Graph Neural Networks

Accurate fault location is critical for distribution network reliability. However, increasing distributed energy resource (DER) penetration complicates fault location due to intermittent generation and bidirectional power flows that reshape fault signatures. Spatio-Temporal Graph Neural Networks (STGNNs) have shown promise by jointly modeling spatial and temporal dependencies, but their behavior under increasing DER penetration has not been studied rigorously. In this paper, we (i) systematically benchmark spatio-temporal graph attention network (STGATv2) against purely temporal (gated recurrent unit, GRU), purely spatial (GATv2) and traditional machine learning baselines, and (ii) evaluate how well models generalize across increasing DER penetration levels (10%, 25%, 50%) on a reconfigured IEEE 123-bus feeder with multiple DER injection points and moderate-to-high impedance faults. Results show that STGATv2 consistently outperforms neural baselines, achieving 92-94% macro F1 in-distribution. Notably, generalization across penetration levels is asymmetric: training at 50% penetration retains near in-distribution F1 score at lower levels, whereas training at 10% degrades considerably at 50% - with STGATv2 retaining 81-84% F1 under these drastic shifts, substantially higher than GATv2 and GRU which drop to 69-74% F1 and 73-75% F1 respectively. Under realistic measurement noise, STGATv2 maintains > 85% F1, while GRU drops as low as 33.5% F1, highlighting the critical role of topological awareness for robust fault location in active distribution networks.

Dynamic matching markets require decisions about whom to match and when: matching now yields value but removes participants who may create better future opportunities. We develop a value-based reinforcement-learning framework for this problem on finite, evolving weighted graphs. We study an infinite-horizon continuous-time model with stochastic arrivals, node-type transitions, edge realizations, and exogenous exits. We prove an event-time reduction: without loss of optimality, the planner acts immediately after each exogenous event and then waits for the next one. We further show that the optimal edge-wise $Q$-function is characterized by a single continuation-value function on post-decision residual graphs, reducing the learned object from state-action values to graph values. Exact action selection still requires combinatorial matching optimization; we approximate the value with a graph neural network, train it by temporal-difference learning, and use it in a forward-greedy matching heuristic. In a binary-type benchmark, the learned policy substantially outperforms immediate and threshold-greedy rules by preserving common nodes for rare arrivals of valuable matches while forming lower-value matches only in thick pools. In a kidney paired donation benchmark, it performs similarly to immediate greedy when exits are unpredictable, recovers the logic of patient matching when warnings are reliable, and outperforms the better of Immediate Greedy and Patient Greedy across intermediate warning probabilities. These results show that residual-graph value learning yields state-dependent dynamic matching policies that adapt to realized connectivity and exit information.

Metallic magnets exhibit complex spin dynamics governed by electronically generated interactions. Predictive simulations of such dynamics typically require repeated solutions of an underlying electronic problem throughout the time evolution, creating a major computational bottleneck. Here we introduce a graph neural network (GNN) magnetic force-field framework that learns the effective magnetic energy functional governing itinerant spin dynamics directly from electronic calculations. Conceptually analogous to machine-learned interatomic potentials, the proposed framework enables efficient evaluation of spin torques while capturing the nonlinear and spatially extended interactions generated by itinerant electrons. We benchmark the method on representative metallic magnetic systems exhibiting collinear, noncollinear, and noncoplanar magnetic order. The learned force fields accurately reproduce electronically generated spin torques and yield nonequilibrium spin dynamics in excellent agreement with direct electronic simulations. Our results establish graph neural networks as a powerful framework for machine-learned magnetic force fields, providing a pathway toward predictive large-scale simulations of nonequilibrium magnetism across multiple length and time scales.

Many real-world graphs support multiple predictive tasks over the same underlying structure, creating an opportunity to reuse supervision across node classification (NC) and link prediction (LP). However, existing evaluations often rely on incompatible splits, observed-graph assumptions, and negative sampling rules, making conclusions about same-graph cross-task transfer unreliable. We formalize same-graph NC-LP transfer and propose a leakage-free protocol that fixes node and edge splits, uses a shared message-passing graph that excludes evaluated edges, and employs fixed negatives for LP. Across three backbones (GCN, GraphSAGE, GPS), we find that transfer is strongly directional and predictable: NC $\to$ LP is consistently beneficial on homophilic graphs, while LP $\to$ NC is fragile and can even degrade accuracy under naive representation reuse. LP $\to$ NC becomes reliably positive mainly in a structure-dominant regime where LP is easy but NC is unsaturated, suggesting that LP acts as structural pretraining. Finally, we introduce the CoTask Score (CTS) to summarize joint NC+LP utility when a shared encoder must serve both tasks, and show that simple dataset statistics, especially homophily, can guide mechanism choice and help avoid negative transfer.

Solving large, sparse linear systems is a core task in scientific computing, and efficient iterative solvers rely critically on effective and robust preconditioning. While classical methods such as algebraic multigrid (AMG) are highly scalable, their robustness can degrade on indefinite or nonsymmetric systems where heuristics originally developed for elliptic PDEs are less reliable. Recently, Graph Neural Networks (GNNs) have emerged as data-driven preconditioners; yet, the practical impact of imposing an AMG-style hierarchy remains underexplored for general sparse matrices. In this work, we propose a Graph Neural Multilevel Preconditioner (GMP) that adopts an AMG hierarchy as a structural prior and learns smoothing, restriction, and interpolation operators in a unified framework. Our method targets general sparse systems and is instantiated as a drop-in preconditioner for standard Krylov solvers. On a benchmark of over 800 sparse matrices, we compare against classical AMG, single-level ILUT, and state-of-the-art GNN preconditioners, and characterize the regimes where multilevel graph neural preconditioning improves convergence or, conversely, introduces overhead relative to strong single-level baselines. These results highlight both the promise and the limitations of enforcing AMG-style multilevel structure in learned preconditioners for large-scale scientific simulations.

Query optimization of Basic Graph Patterns (BGP) SPARQL queries over Knowledge Graphs (KG) requires accurate cardinality estimation. Recently published learned estimators outperform statistics- and sampling-based approaches, but share a limitation preventing their adoption in real-world triplestores: they are transductive and require retraining when the underlying graph changes or when applied to new graphs. We present FICE (Fully Inductive Cardinality Estimation), the first learned cardinality estimator for BGP queries over KGs that generalizes to entirely unseen graphs (including unseen relations), without any retraining. FICE is a graph neural network (GNN) with two coupled components. First, an encoder GNN over a factor-graph view of the KG produces entity and relation embeddings. We prove that BGP cardinality is a local function of the 2-hop neighborhood around bound terms in this view, motivating the local message-passing encoder. A decoder GNN then composes these embeddings along the join topology of the query to predict log-cardinality. The encoder and decoder are trained jointly, making the embeddings specialized for cardinality estimation. FICE is trained using neighborhood sampling to scale to KGs with millions of triples, and decouples embedding generation from cardinality decoding to enable estimation latency below a millisecond. Compared to learned and non-learned baselines over 10 KGs, FICE reduces the overall median q-error from 13.54 (for the best competitor) to 5.34 and dominates all approaches in tail behavior.

Oversmoothing is a fundamental limitation of deep graph neural networks (GNNs), where repeated message passing causes node representations to become increasingly similar, eventually collapsing toward a low-dimensional subspace. This phenomenon limits the effective depth of message-passing architectures and motivates the search for mechanisms that preserve representation diversity. In this paper, we study a recurrent graph neural network in which independent Gaussian noise is injected after every propagation step and analyze the resulting architecture as a stochastic dynamical system. Under a standard global contraction assumption on the deterministic update, we prove that the hidden representations form a geometrically ergodic Markov chain admitting a unique invariant probability measure. Our main theoretical result establishes an explicit positive lower bound on the expected stationary Dirichlet energy, proportional to both the noise variance and the spectral gap of the underlying graph. Consequently, the stationary representations cannot collapse onto the constant manifold, providing a rigorous guarantee that asymptotic oversmoothing is prevented in the sense of non-vanishing Dirichlet energy. Our analysis reveals persistent stochastic perturbations as a fundamentally different mechanism for combating oversmoothing, complementing existing deterministic approaches based on residual connections, normalization, and graph rewiring. Finally, numerical experiments on both linear and nonlinear recurrent graph neural networks closely match the theoretical predictions, illustrating the emergence of a stationary distribution and the predicted dependence of the limiting Dirichlet energy on the noise intensity.

