Graph Neural Networks

Graph neural networks have achieved strong performance in node classification by aggregating information from graph neighborhoods. However, a single aggregation mechanism may be insufficient to capture diverse structural patterns across graph datasets. Moreover, independently training multiple structural branches can introduce substantial overhead without necessarily producing stable node representations. To address these issues, this paper proposes PreGS, a parameter-transfer-based multi-expert graph neural network framework. PreGS first pretrains a multi-head graph attention network (GAT) and transfers the linear transformation weights of its first-layer attention heads to multiple GraphSAGE experts. The transferred experts are frozen and used as complementary structural branches. The fused raw node features, GAT head representations, and GraphSAGE expert representations are fed into a multilayer perceptron (MLP), whose output is further fused with the pretrained GAT logits. Based on PreGS, we further develop PreGSv2, which introduces source-level weighting and a structural gating mechanism for adaptive multi-source feature integration. Experiments on eight public graph datasets show that PreGS and PreGSv2 achieve competitive performance against representative graph neural network baselines. Ablation, parameter-transfer, sensitivity, aggregator, visualization, and training-time analyses further validate the effectiveness and stability of the proposed framework. The code and datasets are available at https://github.com/LH-Czc/PreGS.

Graph Neural Networks (GNNs) achieve state-of-the-art performance on graph-structured data, but training and inference on large graphs are often bottlenecked by memory constraints and sparse linear-algebra workloads. Quantum computing offers an alternative set of primitives that may improve scalability for graph learning. Building on the quantum graph neural network (QGNN) framework of Liao \textit{et al.}, this work implements two representative architectures --- the Simplified Graph Convolution (SGC) and Linear Graph Convolution (LGC) models --- and evaluates them on open benchmark graph datasets and semi-supervised learning tasks using quantum simulation. We compare predictive performance and optimization behavior against classical baselines, showing that the quantum models achieve competitive performance with fewer parameters. Finally, we present a cost gradient analysis that identifies the tasks for which the models showcased are trainable. This is followed by a classical simulability study to find regimes in which the proposed circuits remain robust during training.

Logic resynthesis preserves circuit functionality while changing gate vocabulary, topology, and structural statistics, creating domain shift for circuit graph neural networks (GNNs) without changing task labels. To study this setting, we introduce ReDIL-GNN, a resynthesis domain-incremental learning framework that adapts a fixed prediction or representation head as new synthesis styles arrive and evaluates retention on all previously observed domains. Because not every shift should be adapted blindly, ReDIL-GNN further introduces the Resynthesis Adaptability Index (RAI), a pre-adaptation score that combines adaptation need, source-equivalence recoverability, structural coverage, and update compatibility. We evaluate supervised hardware-security tasks and representation-learning models using task-native metrics for classifiers and source-equivalence retrieval metrics for embedding models, comparing naive fine-tuning with LwF, Online EWC, MAS, ER, A-GEM, DER++, ER+LwF, and equivalence-guided replay. Across the studied pipelines, RAI separates unsupported shifts from promising updates, ranging from 0.001 for a structurally uncovered GNN-RE ABC-rewrite shift to 0.824 for the best original-only GNN-RE adaptation case. In practice, ReDIL-GNN turns resynthesis-aware circuit learning into a deployment control loop: RAI screens each new synthesis flow before update, guiding whether to reuse the current model, apply retention-aware adaptation, or defer adaptation until the shift is better supported.

Graph neural networks are widely used for transductive node classification, with accuracy typically measured on randomly drawn train/validation/test splits. Reported accuracy has been shown to shift substantially across different random splits of the same dataset, making published comparisons between architectures unreliable. The classical remedy in non-graph settings is stratified $k$-fold cross-validation, which ensures each test fold reflects the full class distribution of the dataset. We argue that class stratification alone is insufficient for graphs: nodes are not isolated but connected, and folds that differ in their distribution of local neighbourhood homophily expose the model to systematically different relational conditions that directly affect message-passing behaviour. The resulting cross-fold variation reflects the homophily composition of each split, inflating reported variance beyond what model behaviour alone would produce. To address this, we propose \hp{}, a topology-aware stratification procedure that treats node homophily as the primary stratification axis, aligning folds with respect to local relational consistency alongside the class marginal that standard stratification already controls. Stratifying on homophily alone does not guarantee class balance, so \hp{} incorporates class label as a secondary axis, preserving class representativeness as a natural consequence of the procedure. We evaluate \hp{} on a broad benchmark suite comprising 15 node-classification datasets spanning the full homophily spectrum and 7 GNN architectures. \hp{} achieves a mean stability rank of 1.49 compared to 2.31 for random $k$-fold, achieving the lowest mean stability rank on 13 of 15 datasets while preserving class balance close to class-stratified splits and substantially better than random. We argue that homophily-aware split construction merits broader adoption for GNN evaluation.

Calculating disequilibrium chemistry in exoplanet atmospheres remains a significant computational bottleneck in atmospheric retrievals. The increasing observational precision from facilities such as JWST and the Ariel mission requires including disequilibrium chemistry in these analyses. Previous studies have demonstrated that neural networks can emulate kinetic chemistry, although their spatial inductive bias does not align with the topology of chemical reaction networks. This study introduces a graph neural network surrogate that represents chemical species as nodes and temperature-dependent reaction rates as edges, thereby enabling information propagation along physically meaningful chemical pathways. The model is trained on atmospheres generated using the Venot+2020 chemical scheme and Guillot temperature-pressure profiles. The GNN accurately reconstructs disequilibrium abundances across the sampled parameter space and reduces the mean abundance error by a factor of approximately 3 compared to the previous U-Net model. When applied to transmission spectra, most predictions fall within the observational precision expected for JWST and Ariel, with only about 7% of test atmospheres exceeding a 20 ppm mean spectral error. Performance variations are primarily observed in chemically transitional regimes near a carbon-to-oxygen ratio of one and at low temperatures. An evaluation of the boundary-case planet WASP-39b demonstrates effective performance under a moderate domain shift. Perturbation analysis indicates that disturbances propagate along chemical connectivity rather than spatial adjacency, confirming that the architecture captures the structure of reaction networks. These results suggest that GNN surrogates provide accurate, computationally efficient predictions of disequilibrium chemistry, facilitating integration into the atmospheric retrieval pipeline.

Message-passing Graph Neural Networks (GNNs) iteratively propagate and aggregate local neighborhood information followed by global readout to learn graph representations. However, their discriminative power is upper-bounded by the Weisfeiler--Lehman (1-WL) graph isomorphism test. This prevents GNNs from distinguishing certain non-isomorphic graphs with identical local neighborhood structures, often leading to similar graph representations. Unified Topological Signatures (UTS) capture compact, multi-scale representation of global graph topology derived from persistent homology. We introduce two complementary UTS signatures: Graph_UTS- a static signature of the input graph topology, and Embedding_UTS- a dynamic signature of the evolving embedding topology. They encode structural information inaccessible to 1-WL-based message-passing GNNs, yet their capabilities are explored solely for post-hoc embedding-space analysis. We integrate UTS into GNN training across three architectural interventions: (i) UTS-Aug: augmenting with standard readout feature that encodes graph's true topology; (ii) UTS-Reg: topological regularizer that constrains representation collapse; (iii) UTS-Pool: topology-guided pooling that retains structurally critical nodes. We further leverage UTS as a layer-wise diagnostic to quantify oversmoothing during GNN training. Theoretically, we show that integrating UTS into GNN optimization strictly extends GNN expressivity beyond the 1-WL hierarchy. Experiments on three graph classification benchmarks show consistent benefits: Graph-UTS, Dual-UTS, and UTS-Pool improve accuracy across all three datasets, Embedding-UTS provides smaller but similarly consistent gains, and UTS-Reg's benefit varies across graph domains. Accuracy improves by up to 5.8% with Graph-UTS augmentation, by up to 1.9% with UTS-Reg, and achieves comparable performance to TOGL with UTS-Pool.

Federated learning lets multiple participants train a shared model without pooling raw data, by exchanging locally trained model updates instead. Federated averaging assumes that averaging local models is a reasonable way to solve one shared problem when participants' data are broadly similar. Work on non-IID federated learning has shown that this assumption can withstand differences in label and feature distributions. We ask whether it survives a different strain specific to graph neural networks, where client graphs differ not in label or feature distribution but in structure itself, requiring the same shared weights to operate over fundamentally different topologies. We call the resulting harm structural negative transfer. In a federation of real citation networks and synthetic structural proxies, a structurally atypical client lost more than half its achievable accuracy simply by joining. In an initial six-client federation, two label-free structural statistics computable before training were strongly associated with this harm. Expanding to twenty clients showed that degree divergence remained associated with harm, although more weakly, and survived removal of domain contrast. Spectral divergence did not replicate, which we trace to a confound caused by the composition of the reference pool used for leave-one-out statistics. A causal intervention isolating topology found no significant effect. A degree-normalization mechanism held across twenty-four seeds but did not explain the harm when corrected. The best of five candidate fixes beat a tuned baseline only until a matched, structurally blind control was applied, after which the gain disappeared. What survives is a modest, partially replicated, degree-specific signal that is not yet a validated predictor at scale.

