Graph Neural Networks

Multimodal graph foundation models aim to learn reusable knowledge from graphs enriched with text, images, attributes, and relational topology, thereby supporting diverse graph-centric and modality-centric tasks. In practice, however, such multimodal graphs are often distributed across decentralized clients, where raw contents and local structures cannot be centrally shared due to privacy constraints. This motivates federated multimodal graph foundation learning, which requires not only transferable representation learning but also intrinsic semantic traceability under strict data isolation. Existing methods usually exchange or store knowledge through parameters, prototypes, embeddings, or compact codebooks, which support optimization and transfer but do not explicitly expose how modality evidence, node semantics, and topology context jointly support predictions. To bridge this gap, we propose FedLAB, a traceable semantic codebook framework that organizes multimodal graph knowledge into typed hierarchical codebooks for modality evidence, node semantics, and topology context. FedLAB further refines these trace units through federated semantic barycenter pre-training while keeping raw multimodal contents and graph structures local. Extensive experiments on 10 benchmarks and 6 downstream tasks show that FedLAB improves over state-of-the-art baselines by up to 7.53%, while preserving a native semantic trace interface.

Spontaneous speech is a vital non-invasive biomarker for Alzheimer's Disease (AD), yet many systems overlook non-linear structural disruptions and clinical heterogeneity in pathological language. We propose a Multi-View Gated Graph Attention Network that transcribes audio via Automatic Speech Recognition (ASR) to construct semantic, dependency, and co-occurrence graphs, characterizing speech through a "content-structure-flow" framework. Notably, the co-occurrence graph leverages Pointwise Mutual Information (PMI) from a normative corpus to quantify narrative logic and linguistic deviation. To address symptomatic diversity, an adaptive gated fusion mechanism dynamically integrates these views. Evaluated on the ADReSSo dataset, our model achieves 90.00% accuracy. Ablation results confirm that the PMI-based graph and heterogeneity-aware gating are essential for robust classification across diverse clinical populations. Our source code is publicly available at https://github.com/opeacc/AD.

Text-attributed graphs (TAGs), where each node carries a natural language description, require models to jointly reason over text and graph topology. Existing approaches often handle the two modalities separately: graph neural networks operate on shallow text features, while hybrids of LLMs and graphs use the language model mainly as a text encoder and delegate structure learning to a separate graph module. We propose method that unifies textual reasoning and graph message passing within a masked diffusion language model, a language model with bidirectional attention and generative decoding. For each graph instance, method linearises a sampled local neighbourhood into a token sequence and injects graph structure through a topology attention mask, which realises message passing over the graph. Because the diffusion language model can both interpret and generate text, the method adapts to different tasks simply by changing the prompt, supporting node classification, link prediction, and cross-dataset transfer with no target-specific fine-tuning. Experiments show that method outperforms graph neural networks, graph transformers, and LLM-based baselines on all three TAG benchmarks across two tasks, improving over the strongest baseline by up to 3.9 points.

Graphs are commonly visualized in 2D, where humans readily interpret spatial relationships, yet such layouts often distort higher-dimensional structure. We propose to embed graphs in high-dimensional space and search for informative 2D viewpoints that optimize aesthetic and readability metrics (e.g., edge crossings and angular resolution), enabled by a novel differentiable surrogate for edge crossings. Numerical experiments show that these viewpoints consistently outperform standard 2D layouts, and can even surpass methods explicitly designed to optimize these metrics. We further introduce DataFly, an interactive system for exploring multiple candidate viewpoints through seamless navigation. A usability study demonstrates that our approach reveals structural patterns that remain hidden in conventional 2D visualizations.

The number of trees is a central computational parameter in Random Forests: increasing it reduces finite-ensemble variability but increases training and prediction cost. Plateau-based tuning adapts this parameter through local comparisons of out-of-bag scores at a geometric triplet of tree counts. After the remaining hyperparameters have stabilized, however, the central triplet point need not converge to a deterministic value; instead, it fluctuates around a stationary regime. This paper develops a stationary-distribution theory for this process. The central ensemble size $B_t$ is modeled as a birth-death Markov chain on a geometric grid, and its stationary distribution is derived through local balance. Under a leading centered folded-normal approximation, equilibrium equations are obtained for the original update rule and a symmetric modified variant, implying that the stationary center $B_*=O(\varepsilon^{-2})$ as $\varepsilon\downarrow 0$. The stationary spread is also characterized. A local Gaussian approximation and a Fokker-Planck interpretation give grid-level variance constants. After conversion to the ensemble-size scale, $σ_{B,*}=O(\varepsilon^{-2})$, while the variance is $O(\varepsilon^{-4})$. The leading relative spread is independent of $\varepsilon$ and controlled by the scale factor and update rule. These results interpret plateau-based Random Forest tuning as a stochastic process rather than a deterministic stopping rule.

Text-Attributed Graphs (TAGs) combine textual semantics with graph structure and are central to many graph learning tasks. However, existing fusion methods often treat text and structure as separate inputs in a shallow, one-way pipeline, which limits deep interaction between modalities and weakens performance under sparse connectivity or cross-graph generalisation. To address this issue, we propose PromptGNN-sim, a bi-directional structure-semantic fusion framework for collaborative GNN-LLM learning. PromptGNN-sim uses a Graph Attention Network (GAT) for semantically aware neighborhood selection by combining structural attention with textual similarity. The selected structural context is then used to generate structure-aware prompts for an LLM, including the target node summary, label categories, and representative keywords from similar neighbors. During training, bi-directional cross-modal contrastive learning and cross-attention are introduced to jointly optimize the GNN and LLM components. Experiments on six public datasets, including Cora, Pubmed, and WikiCS, evaluate accuracy, generalisation, and robustness under cross-task transfer, cross-dataset generalisation, and sparse perturbations. Results show that PromptGNN-sim outperforms classical GNNs, LLMs, and recent GNN-LLM fusion methods, demonstrating the effectiveness of interactive structure-semantic collaboration for text-attributed graph learning.