Graph neural networks (GNNs) can operate on large graphs but become infrastructure-sensitive at the scale of millions of nodes and typically require scalable training techniques for even larger graphs. This raises a central question: when can a model trained on a smaller, scaled-down replica of a graph be deployed on the full-resolution graph without retraining? We introduce a zero-shot transfer protocol in which a GNN is trained on a graph coarse-grained by geometric renormalization (GR), and the resulting weights are transferred directly to the original network. Across synthetic and real-world networks, training on GR scaled-down replicas preserves much of the original-scale predictive performance while significantly reducing training cost. We further find that learned representations and predictive trajectories remain aligned across scales. These findings suggest that structural similarity may be more important than network size in determining GNN transferability, opening a path toward scale-equivariant graph architectures.

Functional magnetic resonance imaging (fMRI) is a widely used technique for studying the brain. Recent methods that utilize graph neural networks (GNNs) for analysis of brain functional connectivity have shown great potential for the classification of brain disorders, such as Alzheimer's disease (AD). However, these methods often assume a preset number of functional modules across all subjects, which overlooks inter-subject variability. In addition, the discovered modules are rarely used to directly guide the learned connectivity patterns. Here, to address these issues, we propose a Meta Probabilistic Pooling GNN (MPP-GNN). We frame the model's task as a coupled, bilevel optimization that performs adaptive graph partitioning hierarchically to discover subject-specific modules and then uses the discovered brain modules as an explicit prior to guide edge refinement and representation learning. We validate MPP-GNN on two public datasets for AD classification, achieving the highest AUC in comparison to established baselines for both datasets. Furthermore, our analysis demonstrates that MPP-GNN shows significant alignment with the canonical functional-network organization defined by the Yeo brain atlas and reveals a network-level dedifferentiation pattern for AD.

The information flow in the graph neural networks (GNNs) is fundamentally constrained by over-squashing, where structural bottlenecks impede long range information propagation. Graph-rewiring methods, which modify graph topology, have been extensively used to alleviate this. However, existing approaches often introduce prohibitive structural and computational bottlenecks, fail to preserve the critical properties of original graphs, and increase the edge counts massively. We introduce a novel method Schreier-Coset Graph Rewiring , a group-theoretic rewiring method that augments the input graph with a Schreier-Coset graph derived from a special linear group. Our method provides theoretical guarantees, a graph that exhibits spectral gap and a bounded effective resistance, creating a low-resistance bypass for long-range communication. Empirical evaluations demonstrate that SCGR reduces effective resistance by 5-40% across various learning tasks, effectively mitigating connectivity bottlenecks while maintaining competitive accuracy.

We investigate message-passing graph neural networks with random node features. Random node features are known to enhance the expressiveness of graph neural networks (GNNs) both theoretically and empirically. Here, we establish a novel universality result focusing on permutation-equivariant neural networks (PENNs), a class of GNNs built from feedforward neural network components that subsumes many prominent GNN architectures. We show that PENNs, combined with partially random node features, can approximate arbitrarily well in probability any measurable permutation-invariant or permutation-equivariant function on directed graphs of fixed size with multidimensional node and edge features. For $k$-times continuously differentiable functions, $k\geq 2$, we also derive upper bounds on the approximation rates, relating the complexity of the feedforward components of a PENN in terms of layer depth and number of nonzero weights to the desired approximation accuracy.

Graph Neural Networks (GNN) facilitate effective prediction on graph data such as molecules, media networks and neural network blueprints. GNNs facilitate prediction through message passing techniques which define how information flows from a node to its neighbors. Due to the ubiquity of the graph data type, the development of newer and better GNNs has garnered much interest in the machine learning community. However, GNN evaluation and benchmarking is primarily driven by classification tasks. Thus, prospective GNN message passing layers are evaluated on their ability to outperform prior work in classification contexts. In contrast, GNNs are equally capable of performing scalar regression prediction, yet this class of problem is often overlooked when proposing new GNNs while the best classification GNNs are utilized in an a priori or off-the-shelf manner for regression problems. In response, this paper studies the efficacy of GNN layers in a slew of regression contexts from rank ordering, error minimization and insight extraction. Results show that deep convolutional GNNs, particularly GEN, are more effective at these tasks than attention-based GNNs, while other classical, theoretically-inspired GNNs remain competitive and efficient.

A gradient-based GNN explainer given a molecule with two chemically equivalent nitro groups assigns them attribution scores that are equal to the last bit. It cannot do otherwise: message passing is exactly permutation equivariant, so any automorphism of the input leaves every attribution invariant. Yet the standard report, the top-k edges, names one of the two, and which one is settled by the order of an array. We show this is a structural obstruction rather than an implementation slip. When no minimal valid explanation is fixed by the input's automorphism group, no rule can be single-valued, minimal and symmetry-respecting at once. For the exact-k reports used in practice we give a parameter-free criterion, mechanised in Lean 4 with no axiom dependencies, that decides from the graph alone whether every score-optimal report of that size must split an orbit. Across 21298 instance-budget decisions the criterion agrees with a mechanical model-equivalence check without exception, and no severing case we found admitted a neutral alternative. The obstruction is common. Nontrivial automorphisms occur in 93.4% of Mutagenicity, the dataset the seminal explainability papers use, so the measure-zero dismissal of symmetric inputs, sound on the continuous domains it was made for, collapses here. At the sparsity budget those papers report, 24.0% of molecules with two interchangeable nitro groups (6 of 25) surface exactly one of them, every one arbitrary under mechanical verification. A model's blindness also manufactures symmetry: every MUTAG molecule contains atoms chemistry separates and the network provably cannot, and a matched control shows the resolution is set by what the model reads rather than how it is parameterised. Reporting orbits removes the arbitrariness at 0.11 ms and 0.43 extra edges per graph.

The Word Problem has been a subject of intensive mathematical study for over a century, initially driving advances in combinatorial group theory and more recently emerging as a foundational hardness assumption in post-quantum cryptography (PQC). While generally undecidable, several families of infinite non-abelian groups exhibit solvable or algorithmically fast word problems, making them attractive platforms for cryptographic design. This paper introduces WPNet, a novel Graph Neural Network architecture capable of solving the Word Problem heuristically, which is demonstrated on the Baumslag-Solitar group $BS(1,2)$ and on an Artin group. By mapping unreduced words to dynamic graph structures, the model learns to cluster algebraically equivalent elements in a continuous embedding space, effectively identifying the geodesic representative of a word without executing discrete reduction steps. As an application, a model variant is developed that can predict the geodesic length of an unreduced word in both groups. To demonstrate the cryptographic severity of this structural leakage, WPNet is successfully deployed against the Wagner-Magyarik public-key cryptosystem.

Graph Neural Networks (GNNs) and Large Language Models (LLMs) have each advanced recommendation systems by modeling structural and semantic signals, respectively. However, integrating their complementary strengths remains challenging, particularly in sparse settings where maintaining semantic precision is critical. We propose TRWH (Text-driven Random Walk Heterogeneous Graph Neural Network), a novel framework that fuses LLM-generated textual profiles with heterogeneous graph structures through strategic random walk augmentation. TRWH consists of three core components: (1) Embedding Creation, which produces user and item representations using both Word2Vec and LLM-based profiling; (2) a Heterogeneous Graph Neural Network (HeteroGNN) that propagates information across multi-relational edges; and (3) Random Walk-based Path Construction, which enriches sparse graphs with second-order user-user and item-item links. Experiments on the Amazon-2023 Fashion (2M users, 825K items) and Beauty (631K users, 112K items) datasets demonstrate that TRWH achieves substantial performance gains over state-of-the-art methods, including 80.0% RMSE and 52.6% MAE reductions on Fashion, and 25.7% and 10.8% improvements on Beauty. Notably, while random walks improve performance with traditional embeddings, they can dilute the nuanced representations learned by LLMs, underscoring the importance of adaptive integration strategies.