Power Flow (PF), Optimal Power Flow (OPF), and State Estimation (SE) are fundamental problems in power system analysis, but solving them is computationally expensive. Graph Neural Networks (GNNs) have been proposed as fast surrogates, yet existing solvers are trained for a single problem at a time, producing narrow models that must be rebuilt for each new task. We propose a more general approach: a single Heterogeneous Residual Gated Graph Convolutional Network that solves all three problems with one shared backbone. Rather than learning one mapping, the model learns a reusable representation of how the network behaves, from which PF, OPF, and SE can each be estimated. Trained jointly on the three problems across diverse topologies and loading conditions, and evaluated on the IEEE 14-bus and 118-bus systems, the shared model matches the accuracy of task-specific GNN solvers and stays robust on unseen loading levels and topologies. These results show that a single model can capture the basic operation of a power network and serve several analysis tasks at once, a first step toward a foundation model for power systems.

Accurate cell detection and classification are crucial for pathological analysis, directly affecting diagnostic accuracy and treatment planning. To capture complex cellular interactions beyond visual appearance within the tumor microenvironment, several approaches have employed graph neural networks to model spatial and relational patterns among cell nuclei, yielding promising results. However, these methods typically adopt a two-stage paradigm of visual extraction followed by relational modeling, which necessitates separate tuning for each stage, thereby increasing pipeline complexity and hindering end-to-end joint optimization. In this paper, we propose an end-to-end framework for cell detection and classification that jointly models patch-level visual representations and instance-level interactions, which incorporates a dynamic graph construction module and an instance-aware graph network. Specifically, the graph construction module dynamically builds the graph structure using learnable queries derived from patch-level features as cell instance representations, with adjacency defined by integrating feature similarity and spatial distances. The instance-aware graph network performs adaptive instance filtering and feature reorganization, aggregating them over the cell graph into a topological latent state for a selective state-space transition driven by visual cues, fusing appearance and relational evidence. When evaluated on multiple datasets with different staining protocols for cell and nucleus detection, our method significantly outperforms existing approaches in both detection and classification performance. The code will be released at https://github.com/RuochenLiu23/IGM.

Dynamic-vision-sensor (DVS) cameras generate events on a per-pixel basis with a $μ$s-level temporal resolution, calling for new algorithm-hardware co-design approaches compared to standard frame-based vision. While event-driven graph neural networks (EV-GNNs) emerge as a promising algorithmic solution, they raise new HW challenges by mixing dense-regular compute operations and sparse-irregular memory accesses. We present ETHEREAL, the first EV-GNN accelerator that scales to 640$\times$480 resolutions, thanks to a neighbor-parallel spline convolution engine and a 2D/3D-split memory hierarchy with a novel region-of-interest spatiotemporal caching mechanism. Measurement results demonstrate end-to-end inference with 25.6$μ$s latency and 1.7$μ$J energy per event on state-of-the-art workloads

Recently, researchers have proposed a graph pooling operation, akin to the pooling process in conventional convolutional neural networks (CNN), aimed at reducing the computation cost of Graph convolutional neural networks (GCNNs). While most GCNN-based methods treat graph pooling as a node clustering problem and propose learning a cluster assignment matrix, existing clustering-based pooling methods tend to focus solely on the rough topology information of graphs, neglecting the exploitation of higher-order mutual connections among neighbors. In terms of message passing on graph, the ease of information passing on edges reflects the closeness between neighboring nodes, which significantly relies on the interconnectivity among neighbors. In this study, we address this gap by considering such local connection information and introducing a novel graph pooling method named RicciPool. We introduce discrete graph curvature, particularly Ollivier-Ricci curvature, as a measure of higher-order connectivity around an edge. Subsequently, we construct an Ollivier-Ricci flow formula to reweigh edge weights, leveraging the crucial information provided by Ricci curvature, particularly vital for extracting clusters in graphs. Building upon this foundation, we utilize the spectral clustering technique to learn a new cluster assignment matrix. Experimental results on multiple bioinformatics protein datasets and social networks underscore the effectiveness of our proposed method.

Graph Neural Networks (GNNs) are powerful models for handling attributed graphs in tasks such as classification, link prediction, and community detection, as they enable the aggregation of information from both structural and semantic sources. However, progress in community detection is hindered by the lack of high-quality datasets, since ground-truth community labels are often unavailable and most algorithms proposed in recent literature rely on the same benchmark datasets for model training and evaluation. To address this issue, attributed random graph generators are commonly employed to create synthetic graphs for assessing the strengths and limitations of GNN-based models. Nevertheless, most existing generators rely heavily on power-law degree distributions, despite recent evidence indicating that scale-free networks are rare, particularly in social network contexts. Moreover, state-of-the-art attributed graph generators provide limited flexibility, as they do not allow users to construct communities with varying densities, degree distributions, and sub-community structures. To overcome these limitations, we introduce the Synthetic Community-Aware Attributed Graph Generator (SynCo), a graph generation algorithm that allows users to control the node degree distribution and sub-community structure. We evaluate SynCo across three different tasks: graph mimicking, hyperparameter evaluation, and node clustering tuning. The results show that our model outperforms state-of-the-art approaches in synthetic graph generation and data augmentation, while preserving the original distributions of duplicated and augmented datasets, as confirmed by statistical tests well know in literature. We also demonstrate the ability of SynCo to generate nodes in large scale, up to 2.1 million nodes.

This feature article provides an overview of the theoretical foundations for coVariance neural networks (VNNs), i.e., graph neural networks (GNNs) operating on covariance matrices as graphs. Covariance matrices are ubiquitous across domains, and hence, the deployment of GNNs often leverages graphs of pairwise statistical dependencies. Existing theoretical contributions on GNNs consider abstract graph representations and cannot accommodate the data-driven nuances associated with covariance matrices. This tutorial brings into focus various novel theoretical insights via mathematical analyses of VNNs that have broad signal processing implications, including: (i) a conceptual equivalence between VNNs and principal component analysis (PCA)-based information processing; (ii) refined stability bounds on predictive outcomes in the presence of finite sample-induced covariance matrix perturbations; and (iii) refined characterization of transferability of VNNs across multiscale datasets. The theoretical insights discussed herein provide the underlying principles and justification towards adopting VNNs over workhorse PCA-based learning pipelines, in applications where covariance matrices are useful descriptors of data structure. We also convey how impact of these foundational advances permeates to \textit{principled} designs and applications of learning methods across broad domains where covariance matrices emerge. Notably, we elucidate the conceptual insights facilitated by VNNs to the specific task of characterizing brain age gap for neurodegenerative conditions using neuroimaging datasets, a timely problem in computational neuroscience. Broader impacts to other application domains are discussed as well.

High Performance Computing-Quantum Computing (HPCQC) platforms expose multiple Quantum Processing Units (QPUs) that may differ in size, topology, native gates, and noise characteristics. For current noisy devices, errors compound along the compiled circuits quickly, and minimizing them, that is, maximizing the circuits' execution fidelity, is essential for reliable results. Fidelity depends on the compilation to a specific target device: the same high-level circuit may produce different executables and, therefore, different expected fidelities across QPUs. We present a low-overhead fidelity-aware scheduling framework for multi-QPU systems based on a Graph Neural Network (GNN) that estimates, before compilation, the expected fidelity of each circuit on each available QPU. Then, a tunable scheduler uses these estimates to control the trade-off between execution fidelity and parallelism. Results show that this framework allows for approximating an exhaustive fidelity-based assignment, saving computational resources compared to a brute-force approach that compiles each circuit on every device.