Detecting communities in heterophilic graphs -- where connected nodes often belong to different classes -- is hard for unsupervised methods: classical modularity and spectral methods are feature agnostic, while deep graph-clustering methods rely on contrastive or generative machinery that is opaque. We propose Curvature-Guided Sheaf Diffusion (CGSD), a fully unsupervised community-detection algorithm that uses the discrete Forman--Ricci curvature of each edge as its single topological signal, propagated through every stage of an end-to-end pipeline. CGSD makes three concrete contributions: (i)~a curvature-gated sheaf-diffusion encoder that gates edge messages by $σ(κ_e)$ and is trained from three label-free structural losses (modularity, anti-collapse, curvature-weighted reconstruction); (ii)~a curvature-aware spectral clusterer (CSpec) that re-weights the $k$-NN affinity of the embedding by $σ(ακ_{e^*})$ before Ng--Jordan--Weiss; and (iii)~a unified label-free evaluation against nine truly-unsupervised baselines. On five heterophilic benchmarks (Cora, Cornell, Texas, Wisconsin, Chameleon), CGSD wins outright on Wisconsin and Chameleon and is competitive on the remaining three against nine unsupervised baselines. The gain over the strongest baseline is driven by the clusterer, not the encoder: on the same embedding, CSpec improves mean NMI from $0.091$ with $K$-Means to $0.107$ ($+15\%$, paired $t$-test $p=0.008$). The mechanism is interpretable: intra-community and inter-community curvature distributions are visibly separated. Code is open-sourced at https://github.com/woodywff/cgsd.

Existing robot policies based on learned visual embeddings lack explicit structure and are sensitive to visual distractions. Thus, the representations that drive their behaviour are often opaque, making their decision-making process difficult to interpret. To address this, we introduce Structured Image Representations (SIR), a method that leverages Scene Graphs (SGs) as an intermediate representation for robot policy learning. Our approach first constructs a fully connected graph, using image-derived features as initial node representations. Then, a module learns to sparsify this graph end-to-end, creating a task-relevant sub-graph that is passed to the action generation model. This process makes our model intrinsically explainable. Evaluations on RoboCasa show that our sparse graph policies outperform image-based baselines on average with 19.5% vs 14.81% success rate. Most importantly, we show that the learned sparse graphs are a powerful tool for model analysis. By analysing when the model's sub-graph deviates from human expectation, such as by including distractor nodes or omitting key objects, we successfully uncover dataset biases, including spurious correlations and positional biases. https://github.com/intuitive-robots/SIR_Model

Graph Neural Networks (GNNs) deployed in real-world systems typically have fixed weights, often leading to degraded performance under distribution shifts. This issue can be mitigated by conventional fine-tuning, but in many real-world cases, collecting labeled data is expensive or infeasible. A potential approach is Test-Time Training (TTT), which adapts models' weights using unlabeled test data, yet it is typically limited to shallow updates that affect only a subset of model parameters. We propose T3R, leveraging multiple Rotograd matrices to improve task affinity between the target and auxiliary tasks, essential for effective test-time training. T3R further introduces a rotation technique that reorients self-supervised signals using these matrices to create surrogate gradients for the target task, allowing deeper adaptation across nearly the entire architecture. Empirically, T3R reduces MAE by 0.172 points over standard inference in regression datasets and achieves at least 9.37% relative improvement on cross-domain OGB classification benchmarks compared to models without adaptation. These results highlight the potential to develop an adaptation pipeline for graph-based systems, particularly in settings where conventional fine-tuning or retraining is infeasible.

Graph anomaly detection (GAD) on text-attributed graphs (TAGs) is vital for applications such as fraud detection and academic integrity verification. Existing approaches generally fall into two paradigms. GNN-based methods effectively capture structural patterns but struggle to capture fine-grained textual semantics. Methods integrating LLMs with graphs improve semantic understanding yet fail to fully comprehend topological relationships among neighboring nodes. Moreover, both paradigms overlook the correspondence between textual semantics and graph topological relationships, limiting their ability to identify nodes whose semantics are inconsistent with their neighborhoods. In this paper, we formalize TAG anomaly detection as a node-to-neighborhood semantic consistency problem, where anomalies may arise from either textual semantic mismatch or topological deviation between a node and its neighbors. We propose N2NSC (Node-to-Neighborhood Semantic Consistency), a framework that captures the correspondence between graph topology and textual semantics through two complementary fusion paths. The two pathways work synergistically, enabling the LLM to fully leverage both textual and structural neighborhood information for anomaly detection. Extensive experiments across eight datasets demonstrate that N2NSC consistently outperforms current state-of-the-art methods.

With the rise of data-intensive science, algorithms have become central to scientific research. In academic papers, algorithms are mentioned for different purposes, such as describing, using, comparing, or improving methods for specific research tasks. Identifying these purposes can reveal relationships among algorithms and help assess their roles and value. Taking natural language processing (NLP) as an example, this study proposes a sentence-level framework for identifying, analyzing, and tracing the evolution of motivations for mentioning algorithms. We first identify algorithm entities and algorithm-related sentences from full-text papers through manual annotation and machine learning. We then classify mention motivations using pretrained models and data augmentation, and analyze their distribution and temporal evolution. The results show that deep learning models trained with augmented data outperform traditional machine learning models in motivation classification. In NLP papers, more than half of algorithm-related sentences express direct use, whereas improvement is the least frequent motivation. The diversity of motivations has increased over time. For specific algorithm categories, grammar-based algorithms are more often mentioned for description, while machine learning algorithms are more often mentioned for use. Over time, use motivations have gradually replaced description motivations across different algorithms, and the number of motivation types associated with individual algorithms has declined significantly. This study reveals how authors mention algorithm entities in academic writing and provides a basis for future research on algorithm relationship identification and algorithm impact evaluation.