Learned restriction maps in sheaf graph neural networks are often treated as proof that the model has discovered useful edge geometry. That conclusion does not follow from parameter movement or from a post-hoc ablation: both can show how one checkpoint is organized while leaving open whether learned transport still helps after the rest of the model adapts. We separate these claims with two estimands. Checkpoint reliance intervenes on the maps of a fixed predictor; protocol-relative replacement retrains matched families that remove map capacity, edge variation, or persistent edge assignment. A task-null theorem shows why the claims can diverge: labels identify only the transported classifier directions, leaving $d^2-d$ invisible degrees of freedom in every full $d\times d$ map. An exact frame model then gives the boundary at which reliance becomes unreplaced task value. Label-only training realizes the predicted separation, while audits of public NSD, DNSD, and Directed Sheaf Neural Network (DSNN) implementations recover both replaceable and unreplaced transport regimes on real graphs. All five DNSD benchmarks exhibit fixed-checkpoint reliance. After retraining, assignment-breaking or shared-map controls recover Full performance on four; Roman-Empire retains a $.0675$ advantage over continually resampled assignment and a $.0391$ advantage over a parameter-matched shared map across ten official splits. Thus, a learned map can govern a fitted computation without constituting indispensable edge geometry. Claims of learned transport should pair checkpoint interventions with matched retraining.

Conformal prediction (CP) provides distribution-free uncertainty quantification, and its extension to graphs is an active research direction. Diffused Adaptive Prediction Sets (DAPS) is a widely used graph-aware diffusion baseline, propagating Adaptive Prediction Sets (APS) non-conformity scores along edges with a uniform coefficient $λ$. We identify a fundamental shortcoming of this design: the uniform low-pass diffusion presupposes graph homophily and proves detrimental on heterophilic graphs, enlarging the mean prediction-set size by up to 10.6% relative to plain APS. To mitigate this, we propose HeAD-CP, a family of node-wise diffusion variants whose coefficients are determined by a label-free local-homophily estimate derived from the GNN softmax. Three variants, namely signed-$γ$, edge-compatibility, and a DAPS-baseline-with-correction, are most effective at extreme heterophily, intermediate heterophily, and moderate-to-high homophily, respectively, and all preserve the marginal coverage guarantee. On ten benchmarks, the HeAD-CP family stays at or below plain APS on every dataset, while DAPS exceeds APS on six. The post-hoc oracle over the family improves over DAPS on 8/10 datasets at $p<0.01$ (paired Wilcoxon), with the largest gains on heterophilic graphs (10.3% on Texas); on the two homophilic datasets where DAPS still wins (CiteSeer, PubMed), it retains a marginal advantage of at most 0.002, statistically insignificant on CiteSeer ($p=0.23$). Designing a calibrated label-free selector that approaches this oracle is the main outstanding empirical question.

Curvature notions on graphs, particularly Ollivier-Ricci and Forman, have emerged as powerful tools for addressing fundamental issues in Graph Neural Networks (GNNs) such as oversmoothing and oversquashing, but rely almost exclusively on local edge-level comparisons and therefore fail to certify how information actually propagates over long distances. We introduce Entropic Curvature, a global, transport-based curvature obtained by extending the Lott-Sturm-Villani framework to graphs through the displacement convexity of entropy along Wasserstein geodesics. We define a tractable Weak Entropic Curvature proxy that lower-bounds the global entropic curvature, and from it derive (i) a Poincare-type inequality controlling oversmoothing, (ii) a transport-entropy generalization bound, and (iii) an expansion paradox proving that sparsity, strong spectral expansion, and positive entropic curvature cannot coexist in large graphs, unifying oversmoothing and oversquashing as opposite ends of a single curvature spectrum. We translate the theory into three practical mechanisms, the E-Gate aggregator, the ENT structural encoding, and Midpoint-Completion Rewiring (MCR), and benchmark them against SDRF, FoSR, BORF, LCP, and Graph Ricci Flow on six node-classification benchmarks, and graph-classification.

Graph-based recommendations are widely adopted in real-world industrial applications. However, graphs in these systems often reach a massive scale, posing notable scalability and efficiency challenges. This requires techniques that can effectively balance predictive quality with computational cost. One promising approach is graph coarsening, an adaptive graph reduction technique that offers a way to systematically construct smaller, yet structurally representative, versions of the original large-scale graphs. In this work, we propose a flexible two-stage diffusion framework that combines graph coarsening with multi-step label propagation in the telecommunications domain. Domain-specific heuristics are applied to first aggregate nodes into meaningful communities, reducing graph size while preserving essential business-relevant relationships. An initial diffusion process done by a Label Propagation Algorithm (LPA) or a Graph Neural Network (GNN) propagates labels across the coarsened graph to produce coarse-grained predictions. Finally, a second LPA within subgraphs generates the final recommendations for individual users. On a real-world telecommunications dataset, when using LPA in both stages, our method achieves up to +24% NDCG@5 over the full-graph LPA baseline. Incorporating a lightweight GNN in the first stage further boosts NDCG@5 by more than 50%, but requires substantial training and inference time. Through extensive experiments and a detailed ablation, we quantify these trade-offs and demonstrate that our coarsening-driven approach delivers an optimal balance between scalability, latency, and recommendation quality.

Accurate yet low-latency depth is essential for radar-camera perception in autonomous systems. Cameras provide rich appearance but lack metric scale, whereas automotive radar offers metric range but is sparse and noisy. Many pipelines are multi-stage or depend on auxiliary annotations, increasing latency and limiting portability. We introduce JustDepth, a single-stage radar-camera depth estimator trained only with radar, camera, and single-scan LiDAR. All radar returns are aggregated into a fixed-width 1D representation, decoupling runtime from point count. A Height Fusion Block fuses modalities, a lightweight GNN propagates depth globally, and a training-only confidence decoder stabilizes learning with zero test-time cost. We mitigate stripe artifacts via simple augmentations and quantify them using the Vertical-Horizontal Gradient Ratio (VHGR). On nuScenes, compared to recent state-of-the-art methods, JustDepth maintains accuracy while reducing inference time by 39.7x and stripe artifacts by 66% as measured by VHGR.

Chemists and materials scientists increasingly use machine learning models, such as graph neural networks (GNNs), to predict properties of molecules and the outcomes of their reactions. Beyond predictive performance, understanding how these models organize chemical information internally in their latent spaces, i.e., the embeddings of the molecules, is critical. Analyzing latent spaces helps diagnose model behavior and assess whether the learned embeddings are organized in ways that reflect meaningful chemical relationships. Unfortunately, existing methods provide limited support for analyzing latent spaces across layers and across different model states (e.g., training epochs, model configurations, and input data), making it difficult to understand how these latent spaces evolve throughout a model or relate to chemical concepts. We present LatentFlow, a visual analytics system developed in collaboration with a domain expert for analyzing latent spaces in molecular GNNs. LatentFlow groups embeddings into clusters and supports exploration of latent spaces by tracking how these clusters change across layers and model states using a modified Sankey diagram. To support interpretation, LatentFlow links these clusters to representative molecules and their shared substructures, and it allows scientists to introduce their own domain knowledge and compare it with the patterns found in the latent spaces. We evaluate LatentFlow through two case studies. The results show that LatentFlow helps scientists understand how latent spaces evolve, identify meaningful molecular patterns, and better interpret model behavior.

Coarsening-based training for graph neural networks (GNNs), i.e.\ training on coarsened graphs rather than the original large ones, has become a promising direction for scaling GNNs to massive graphs. However, prior work has been evaluated almost exclusively on \textit{homophilic} graphs, leaving the more challenging \textit{heterophilic} settings underexplored. We show, both empirically and theoretically, that existing coarsening-based training methods suffer significant performance degradation on heterophilic graphs due to inevitable loss of graph information during coarsening. To address this, we propose {\bf A}daptive {\bf C}omplementary {\bf E}nhancement, a plug-and-play, model-agnostic strategy that reintegrates the information discarded in coarsening: ACE learns a projector for re-constructing original node features and applies \textit{anisotropic structural regularization} to embed local heterophily. We further adopt \textit{homoscedastic uncertainty weighting} to adaptively balance the combined training objective of primary coarsened-graph training loss and full-graph auxiliary loss with augmented node features re-constructed by the heterophily-aware projector. Extensive experiments show that ACE drives consistent gains on heterophilic benchmarks while preserving competitive results on homophilic graphs with minimal computational overhead. Code is available at the GitHub repository: https://github.com/vasile-paskardlgm/ACE.

We present a traffic-signal control interface in which a shared graph neural network assigns scores to individual traffic movements. Each junction converts these scores into its own variable-sized set of legal signal phases using a deterministic incidence matrix. Directed corridor nodes provide traffic context, while movement nodes represent controlled input-to-output paths through junctions. Typed mean aggregation produces one scalar per movement; phase definitions and signal timing remain outside the learned network. This makes graph size and junction-specific action count independent of the learned parameter shapes. PPO experiments evaluate the interface on unseen synthetic grid geometries, altered signal coverage, and five heterogeneous city graphs. The policies retained performance across unseen geometries within the synthetic grid family, while changes in signal coverage exposed sensitivity to a signal-coverage distribution shift. A single trained city-policy instance executed across all five city graphs, with heterogeneous outcomes. These results provide feasibility evidence rather than a general estimate of transfer to arbitrary road networks.