Malocclusion skeletal grading is a fundamental task in orthodontics, critical for diagnosis and treatment planning. Traditionally, cone-beam computed tomography (CBCT) is used for visual measurement, and the reconstructed lateral cephalograms are handed over to expert dentists for diagnosis. However, manual review is time-consuming, labor-intensive, and subject to inter-operator variability. Therefore, an automatic CBCT-based system is needed for reliable malocclusion skeletal grading. In this case, we develop TeethGNN, a novel graph-based framework designed to combine CBCT image features with morphological information for accurate and efficient malocclusion grading. TeethGNN utilizes a decoupled learnable decoder to directly predict key morphological indicators from CBCT images, eliminating the need for manual measurements. These morphological features are then fused with image features using a graph neural network (GNN), which effectively models the relationships between the modalities. To further enhance robustness and calibration, we introduce a collaborative calibration strategy. This strategy combines multi-scale graph adversarial perturbation for explicit calibration and nonlinear topological graph calibration for implicit confidence adjustment. Extensive experiments and ablation studies on our collected clinical dataset demonstrate that our malocclusion measurement system achieves 77.08% in accuracy and 89.61% in AUC, outperforming the compared state-of-the-art methods. These results validate the effectiveness of graph-based multimodal fusion and collaborative calibration in improving malocclusion grading performance. Our system shows strong potential for advancing computer-aided orthodontic diagnosis, providing an accurate and reliable solution for vision-based clinical measurement and diagnosis.

6G wireless technology is poised to adopt higher and wider frequency bands, leveraging highly directional beamforming. However, the vast bandwidths amplify the impact of beam squinting. Traditional solutions, such as adding a true-time-delay filter to each antenna, are cost-prohibitive due to the required hardware scale. This paper proposes a signal processing alternative using Graph Neural Networks (GNNs) to optimize hybrid beamforming in multicarrier wideband systems. Using a bipartite graph to represent a shared analog beamformer among multiple subcarriers, we develop three GNN structures with distinct digital beamformer representations (i) at the subcarrier nodes, (ii) at the edges, or (iii) integrating traditional singular-value decomposition solutions. By designing an efficient message-passing mechanism, these structures offer insights into the impact of different GNN designs on communication system performance and computational complexity. Extensive analysis and ablation studies show that our proposed GNN structures outperform traditional optimization methods and existing ML-based solutions. Furthermore, the proposed GNNs exhibit strong resiliency to beam squinting and better robustness against imperfect CSI than even fully digital beamforming and all existing hybrid designs. These GNNs can also be extended to multi-user scenarios and demonstrate excellent generalization capabilities, allowing trained models to adapt to diverse multicarrier and multi-user settings without retraining.

Graph Neural Networks (GNNs) have achieved remarkable success across diverse applications, yet they remain highly vulnerable to adversarial attacks that maliciously perturb graph structure. Existing defenses often lack rigorous theoretical grounding, rely on attack-specific heuristics, or require costly retraining procedures such as adversarial training. To address these limitations, we propose Kernel-Complexity Edge Sanitization (KCES), a training-free and model-agnostic framework for defending against structural attacks. KCES is built upon Graph Kernel Complexity (GKC), a principled metric derived from the graph Gram matrix that appears in a generalization upper bound on the GNN test error. From this bound, we define an edge-specific KC score that quantifies each edge's structural influence via its induced change in GKC. KCES then identifies and prunes high-KC edges, which are empirically enriched with adversarial perturbations under structural attacks, to mitigate their harmful impact. Computationally efficient and scalable, KCES operates as a lightweight preprocessing step without retraining and can be seamlessly integrated with existing defenses. Extensive experiments demonstrate that KCES consistently outperforms representative robust baselines across diverse attack settings and scales effectively to large graphs. Supported by theoretical analysis and extensive empirical validation, KCES provides a principled and efficient framework for securing GNNs. Our code is available at https://github.com/karpning/KCScore.

Camera pose estimation is a key step in 3D reconstruction and view-synthesis pipelines. We present a deep, global Structure-from-Motion framework based on learned view-graph aggregation. Our method employs a permutation-equivariant, edge-conditioned graph neural network that takes noisy pairwise relative poses as input and outputs globally consistent camera extrinsics. The network is trained without ground-truth supervision, relying solely on a relative-pose consistency objective. This is followed by 3D point triangulation and robust bundle adjustment. Our approach is efficient, scalable to more than a thousand images, and robust to graph density. We evaluate our method on MegaDepth, 1DSfM, Strecha, and BlendedMVS. These experiments demonstrate that our method achieves superior rotation and translation accuracy compared to deep track-centric methods while registering more images across many scenes, and competitive results compared to state-of-the-art classical pipelines, while being much faster.

We present a method for recovering the moral graph of a causal DAG from a probability distribution over discrete variables, using fully connected tensor networks (FCTNs) with nuclear-norm-regularized bond corrections. Each bond matrix is parameterized as a baseline all-ones matrix plus a low-rank correction $C_{ij} = U_{ij}V_{ij}^\top$, and the nuclear norm of the correction implemented via the variational Frobenius norm penalty on the factors drives unnecessary bonds to zero. We prove that under faithfulness, positivity, and a no-implicit-rerouting assumption on the local tensor architecture, \textbf{every} optimal FCTN with zero reconstruction error $\varepsilon = 0$ has effective graph exactly equal to the moral graph. For the approximate regime ($\varepsilon > 0$), we provide explicit recovery bounds using the Fannes-Audenaert continuity of conditional mutual information, and derive a sufficient condition on the regularization parameter $β$. The effective graph is read directly from the optimized bond matrices.

Standard open-set node classification methods rely on the homophily assumption, where connected nodes share labels. However, real-world graphs are often heterophilic, exposing the limitations of current methods and posing new challenges to open-set node classification. On the one hand, cross-class connectivity causes representations from different known or unknown classes to become intertwined after aggregation, undermining their discriminative capacity. On the other hand, structural mixture invalidates threshold-based open-set methods and cross-class feature interpolation, leading to unreliable unknown-class rejection. To address these challenges, we propose HOPE, a Heterophily-aware Open-set node classification method with Pseudo-Extrapolation. To adapt open-set graph neural networks (GNNs) to heterophilic scenarios, HOPE uses a structure-augmented feature initialization layer to capture multi-hop structural patterns. Meanwhile, we design a trustworthy neighborhood aggregation mechanism for standard GNNs to dynamically filter noisy cross-class neighbors. To enhance unknown-class rejection, we introduce a heterophily-guided pseudo-extrapolation strategy. It dynamically maintains known-class centers and extrapolates along cross-class neighborhood displacement directions, synthesizing pseudo-unknown proxies near structurally ambiguous regions. Finally, we optimize the network with joint classification and logit margin regularization, routing synthetic proxies into a dedicated rejection slot without imposing geometric margin constraints in the representation space. Extensive experiments on multiple datasets show that HOPE consistently outperforms state-of-the-art models, validating its effectiveness, robustness, and efficiency.

Graph modeling, a crucial task for representing complex relationships in graph-structured data, has achieved significant success in recent years. However, current graph modeling methods rely on traditional Graph Neural Networks and pre-training approaches to implicitly learn the underlying relational structure of graph data. Thus, these prior methods cannot capture the complex graph structure and correlations among inputs. In this paper, we introduce a novel Attention-based Normalizing Flow-based Approach\footnote{Our implementation and models will be released publicly for research reproducibility.} (ANFA or $α$) that provides an explicit, interpretable, and tractable Graph Modeling ($α$-Graph). In particular, we propose a new Unconditional Graph Normalizing Flow with an Invertible Attention Mechanism to capture the complex relational structure of graph data. To further enhance the expressiveness of the model, we introduce Conditional Graph Normalizing Flow with Learnable Queries that enables efficient modeling of correlations in graph-structured data. We show that our Conditional Graph Normalizing Flows behave similarly to Unconditional Graph Normalizing Flows, enhancing expressiveness while maintaining training stability and efficiency. Our experimental results on three benchmarks will illustrate the effectiveness and the state-of-the-art (SoTA) performance of the proposed $α$-Graph method.

We study the use of graph neural networks (GNNs) for finding approximate ground states of Ising models. Efficiently finding these ground states is of broad significance because many combinatorial optimization problems can be formulated as an Ising model with the appropriate choice of couplings and fields. Exactly solving these problems is hard but there are many good heuristic methods. A lineage of these heuristics build from mean-field approximations: one approach uses the leading eigenvector of an appropriately defined matrix, another is the min-sum algorithm, also known as the energetic cavity method. Without modification, GNNs perform worse than both of these methods. We consider small modifications to the GNN to incorporate these heuristics and find that this considerably improves performance. While the modified approach is competitive against other deep-learning approaches, we still find that simulated annealing is reliably at least as good as deep learning methods for the same computational cost.