Graphs are widely used to model relational systems, with applications in domains such as social networks, finance, and biomedicine. Graph neural networks (GNNs) have become a mainstream approach for learning graph representations. With the rise of large language models (LLMs), recent studies have attempted to combine GNNs with LLMs. However, most existing works concentrate on node-level and edge-level tasks, while graph-level tasks, which require capturing more complex structural and feature information, remain relatively underexplored. Moreover, graph pretraining is a widely adopted strategy to alleviate the challenge of label scarcity. Most existing approaches are designed solely for GNNs such as GraphCL, leaving LLMs uninvolved in the process. To address these limitations, we propose GLIP, a Graph-LLM JoInt Pretraining framework for graph-level tasks. GLIP first performs graph augmentation to construct positive and negative pairs and introduces a multi-token selection strategy to identify patches informative in both structure and features. It further leverages a diffusion-based projector to enrich them with contextual information, enabling GLIP to capture signals from both global and local perspectives. Finally, GLIP employs a joint objective that integrates the LLM's semantic judgments with a contrastive alignment loss, ensuring consistent supervision at both the semantic and structural levels. After pretraining, GLIP is fine-tuned with limited labeled data for downstream tasks, and extensive experiments show that it outperforms state-of-the-art methods on graph-level classification and reasoning tasks. Our source code is publicly available at https://anonymous.4open.science/r/GLIP.

The application of graph data in numerous disciplines raises the need for gathering and analyzing huge volumes of data, some of which is private and sensitive. The non-Euclidean nature of the graph data makes the analysis computationally challenging, leading to the use of Graph Neural Networks (GNNs) in the age of AI. GNNs may inadvertently leak sensitive data they are trained on, which raises serious data security issues, including the model inversion attack. In this study, we analyze GNNs' vulnerabilities by introducing two novel graph inversion (i.e., reconstruction) attacks: graph-label conditioned (GLC) attack and embedding-label conditioned (ELC) attack, utilizing targetmodel predictions and their intermediate representations, respectively. We perform a comprehensive analysis of our introduced privacy attacks and compare them with existing baselines across three benchmark graph datasets (i.e., NCI1, PROTEINS, and AIDS) and four graph distributional/structural metrics (i.e., FGD, EGD, MMD, and GKS). Our work demonstrates that an adversary can use the generator-discriminator technique to reconstruct high-quality graphs in real-world black-box attack scenarios against GNNs. Additionally, we present a variant of our attacks (Ours--) with 50% reduced queries, achieving good or comparable reconstruction attack performance. In addition, we show that GNNs are highly vulnerable to privacy attacks, varying Laplacian noise-scales.

Predicting a material's properties from its structure is a central, fast-advancing problem in computational materials science. A decade of work has produced standard public benchmarks and many published machine-learning models for the task (Dunn et al., 2020). The task's fixed metric and these baselines make it a natural setting for autonomous agent research (Karpathy, 2026). On the MatBench band-gap benchmark ($>$100k crystals), a general-purpose coding agent autonomously built the most accurate model trained without external pretraining, ahead of all seventeen expert-designed models reported for the task. A closer analysis shows it reached this by implementing known methods: either already standard in crystal neural-network models, or borrowed from other areas of machine learning. The contributing implementations include element-pair features on each message-passing edge and a crystal space-group embedding. The work not only demonstrates that LLM-agent autonomous research can optimize an expert-designed machine learning model for material property prediction, but also investigates the limitations of such autonomous research.

Heterogeneous graph neural networks (HGNNs) have achieved strong performance in modeling complex graph-structured data with multiple node and relation types. However, their robustness under realistic black-box adversarial settings remains insufficiently explored. Existing attacks on HGNNs usually assume access to model gradients, soft prediction scores, or the complete graph structure, which is often unavailable when HGNN-based services are deployed as closed systems. In this paper, we propose Blackknife, a hard-label, query-limited, and structure-limited black-box evasion attack framework for heterogeneous graph neural networks. Blackknife assumes no access to the victim model architecture, parameters, gradients, logits, confidence scores, or the full graph structure. Instead, it only relies on locally observable one-hop heterogeneous structures and a small number of hard-label queries. To generate effective perturbations under these strict constraints, Blackknife first constructs a local relation-aware surrogate model from observable heterogeneous neighborhoods. It then relaxes discrete edge addition and deletion operations into continuous soft weights and optimizes them through projected gradient descent. Finally, the optimized perturbations are discretized into relation-preserving structural rewiring operations and verified using limited hard-label feedback from the victim model. Extensive experiments on three benchmark heterogeneous graph datasets, including ACM, DBLP, and IMDB, demonstrate that Blackknife consistently achieves strong attack success rates against representative HGNN models. The results further show that Blackknife remains effective under topology-based defense strategies, revealing the vulnerability of HGNNs to local structure-limited black-box attacks.

A Knowledge Graph (KG) represents facts as structured triples and is widely used to organize relational knowledge across diverse domains. Just as textual information ranges from words and sentences to complete documents, KG information can be interpreted at multiple levels, from entities, relations, and triples to subgraphs and entire KGs. However, existing KG embedding methods mainly focus on entities, relations, and triples, leaving graph-level semantics largely unaddressed. Conventional graph-level methods, which typically compare graphs based on structural patterns, are also insufficient because structural similarity alone cannot guarantee semantic similarity between KGs. To evaluate how well different methods capture such graph-level semantic information, we study graph-to-graph semantic similarity, which determines whether a pair of KGs represents semantically corresponding underlying information. To obtain reliable ground-truth correspondences, we construct a semantic matching dataset by modifying text documents, extracting KGs from both original and modified documents, and transferring their known correspondences to KG pairs. We compare text-based, structure-based, and KG embedding-based approaches on each dataset. For the KG embedding-based approach, we introduce two scoring functions: \textit{EmbPairSim}, which uses maximal pairwise entity similarity, and \textit{AvgEmbSim}, which uses a frequency-weighted centroid. Experiments on WikiText-2 and CC-News show that \textit{EmbPairSim} achieves up to 5.3 pp higher MRR than Sentence-BERT while using substantially fewer parameters. These results suggest that KGE representations can serve as compact and effective signals for graph-to-graph semantic similarity in KGs. Our code is available at https://github.com/SeungRyeolBaek/KG-to-KG-Semantic-Similarity.