Molecular property prediction from structure often uses a single representative conformation, even though many molecules exist as conformational ensembles in solution. We introduce EnsembleEGNN, a molecular ensemble foundation model that encodes an ensemble by first encoding each conformer with shared Equivariant Graph Neural Network (EGNN) layers, then pooling the resulting conformer representations with a Set Attention Block. We pretrain the model on CREMP, a cyclic peptide ensemble dataset, using a multi-task self-supervised objective combining masked token recovery, noisy-coordinate reconstruction, and pairwise distance reconstruction. On the CREMP-CycPeptMPDB dataset, training EnsembleEGNN from scratch fails entirely ($R^2=0.005$). However, the pretrained model reaches $R^2=0.477$ and Pearson $r=0.699$, outperforming the sequence-only BERT baseline ($R^2=0.439$, Pearson $r=0.667$). When EnsembleEGNN is co-trained end-to-end with the BERT sequence encoder, the hybrid model improves further to $R^2=0.538$ and Pearson $r=0.737$. These results demonstrate that encoding conformational ensembles into a single thermodynamically informed embedding improves cyclic-peptide property prediction.

Instance-level explanations aim to reveal the rationale behind a model's decisions for a specific graph. Previous methods explain graph neural networks (GNNs) by selecting important edges to induce subgraphs, where edge importance is assessed by perturbing each edge and observing changes in the model predictions. However, they often neglect the synergistic effects among edges, which are crucial for accurately characterizing edge importance. To address this issue, we propose SeeExplainer, a parameter-free explainer to interpret GNNs. Specifically, we first introduce a granular-ball graph refinement mechanism that decomposes a graph into several disjoint granular-balls with no fixed size, and utilize them as nodes to construct a structural graph. This process can better capture the synergistic effects among edges. Then, we perturb nodes and edges in the structural graph to generate explanatory subgraphs based on their respective contributions. Experiments on several graph classification datasets of different networks show that SeeExplainer outperforms state-of-the-art baselines.

We study feature-level and node-level explanations for graph neural networks (GNNs) through the lens of Aumann-Shapley attribution. Path-integral methods such as Integrated Gradients provide an axiomatic formulation of attribution, but their practical use in deep GNNs typically relies on finite-sample numerical approximations to the path integral, requiring a trade-off between quadrature error and computational cost. This paper proposes APEX, a model-attribution co-design framework that makes the attribution integral exactly computable under a polynomial GNN architecture. The key component is PolyGIN, a GIN-style graph network whose message-passing, normalization, and transformation operations preserve a bounded multivariate polynomial form for scalar model scores, such as pre-softmax logits. We show that, for a PolyGIN with $L$ polynomial transformation blocks, the derivative along the attribution path has degree at most $2^L-1$. Therefore, Gauss--Legendre quadrature can evaluate the Aumann--Shapley path integral exactly, up to floating-point precision, with $2^{L-1}$ deterministic evaluation points. The resulting attributions can be computed at the feature level and then aggregated into node-level scores while preserving completeness. Experiments on synthetic and real-world graph benchmarks show that PolyGIN maintains competitive predictive performance, while the complete APEX framework achieves higher attribution fidelity than the compared baselines and substantially reduces the number of evaluations required for path integration.

User modeling is a critical task in a variety of personalized systems. Recognizing their effectiveness in learning from graph-structured data, Graph Neural Networks (GNNs), particularly Graph Convolutional Networks (GCNs), are increasingly employed for user modeling. However, existing approaches typically treat different relation types in a graph as homogeneous, limiting their ability to capture richer semantics and construct more informative user models. While multi-relational GNNs (MR-GNNs) have been adopted for representation learning and recommendation, their application for user modeling remains unexplored. Moreover, existing GNN-based user modeling approaches ignore the user interaction sequence. To address these research gaps, in this work we propose MR-ConceptGCN, a novel fully unsupervised approach focused on concept-based sequential learner modeling using multi-relational GCNs (MR-GCNs). MR-ConceptGCN effecively combines Personal Knowledge Graphs (PKGs), MR-GCNs, and the pre-trained language model SBERT to obtain enhanced relation- and semantic-aware representations of the PKG items. The enriched embeddings of the knowledge concepts that a learner did not understand when interacting with learning materials in CourseMapper are then used to construct a sequential learner model that combines long-term and short-term learner interactions. We report the results of an online user study (n = 31), demonstrating the benefits of MR-ConceptGCN in terms of several important user-centric aspects including accuracy, usefulness, diversity, and satisfaction with an educational recommender system.

Neural Markov Logic Networks (NMLNs) are a flexible neurosymbolic relational model. Previous work has shown that, although NMLNs achieve strong performance as generative models for small relational structures, they underperform diffusion-based generative graph models on larger structures. In this paper, we strengthen NMLNs along two main dimensions: (i) we increase the expressive capacity of their potential functions using graph neural networks, and (ii) we develop a new training and inference algorithm inspired by parallel-tempering Markov chain Monte Carlo methods, which we name parallel noising. Together, these enhancements enable NMLNs to attain strong performance in graph generation relative to general diffusion-based generative graph models. Furthermore, they allow NMLNs to match the performance of specialized text-based recurrent models when generating small molecular structures.

Equivariant graph neural networks provide a powerful modeling language for three-dimensional scientific data, but their reuse is often limited by implementations tied to specific tasks, outputs, and training regimes. We present GEqTrain, a configuration-driven framework that separates dataset semantics, model composition, and training objectives. Raw data are mapped to typed node-, edge-, and graph-level fields, while model stacks, losses, and training workflows are assembled declaratively through Hydra configurations. A shared equivariant backbone and training infrastructure can therefore be retargeted to a new task primarily through configuration. We demonstrate this flexibility on three different problems handled within one software stack: coarse-grained-to-atomistic backmapping of biomolecular systems, prediction of NMR chemical shifts in molecular solids, and equivariant generative modeling. Our aim is not to surpass individually optimized task-specific systems, but to show that a shared representation and training infrastructure can achieve competitive accuracy across qualitatively different tasks at the cost of a configuration change. We further introduce GEqDiff, a generative extension based on equivariant flow matching. GEqDiff treats user-defined equivariant fields as first-class generation targets, jointly transporting Cartesian positions and non-scalar node fields spanning representations up to l=3 within a single equivariant flow. We validate this capability on a controlled synthetic benchmark inspired by protein secondary-structure motifs, showing that fields with heterogeneous transformation properties can be reconstructed jointly and with high fidelity. By reducing the software overhead of moving between predictive and generative, scalar and tensorial settings, GEqTrain aims to make equivariant modeling more reproducible, extensible, and reusable.

Automated Algorithm Selection (AS) aims to improve problem-solving performance by selecting, for each problem instance, the most suitable algorithm from a predefined portfolio. This is particularly relevant to the Traveling Salesman Problem (TSP), where solver performance is strongly instance-dependent. We introduce GNNAS-TSP, a Graph Neural Network (GNN)-based AS framework that learns TSP instance representations directly from raw graph data, avoiding manual feature engineering. GNNAS-TSP formulates AS as a joint cost-prediction and ranking task. We evaluate cost-based (mean squared error (MSE), mean absolute error (MAE), and Huber), rank-based (RankNet, ListNet, and LambdaRank), and hybrid learning objectives for a portfolio comprising Chained Lin-Kernighan, Edge Assembly Crossover, Lin-Kernighan-Helsgaun, Multiagent Optimization System, and Concorde. Experiments use fixed computational budgets of 10 and 60 seconds. On the held-out test set, the selected configurations improve on the Single Best Solver (SBS) in normalized solution cost at both budgets. For the 10s budget, AS achieves substantial and statistically significant cost improvement over SBS. Overall, the results suggest that GNNAS-TSP is a useful meta-solving strategy when exploitable variation exists across solver performance.

In recent years, interest in single-atom catalysts supported on carbon-based structures has grown considerably due to their high catalytic activity and efficient uses of metal atoms. However, the design and characterization of these materials through first-principles calculations are computationally expensive, limiting the exploration of a large number of possible configurations. Here, we developed a framework based on graph neural networks (GNNs) to predict the adsorption energies of transition metals on graphene quantum dots (GQDs). The model was trained using data obtained from density functional theory calculations and achieved an $R^2$ of 0.906 with an MAE of 0.101 eV, while reducing computational cost by roughly six orders of magnitude relative to DFT. This methodology provides an efficient tool for the accelerated screening and rational design of new catalysts based on carbon nanostructures.