As integrated circuit technology scales into the nanometer regime, the traditional disconnect between logic synthesis and physical design has led to significant PPA (Power, Performance, and Area) degradation and prolonged design closure cycles. Traditional logic synthesis relies on non-physical Wire Load Models (WLMs), while recent spectral-based placement predictors often neglect the inherent hierarchical logic depth and signal flow of netlists, which leads to low-fidelity spatial estimations. To bridge this gap, we propose LevelSyn, a novel physical-aware logic synthesis framework that integrates hierarchical representation learning with a wirelength-driven optimization engine. At its core, LevelSyn leverages a level-asynchronous Graph Neural Network (GNN) to predict high-fidelity gate coordinates by capturing the structural and directional semantics of And-Inverter Graphs (AIGs). To handle industrial-scale designs, a level-aligned subgraph partitioning strategy is introduced to eliminate memory bottlenecks while preserving local logical dependencies. These spatial insights are seamlessly integrated into a newly developed physical-informed synthesis engine within the Berkeley ABC framework. Experimental results on the EPFL benchmark suite demonstrate that LevelSyn significantly outperforms state-of-the-art (SOTA) methods, achieving an average power reduction of 6.89% and a timing delay improvement of 27.48%. Furthermore, post-place-and-route validation shows a 99.59% reduction in design rule check (DRC) violations, highlighting its effectiveness in accelerating design convergence.

Learning-based schedulers have been proposed to provide real-time user, target, and access point (AP) association in distributed cell-free integrated sensing and communication systems. In a typical approach, a graph neural network (GNN), trained on labels from a mixed-integer linear program, maps lightweight per-AP statistics to decisions on AP clustering, user and target scheduling, and mode selection in one forward pass. Such solutions assume that hard constraints, enforced only as soft training penalties, hold at inference, and that the self-reported statistics are truthful. Using our ASSENT algorithm as an example, we find that despite high $F_1$ scores, many solutions violate at least one hard constraint, demonstrating that high prediction accuracy does not ensure joint feasibility. Projecting the GNN output onto a feasible solution restores constraint satisfaction with low utility loss, even with a simple greedy repair procedure. We further show that feasibility alone does not guarantee robustness to false data injection attacks. A single malicious AP that reports false information cannot substantially increase its user associations, but can greatly increase the rate of infeasible solutions. The effect of such attacks depends on the type of information being falsified. Misreporting information that affects the objective can largely be mitigated through feasibility projection, whereas falsifying information that affects the constraints cannot. The latter can, however, be detected using a low-complexity cross-AP consistency check. These results show that learned ISAC schedulers should be evaluated using constraint-aware feasibility metrics in addition to conventional accuracy measures.

Graph neural networks (GNNs) are a class of neural networks suitable for learning on graph-structured data. Their application to spatial data is a natural extension, however its relatively unclear which message-passing operations, architectural configurations, and graph representation is best suited for classifying changes to objects in electronic navigational charts (ENCs)--geospatial vector datasets used for marine navigation. Maintaining these datasets is a challenge, and categorizing changes to objects in the ENC based on their significance to navigational safety is of particular importance. Here, we propose to represent these vector navigation datasets as a graph structure where the spatial objects serve as nodes and their spatial and semantic relationships form edges. We encode both the old ENC dataset and new ENC dataset into a pair of graphs and frame the task as a graph-pair classification problem. Building on this representation, we investigate the use of GNN architectures to classify whether the encoded graphs constitutes a critical or non-critical risk to navigational safety. We train and evaluate several GNN architectures and model configurations on ENC changes reviewed by maritime experts. Our results demonstrate that graph-based representations improve the classification of ENC updates, providing a scalable approach for automating or improving ENC maintenance workflows.

Scientific knowledge graphs organize entities and relations extracted from scientific literature, but they remain inherently incomplete. Missing typed links in such graphs can therefore represent plausible scientific hypotheses, such as unexplored associations between materials and applications. However, scientific hypothesis discovery is challenging because true discoveries are extremely sparse among typed candidate pairs: graph neural networks (GNNs) are efficient but unreliable for ambiguous cases, while large language models (LLMs) are knowledgeable but too costly to apply exhaustively and are not naturally grounded in graph structures. We propose HyGRAIL, a cost-aware and evidence-grounded framework that combines heterogeneous GNN triage with LLM-based hypothesis review. HyGRAIL first uses a GNN to score candidate hypotheses and identify a validation-calibrated ambiguous region, routing only graph-uncertain cases to LLM review. For each routed hypothesis, HyGRAIL retrieves node-level associations and multi-hop relational paths from the knowledge graph (KG), then converts this structured evidence into natural language through template-based or LLM-based naturalization. An LLM review agent finally judges each hard hypothesis using the naturalized evidence and validation-selected decision criteria. On MatKG, HyGRAIL achieves the best F1 score of 0.429, improving over the strongest prior baseline by 0.242 F1 points and over the GNN-only baseline by 0.322. Meanwhile, GNN triage reduces the LLM call rate by 54.36% on average. Ablation studies further show that retrieved graph evidence is crucial for reliable hypothesis verification and that compact, two-sided evidence is more effective than simply increasing retrieval quantity.

Bitcoin's pseudonymous nature makes it challenging to analyze user-level activity, since a single user may control multiple identifiers (addresses). Existing heuristic-based methods attempt to identify addresses belonging to the same user, but they often produce flat cluster assignments with limited modularity and are prone to errors such as merging different users together. In this work, we propose a method for refining heuristic-obtained clusters by grounding our clustering on contrastive embeddings yielded by graph neural networks. Our contributions are threefold: (i) we release a publicly available dataset of Bitcoin transaction graphs containing a substantial number of clusters; (ii) we propose a methodology for learning address embeddings consistent with heuristics, and back it up with theoretical guiding intuitions; (iii) through hierarchical clustering, we enable a finer analysis of heuristic clusters and provide a quantitative criterion for flagging suspicious merges.

Graph neural networks (GNN) based on message passing are provably no more powerful than the one-dimensional Weisfeiler--Leman colour-refinement test (1-WL): two graphs it cannot tell apart receive identical representations, however deep or wide the network. A common remedy augments node or edge features with precomputed structural descriptors, most often counts of a fixed small subgraph such as triangles or longer cycles, but such counts require committing in advance to the size of the substructure counted, a choice usually made blind to the data. We study a descriptor that avoids this choice. The edge-girth of an edge is the length of a shortest cycle through it, and its multiplicity is the number of such shortest cycles; together they form a per-edge invariant that reports cycles of arbitrary length, computable exactly by a single breadth-first search per edge. Injected into a gated message-passing architecture, EGAGNN, it reaches a test MAE a factor three below the closest gated comparator on the ZINC-12k regression benchmark at 104k parameters; against bounded cycle-counting descriptors under the same architecture, it matches only a dictionary counting cycles up to length eight, using twice as many channels, while a dictionary capped at length four performs no better than no structural information at all. On graph discrimination we prove a matching limitation: on graphs where every edge sees the same number of shortest cycles of the same length, the descriptor becomes constant and any model built on it collapses back to the 1-WL bound. This holds without exception across all 400 pairs of the BREC benchmark: not one of the 90 such pairs is distinguished.

Optimizing absorption, distribution, metabolism, and excretion (ADME) is an important part of small molecule drug discovery. Many machine learning models have been built to predict ADME properties to facilitate this optimization process, but explaining model predictions is challenging. We propose a new graph neural network architecture with built-in meaningful per-atom attributions. Our model MolLedger outputs predictions that are the sum of per-atom scores. MolLedger's additive framework obtains exact interpretability at no cost to performance because the global context vector gives the additive head enough context to produce good per-atom scores. Furthermore, MolLedger produces attributions that are more faithful to chemical properties than other interpretability methods because the auxiliary loss in MolLedger anchors the atom scores to chemical properties. Our case studies comparing interpretations from multiple methods on molecular pairs reveal that MolLedger is much better at producing sensible explanations for predicted property changes.

Beamforming methods in millimeter-wave (mmWave) cell-free massive multiple-input multiple-output (CFmMIMO) systems require accurate channel state information (CSI), whose acquisition entails significant training overhead. This paper shows that fully digital cell-free mmWave beamforming can be effectively learned from sub-6 GHz CSI using a graph neural network (GNN). Specifically, we represent a CFmMIMO system as a wireless graph, and the GNN is trained to approximate beamformers that maximize the downlink sum-rate based on the available sub-6 GHz CSI. A message-passing mechanism is proposed to capture inter-user interference and inter-base-station cooperation across different network topologies. Simulation results demonstrate that the proposed sub-6 GHz-assisted GNN-based beamformer achieves competitive and often superior sum-rate performance compared to classical baselines that rely on full mmWave CSI.