Detecting security threats in an organization's cloud computing environment has become necessary due to the increased reliance on cloud infrastructure. Logging of all cloud computing events enables investigation into any incidents after they are detected. Automated detection of threats using the logs based on heuristics or anomaly detection could result in a high false positive rate due to its relatively static nature. In this article, we present an industrial case study of a self-supervised learning method using graph neural networks applied to AWS CloudTrail logs to surface suspicious events for analyst review. The model produces an anomaly score for each event and dynamically adapts to changes in the organization without requiring periodic retraining. Based on our experiments across five organizations, the proposed model produced substantially fewer alerts than a domain expert rule-based baseline in almost all cases, reducing alert volumes to approximately 1 per hour from thousands generated by traditional methods. We note that this evaluation covers only flagged events, and false negatives cannot be estimated from the current data; findings should therefore be interpreted as a practical deployment study offering insights into real-world constraints rather than a fully validated detection system. We discuss these limitations and the requirements for extending the approach to other cloud environments as future work.

Modern machine learning models are trained by optimizing high-dimensional non-convex empirical risk functions. Such cost functions can have a multitude of local optima and yet, gradient-based optimization appears to converge to near-global optima. Within a simple supervised learning setting, we develop a precise picture of which parts of the empirical risk landscape are accessible by polynomial-time algorithms. We are given i.i.d. pairs $\{(\boldsymbol{x}_i,y_i):\; 1 \le i\le n\}$ with $\boldsymbol{x}_i\in \mathbb{R}^d$ standard Gaussian feature vectors, and $y_i\in\mathbb{R}$ response variables that depend on $\boldsymbol{x}_i$ through their projections on an unknown $k$-dimensional subspace. We use empirical risk minimization to learn a model that depends on an $m$-dimensional projection of the data (e.g., an $m$-neurons neural network). We propose an incremental approximate message passing (IAMP) algorithm and precisely characterize the training error it achieves, as well as the relation between test and training error, in the high dimensional asymptotics $n,d\to\infty$, with $n/d\toα\in (0, +\infty)$. Based on earlier work in related models, we expect that the performance achieved by our algorithm is optimal among polynomial-time algorithms.

Graph-based fraud detection is essential for safeguarding large-scale transaction systems, where undetected anomalies may lead to substantial financial losses and security risks. Real-world fraud graphs pose two coupled challenges: sparse and imbalanced supervision, where verified fraudulent labels are scarce and heavily skewed toward benign accounts, and representation dilution, where spatial message passing may oversmooth camouflaged anomalies while spectral filters may suppress fraud-relevant mid- and high-frequency irregularities. To address these challenges, we propose ADC-GNN, short for Attention-guided Diffusion-Contrastive Graph Neural Network, a unified framework that combines diffusion-guided feature augmentation, contrastive representation learning, and multi-hop spectral attention for few-shot graph fraud detection. The diffusion component is formulated as a feature-space denoising augmentation mechanism rather than a full topology-generative graph diffusion model: it constructs noise-perturbed node-feature views under a cosine schedule and uses contrastive learning to stabilize node representations across perturbations. The spectral attention module further adaptively emphasizes fraud-relevant hop-level and relation-level cues. We evaluate ADC-GNN primarily on three public benchmarks and additionally report a proprietary real-world telecom transaction dataset with approximately 60,000 records as a private case study. Under the 1% training setting, ADC-GNN achieves consistent improvements over original graph fraud baselines and four protocol-consistent recent graph anomaly/fraud baselines on the public benchmarks. Additional analyses on split stability, training ratios, oversampling alternatives, module-level ablations, diffusion schedules, and runtime and memory-consumption comparisons further characterize the effective operating regime of ADC-GNN.

Single-cell RNA sequencing (scRNA-seq) clustering is essential for identifying cell types, but high dimensionality, sparsity, dropout, and technical noise hinder robust expression representation and cell graph construction. Existing masked autoencoders mainly use expression recovery for feature reconstruction, while graph clustering methods usually depend on fixed KNN graphs and do not feed recovered expression back into graph optimization. We propose scKDGM, a KAN-guided dynamic graph masked learning framework for scRNA-seq clustering. scKDGM uses graph-aware distribution preserving gene masking (GDP-Mask) to perturb cell identity, a KAN-based TAKGCN encoder to learn masked-view representations, mask-guided expression recovery to construct a dynamic graph, and cross-view contrastive learning to transfer recovery signals into topology updates. A ZINB loss models overdispersion and zero inflation. Experiments on 12 real scRNA-seq datasets show that scKDGM outperforms 10 baselines in average NMI and ARI.

This paper formulates frame-level freeway risk assessment as a multi-agent scene graph-level binary classification problem, where each video or trajectory frame is labeled risky if any TTC- or PET-based conflict violates a specified severity threshold. We construct a relation-aware graph per frame with vehicles as nodes and two interaction types as edges: same-lane (longitudinal) and adjacent-lane (lateral), augmented with physics-informed edge features aligned to rear-end and lane-change conflict mechanisms. Building on a structured benchmarking suite of non-graph models and graph baselines, we propose HIA-GAT, a dual-stream heterogeneous graph attention network that processes longitudinal and lateral interactions through dedicated attention pathways and fuses them via a conflict-type-aware gating mechanism with event-level gate supervision derived from SSM conflict attribution. Experiments on the NGSIM I-80 and US-101 freeway datasets across nine TTC and PET threshold configurations show that HIA-GAT achieves the best average risk-ranking performance (AUC 0.835 on I-80 and 0.867 on US-101), with the largest gains on PET-only (lane-change) settings where relational structure is essential. Beyond accuracy, the learned gate provides interpretable per-vehicle attribution of dominant conflict type, supporting actionable, real-time freeway safety monitoring. We show that graph structure is critical for modeling lateral conflict risk, while longitudinal risk can often be captured by non-relational aggregation.

