typically rely on local neighborhood aggregation and overlook global community structure, despite semantic document graphs exhibiting strong class-consistent clustering. Ignoring this can blur class boundaries and lead to over-smoothing. We propose ModTGCN, a modularity-aware graph neural network for text classification that jointly optimizes cross-entropy and a modularity-based auxiliary objective to promote class-coherent document communities while preserving discriminative representations. The modularity term is computed on a document-document similarity graph derived from transformer embeddings (pretrained or fine-tuned). To improve scalability, we decouple the original heterogeneous TextGCN graph into separate document-word and word-word components, achieving 2x-10x faster training. We further study graph construction strategies, label-aware edge reweighting, and supervision choices for modularity optimization. Experiments on five benchmarks show consistent gains, with larger improvements on complex, low homophily datasets such as Ohsumed and 20NG.

This paper addresses the problem of anomaly detection in accounting subject association structures, proposing a structured modeling and unsupervised discriminant framework based on graph neural networks. This framework is used to mine stable correspondences between subjects and identify structural deviations from general ledger details and voucher entries. The method first abstracts accounting subjects as graph nodes, and the co-occurrence and debit/credit correspondence of subjects in the same business record are abstracted as weighted edges. The edge weights are characterized by statistical measures such as co-occurrence frequency or amount aggregation, thus forming a period-level accounting subject association graph. In the representation learning stage, a message passing mechanism is used to fuse the node's own attributes and neighborhood context to obtain node embeddings containing structural information. In the anomaly detection stage, the rationality of subject pair connections is estimated through a relation reconstruction decoder, and edge-level anomaly scores are defined based on the degree of deviation in reconstruction probabilities. These scores are then aggregated to obtain node-level risk ranking and local anomaly localization. This framework can simultaneously capture local substructure anomalies and cross-community anomaly connections without relying on anomaly labeling, outputting traceable subject pair risk clues. Comparative experiments demonstrate more stable comprehensive discriminant capabilities and higher top-ranking accuracy.

Graph neural networks (GNNs) have emerged as a versatile and efficient option for modeling the dynamic behavior of deformable materials. While GNNs generalize readily to arbitrary shapes, mesh topologies, and material parameters, existing architectures struggle to correctly predict the temporal evolution of key physical quantities such as linear and angular momentum. In this work, we propose MomentumGNN -- a novel architecture designed to accurately track momentum by construction. Unlike existing GNNs that output unconstrained nodal accelerations, our model predicts per-edge stretching and bending impulses which guarantee the preservation of linear and angular momentum. We train our network in an unsupervised fashion using a physics-based loss, and we show that our method outperforms baselines in a number of common scenarios where momentum plays a pivotal role.

Graph neural networks such as ParticleNet and transformer based networks on point clouds such as ParticleTransformer achieve state-of-the-art performance on jet tagging benchmarks at the Large Hadron Collider, yet the physical reasoning behind their predictions remains opaque. We present different methods, i.e. perturbation-based (GNNExplainer), Shapley-value-based (GNNShap), and gradient-based (GRADCam); adapted to operate on LundNet's Lund-plane graph representation. Leveraging the fact that each node in the Lund plane corresponds to a physically meaningful parton splitting, we construct Monte Carlo truth explanation masks and introduce a physics-informed evaluation framework that goes beyond standard fidelity metrics. We perform the analysis in three transverse-momentum bins ($\mathrm{p_T} \in [500,700]$, $[800,1000]$, and the inclusive region $[500,1000]$ GeV), revealing how explanation quality and focus shift between non-perturbative and perturbative regimes. We further quantify the correlation between explainer-assigned node importance and classical jet substructure observables -- $N$-subjettiness ratios $τ_{21}$ and $τ_{32}$ and the energy correlation functions -- establishing the degree to which the model has learned known QCD features. We find that overall the weight assigned by explainability methods has a correlation with analytic observables, with expected shift across different phase space regimes, indicating that a trained neural network indeed learns some aspects of jet-substructure moments. Our open-source implementation enables reproducible explainability studies for graph-based jet taggers.