Existing GNN quantization methods suffer from considerable quantization overhead, which severely limits their practical usage in real-world scenarios. To this end, we present TopGQ, an accurate post-training GNN quantization framework, alleviating redundant quantization overhead. We propose dual-axis scale absorption, which enables activation quantization along both the outer and inner dimensions by merging one into the adjacency matrix. On top of that, we introduce TopPIN, a proxy for nodes' local structure, and use it to group nodes with similar topology during quantization. Experimental results show that TopGQ reduces quantization time by an order of magnitude while preserving accuracy.

Graph positional encodings are widely used in graph neural networks and graph Transformers, yet it remains unclear when the code itself can identify nodes. We study a hybrid distance-spectral encoding that combines anchor-distance profiles with quantized low-frequency Laplacian-energy coordinates. Treating the encoding as an observation map yields a simplex-refined converse, an exact collision factorization $κ_H=κ_Dκ_{S|D}$, and the collision information $I_H=-\logκ_D-\logκ_{S|D}$. On random regular graphs, the criterion is made explicit through a bounded-correlation Gaussian-wave surrogate; for actual Laplacian-energy coordinates, we give the distance-conditioned spectral collision condition sufficient for conditional actual-coordinate achievability. Experiments show that $I_H/\log n$ calibrates localization success, and PE-only structural task probes on Universal Dependencies trees show that hybrid encodings better recover syntactic-tree geometry than distance-only or spectral-only baselines.

Bilevel mixed-integer linear optimization problems model hierarchical decision processes in which a leader anticipates the optimal response of a follower. Although expressive, these problems are computationally challenging because lower-level optimality is embedded in the leader's feasible region. Value-function reformulations replace the nested follower optimization with a constraint involving the follower's optimal value, but evaluating this value function exactly can itself be expensive. This paper introduces Graph4BiLO, a graph neural network (GNN) approach for learning bilevel value functions from variable--constraint graph representations. In contrast to fixed-length multilayer perceptron (MLP) representations, the GNN uses shared message-passing parameters and can therefore be applied across multiple problem sizes with a single trained model. The learned ReLU network is encoded exactly as mixed-integer linear constraints and embedded in an approximate single-level formulation. A repair step subsequently re-solves the follower problem for the selected leader decision to recover a bilevel-feasible follower response. We evaluate Graph4BiLO on knapsack interdiction instances with 20--100 items against the exact MibS solver and the learning-based Neur2BiLO method. Graph4BiLO obtains objective values comparable to Neur2BiLO across all tested sizes while avoiding size-specific neural networks. An additional out-of-distribution experiment demonstrates zero-shot transfer from 20-item training instances to previously unseen 40- and 60-item instances. However, embedding message passing at every graph node substantially increases the resulting mixed-integer formulation size and solve time. These results identify a central tradeoff between size-generalizable graph representations and the computational cost of embedding GNNs within optimization models.

Accurate traffic flow prediction is fundamental to intelligent transportation systems, playing a pivotal role in urban mobility optimization and smart city development. While Graph Neural Networks (GNNs) integrated with time series forecasting have emerged as promising solutions, two critical limitations persist: (1) the quadratic complexity of attention-based architectures hinders real-time deployment in large-scale networks, and (2) high-frequency noise in sensor data significantly degrades prediction reliability. These challenges are particularly acute in metropolitan scenarios where both computational efficiency and noise robustness are paramount. To address these limitations, we introduce \textbf{ButterMamba}, a novel and efficient framework based on State Space Models (SSMs). ButterMamba consists of two key components: (1) a Butterworth Spectral Filtering module that preprocesses the data by removing high-frequency noise, allowing the model to focus on significant underlying trends, and (2) a Spatial-Temporal State Mixer that uses a parallel Mamba architecture to efficiently capture both long-range temporal dependencies and complex spatial correlations across the road network. By decoupling noise filtering from spatial-temporal modeling, ButterMamba achieves superior predictive accuracy with linear computational complexity. Extensive experiments on three public datasets demonstrate that ButterMamba not only outperforms existing state-of-the-art models in terms of prediction accuracy but also considerably reduces training time and memory usage.

Protein structure modeling rests on a single computational primitive: the interaction between what a residue is (sequence content) and where it sits (three-dimensional geometry). What is the expressive limit of this layer class? We show that the complete bilinear operator over content-geometry outer products--the sufficient statistic of all second-order interactions--is the expressive ceiling, while the additive message passing of mainstream geometric GNNs is provably blind to content-geometry binding. We then introduce Hyper-Fold, a rank-K separable convolutional backbone approaching this ceiling at message-passing cost: each radius neighborhood is organized into a sequence hyperedge and a contact hyperedge, modulated by an edge-conditioned matrix-valued operator factorized into K learned basis operators with geometry-generated coefficients. Across enzyme function prediction, fold classification, and ligand binding site detection, Hyper-Fold and its hierarchical variant Hyper-Fold-Deep achieve the best results among protein-specific structure encoders; Hyper-Fold-Pocket, an anchored set-prediction head, surpasses UniSite-3D on UniSite-DS and two zero-shot benchmarks with no sequence language model features, 68x fewer parameters, and 4.8x lower latency--suggesting that a sufficiently expressive 3D backbone recovers information that fusion architectures previously borrowed from evolution-scale pretraining.

RNA-Protein Interactions (RPIs) are critical for regulating cellular functions. While traditional wet-lab experiments for RPI detection are costly and time-consuming, Deep Learning (DL) methods provide an efficient computational alternative for RPI Prediction (RPIP). In particular, Graph Neural Networks (GNNs) are promising, as they naturally model RPI networks. However, existing GNN-based methods often rely on homogeneous graphs or predefined meta-paths, which limit their ability to handle data sparsity and to generalize to cold-start scenarios involving unknown molecules. To address these limitations, we propose Edge Generation-guided Relation-aware Learning (EGRL), a novel framework with several key components: implicit meta-path learning to capture relational semantics without handcrafted paths; a multi-relation-aware attention mechanism for adaptive fusion of interaction patterns; a graph generator that predicts potential ("soft") edges to support cold-start nodes; and a multi-feature fusion predictor for final interaction scoring. EGRL is jointly trained with a primary task loss and an auxiliary generator loss. Comprehensive evaluations on four benchmark datasets demonstrate that EGRL achieves competitive overall performance. More importantly, it exhibits superior generalization in cold-start settings, achieving an Area Under the Receiver Operating Characteristic curve (AUROC) of 0.867 and an Area Under the Precision-Recall curve (AUPR) of 0.861 on unknown molecules, corresponding to improvements of 8.6% in AUROC and 5.0% in AUPR over prior state-of-the-art methods. The code will be released soon.

Deep graph neural networks(GNNs) suffer from oversmoothing- a progressive collapse of node representation towards a low information subspace as network depth increases because the normalized graph propagation operator is repeatedly applied directly to the hidden representations. In this work we study Householder Graph Neural Network (HouseGNN). Rather than updating the hidden state like standard GCN, HouseGNN uses the aggregated neighbourhood message solely to estimate a reflection direction; the node embedding is then updated by a Householder reflector followed by GroupSort, yielding a piecewise orthogonal layer that preserves Euclidean norm at every node and at every depth. We prove three core properties: (i) every internal layer preserves the node-wise Euclidean norm; (ii) the Householder reflector is scale scale and sign-invariant in the message; and (iii) pairwise distance between nodes can change through mismatch between node-wise orthogonal operators.

Graph Neural Networks (GNNs) achieve strong predictive performance on graph-structured data across domains such as chemistry, biology, and network analysis, yet they provide no intrinsic explanation of their predictions. This limits their adoption in high-stakes and safety-critical settings. Counterfactual explanations address this by revealing the minimal structural modifications that would change a model's prediction. On graphs, however, such a modification is hard to produce. The search space is discrete and combinatorial, and a valid answer must respect categorical node and edge types together with domain rules such as chemical valency in the case of molecular graphs. Existing explainers give up one of two things. Either edits are not held on the data manifold, or the search does not span the full edit space. We propose Graph Diffusion Counterfactual Explanation via Inversion (GDCE-I), which gives up neither. A discrete denoising diffusion model with a novel discrete inversion scheme enables distribution-aware edits leveraging the whole domain edit space. We further address the incomplete and inconsistent evaluation of graph counterfactuals by deriving a framework of explanation desiderata and applying it to every method under one shared protocol. Across four benchmarks, GDCE-I outperforms related work by a large margin on the defined framework. For the molecular domain, we further qualitatively show that GDCE-I attains interpretable in-distribution solutions.