Understanding which genes control which traits in an organism remains one of the central challenges in biology. Despite significant advances in data collection technology, our ability to map genes to traits is still limited. This genome-to-phenome (G2P) challenge spans several problem domains, including plant breeding, and requires methods capable of reasoning over high-dimensional, heterogeneous, and biologically structured data. Current datasets and data repositories, however, are not well-equipped for this task. Current studies do not link gene expression and trait data, and most focus on very specific traits, limiting the breadth of possible correlations. To address this gap, we present the novel Gene-Graph Regression for Arabidopsis Functional Traits (GRAFT) dataset, a curated multi-modal dataset linking gene expression profiles with phenotypic trait measurements in Arabidopsis thaliana, a model organism in plant biology. GRAFT supports tasks such as phenotype prediction and interpretable graph learning. In addition, we benchmark conventional regression and explanatory baselines, including a biologically-informed hypergraph baseline, to validate gene-trait associations. To the best of our knowledge, this is the first dataset to provide multimodal gene information and heterogeneous trait or phenotype data for the same Arabidopsis thaliana specimens. With GRAFT, we aim to foster research to accurately understand the relationship between genotypes and phenotypes using gene information, higher-order gene pairings, and trait data from multiple sources.

Graph neural networks have moved from a niche representation-learning technique to the default model class wherever data carry relational structure. The interesting question is no longer whether message passing helps on a given dataset, but where graph structure earns its computational cost and where it does not. This survey organises the field around a single design space, derives the spectral and spatial formulations from shared first principles, and connects expressive power to the Weisfeiler-Leman hierarchy with explicit statements of what current architectures can and cannot separate. Against that methodological backbone we examine twelve application domains, among them recommendation and social networks, knowledge graphs and language-model integration, drug discovery and molecular property learning, healthcare and neuroscience, computer vision, traffic and urban computing, power and renewable-energy systems, wireless and sixth-generation networks, fraud and cybersecurity, industrial prognostics, materials science, and climate modelling. For each domain we specify the graph-construction choices and their costs, identify which architecture families dominate and why, and separate reported gains from artefacts of weak baselines or favourable splits. A cross-domain comparison exposes recurring patterns: heterophily and scale undercut the same models almost everywhere, temporal graphs remain harder than their static counterparts, and the architectures that top public leaderboards are seldom the ones that reach deployment. We treat over-smoothing, over-squashing, robustness, distribution shift, fairness, and explainability not as a closing checklist but as the constraints that decide adoption.

Kolmogorov Arnold networks (KAN) have recently been introduced as a (deep) neural network architecture whose trainable parameters adapt the activation functions, instead of the coefficients of the affine transformations at the core of traditional architectures such as deep multilayer perceptrons (MLPs). This architecture builds on the Kolmogorov-Arnold theorem, which endows it with universal approximation properties. While the advent of KANs has been received with excitement, there is a current debate about the possible KAN supremacy over deep multilayer perceptrons (MLPs) for classic fields such as symbolic regression, generic-purpose machine learning, natural language processing or computer vision. Here we assess the performance of KANs --and its nuanced comparison against MLPs and graph neural networks (GNNs)-- in the realm of fluid dynamics surrogate modelling. To that aim, we consider the task of predicting the surface pressure distribution over subsonic and transonic airfoils, a canonical task in aerodynamics. Our results show that KAN models show good performance in predicting the whole pressure coefficients and is able to interpolate across Mach numbers and angles of attack, however its performance is comparable --marginally inferior-- to a suitably trained MLP, where best performance is achieved by a GNN at the expense or requiring lengthier training. While the optimal KAN model have typically much lower complexity than MLP and GNN --hence resulting in faster training--, we find that KANs suffer from training instabilities, and their performance is highly dependent on a proper hyperparameter optimisation.

Existing homomorphic encryption (HE)-based GNN systems adopt a graph-centric paradigm that couples per-query cost to global graph size, limiting evaluations to at most ~20k nodes and making them incompatible with dynamic, large-scale financial graphs. We propose TGHE (Template-based Graph Homomorphic Encryption), an ego-centric framework that resolves this by exploiting a template phenomenon: local computation trees in transaction graphs converge into a small set of structural shapes. TGHE canonicalizes ego-graphs at the edge and packs structurally identical trees into shared CKKS ciphertexts for SIMD-parallel encrypted inference, with two long-tail optimizers (Approximate Template Fitting and Topology Collapse) ensuring full SIMD coverage. On DGraphFin (3.7M nodes, 4.3M edges), TGHE-Collapse achieves a 66.9x speedup over the sequential encrypted baseline with less than 0.002 AUC loss.

Graph Neural Differential Equations (GNDEs) model continuous-time graph dynamics by parameterizing Neural ODE velocity fields with Graph Neural Networks. Their local, size-independent filters suggest a zero-shot size-transfer principle: train on a small graph and deploy on larger, similar graphs without retraining. We develop a quantitative theory for this principle on sparse random graphs sampled from graphons. We consider Graphon Neural Differential Equations (Graphon-NDEs) and adjoint Graphon-NDEs as the infinite-node limits of the forward and adjoint GNDE systems, and establish well-posedness. For an $n$-node random graph with sparsity parameter $α_n$, we prove trajectory-wise convergence of GNDE solutions to Graphon-NDE solutions at rate $O((α_n n)^{-1/2})$, up to logarithmic factors, with high probability. We also establish uniform-in-time convergence bounds for adjoint systems governing hidden-state and parameter gradients. We further study discretize-then-optimize (DTO) and optimize-then-discretize (OTD) training. Under explicit Euler discretization with $M$ steps, we show that DTO and OTD are asymptotically consistent, with hidden-state and local parameter-gradient discrepancies of orders $O(1/M)$ and $O(1/M^2)$, respectively, up to sparsity and logarithmic factors. Experiments on HSBM and tent graphons support the theoretical rates, while zero-shot transfer experiments across four graphon classes demonstrate accurate deployment of learned GNDEs on larger independently sampled graphs.

Spatial pattern matching is the process of matching query entities and constraints with database entities and relations. It has many applications, including similar region search, housing market search, landmark search, and road network matching. To our knowledge, all existing spatial pattern matching approaches frame the problem in a 2 dimensional space, where entities lie in a cartesian plane and relationships defined between them are contained in 2 dimensions. However, this problem framing has significant limitations when searching for real world entities that have height in addition to position. To address this limitation, we extend spatial pattern matching to 3 dimensions and provide a generalized definition of the problem. We describe a subgraph matching algorithm capable of resolving 3D spatial patterns over distance relations and release two 3D spatial pattern matching datasets, one synthetic and one containing real 3D building data from the city of Hamburg, Germany. We test our subgraph matching algorithm on both datasets and present results as a baseline for future methods to build upon.