Machine olfaction for gas unmixing is an underconstrained inverse problem in which gas compositions must be inferred from low-dimensional, delayed, and entangled sensor responses produced by interacting chemical transport, surface adsorption, and sensor transduction. One of the key obstacles is physics closure misspecification, where a neural network is designed to fit sensor traces rather than infer a physically closed olfactory process. In this work, we formulate gas unmixing as a multi-physics-constrained inverse problem governed by Maxwell--Stefan multicomponent transport PDEs, competitive adsorption ODEs, and nonlinear sensor transduction ODEs. Directly solving such a high-dimensional coupled system is computationally expensive and often numerically unstable. To this end, we propose UnMixNet, a physics-closed graph neural solver that embeds this multi-physics forward process into end-to-end gas unmixing. UnMixNet discretizes Maxwell--Stefan cross-diffusion on spatial graphs and formulates the multicomponent flux on each edge. This design enables local, differentiable, and flux-conservative inference for multicomponent cross-diffusion. Evaluations on SmellNet show improved single-odor recognition, seen-mixture unmixing, and unseen-mixture generalization. In addition, an external validation on UCI Dynamic Gas Mixtures shows that the inferred concentration process agrees with ground truth concentration set points under dynamic transitions. Process-consistency diagnostics further show that the proposed model learns transferable dynamic physical fingerprints that better satisfies transport, conservation, adsorption, and readout closure.

Equivariant graph neural networks repeatedly apply edge-conditioned tensor-product convolutions over graph edges. Conventional implementations materialize edge-specific weights, messages, and adjoints, causing tensor-product workspace and memory traffic to grow rapidly with graph size and operator width. This limits feasible workloads and can prevent larger problems from fully utilizing the GPU. We show that these edge-sized intermediates are artifacts of the execution schedule, not requirements of the equivariant operator. By reassociating radial projection, spherical-harmonic coupling, and graph aggregation, edge-local products can be consumed directly into bounded receiver-side state. The resulting streaming formulation preserves fully connected multiplicity mixing and extends through forward, backward, and double backward. We implement this formulation in Sobek, a generated-CUDA backend, and evaluate it across edge-scaling regimes and varied feature structures. Across two operator families and all three differentiation orders, Sobek is faster in all 75 capacity-matched comparisons, with speedups ranging from $1.2\times$ to $49.7\times$, and reduces peak allocated memory by up to 99%. It also executes workloads up to two orders of magnitude beyond OpenEquivariance's capacity while retaining near-peak throughput. These results show that edge-scaled tensor-product workspace is a property of the conventional schedule, not of equivariant convolution itself.

Graph Neural Network (GNN) inference on billion-scale graphs is challenging due to the large memory footprint of features and embeddings and high disk I/O costs in out-of-core settings. Existing distributed GNN systems incur high communication times and infrastructure costs, while disk-based GNN systems are primarily tailored to training and experience massive wasted reads during inference on the entire graph. We present Taurus, a single-machine system for GNN inference on graphs that do not fit in RAM, supporting both \textit{exact} full-graph inference and fanout-sampled inference. To avoid random and repeated feature gathers, Taurus reformulates layer-wise inference as source-centric broadcasts over sequential SSD scans, backed by a pipelined GPU-CPU-SSD hierarchy, topology-aware reordering, pending-message eviction, and a GPU-resident store for high-degree vertices. It further uses non-buffered sequential reads and GPU-backed writes to reduce page-cache pollution, host-memory pressure, and write overheads. On out-of-core graphs with up to $269M$ vertices, $4B$ edges, and $514$ GiB of features, Taurus outperforms the strongest layer-wise baseline, DGI, by $7$-$25\times$, and vertex-wise baselines by $40$-$140\times$.

High quality temporal graph benchmarks with rich semantics and ground-truth anomaly labels are essential for training graph neural networks, yet remain scarce due to privacy constraints and annotation costs. We present SAGA (Synthetic Agentic Graph Architecture), a system for generating large-scale, semantically rich temporal graphs via a four-phase pipeline. Our Skeleton-First, Semantics-Second architecture decouples structure from semantics: (S) an O(1)-per-edge skeleton generator produces power-law graphs; (A) a dispatcher partitions causally ordered time blocks for parallel execution; (G) LLM agents inject domain semantics using RAG-based rule bases across four domains; and (A) a state alignment engine resolves conflicts via temporal replay, yielding anomaly labels as natural byproducts. Unlike structural generators (e.g., LDBC SNB, Kronecker/R-MAT) or purely LLM-based approaches, SAGA achieves structural realism, semantic richness, and automatic anomaly labeling in a unified framework. On a single H100 GPU with vLLM batching, SAGA generates 500,000 temporal edges with controlled anomalies in under 90 minutes, scaling to 100,000 nodes while maintaining clustering coefficients above 0.99. The system supports real-time pipeline visualization, interactive multi-domain tuning (Finance/AML, Network/IDS, Cyber/APT, Transportation), and a CLI for large-scale GPU-based experiments.

Graph Neural Networks (GNNs) have emerged as a powerful, differentiable class of learning models for graph-structured systems. Their ability to generalize across topologies opens the prospect of a surrogate for combined structural and parametric optimization, which classical metamodels cannot offer. Supply chains are a natural target, yet the use of GNN surrogates for supply chain problems is largely unexplored. This paper lays the foundation, presents initial steps, and discusses key research directions. As a foundation, we formulate the problem and create a large public training dataset of programmatically generated supply chain graphs with input parameters and steady-state performance metrics obtained using our SupplyNetPy simulation library. As initial steps, we explore GNN architectures that work well as surrogates for node- and network-level predictions, and analyze their accuracy-compute trade-off against simulation. Most importantly, we outline the exciting directions this opens, namely gradient-based optimization over topology, fast design-space exploration, and sensitivity analysis.

Comparing phylogenetic tree topologies is essential for understanding epidemic dynamics, yet biologically meaningful distances such as the Subtree Prune and Regraft (SPR) distance are NP-hard to compute and intractable on large datasets. We investigate whether a Graph Neural Network (GNN) can approximate SPR distances in near-constant time per comparison after training. Our contributions are fourfold. First, we build and publicly release a dataset of 864 phylogenetic trees inferred with UPGMA and Neighbor-Joining over four bacterial species, spanning up to 9{,}500 isolates, together with 388 labelled tree pairs. Second, we establish a reproducible pre-processing pipeline including midpoint re-rooting, which reduces tree depth and supplies the rooting required for exact distance computation and for the model's root-based features. Third, we validate the supervision target: on small trees, where exact SPR is tractable, the unrooted phangorn::SPR.dist heuristic correlates almost perfectly with the exact rooted distance computed by rspr (Pearson $0.98$--$0.99$), making it an excellent monotonic surrogate. Lastly, we train a Siamese Graph Isomorphism Network (GIN) regressor. In-distribution, i.e., held-out trees from the same species and size range as training, it explains roughly 87--90% of the variance ($R^2 \approx 0.87$ on a held-out split; $0.90 \pm 0.19$ under stratified cross-validation), with about four times lower error than a mean-predictor baseline, and shows partial transfer to unseen species ($R^2 \approx 0.37$). Its main limitation is extrapolation to trees larger than those seen in training, where accuracy collapses. The released dataset and the validated heuristic versus exact relationship provide a reproducible basis for scaling learned SPR approximation.

Unsteady aerodynamic phenomena, such as gusts, turbulence, and fluid-structure interactions affect an aircraft during flight. For design, optimisation and certification, it is indispensable to quantify such unsteady aerodynamic effects. Industry-standard computational fluid dynamics methods, such as solving the unsteady Reynolds-averaged Navier-Stokes equations or the linearized frequency domain method, are either computationally expensive or restricted by assumptions like linearity. Once trained, machine learning methods are capable of computing non-linear relationships very fast, making them suitable as surrogate models. By autoregressively applying graph neural networks (GNNs), operating on a discretised spatial domain, spatio-temporal predictions can be made. However, autoregressive GNNs suffer from error accumulation leading to unstable rollouts over time. Here we show that combining GNNs with augmented Neural Ordinary Differential Equations yields temporally stable predictions of the surface forces on a pitching airfoil. We found that our approach, called GNODE, based on Graph Neural Ordinary Differential Equations, provides temporally more stable, spatially smoother, and overall more accurate results than an autoregressive GNN baseline. Tests are conducted on a dataset consisting of a simulations of a pitching airfoil, including transonic shocks, transient behaviour and dynamic non-linearities. Augmenting GNODEs with additional latent dimensions improves the expressivity and accuracy by capturing underlying history effects. The developed method demonstrates an approach that is suitable to model non-linear spatio-temporal systems with exogenous inputs.