Graph Neural Networks (GNNs) serve as the backbone for high-stakes applications in Machine-Learning-as-a-Service (MLaaS). Still, their black-box deployment exposes them to Model Extraction (ME) attacks, in which adversaries steal intellectual property by querying APIs. Existing defenses suffer from a critical ''Euclidean bias'': they transfer image-based strategies (e.g., random noise) to graphs, ignoring the complex topological dependencies between nodes, which often results in severe utility degradation. Passive methods like watermarking also fail to prevent theft in real time. To bridge this gap, we propose GraphRP (Graph Reprogramming Protection), a proactive defense framework that repurposes Model Reprogramming for security. Unlike static perturbations, GraphRP introduces a Structure-Aware Gating Mechanism driven by learnable topological prototypes. This creates a dynamic ''structural firewall'' that selectively modulates the model's decision boundary: it preserves fidelity for benign queries residing on the training manifold, while maximizing the Fisher Information along the perturbation direction for adversarial queries. Under standard assumptions (bounded loss, optimal attacker, and local second-order approximation), we prove a lower bound on the attacker's estimation error that increases with the structural sensitivity of the reprogramming noise. Extensive experiments on both hard-label and soft-label ME attacks demonstrate that GraphRP significantly degrades attack effectiveness while preserving benign utility.

Deep learning systems perform mainly within the 2D for a single image domain and take the face as a single-dimension representation, losing sight of the 3D anatomy of sheep and cross-landmark spatial relationships that are intrinsic to the clinically proven Sheep Pain Facial Expression Scale (SPFES). This paper presents the \textbf{3D Sheep Pain Facial Expression System (3D-SPFES)}, a novel, monocular depth-aware geometric graph neural network system that integrates each SPFES facial landmark, such as the ears, eyes, and nose, into 3D Euclidean space estimated from a single RGB camera by using VideoDepthAnything, thus preventing the need for specialized depth hardware. Each landmark node includes a feature vector containing its 3D spatial coordinates, estimated surface normal, and facial attribute class embedding. Edges linked to nodes are assigned weights based on an aggregate metric that combines both Euclidean distance and surface co-planarity in a 3D space. A Weighted Geometric Graph Neural Network (WG-GNN) studies this graph using $\mathcal{K} = 3$ geometry-aware message-passing layers enhanced by a scaled dot-product attention method that selectively enhances anatomically relevant inter-landmark messages. The resultant node embeddings are combined into $\mathcal{O} = 3$ pain-level clusters and integrated into a Normalized Pain Score (NPS) within the range of $[0, 100$ a confidence-weighted, SPFES-derived scoring method.

Graph Neural Networks (GNNs) suffer from two fundamental limitations: over-smoothing, where node representations become indistinguishable with depth, and over-squashing, where long-range information is compressed through limited message-passing channels. Existing metrics such as Dirichlet energy provide global characterizations of over-smoothing but lack the resolution to analyze node-level behavior and guide architectural improvements. In this paper, we propose LEED (Local Embedding Evolution Distance), a novel local metric that quantifies over-smoothing by tracking the evolution of individual node embeddings across layers. By operating at the node level, LEED enables fine-grained analysis of representation dynamics during training, revealing heterogeneous over-smoothing patterns that are invisible to global energy-based measures. This locality induces informative node importance scores, interpreted as embedding-driven centrality measures. We leverage LEED to design a more efficient strategy for virtual node selection. Unlike existing approaches that depend on multiple heuristic centrality measures, our method uses LEED as a unique criterion to guide the construction of Local Virtual Nodes to mitigate over-squashing. Experiments show that LEED provides more informative diagnostics than Dirichlet energy while preserving global evaluation, and enables more effective virtual node integration, improving GNN performance across datasets.

Industrial processes are complex systems composed of multiple interacting sensors that generate multivariate time series (MTS). Detecting anomalies in such systems is critical for reliability and safety, yet understanding their origin is equally important. Existing Graph Neural Network (GNN)based methods for anomaly detection primarily focus on sensor-level deviations and either attribute anomalies directly to the deviating sensors. When diagnosis is attempted, generally, the most deviated sensor is identified as a root cause of a system fault. However, in many industrial systems, anomalies do not arise from faulty sensors but from disruptions in the influences governing the system dynamics. We propose an explainable GNN-based anomaly detection framework that shifts the perspective from sensor-level anomalies to component-level diagnosis, hypothesizing that anomalous measurements are symptoms of altered inter-sensor influences. Experiments show that the method effectively identifies and prioritizes the true faulty components, providing interpretable insights into system failures.

A central obstacle in building graph foundation models is the input heterogeneity in terms of feature space dimensionality, semantics, and structure. Such heterogeneity limits the capability of graph neural networks to generalize to new graphs with unseen feature spaces. We address the transferability challenge with SIGIL, a framework that maps any attributed graph to a unified representation space of fixed dimension. Given a graph, SIGIL lifts it to a structural interaction graph, where nodes are the input feature dimensions and weighted, typed edges encode feature alignment across multiple orders of the graph's connectivity. A relational message-passing network embeds each feature dimension into a shared space, transforming the original node features, of arbitrary dimensionality, into representations transferable to any downstream graph. By construction, SIGIL is equivariant to permutations of nodes, feature dimensions, and labels. Additionally, when the input features are one-hot indicators of discrete relations, SIGIL recovers and strictly generalizes existing foundation models for knowledge graph reasoning. A single SIGIL model, pretrained on one graph, delivers strong fully-inductive link prediction. Also, SIGIL can be used to implement existing knowledge graph foundation models. As such, SIGIL unifies several existing regimes in graph foundation model design under a single framework

Circuit localization is a mechanistic interpretability task whose goal is to identify a sparse subgraph of a transformer's computation graph sufficient to reproduce a particular behavior. Most established methods localize circuits independently for each model--task pair. We instead frame circuit localization as a graph machine learning problem in which the edges of a computation graph represent computational pathways, and graph neural networks (GNNs) model interactions among these pathways. We introduce Graph Circuit Learning (GCL), a supervised, amortized framework that trains a GNN across multiple model--task pairs and applies it to unseen cases. To provide sufficient data, we augment the InterpBench benchmark with additional cases derived from the TracrBench programs. Of the 14 evaluated GCL configurations, the highest scored a median edge AUROC of $0.902$ (interquartile interval $[0.861, 0.942]$) on the 16 original held-out InterpBench cases. This is close to the published InterpBench median of $0.910$ for EAP-IG while remaining below ACDC's $0.959$. Removing all message-passing edges reduces the median to $0.825$. We also adapt PGExplainer, a GNN explainability method, to circuit localization, obtaining a median edge AUROC of $0.858$ on the same cases. These preliminary results suggest that graph machine learning offers a natural and potentially powerful perspective on circuit localization, and we hope this perspective encourages closer exchange between the two communities.

Graph Neural Networks (GNNs) are widely used across domains such as natural sciences, social network analysis, chip design, and recommendation systems. However, as graph sizes grow, storing and processing them entirely on a single-node CPU-GPU system becomes increasingly impractical. A promising approach is to distribute the graph across multiple remote memory nodes, though this introduces a major bottleneck: inter-node network congestion during training. To address this, we propose LGNNIC, a novel inter-node system architecture that leverages SmartNICs co-located with remote memory nodes-a configuration already available in modern systems-to reduce communication overhead in distributed GNN training. LGNNIC offloads key preprocessing tasks to SmartNICs, reducing the volume of data transferred to computational (training) nodes and alleviating network congestion. We introduce two complementary techniques executed on the SmartNICs during the preprocessing phase: Neighbor Sampling, which performs mini-batch sampling, and Quantization of the sampled batches. To evaluate LGNNIC under different communication infrastructures, we designed both an optimized low-overhead DMA-based synchronization mechanism and a high-overhead socket-based alternative used as a benchmark. We evaluate the core SmartNIC offloading mechanisms across standard GNN workloads and sampling hyperparameters using a proof-of-concept (PoC) system comprising one remote-memory node with an NVIDIA BlueField-2 SmartNIC and one compute node with an A100 GPU. Both Neighbor Sampling and Quantization on the remote node demonstrated substantial training speedups in most configurations. Neighbor Sampling achieved up to 62.4x and 17.5x speedups with Sockets and DOCA-DMA, respectively, primarily due to reduced data transaction time. Quantization provided additional speedups of up to 3.6x and 1.3x, respectively, by reducing data transfer.