Prior work on node classification has shown that Graph Neural Networks (GNNs) can learn representations that transfer across graphs, when underlying graph properties are shared. For a fixed graph, one would then expect GNNs trained for link prediction to learn a representation consistent with that learnt for node classification. We show this intuition does not hold in the general case. Instead, we find popular link prediction models can learn a trivial mini-batch dependent heuristic, enabled by batch-normalisation layers, to solve the edge classification task. When correcting for this, we observe increased alignment of the network representation with node-class relevant features, suggesting the network has learnt a graph representation that better aligns with the underlying graph's properties. Our findings suggest that standard link prediction training may be leading us to overestimate link predictors' ability to learn a generalised representation of a graph that is consistent across tasks.

Code understanding models increasingly rely on pretrained language models (PLMs) and graph neural networks (GNNs), which capture complementary semantic and structural information. We conduct a controlled empirical study of PLM-GNN hybrids for code classification and vulnerability detection tasks by systematically pairing three code-specialized PLMs with three foundational GNN architectures. We compare these hybrids against PLM-only and GNN-only baselines on Java250 and Devign, including an identifier-obfuscation setting. Across both tasks, hybrids consistently outperform GNN-only baselines and often improve ranking quality over frozen PLMs. On Devign, performance and robustness are more sensitive to the PLM feature source than to the GNN backbone. We also find that larger PLMs are not necessarily better feature extractors in this pipeline, and that the PLM choice has more impact than the GNN choice. Finally, we distill these findings into practical guidelines for PLM-GNN design choices in code classification and vulnerability detection.

Recurrent Graph Neural Networks (RGNNs) extend standard GNNs by iterating message-passing until some stopping condition is met. Various RGNN models have been proposed in the literature. In this paper, we study three such models: converging RGNNs, where all vertex representations must stabilise; output-converging RGNNs, where only the output classifications must stabilise; and halting RGNNs, where a per-vertex halting classifier determines when to stop. We establish expressiveness relationships between these models: over undirected graphs, converging RGNNs are equally expressive as graded-bisimulation-invariant halting RGNNs, while output-converging RGNNs are at least as expressive. Combined with prior results on halting RGNNs, this shows that, relative to the classifiers expressible in monadic second-order logic (MSO), converging RGNNs express exactly the graded modal $μ$-calculus ($μ$GML), and output-converging RGNNs express at least $μ$GML. These results hold even when restricting to ReLU networks with sum aggregation. The main technical challenge is simulating halting RGNNs by converging ones: without a global halting classifier, vertices may locally decide to halt at different times, causing desynchronisation. We develop a "traffic-light" protocol that enables vertices to coordinate despite this asynchrony. Our results answer an open question from Bollen et al. (2025) and show that the RGNN model of Pflueger et al. (2024) retains full $μ$GML expressiveness even when convergence is guaranteed.

Current research on distributed multi-modal learning typically assumes that clients can access complete information across all modalities, which may not hold in practice. In this paper, we explore patchwork learning, in which the modalities available to different clients vary, and the objective is to impute the missing modalities for each client in an unsupervised manner. Existing methods are shown not to fully utilize the modality information as they tend to rely on only a subset of the observed modalities. To address this issue, we propose GraphPL, which combines graph neural networks with patchwork learning to flexibly integrate all observed modalities and remains robust with noisy inputs. Experimental results show that GraphPL achieves SOTA performance on benchmark datasets. Our results on real-world distributed electronic health record dataset show GraphPL learns strong downstream features and enables tasks like disease prediction via superior modality imputation.