Industrial processes often generate complex, interdependent time-series data from multiple sensors across multiple stages, forming complex dependencies among variables and process stages. Effective monitoring and timely anomaly detection of these time series through multivariate time series anomaly detection (MTAD) is crucial for preventing failures and ensuring the reliability of automated systems. Graph neural networks (GNNs) have advanced MTAD by leveraging data-driven graphs to model complex dependencies among variables, effectively capturing relational structures within multivariate time series to enhance anomaly detection performance. However, existing GNN-based approaches often overlook critical process knowledge, and even when this knowledge is considered, seamlessly incorporating it into existing models remains inherently challenging, leading to suboptimal performance. To address this limitation, we propose a knowledge-assisted multi-graph framework for modeling sensor dependencies in multi-stage industrial processes for MTAD, which explicitly incorporates process knowledge into graph learning to enhance dependency modeling and improve anomaly detection performance. Our method constructs three complementary graphs: one purely data-driven and two refined by integrating structural constraints derived from process knowledge. To effectively leverage these graphs for anomaly detection, we employ a multi-graph attention network, enabling a more accurate and robust representation of complex dependencies. Comprehensive experiments on two real-world, multi-stage industrial datasets demonstrate that incorporating process knowledge substantially enhances anomaly detection performance.

Accurate prediction of crystal properties remains a key challenge in computational materials science. While graph neural networks (GNNs) such as CGCNN, MEGNet, ALIGNN, and SchNet have shown strong performance, they primarily represent crystals at the atomic level and implicitly learn local chemical environments through message passing. However, many material properties are governed by coordination polyhedra, the fundamental structural units formed by atoms and their neighboring atoms. To address this limitation, we propose the Coordination Polyhedron Graph Network (CPGN), a multi-scale GNN that jointly learns atomic, bond, and coordination-polyhedron representations. CPGN constructs three coupled graphs: an atom graph encoding elemental and bonding information, a line graph capturing angular interactions, and a coordination polyhedron graph describing Voronoi-derived local environments through corner-, edge-, and face-sharing relationships. Physically meaningful geometric descriptors are incorporated for each polyhedron, while an interleaved message-passing mechanism with bidirectional cross-attention enables effective information exchange across structural levels. Extensive evaluations on the Materials Project, JARVIS-DFT, and QM9 benchmark datasets demonstrate that CPGN outperforms existing state-of-the-art GNN models. It achieves a formation-energy MAE of 0.060 eV/atom and a band-gap MAE of 0.292 eV on the Materials Project, while providing competitive multi-property prediction on JARVIS-DFT and superior HOMO prediction on QM9. The results highlight that explicit modeling of coordination polyhedra improves crystal representation learning and enables accurate, physically interpretable prediction of material properties.

Graph neural networks (GNNs) frequently encounter group fairness issues, often yielding biased predictions against specific demographic groups defined by sensitive attributes such as gender or race. While this challenge has motivated extensive research, most existing solutions rely on the strong assumption that demographics are fully available. To bypass this strict requirement, a few recent studies have attempted to use predicted demographics as proxies to enforce fairness constraints. However, predicted demographics may be inaccurate, resulting in the failure to improve fairness. In this work, we investigate the problem of graph fairness without demographic information and avoid the utilization of predicted demographics. Motivated by our observation that the gradient distributions of misclassified nodes implicitly encode demographic information, we first propose GradDist, a gradient-based metric that quantifies bias by measuring the distance between local modes within these distributions. To mitigate this bias, we propose Gradient-to-Fairness (Grad2Fair), a gradient-guided approach for group fairness without demographics. Due to the potential demographics in gradients, Grad2Fair directly leverages gradients to debias and eliminates demographic prediction, thereby enabling stable fairness performance. Experiments on several real-world datasets demonstrate the effectiveness of Grad2Fair, as evidenced by superior performance over baselines in most cases. Our code is available at https://github.com/ZzoomD/Grad2Fair.

In real-world applications, node classification on graphs often faces the challenge of class imbalance, where majority classes dominate training, resulting in biased model performance. Traditional GNNs often struggle in such scenarios, as they tend to overfit to majority classes while underrepresenting minority classes. Existing solutions, which either prioritize nodes based on class size or synthesize new nodes for minority classes, often fall short of effectively addressing this imbalance issue. This paper introduces an approach to class-imbalanced node classification by utilizing a balanced meta-set for importance measurement, where a training node is considered significant if it enhances model performance under an unbiased setting. Our method identifies important nodes that can counteract class imbalance and utilizes them for model training, allowing for fine-grained and dynamic node selection throughout the training process. We theoretically derive a formula to directly assess node importance, reducing computational overhead and providing an intuitive threshold for node selection. Guided by this metric, we develop a novel framework that filters valuable labeled, unlabeled, and synthetic nodes that enhance model performance in an unbiased context. A key advantage of this framework is its separation of the synthetic node generation process from the filtering process, ensuring compatibility with various node generation methods. Furthermore, we introduce a strategy to construct a high-quality meta-set that closely approximates the overall feature distribution, ensuring robust representation of each class. We evaluate our framework, NodeImport, across multiple datasets using popular GNN architectures, demonstrating its superiority over existing baselines. Our results highlight the flexibility and effectiveness of the framework in mitigating class imbalance, leading to improved outcomes.

Recovering a latent potential from observed flow on a directed graph (a discrete Poisson problem with Dirichlet boundaries) is ill-posed, and the standard fix backfires: ridge regularization shrinks toward a gauge-meaningless origin, collapsing and reversing the recovered ordering ($+0.81\to-0.42$ rank correlation against a planted ground truth). The gauge-invariant graph Dirichlet energy removes the hazard and delivers parameter-insensitivity: the estimate is stable across four orders of magnitude in $λ$, whereas ridge inverts the ordering for every $λ>0$. We prove the reduced solve is SPD and preserves dynamic range exactly where ridge collapses it, and localize absorbing boundaries from flow alone via a Poisson residual. The $H^1$ seminorm is classical; what is new is the gauge diagnosis, the parameter-insensitivity it buys, and an ablation showing the result is robust to the extraction method. On three public clickstream corpora the gauge-invariant estimate retains $28$--$41\%$ of the interior dynamic range while ridge collapses to as little as $0.2\%$. The same gauge invariance carries into graph neural networks -- neutralizing the constant mode per layer prevents the oversmoothing that collapses a deep directed GCN -- linking this classical inverse problem to a central question in graph learning.

Industrial design in fields such as vehicle and aerospace engineering often relies on large-scale numerical simulations to evaluate fluid dynamics performance, which can incur substantial computational costs. Deep neural networks have shown promise in improving simulation efficiency, especially graph neural networks (GNNs), which demonstrate great potential due to their flexibility with unstructured data. However, GNNs face challenges when dealing with tasks involving complex geometries and large-scale meshes. In this paper, we propose the Multi-scale Feature Enhanced Graph Neural Network (ME-GNN) to tackle these challenges. ME-GNN employs a graph neural network with a two-step message-passing mechanism to capture detailed local features effectively. Additionally, it integrates an Attention U-Net with uniform grid discretization, enabling the extraction of both fine and coarse features. The model also utilizes K-hop sampling to construct subgraphs, facilitating efficient training on large datasets while preserving detailed local features. We evaluated ME-GNN on three benchmark datasets and achieved state-of-the-art results: a relative L2 error of 0.0196 for the velocity field and 0.0556 for the surface pressure on ShapeNet-Car, a normalized mean squared error of 0.0033 for the flow field on AirfRANS, and a relative L2 error of 0.1416 for the surface pressure on DrivAerNet.