A Graph Neural Network (GNN) framework for predicting the solvability of finite groups from their Cayley graph representations was introduced in [1]. In the present work, we generalize this approach and develop a property-independent framework for learning algebraic properties of finite groups directly from Cayley graphs. As representative case studies, we consider abelianity, nilpotency, and solvability. Using a common GNN architecture and training pipeline, we investigate the extent to which algebraic structure can be recovered from graph-based representations alone. Results on a collection of finite groups drawn from several families demonstrate that the framework successfully learns and distinguishes multiple algebraic properties from their associated Cayley graphs. These findings suggest that substantial algebraic information is encoded in graph representations and can be extracted through GNNs. More broadly, the proposed framework provides a proof of concept for applying graph representation learning to the study of algebraic properties of finite groups.

Risk stratification for pulmonary embolism (PE) is critical for clinical decision-making. Stratification guidelines are based on patient medical records, parameters measured from computed tomography pulmonary angiography (CTPA), and blood tests. However, blood tests are often missing in routine practice. This work studies whether state-of-the-art models can accurately classify risk stratification from only medical records and biomarkers extracted from CTPA images. We benchmark different approaches to combine medical records and cardiac biomarkers with rich pulmonary vascular information; we add vascular biomarkers to tabular models and apply graph neural networks (GNNs) on the vascular tree's intrinsic graph representation. We use a private dataset (n=353) with uniquely complete data for PE risk stratification. Our results show that, among global features, medical records and cardiac biomarkers are the most significant predictors, while vascular biomarkers do not further improve stratification. Even more surprising, even GNNs on vascular graphs fail to outperform strong tabular baseline on global features. We consider hypotheses, on both models and data, that could explain this suboptimal performance. Our investigation suggests that, counter-intuitively, vascular graphs might hold no discriminative information for PE risk stratification. Code is available from https://github.com/creatis-myriad/GENESIS.

Commodity futures can be represented hierarchically, with underlying assets at the upper level and individual futures contracts at the lower level. Entities at each level can be connected by edges reflecting inherent correlations, with cross-level edges capturing contract-to-underlying asset connections. Building on our observations of these structures, we propose a hierarchical graph learning approach for calendar spread (CS) strategies in commodity futures markets, addressing two significant gaps in the machine-learning literature: (i) the absence of learning-based methods for CS strategies in futures markets, and (ii) the lack of consideration of maturity-dependent interrelationships across commodity futures. We first establish the efficacy of CS strategies by analytically showing that CS strategies can possess higher risk-adjusted returns, measured by the information ratio, and lower risk, measured by variance and delta, than long-only strategies. We then introduce a method to convert learning-based predictions into CS positions. Next, we develop a hierarchical graph learning method that predicts futures price movements by utilizing the maturity-dependent interrelationships, thereby yielding a CS trading algorithm. Empirical results on commodity futures markets traded on the Chicago Mercantile Exchange Group demonstrate that our method outperforms benchmark models in both prediction and trading performance. We find that maturity-dependent interrelationships across commodity futures are instrumental in prediction and that CS trading based on hierarchical graph learning is effective for statistical arbitrage.

As graph neural networks (GNNs) become standard tools for critical tasks in circuit design and analysis, their security and privacy risks require careful attention. Here, we present the first comprehensive evaluation of gradient leakage attacks (GLAs) on GNNs in circuit-design and hardware-security tasks, a practical threat that has been largely overlooked. We assess state-of-the-art (SOTA) GNNs, including GraphSAGE, GCN, GIN, and GAT, trained on standard netlist benchmarks (ISCAS'85, EPFL, and TrustHub), for their fundamental vulnerability to GLAs. We find that GLAs can expose sensitive information, such as gate types and distinctive properties of hardware Trojans, which may assist adversaries in analyzing logic locking schemes or evading Trojan detection mechanisms. Our analysis shows that these risks are influenced by architectural features, with attention mechanisms (GAT) exacerbating leakage, while injective aggregation (GIN) provides comparatively stronger resilience. We further evaluate several SOTA defense techniques, including differential privacy, gradient clipping, secure aggregation, model compression with quantization, and adversarial training. We find that these techniques improve resilience only in specific settings and can also compromise model performance. Overall, our work provides key insights toward privacy-preserving GNNs and highlights the need for more robust and efficient defenses. We release our full methodology and artifacts.

Mathematical knowledge is organized around statements and their dependencies, but this structure is exposed unevenly: informal papers cite mostly at the document level, while formal libraries record fine-grained dependencies over a much smaller body of mathematics. We introduce TheoremGraph, a unified statement-level dependency graph spanning both informal and formal mathematics. On the informal side, we parse 11.7M theorem-like environments from mathematics arXiv and recover 18.3M candidate directed dependencies, each labeled by the extractor that proposed it so downstream users can trade coverage for precision. On the formal side, we release LeanGraph, a Lean 4 elaborator-level extractor producing 388,105 declaration nodes and 11.3M typed edges across 25 Lean projects. We bridge the two graphs by embedding generated natural-language slogans into a shared semantic space, linking related statements across papers and across the informal/formal divide; an LLM judge affirms 47,952 such matches above a 0.8 cosine floor, with the judge-acceptance rate rising from 48% across the floor to 87% in the >=0.9 tier. On formal concept retrieval, our name-and-signature representation with graph expansion comes within 0.5pp of LeanSearch v2's reranked Recall@10 (0.775 vs. 0.780) without an LM reranker. We release the dataset, extractors, HTTP API, and MCP interface as infrastructure for mathematical search, attribution, and retrieval-augmented reasoning, available at theoremsearch.com and huggingface.co/datasets/uw-math-ai/theorem-matching.