Modeling multivariate time series by representing them as graphs, where individual series act as nodes and pairwise temporal corre- lations serve as edges, has gained significant traction. Recent advances in Graph Neural Networks (GNNs) have demonstrated strong perfor- mance by assuming a static graph topology and aggregating information from neighboring series. In this work, we investigate the representa- tional power of GNNs for forecasting under both static and dynamic settings (i.e., when pairwise correlations evolve drastically over time) and identify critical limitations in current architectures. To formalize this, we first propose Temporal Correlation Volatility (TCV), a model- agnostic metric designed to quantify the distributional evolution of these latent structures. We establish a clear connection between TCV and performance degradation, demonstrating that many popular models, including Transformers, generalize poorly in high-TCV settings and are often outperformed by simple structure-agnostic baselines. To address these limitations, we propose Graph Layer for Inference in Dynamic En- vironments (GLIDE), a novel GNN layer enhanced by two theoretically grounded design mechanisms: (D1) Path-based Message Passing, which captures path-based neighborhoods and (D2) Static and Dynamic Propagation Separation, which identifies optimal dynamics via local static approximation. These components significantly improve learning under dynamic topology while preserving robustness in static scenarios. Ex- tensive experiments on synthetic and real-world benchmarks show that GLIDE improves average performance by up to 45.6% across static and dynamic settings, with the largest gain reaching 85.7%. The source code is available at https://github.com/ChenS676/GLIDE.

Cognitive distortion detection is a key task in computational mental health, yet existing approaches often overlook the psychological structure of distorted thoughts. We propose MTI-GNN (Multi-Perspective Triad Interaction Graph Neural Network), which models Beck's cognitive triad---negative views of the self, world, and future---as complementary perspectives for classification. An LLM decomposes each utterance into the three perspectives, from which perspective-specific similarity graphs are constructed and encoded by a Multi-Perspective GNN. A Triad Interaction module models cross-perspective dependencies through sequential source-conditioned updates and feature-wise gating, while Prototype-Guided Perspective Fusion performs label-conditioned aggregation. Label-expanded supervision incorporates all available distortion annotations during training. We evaluate MTI-GNN on 9,764 samples from four Korean, English, and Chinese datasets spanning ten distortion categories. MTI-GNN significantly outperforms all supervised variants and exceeds eight prompted generative models under zero-shot and few-shot settings. Leave-one-perspective-out ablations show that all three perspectives contribute significantly, while human expert evaluation provides preliminary evidence of their alignment with the intended cognitive dimensions.

Full-graph GNN training delivers high accuracy but scales poorly on multi-server clusters due to heavy, irregular inter-node embedding exchanges. We present SNI-GNN, a SmartNIC-assisted full-graph training system that reduces communication while preserving accuracy by predicting remote embeddings in-network. SNI-GNN deploys a lightweight linear-trend predictor on SmartNICs to refine cached historical embeddings, coupled with an importance-based boundary-node sampling policy and an asynchronous DPU--GPU data pipeline with intermediate-result reuse. We provide error and convergence bounds showing that predictor bias remains controlled under bounded second-order dynamics and yields standard non-convex convergence with inexact gradients. Implemented on NVIDIA BlueField-3, SNI-GNN integrates with state-of-the-art full-graph systems, cuts communication by 21--45%, achieves 1.3--3.6$\times$ end-to-end speedups over BNS-GCN and up to 1.29$\times$ over baseline SANCUS, with accuracy loss $\leq 0.01$, and scales efficiently to 16 GPUs on graphs with up to tens of millions of edges. These results indicate SmartNIC-based in-network prediction is a practical complement to partitioning and compression techniques for communication-efficient full-graph GNN training at scale.

The quantitative analysis of 3D neuronal morphologies requires capturing both graph topology and spatial geometry. Current message-passing Graph Neural Networks (GNNs) are bounded by the 1-Weisfeiler-Lehman (1-WL) test, limiting their ability to capture cycles induced by spatial proximities. To address this, we propose a training-free geometric prior based on tropical algebraic geometry. We apply the recently established tropical Abel-Jacobi transform and polarization distances to machine learning on tree-structured data. We introduce a structural transformation pipeline, comprising cycle space augmentation and quotient space construction, to convert spatial trees into cyclic metric graphs suitable for embedding into the Tropical Jacobian. Computing exact tropical polarization distances requires solving the NP-Hard Closest Vector Problem (CVP) on integer lattices. Instead of relying on explicit approximations with quantization errors (e.g., Babai's rounding), we adopt a continuous relaxation on the universal cover of the Albanese torus. We show that the discrete Arakelov-Green measure, computed in closed form via the graph Laplacian's generalized inverse, decomposes exactly into the intrinsic path metric minus the unquantized polarization distance on this cover, avoiding integer lattice searches. This metric yields two descriptors: eigenvectors provide node-level structural coordinates, and the permutation-invariant eigenvalue spectrum provides a graph-level signature. On the BREC benchmark, the eigenvector formulation demonstrates expressivity beyond the 1-WL limit. On 3D morphology datasets (ACT-4, JML-4, BIL-6), the spectrum seamlessly integrates into standard architectures (VAEs, GNNs, Tree-LSTMs) without additional trainable parameters, outperforming explicit lattice approximations and improving classification accuracy over existing spatial models.

Blood-brain barrier permeability (BBBP) prediction is a critical screening task in central nervous system drug discovery, where candidate molecules must be assessed for whether they can cross, or should be prevented from crossing, the blood-brain barrier. However, this task remains challenging because of limited, class-imbalanced datasets and sensitivity to molecular structure. Recent advances in deep learning have established graph neural networks (GNNs) as a powerful approach for molecular representation learning, while pre-trained molecular GNNs provide transferable knowledge for downstream tasks. However, full fine-tuning is often parameter-inefficient and prone to overfitting, whereas existing parameter-efficient fine-tuning (PEFT) methods mainly adapt node features or the two-dimensional covalent graph, limiting their ability to capture three-dimensional geometry and second-order interactions. To address these limitations, we propose BBBP-GeoPEFT, a geometry-informed PEFT framework for pre-trained molecular GNNs. BBBP-GeoPEFT constructs distance-based graphs at multiple cutoffs and their corresponding line graphs from molecular conformers to capture spatial atom and second-order edge interactions. Lightweight auxiliary geometric graph encoders generate cutoff-specific representations, which are incorporated into each pre-trained layer through node-wise cutoff attention and gated residual connections. This design preserves pre-trained knowledge while incorporating permeability-relevant geometric information with a small trainable-parameter budget. Experiments on a curated BBBP dataset show that BBBP-GeoPEFT achieves competitive performance compared with full fine-tuning and representative PEFT baselines. Under both random and scaffold splitting, BBBP-GeoPEFT achieves competitive or improved ROC-AUC and accuracy in most experiments while updating only 10.1% of the model parameters.

Language models (LMs) offer strong textual representations for electronic health records (EHRs), but they encode patient sequences in isolation and provide limited explainability. Graph neural networks (GNNs) complement LMs by incorporating inter-patient relationships and enabling reference-patient attribution, yet they rely on high-quality patient representations. We propose Patients-like-me (PLM), a unified LM--GNN framework that integrates local patient semantics with global cohort structure. To train PLM efficiently, we introduce a Variational Expectation-Maximization algorithm that alternates LM and GNN updates under a supervised variational objective. Extensive experiments on MIMIC-III and MIMIC-IV show that PLM consistently outperforms state-of-the-art methods, with improvements generalizing across encoder-only and decoder-only LM backbones. These gains are achieved with only modest additional computational overhead. PLM also provides reference-patient explanations by retrieving influential similar patients, while edge-masking experiments confirm that the highest-ranked references have the greatest impact on model predictions.

This work focuses on the problem of learning on temporal graphs, with particular emphasis on the task of clustering: obtaining coarse-grained representations by aggregating information from nodes, edges, and temporal dynamics - a task related to pooling in machine learning on graphs, or community detection in network science. Although graph neural networks reach state-of-the-art performance across many downstream graph tasks, their advantage over established descriptive and inferential clustering algorithms is far less settled, especially under demands of efficiency and recovery accuracy. We frame this tension through three linked perspectives: principles, connecting graph learning and community detection through shared spectral foundations and detectability thresholds in stochastic block model regimes; primitives, making spectral clustering and multislice modularity optimization tractable through GPU-accelerated temporal backends; and pooling, viewing principled community detection as a theory-grounded coarse-graining operator for temporal graphs. Our results indicate that algorithmic methods remain the appropriate tool where attributes are absent or weak - scalability rather than accuracy being the binding obstacle - while neural models are most compelling when structural, temporal, and attribute signals align. By making temporal clustering scalable, GPU-accelerated primitives suggest a route toward theory-grounded pooling, while raising a central question: when does community-based coarse-graining preserve the dynamics needed for downstream learning tasks?