We introduce a constrained two-view framework for node prediction that aligns structure-conditioned GNN embeddings with a structure-free feature prior learned by an anchor model. Conventional Graph Neural Networks (GNNs) couple feature transformation and neighborhood aggregation, which renders them vulnerable to topology noise and heterophilous connections. To decouple this dependency, our framework utilizes an independent anchor network to capture intrinsic attribute features via a self-supervised reconstruction objective. Furthermore, we propose a Channel-Split Adaptive Gated GNN (CSAG-GNN) that dynamically routes representations between global spectral smoothing and local spatial discrimination through a node-wise gating mechanism. We propose a stable cyclic alternating optimization strategy to solve the resulting coupled bi-level objective, preventing mutual representation drift during training. Empirical results on both homophilous and heterophilous benchmarks show balanced performance gains and structural robustness over competitive baselines.

Determining whether one finite group is isomorphic to a subgroup of another is a fundamental problem in computational group theory. In this work, we propose a Siamese Graph Neural Network (Siamese GNN) for subgroup prediction using Cayley graph representations of finite groups. Each input group is represented by its undirected Cayley graph and encoded by one branch of a Siamese GNN to produce a graph embedding. The resulting graph embeddings are combined with algebraic features derived directly from the input groups to construct a joint feature vector, which is processed by a fully connected classifier to predict subgroup relations between finite groups. By integrating graph-based structural representations with algebraic features, the proposed framework provides a unified approach for learning subgroup relations from finite groups. Experimental results demonstrate the effectiveness of the proposed architecture, achieving a test accuracy of 95.9% (47/49) on an independent test set and illustrating the potential of geometric deep learning for subgroup prediction.

Indoor spatial understanding remains a fundamental challenge for intelligent systems operating in physical environments. Traditional RFID localization techniques typically estimate positions of tags using signal strength measurements but fail to capture higher-order spatial relationships between objects and infrastructure. Recent work on RFID and wireless indoor localization has increasingly emphasized robust learning under noisy propagation, while recent graph-based localization methods demonstrate the value of relational modeling over isolated samples. This paper introduces a graph-based learning framework that leverages Graph Neural Networks (GNNs) to infer spatial geometry from RFID observations. Rather than predicting isolated coordinates, the proposed system models relationships between RFID readings, antennas, and physical structures within an indoor floorplan. This framing is aligned with recent graph-based indoor positioning and graph construction literature, where topology is a first-class source of information for downstream inference. The approach integrates signal strength data, floorplan semantics, and spatial constraints into a graph representation where nodes correspond to RFID observations and edges encode proximity and contextual relationships. A GNN is then trained to predict geometric patterns such as linear trajectories, rectangular bounding regions, and movement paths of objects in space.

Graph neural networks (GNNs) are increasingly deployed in real-world applications where distribution shift is un-avoidable. However, how such shifts affect model calibration, defined as the agreement between predictive confidence and actual accuracy, remains poorly understood, and existing graph calibration methods typically rely on labeled validation data from the deployment distribution. In this work, I present the first closed-form theoretical characterization of GNN calibration under distribution shift. I show that calibration is governed by a single scalar quantity that explicitly depends on structural changes between the source and target graphs, as well as feature quality. This characterization precisely identifies when a model becomes over-confident, under-confident, or remains calibrated, and directly yields the optimal temperature scaling strategy. I further extend the analysis to graph convolutional networks with symmetric normalization, multi-class classification, and covariate shift, and derive a theoretical upper bound on the expected calibration error. My analysis also reveals that, under homogeneous distribution shift, a single global temperature is theoretically optimal, providing a principled explanation for why more complex node-wise recalibration methods offer no additional benefit. Building on these theoretical insights, I propose STAC, a source-free, label-free calibration method. Experiments on synthetic benchmarks demonstrate substantial calibration improvements, while evaluations on five real-world graph datasets show that reliable calibration without target labels remains challenging despite the strong predictive power of the theory.

Graph Neural Networks (GNNs) provide a learning-based framework for approximating graph quantities that are expensive to compute exactly. This paper investigates GNNs for scalable approximation of betweenness and closeness centrality, formulated as a node-ranking problem. Exact centrality values are used as supervision, and ranking quality is evaluated using Kendall's tau rank correlation. We study whether message-passing GNNs can learn transferable structural representations across different graph topologies rather than only fitting the distribution used during training. On unseen Erdos renyi graphs, the proposed models achieve tau = 0.851 for betweenness and tau = 0.894 for closeness. A large-scale betweenness model trained on graphs with N = 5,000 nodes achieves tau = 0.938, demonstrating scalability. Mixed-distribution training on Erdos renyi, Barabasi-Albert, and Gaussian Random Partition graphs improves betweenness transfer across graph families. In contrast, closeness centrality remains more sensitive to community-structured graphs and shows reduced transfer to real-world topologies. Finally, GNN inference achieves up to a 97.7x speedup over exact computation. These results show that mixed-distribution training can improve structural transfer in GNN-based centrality approximation, while identifying closeness centrality's sensitivity to topology as an open challenge.

Legal precedent retrieval is a fundamental task in legal case preparation, planning, litigation strategy, and legal research. Current approaches for automatic precedent retrieval map legal documents to a low-dimensional semantic space and compute similarity based on the proximity of their representations. These approaches treat legal documents as monolithic texts, ignoring the rhetorical organization of the legal technicalities. Ergo, they overlook nuanced legal meanings and fail to distinguish the contextual significance of legal entities and concepts that vary based on their rhetorical roles within the document. To address this insufficiency, we propose the PRecG pipeline that computes the similarity between pairs of legal judgments by hierarchically learning their representations. The process begins by decomposing each document into distinct semantic units (segments) based on the rhetorical roles of sentences. For each rhetorical segment, a knowledge graph is constructed to capture the legal entities and their relationships within the segment. Contextual representations of the entities are then learned and aggregated to derive segment-level embeddings. These embeddings are further integrated to produce a unified document-level representation, and finally, the semantic similarity between a pair of documents is computed. We validate the performance of the proposed approach through extensive experiments on a benchmark Indian legal dataset, comparing it against state-of-the-art baselines to demonstrate its effectiveness.

Graph Neural Networks have emerged as a powerful tool for the fast and accurate prediction of various crystal properties. These models often encode domain-specific knowledge into their graph encoding modules, which increases their parameter size and makes their performance heavily dependent on domain expertise. Added to this, explicitly incorporating all chemical and structural features, that might influence a specific crystal property into the GNN encoder, is a challenging task. In this work, we propose a soft prompt learning framework that captures latent features essential for property prediction, which are not explicitly provided to the GNN. We introduce a novel multilevel graph prompt learning framework comprising both node-level and graph-level soft prompts. At the node level, we capture the local chemical semantics of different atom types, while at the graph level, we encode the global structural symmetry of the crystal graph. Our proposed prompt learning framework is lightweight and seamlessly integrates with any existing GNN encoder. Extensive experiments on popular benchmark datasets show that incorporating prompt learning significantly improves (3% - 15%) the performance of state-of-the-art GNN models in crystal property prediction tasks. Furthermore, the learned soft prompts enable cross-property knowledge transfer, enhancing prediction performance for properties with limited training data. Code is available at https://github.com/shrimonmuke0202/Prompt.git

Missing data is ubiquitous in real-world datasets. Traditional methods either discard incomplete samples or apply imputation techniques that ignore potentially informative missingness patterns, implicitly assuming that missingness occurs randomly. However, missingness patterns might provide additional information. We propose pattern-aware graph neural networks that explicitly encode which features are missing alongside observed values. We used four encoding strategies -- learned embeddings, frozen random embeddings, statistical features, and hierarchical representations -- across seven UCI datasets with naturally occurring missingness. Our Pattern-aware methods achieve substantial improvements over baselines, with an average improvement of 17% in balanced accuracy and 22% in F1-macro across all datasets. The benefits vary significantly by dataset: annealing shows dramatic improvement (+80% balanced accuracy), while hepatitis and soybean show minimal gains (+4--5%). Notably, even simple random pattern embeddings perform comparably to learned embeddings (0.650 vs 0.663 balanced accuracy), suggesting that distinguishing between patterns may be more important than task-specific optimization. Our ablation study reveals that attention mechanisms, while helpful, are not critical when pattern information is available -- simple mean aggregation with pattern awareness achieves 0.640 balanced accuracy compared to 0.645 for attention-based variants.