Positional encodings (PEs) are essential for Transformers. Yet designing effective PEs for non-Euclidean graphs remains challenging. Such encodings should ideally induce an Attention-Compatible Geometry for self-attention: not merely describing graph structure, but defining a geometry whose inner products reflect meaningful structural relatedness. To realize this geometry, we propose Communicability-Inspired Positional Encoding (CIPE), built from communicability, a measure between pairs of nodes that aggregates contributions from paths of all lengths. By construction, CIPE inner products recover communicability, converting global multi-path connectivity into an attention-ready similarity geometry. For practical Transformer training, we introduce dimensionality alignment, mapping graph-size-dependent CIPE representations to prescribed dimensions while faithfully preserving the induced geometry. Empirically, CIPE improves structure-agnostic Transformers by 35.5% on average across seven benchmarks, outperforming representative PEs; it also consistently improves structure-biased graph Transformers, where competing PEs often yield only marginal benefits. These results position CIPE as a principled framework for attention-compatible graph positional encodings.

Unmanned aerial vehicles (UAVs) are increasingly employed in urban inspection tasks, where reliable communication is critical but challenging due to the severe spatial channel heterogeneity. To address the issue, in this paper, we focus on the communication-aware path planning for multi-UAV tasks, and propose a channel knowledge map (CKM)-driven trajectory planning framework which integrates the channel modeling and trajectory decision-making. Specifically, we apply the diffusion model to construct a time-accumulated CKM and achieve the accurate perception with low flight overhead, which leverages the sparse observation data to reconstruct the high-fidelity global channel quality distribution. Based on the CKM, we propose a global-to-local graph attention network soft actor-critic algorithm. The graph attention network optimizes the complex combinatorial node ordering problem, generating an optimal and communication-aware sequence for the inspection targets. Subsequently, the soft actor-critic algorithm performs continuous action control to ensure the smoothness of the flight path and dynamically avoid communication attenuation areas. Simulation results demonstrate that the proposed method effectively guides UAVs through high-quality channel regions without dependence on real-time channel feedback, significantly improving both the trajectory efficiency and communication reliability.

Due to the wide use of graph-structured data in different fields of industry and science, the development of Graph Foundation Models (GFMs) has recently attracted a lot of attention. While many different types of models are called GFMs, particular interest has been paid to GFMs designed for node property prediction tasks, which is one of the most popular settings in Graph ML with lots of real-world applications from fraud detection in financial and social networks to recommendation systems for e-commerce and user-generated content platforms. While a number of GFMs for this task have been recently proposed, the field has not converged to a unified evaluation setting, and different works evaluate their models in widely different ways, preventing reliable comparison of GFMs with each other and with other types of models. In this work, we conduct a fair and rigorous reevaluation of 9 recent GFMs for node property prediction, comparing them to strong Graph Neural Network (GNN) baselines. We find that, among these GFMs, only the most recent ones based on the Prior-data Fitted Networks paradigm outperform well-tuned GNNs in predictive performance, although at a higher inference cost.

Accurate particulate matter (PM) prediction is crucial for mitigating air pollution. Graph Neural Networks (GNNs) effectively model spatiotemporal dependencies, but predefined graphs limit adaptability, and some datasets complicate learning. This study introduces a graph construction method based on a confusion matrix from a supervised learning process to dynamically capture inter-class relationships. Additionally, a hybrid loss function that combines energy distance and Huber loss is applied to address the vanishing gradient problem and improve learning stability. The approach is evaluated using air pollution data from the University of Utah AirU Pollution Monitoring Network in Salt Lake City, UT, with five GNN models: Graph Convolutional Networks (GCNs), Simple Graph Convolutional Networks (SGConv), Graph Isomorphism Networks (GINs), Graph Attention Networks (GATs), and GraphSage. The experimental results of single- and multistep predictions confirm that GraphSage achieves the highest accuracy in predicting the concentrations of PM${1}$, PM${10}$, and PM$_{2.5}$ over different time horizons. Furthermore, {\color{black} GNNExplainer (Graph Neural Network Explainer) and PGExplainer (Probabilistic Graph Explainer)} are applied to interpret feature importance and graph structure, ensuring model transparency. Results show improved prediction accuracy, with GNN models outperforming traditional machine learning \textcolor{black}{and deep learning models (i.e., Prophet, Long short-term memory, Gated recurrent units} in air pollution forecasting.

Spectral filtering recently delivered substantial pruning for \emph{static} subgraph matching: Laplacian interlacing rejects candidates whose neighborhoods cannot host the query. We study whether such aggregate structural tests can accelerate \emph{continuous} subgraph matching (CSM) over dynamic graphs, and answer in three parts. First, lazily maintained spectral bounds are infeasible exactly where spectral pruning has value: we characterize the tightest safe rule over a formalized perturbation relaxation and show that even it loses essentially all pruning power within four touching updates. Second, exact maintenance is affordable when selective: pruning utility and recomputation cost are anti-correlated across vertices -- hubs provably never prune -- so recomputing small-neighborhood spectra on touch sustains exact local spectra at microseconds per update, complete by construction. Third, integrated into a decoupled CSM benchmark against an identical-minus-spectra control, the tests remove up to $51\%$ of candidates or safely skip up to $47\%$ of update enumerations, yet enumeration intermediates remain unchanged -- beyond the gates' skipped first-level bindings, typically zero -- across two engines, four real graphs, two stream types, and $77$ solved queries; a constructed radius-stratified workload confirms the instrument detects the exception when one exists ($-99.9\%$ intermediates, $748\times$ faster). Aggregate tests accelerate what scales with candidate sets -- construction, list scans -- never adjacency-guided exploration. We distill an intermediate-invariance methodology for evaluating CSM filters and release a reusable dynamic local-spectra index.

Spectral graph neural networks (GNNs) interpret message passing as frequency-selective filtering. While low-order spectral filters are efficient, their limited selectivity often leads to weak attenuation outside the passband, whereas high-order alternatives introduce optimization challenges. We propose DCQ-GNN, a spectral GNN based on a compact bank of adaptive convex--concave quadratic filters. By restricting the filter order to two while explicitly exploiting complementary curvature, DCQ-GNN improves spectral selectivity as quantified by Dirichlet energy and entropy measures without resorting to high-order polynomial expansions. The model fuses filter outputs through a node-adaptive gating mechanism to enable node-wise structure-aware spectral selection. We provide a formal spectral analysis grounded in Dirichlet energy attenuation, von Neumann entropy, and curvature polarity, and derive explicit characterizations of filter behavior across varying levels of homophily and structural perturbations. Extensive benchmarks on 10 datasets show that DCQ-GNN ties for the top average rank (3.0) on heterophilic graphs and obtains the second-best rank (4.2) on homophilic graphs, remaining competitive with representative high-order polynomial spectral filters. Furthermore, under strong structural perturbations, DCQ-GNN exhibits substantially smaller performance degradation compared to both first-order and high-order baselines. These results demonstrate that curvature-aware quadratic banks provide a robust and efficient alternative to high-order spectral models while preserving optimization stability and computational efficiency.