Sheaf Neural Networks (SNNs) generalize message passing by replacing scalar edge weights of standard Graph Neural Networks (GNNs) with learnable, edge-dependent restriction maps between node stalks. Despite their strong theoretical foundations and promising transductive results, SNNs have been evaluated almost exclusively on transductive node classification, leaving their behaviour under inductive protocols unknown. We address this gap through the first systematic benchmark of the sheaf design space, evaluating three diffusion mechanisms (neural sheaf diffusion, sheaf attention, and sheaf attention with Graph Attention Network v2), three restriction-map parameterizations, three stalk dimensions, and six modern GNN architectural components, within a message-passing reformulation that never assembles the heavy sheaf Laplacian, making the full design space trainable under cross-graph batching. Across $1{,}890$ controlled experiments on 14 inductive datasets, multiple insights emerge: restriction maps are the dominant design choice and general maps are preferable, larger stalks add capacity but not long-range reach, architectural components explain more performance variation than the entire sheaf-specific design space itself. Under a matched protocol, SNNs transfer to inductive settings but do not reach the strongest baselines, with gaps being dataset-dependent. Practically, a single sheaf configuration can generalize across datasets, so effort is better spent tuning the surrounding architectural recipe than the sheaf operator itself.

Content-based detection of unreliable news is increasingly difficult, as low-reliability sources mimic credible journalism and generative AI makes fabricated content harder to flag. We ask whether network structure can improve news reliability classification, taking a domain-level approach that shifts the focus from individual articles to source reliability. From URL-sharing patterns in Telegram chats, we build a statistically validated domain co-sharing network and find assortative mixing by reliability: low-reliability domains group together, as do reliable ones. Exploiting this structure, we compare Graph Neural Networks against network-unaware baselines using both content-aware features (multilingual text embeddings) and content-agnostic features (spreading dynamics). GNNs consistently outperform Multi-Layer Perceptrons on identical features, with GraphSAGE best in both settings (accuracy 0.63 with content, 0.53 without), a 13-14% relative gain over the network-unaware baseline. Network topology thus systematically improves domain reliability assessment, and remains effective even when content analysis is infeasible.

Credit risk detection, particularly mitigating individual fraud, is crucial for maintaining the stability of digital financial ecosystems. Accurately identifying credit fraud among billions of users is critical for minimizing financial losses and safeguarding the sustainability of inclusive financial services. Given that credit fraud risks are often concealed within heterogeneous user-risk graphs, Graph Neural Networks (GNNs) have emerged as an effective tool for risk mining by capturing complex dependencies. To address the scalability bottleneck of industrial GNNs, distributed training based on subgraphs is indispensable. However, existing strategies often compromise topological integrity for load balancing. This can be catastrophic for risk detection, as it indiscriminately severs the long-tail evidence chains essential for risk propagation. Overlapping subgraphs can restore severed risk contexts but inevitably introduce redundancy and noise, while overlooking the representation alignment across different local subgraphs. In this paper, we propose a risk-aware overlapping subgraph learning framework for large-scale credit risk detection. We first construct base partitions to ensure load balance. Then, we perform budget-constrained sampling that selects informative long-tail nodes, thereby preserving critical risk diffusion patterns while filtering out noise. To mitigate representation inconsistency, we design a cross-subgraph consistency alignment mechanism. By enforcing alignment constraints on the overlapping nodes, we harmonize the local representations into a globally consistent latent space. Extensive experiments on Weixin Pay's production dataset demonstrate that our model significantly outperforms existing strategies for risk detection, offering a scalable and effective solution for industrial graph learning.

Training Graph Neural Networks on large graphs is challenged by the memory cost of storing all node representations across layers. We show that several existing scalable approaches can be written as structured modifications of the GNN propagation matrix, providing a unified perspective that exposes their respective limitations. In particular, graph coarsening replaces it by a low-rank approximation that enables spectral guarantees but assigns uniform representations to clustered nodes, while Cluster-GCN restricts the propagation matrix to intra-cluster connections that allow efficient batching but sever long-range information. These are complementary failures of the \emph{same} decomposition of the graph into groups of nodes. To obtain the best of both worlds, we propose \textbf{CoRe-GNN}, which performs both propagations in parallel at each layer: a coarsened inter-cluster term capturing long-range structure, and a local intra-cluster term preserving per-node discriminability. We prove that CoRe-GNN inherits analogous approximation guarantees to those of graph coarsening, and introduce a natural cluster-based \emph{batching scheme} that scales to graphs with millions of nodes. On node classification benchmarks spanning homophilic, heterophilic, large-scale, and long-range graphs, CoRe-GNN outperforms both graph coarsening and Cluster-GCN baselines. Notably, CoRe-GNN reaches competitive accuracy on \emph{long-range} tasks, while remaining memory-efficient through batching.

Topological neural networks (TNNs) enable leveraging high-order structures on graphs (e.g., cycles and cliques) to boost the expressive power of message-passing neural networks. In turn, however, these structures are typically identified a priori through an unsupervised graph lifting operation. Notwithstanding, this choice is crucial and may have a drastic impact on a TNN's performance on downstream tasks. To circumvent this issue, we propose $\partial$lift (DiffLift), a general framework for learning graph liftings to hypergraphs and cellular- and simplicial complexes in an end-to-end fashion. In particular, our approach leverages learned vertex-level latent representations to identify and parameterize distributions over candidate higher-order cells for inclusion. This results in a scalable model which can be readily integrated into any TNN. Our experiments show that $\partial$lift outperforms existing lifting methods on multiple benchmarks for graph and node classification across different TNN architectures. Notably, our approach leads to gains of up to 45% over static liftings, including both connectivity- and feature-based ones.

Kinematic models provide reliable motion constraints for odometry estimation in featureless environments, where exteroceptive sensing degrades and IMU integration drifts. Learning-based kinematic models can achieve more accurate odometry estimation than model-based methods by capturing nonlinear effects; however, most existing learning-based models are trained on a single embodiment and generalize poorly to new embodiments. This generalization is difficult because the meanings and structures of proprioceptive measurements vary across embodiments, including the number of joints and ground-contact elements (e.g., wheels, feet). To address this challenge, we propose KING, a Graph Neural Network (GNN)-based kinematic model that explicitly incorporates robot embodiments by representing them as a common graph. We show that wheel and leg kinematic models can be expressed by a unified representation, enabling a single model for both wheeled and legged robots. Trained on datasets spanning diverse embodiments, KING provides a unified representation of wheeled and legged kinematics and achieves high-accuracy odometry estimation in real environments. KING estimates accurate odometry using only an embodiment description (e.g., a URDF file) and on-board proprioception (encoders and an IMU) and can be adapted to new robot embodiments through few-shot learning with only one minute of data, avoiding retraining from scratch on a new dataset for each robot. The project page is available at: https://smrg-aist.github.io/king_project_page/

While signed-directed graphs have been studied using linear Laplacians in the design of graph neural networks, relatively little research has focused on developing non-linear Laplacian operators for such networks. We introduce a non-linear Laplacian operator specific to signed and directed networks (NLSD). This non-linear operator extends the concepts of the signed Laplacian for signed graphs and the Laplacian for directed graphs. The NLSD calculates node-specific potentials based on features More precisely, if the potential discrepancy is not aligned with the edge direction, we ignore it (and vice versa) leveraging message-passing techniques only across edges where potential discrepancies align with the edge's direction. Utilizing this novel operator, we propose an efficient spectral GNN framework (NLSD-GNN). We conducted comprehensive evaluations focusing on node classification and link prediction, examining scenarios involving signed, directional, or both types of information. Our findings reveal that this spectral GNN framework not only integrates signed and directional data effectively but also achieves superior performance across diverse datasets.

High-entropy perovskite oxides (HEPOs) represent a chemically complex class of materials with promising functional properties, yet their vast compositional space and, chemical/structural disorder pose significant challenge for accurate property prediction. Graph neural networks (GNNs) enable rapid exploration of materials space but are often limited by the availability of representative training data. Here, we investigate ordered-to-disordered transfer learning using GNNs for formation-energy and HOMO-LUMO gap prediction in HEPOs by transferring knowledge learned from chemically ordered perovskites. Four representative GNN models, including CGCNN, GATGNN, ALIGNN and M3GNet are evaluated to understand the role of structural representations, spanning pairwise two-body and angular three-body interactions in transfer performance. We find strong property-dependent transfer behavior: formation-energy prediction transfers effectively to disordered HEPOs, whereas HOMO-LUMO gap prediction shows limited transferability due to its sensitivity to local chemical environments. Incorporating a small HEPO-specific training dataset substantially improves HOMO-LUMO gap prediction. Representation-level analysis using UMAP further highlights the importance of encoding three-body geometric information such as in ALIGNN for capturing complex structure-property relationships and improving transferability.