Graph Neural Networks (GNNs) have shown considerable success in learning from graph-structured data, but their use in privacy-sensitive areas remains difficult because graph structure can leak sensitive link information. To satisfy edge-level differential privacy, a common approach is to inject noise into all elements of the graph's adjacency matrix, thereby obfuscating the existence of any single edge. However, stronger privacy requires more noise, and excessive noise reduces utility, making the privacy-utility balance a major barrier to practical privacy-preserving graph learning. To address this issue, we propose EdgeRefine, a local differential privacy framework that improves this trade-off through adaptive edge refinement. EdgeRefine first estimates edge-existence probabilities using Jaccard similarity and ranks edges for noisy edge removal. To ensure the sparsity and reliability of the final graph, it uses the privacy budget $ε$ to determine the ratio of true to false edges, samples them separately based on this probability ranking, and controls the total number of edges with a separate sampling rate $k$. Extensive experiments show that EdgeRefine achieves accuracy comparable to the noise-free baseline and substantially outperforms other privacy-preserving methods across datasets and GNN architectures. Under privacy budget $ε= 2.5$, EdgeRefine improves node classification accuracy over state-of-the-art baselines by 17.8% on ACM under GAT and 19.7% on Cora under GCN. In graph classification, it achieves an average accuracy degradation of around 5% compared to the noise-free baseline. Under graph reconstruction attacks, EdgeRefine maintains relative absolute error levels above 1 across all privacy budgets, averaging 1.962 on Cora and 1.472 on AMAP, indicating strong resilience against privacy leakage.

We present path_boost, a Python package for interpretable supervised learning on graph-structured input data. The package implements PathBoost, a gradient boosting algorithm that automatically discovers predictive labeled paths within graphs during the learning process. Unlike graph neural networks, which are generally difficult to interpret, PathBoost produces an additive prediction model over path-based features that explicitly reveals which substructures drive predictions. To avoid an exhaustive enumeration of all possible paths, the algorithm iteratively selects and extends paths during learning based on their predictive power, using boosting to combine weak learners into a strong ensemble. The package supports both regression and binary classification. Key features include compatibility with scikit-learn workflows, support for custom base learners and selectors, automatic starting node selection, parallel training across anchor nodes, and built-in variable importance computation. We demonstrate PathBoost on molecular property prediction of transition metal compounds, where atoms serve as nodes and bonds as edges, and further benchmark PathBoost against an established graph neural network and a graph kernel method across six molecular datasets. The package is available on PyPI and GitHub under an open-source license.

For seemless control of advanced hand prostheses and augmented reality, accurate and immediate hand gestures recognition is essential. Surface electromyography (sEMG) signals obtained from the forearm are commonly employed for this purpose. In this paper, we present a novel approach for sEMG representation that utilizes graph networks which contain information about muscle activation patterns in the forearm. Based on these graph networks, we have developed a machine learning algorithm capable of real-time hand gesture recognition using a graph neural network. The algorithm's performance was evaluated using sEMG signals acquired from myoband, which has 8 electrodes placed around the forearm, involving 8 healthy subjects. The proposed method demonstrated an average classification accuracy of 99%, surpassing the performance of state-of-the-art techniques. The average time for both graph construction and prediction stood at 48ms utilizing a M1 pro CPU, rendering the approach well-suited for real-time applications.

Alzheimer's disease (AD) is a common neurodegenerative disorder, and early diagnosis is of great significance for delaying disease progression and enabling timely intervention. Mild cognitive impairment (MCI), which represents an intermediate clinical stage between cognitively normal aging and AD. Structural magnetic resonance imaging (sMRI) provides detailed characterization of anatomical structures and plays an important role in AD-related brain analysis. However, existing sMRI-based brain network methods typically rely on a single graph construction strategy, limiting their ability to jointly capture spatial relationships and morphological similarities between brain regions. To address these issues, this paper proposes an sMRI-based multi-view masked graph neural network model (MVMGNN) for AD diagnosis. A joint node-edge masking mechanism is proposed to simultaneously select radiomics feature dimensions and structural connections, reducing redundancy during graph learning. Furthermore, a patient-level cross-view gated fusion mechanism is proposed to integrate multi-view representations. Experimental results on the ADNI dataset demonstrate that MVMGNN outperforms several competing approaches in AD classification. Interpretability analysis further demonstrates that MVMGNN is able to identify key brain regions associated with AD, providing useful insights into discriminative patterns in sMRI-based brain networks.Our implementation is publicly available at https://github.com/chenzhao2023/MVMGNN_AD

Event-based cameras are gaining popularity as the sensor of choice for mobile robotics, due to their high performance in dynamic environments. However, these applications require efficient real-time data processing with low latency and power consumption. One strategy to meet these stringent requirements is hardware acceleration of efficient algorithms that preserve the temporal sparsity of event data. In this work, we propose an optimization strategy for Graph Convolutional Neural Networks models aimed at adapting their architecture to the limited resources of embedded heterogeneous FPGA platforms. Our method incorporates hardware-aware pruning and quantization, taking into account the trade-off between on-chip memory savings and inference accuracy. Strategic exploration of the design space with Fine Grid Search and Greedy layer-wise Iterative Deepening Search methods enables flexible adaptation of the model architecture to the target platform. Our approach was evaluated across various network configurations and multiple datasets, resulting in BRAM memory reductions of 28.8% for CIFAR-10 (with a 1.65% decrease in accuracy), 31.4% for MNIST-DVS (accuracy drop of 3.55%), and 26.5% for N-Caltech101 (with a 5.18% accuracy reduction).

Molecular property prediction often relies on isolated data modalities, where continuous 3D graph neural networks (GNNs) struggle to efficiently capture long-range topological dependencies and exact macroscopic heuristics. In this work, we introduce a parameter-efficient Tri-Branch Modular Fusion Neural Network that synthesizes three orthogonal modalities: 3D spatial geometry (SchNet), discrete topological grammar (SMILES via ChemBERTa), and explicit macroscopic physicochemical descriptors (Deep & Cross Network). By bypassing standard scalar readouts and employing a shared late-fusion architecture, the framework establishes a mathematically rigorous multimodal latent space that effectively resolves the arithmetic and oversmoothing limitations of local message passing. We evaluate the proposed architecture on the QM9 benchmark, targeting the extensive thermodynamic property of atomization energy at 0 K ($U_0^{\mathrm{atom}}$). Through systematic combinatorial ablation and latent bottleneck optimization ($d_e=64$), the tri-modal framework achieves a validation Mean Absolute Error (MAE) of 0.0207 eV. Operating with fewer than one million parameters, this architecture decisively surpasses the sub-chemical accuracy threshold and yields a substantial 20.6% error reduction over a strictly controlled geometric baseline. Ultimately, our findings demonstrate that integrating orthogonal macroscopic and topological data streams provides a synergistic, $\mathcal{O}(1)$ physical shortcut. This multimodal alignment offers a highly efficient alternative to brute-force parameter scaling, establishing a robust surrogate model for high-throughput virtual screening (HTVS) pipelines.

The performance of deep learning models crucially depends on the settings of hyperparameters like learning rate, initialization scale, and weight decay. Hyperparameter transfer aims to make near-optimal hyperparameter settings consistent across model scale, so that large models can be optimized by proxy tuning their smaller, cheaper-to-optimize counterparts. While transfer principles are well-studied in the context of dense neural networks in language and vision tasks, they remain comparatively under-explored for graph neural networks (GNNs). We develop and validate a transfer parameterization for GNNs trained with SGD, Adam, and AdamW. Through theoretical scaling analyses and controlled experiments, we show that the proposed parameterization yields stable feature updates, learning rate transfer, and improved performance as width and depth increase. For SGD, we identify graph-dependent first-layer correction factors and show that their use can accelerate early training in graphs with sparse bag-of-words inputs. For Adam, we explore how different message passing normalizations affect early- and late-training transfer behavior, illustrating the importance of message passing normalization and advocating for an associated hyperparameter. For AdamW, we adapt a parameterization that allows for the joint transfer of weight decay and learning rate. Together, these results provide a practical recipe for scaling GNNs across a variety of learning tasks and training scenarios.

Graph eXplainable AI (G-XAI) is increasingly important for making Graph Neural Networks interpretable and accountable. While a growing number of explainers are available, choosing the right method and assessing the trustworthiness of its outputs remains unclear. Consistent evaluation practices and actionable guidance are still missing, hindering practical adoption. In this paper, we introduce a unified, quantitative benchmarking framework for G-XAI that requires no ground-truth assumptions. We formalize tabular explainability metrics for graph data, evaluating topological structure and node features as independent components. Our large-scale benchmarking study identifies explainers that consistently lie on the Pareto front across metric pairs and tasks, establishing robustly non-dominated solutions - while confirming that no single explainer achieves universal superiority. We distill our findings into actionable G-XAI usability guidelines to support Machine Learning practitioners in evaluating and deploying trustworthy GNN-based pipelines.