In multi-agent reinforcement learning (MARL), the integration of a communication mechanism, allowing agents to better learn to coordinate their actions and converge on their objectives by sharing information. Based on an interaction graph, a subclass of methods employs graph neural networks (GNNs) to learn the communication, enabling agents to improve their internal representations by enriching them with information exchanged. With growing research, we note a lack of explicit structure and framework to distinguish and classify MARL approaches with communication based on GNNs. Thus, this paper surveys recent works in this field. We propose a generalized GNN-based communication process with the goal of making the underlying concepts behind the methods more obvious and accessible.

High-entropy alloys (HEAs) have attracted growing attention for their exceptional mechanical and thermal properties arising from complex atomic configurations. In this paper, we propose crystal fractional graph neural network for predicting the energy of high-entropy alloys by explicitly integrating both local atomic environments and global compositional information. The model consists of three components: a crystal graph neural network, which employs graph attention network layers to learn local interactions among 16 on-site atoms within the crystal lattice; fractional neural network, a fully connected network that embeds the global fraction of constituent elements; and feature fusion neural network, which fuses the outputs of the two submodels to predict the total crystal energy. We train the model on a dataset of 1,049 crystal structures and validate it on 198 quaternary structures, optimizing all hyperparameters via Optuna. Our results show that our model achieves an RMSE comparable to first-principles calculations and maintains high accuracy even for low-energy configurations. However, the model exhibits limitations in handling large crystal cells, which we aim to address in future work to extend its applicability to more complex systems.

Lattice Hamiltonian systems underpin models across condensed matter, nonlinear optics, and biophysics, yet learning their dynamics from data is obstructed by two unknowns: the interaction topology and whether node dynamics are homogeneous. Existing graph-based approaches either assume the graph is given or, as in $α$-separable graph Hamiltonian network, infer it only for separable Hamiltonians with homogeneous node dynamics. We introduce the Hamiltonian Graph Inference Network (HGIN), which jointly recovers the interaction graph and predicts long-time trajectories from state data alone, for both separable and non-separable Hamiltonians and under heterogeneous node dynamics. HGIN couples a structure-learning module -- a learnable weighted adjacency matrix trained under a Hamilton's-equations loss -- with a trajectory-prediction module that partitions edges into physically distinct subgraphs via $k$-means clustering, assigning each subgraph its own encoder and thereby breaking the parameter-sharing bottleneck of conventional GNNs. On three benchmarks -- a Klein--Gordon lattice with long-range interactions and two discrete nonlinear Schrödinger lattices (homogeneous and heterogeneous) -- HGIN reduces long-time energy prediction error and trajectory prediction error by six to thirteen orders of magnitude relative to baselines. A symmetry argument on the Hamiltonian loss further shows that the learned weights encode the parity of the underlying pair potential, yielding an interpretable readout of the system's interaction structure.

The health condition of components in civil infrastructures can be described by various discrete states according to their performance degradation. Inferring these states from measurable responses is typically an ill-posed inverse problem. Although Bayesian methods are well-suited to tackle such problems, computing the posterior probability density function (PDF) presents challenges. The likelihood function cannot be analytically formulated due to the unclear relationship between discrete states and structural responses, and the high-dimensional state parameters resulting from numerous components severely complicates the computation of the marginal likelihood function. To address these challenges, this study proposes a novel Bayesian inversion paradigm for discrete variables based on Probabilistic Graphical Models (PGMs). The Markov networks are employed as modeling tools, with model parameters learned from data and structural topology prior. It has been proved that inferring this PGM produces the same probabilistic estimation as the posterior PDF derived from Bayesian inference, which effectively solves the above challenges. The inference is accomplished by Graph Neural Networks (GNNs), and a graph property-based GNN training strategy is developed to enable accurate inference across varying graph scales, thereby significantly reducing the computational overhead in high-dimensional problems. Both synthetic and experimental data are used to validate the proposed framework

Graph Neural Networks (GNNs) have demonstrated impressive performance in learning representations from graph-structured data. However, their message-passing mechanism inherently relies on the assumption of label consistency among connected nodes, limiting their applicability to low-homophily settings. Moreover, since message passing operates as a hierarchical diffusion process, GNNs face challenges in capturing long-range dependencies. As network depth increases, the structural noise along heterophilic edges tends to be amplified, resulting in over-smoothing. This issue becomes especially prominent in highly heterophilic graphs, where the propagation of inconsistent semantics across the topology continually exacerbates misaggregation. To address this issue, we propose a novel framework named Layer Embedding Deep Fusion Graph Neural Network (LEDF-GNN). Specifically, we design a Layer Embedding Deep Fusion (LEDF) operator that nonlinearly fuses multi-layer embeddings to capture inter-layer dependencies and effectively alleviate deep propagation degradation. Meanwhile, to mitigate structural heterophily, LEDF-GNN employs a Dual-Topology Parallel Strategy (DTPS) that simultaneously leverages the original and reconstructed topologies, allowing for adaptive structure-semantics co-optimization under diverse homophily conditions. Extensive semi-supervised classification experiments on the citation and image benchmarks demonstrate that, under both homophilic and heterophilic settings, LEDF-GNN consistently outperforms state-of-the-art baselines, validating its effectiveness and generalization capability across diverse graph types.

We study the expressive power of message-passing aggregate-combine-readout graph neural networks (ACR-GNNs). Particularly, we focus on the first-order (FO) properties expressible by this formalism. While a tight logical characterisation remains a difficult open question, we make two contributions towards answering it. First, we show that sum aggregation and readout suffice for GNNs to capture FO properties that cannot be expressed in the logic C2 on both directed and undirected graphs. This strengthens known results by Hauke and Wał{\k e}ga (2026) where aggregation and readout functions are specially crafted for the task. Second, we identify two natural ways of restoring characterisability (with regard to C2) for ACR-GNNs. One option is to limit local aggregation (without imposing restrictions on global readout), whilst the second is to run ACR-GNNs over graphs of bounded degree (but unbounded size). In both cases, the FO properties captured by GNNs are exactly those definable by a formula in graded modal logic with global counting modalities. Our results thus establish an innate lower- and upper-bound in terms of how far (fragments of) C2 can be taken to characterise GNNs, and imply that is indeed the unbounded interaction of aggregation and readout that pushes the logical expressive power of GNNs above C2.

Vision Graph Neural Networks (ViGs) represent an image as a graph of patch tokens, enabling adaptive, feature-driven neighborhoods. Unlike CNNs with fixed grid biases or Vision Transformers with global token interactions, ViGs rely on dynamic graph convolution: at each layer, a feature-dependent graph is built via k-nearest-neighbor (kNN) search on current patch features, followed by message passing. This per-layer graph construction is the main bottleneck, consuming 50--95% of graph convolution time on CPUs and GPUs, scaling as $O(N^2)$ with the number of patches $N$, and creating a sequential dependency between graph construction and feature updates. We introduce GraphLeap, a simple reformulation that removes this dependency by decoupling graph construction from feature update across layers. GraphLeap performs the feature update at layer $\ell$ using a graph built from the previous layer's features, while simultaneously using the current layer's features to construct the graph for layer $\ell+1$. This one-layer-lookahead graph construction enables concurrent graph construction and message passing. Although using prior-layer features can introduce minor accuracy degradation, lightweight fine-tuning for a few epochs is sufficient to recover the original accuracy. Building on GraphLeap, we present the first end-to-end FPGA accelerator for Vision GNNs. Our streaming, layer-pipelined design overlaps a kNN graph construction engine with a feature update engine, exploits node- and channel-level parallelism, and enables efficient on-chip dataflow without explicit edge-feature materialization. Evaluated on isotropic and pyramidal ViG models on an Alveo U280 FPGA, GraphLeap achieves up to $95.7\times$ speedup over CPU and $8.5\times$ speedup over GPU baselines, demonstrating the feasibility of real-time Vision GNN inference.