Federated Graph Learning facilitates collaborative graph modeling across distributed clients while preserving data privacy. However, real-world data categories frequently exhibit long-tailed distributions. Such statistical scarcity severely degrades performance in two ways: it biases the global model toward majority classes, and it structurally isolates minority nodes by submerging them in heterophilic, head-dominated neighborhoods. While existing methods attempt topology-agnostic statistical compensations, they often fail under data scarcity. Instead of recovering tail nodes, they overfit the structural noise from adjacent dominant classes, leading to representation degradation. To address these limitations, we propose FedEPD, a framework built on a dual decoupling paradigm that separates topological purification from semantic recalibration. Specifically, FedEPD utilizes distribution-aware Dirichlet energy pruning to filter spatial heterophilic edges. It then overcomes Non-IID distribution shifts by extracting robust global prototypes from topologically central nodes, which are incorporated into local representations via a spatial low-pass prototype injection. Furthermore, a two stage alternating optimization strategy strictly protects majority decision boundaries while improving minority accuracy. Extensive experiments demonstrate that FedEPD achieves state-of-the-art performance across diverse long-tailed benchmarks, yielding absolute improvements of up to 4.97% in Accuracy and 5.48% in Macro-F1.

We develop a spectral theory for \emph{normalized corrected GNN propagation}. The object of study is the symmetric normalized adjacency with its degree-stationary component removed, matching the normalization used by standard GCN-style models while isolating the stationary direction most directly tied to oversmoothing. The central theoretical question is whether this corrected normalized operator preserves class-discriminative signal after many propagation layers. Our main result is a high-probability exact-recovery theorem for the binary Contextual Stochastic Block Model after $k=O(\log n)$ propagation steps in the dense polylogarithmic regime $p\ge C\log^B n/n$, for any fixed $B>4$, under explicit graph-signal and feature-SNR conditions. We also establish a multi-class partial recovery theorem showing contraction toward class centers for most nodes. Synthetic and real node-classification experiments are included as empirical checks of the theory's predicted dependence on depth, graph signal, and feature noise.

This paper presents SuperCond-GNN, a graph neural network-based surrogate model for predicting the voltage distribution in high-temperature superconducting (HTS) magnets. HTS magnets are modeled as lumped-element equivalent circuits and mapped onto graph representations, enabling message passing GNNs to learn the electrical response as a function of circuit topology, material properties, and operating current. As a proof of concept, tape stacks of up to 10 tapes are considered across a range of circuit topologies and operating conditions. The surrogate is trained on data generated from circuit simulations and achieves a mean MAPE of 4.3 % within the prescribed design space. The predicted nodal voltages enable fast and scalable inference of current redistribution and local operating conditions across a wide range of circuit configurations. The effect of incorporating physics-informed regularization via Kirchhoff's current law is also evaluated, and generalizability to unseen topologies is assessed through zero-shot inference and few-shot fine-tuning. While demonstrated on tape stack circuits, the graph-based framework is topology-agnostic and naturally extensible to more complex HTS cable and magnet configurations, offering a scalable alternative to conventional circuit solvers for downstream applications such as design space exploration, current sharing analysis, and real-time magnet monitoring.

Thin-structure segmentation--power lines, cracks, lane markings at 1-3 pixel width--requires preserving connectivity that standard representations preclude: patching severs continuous structures and conventional superpixels merge thin targets into background before classification. Topology-aware losses penalize connectivity breaks at the objective level but cannot recover what the representation has already destroyed. We propose SEMIR, a framework that replaces the pixel lattice with a parameterized graph minor whose contraction map preserves thin-structure connectivity under the contraction criterion. The minor collapses millions of pixels into tens or hundreds of boundary-aligned supernodes, enabling full-resolution inference without patching at scales demonstrated up to 21 MP in this paper; a lightweight GNN classifies the reduced graph and an exact map lifts predictions to pixel resolution. One pipeline--identical architecture, features, loss, and GNN hyperparameters across all dataset--matches or exceeds domain-specific baselines on TTPLA (power lines), CrackSeg9k (pavement cracks), and SkyScapes Lane (aerial markings) on Dice, IoU, and Boundary F1 while reducing mask fragmentation by at least 4.6x relative to SLIC at matched inference.

Attributed graph clustering partitions nodes by jointly exploiting node attributes and graph topology. It remains challenging due to attribute heterogeneity and representation degradation during graph learning. Real-world datasets often contain heterogeneous attributes, i.e., numerical and categorical attributes, complicating unified representation learning. This challenge becomes more complex in attributed graphs, where constructing a clustering-friendly graph structure from attributes and topology remains difficult. Under deep graph architectures, repeated graph propagation causes node embeddings to become overly similar, leading to the over-smoothing (OS) effect. Meanwhile, graph representation learning amplifies topological influence, making discriminative attribute information harder to exploit for clustering, an effect we refer to as over-dominating (OD). To bridge these gaps, an end-to-end framework, Any-type attributed Graph REpresentation lEarning (AGREE), is proposed. It unifies attributed graphs and any-type attributed data through multi-level alignment and similarity-based graph construction. Quaternion-based graph convolution strengthens attribute interaction to alleviate OD, while shallow graph architectures help relieve OS. The learned embeddings are jointly optimized for graph reconstruction and clustering, without requiring a predefined number of clusters during training. Experiments on diverse benchmarks show that AGREE achieves strong overall performance in accuracy, robustness, and adaptability.

Text-attributed graphs (TAGs) are widely used in many real-world domains, and learning on TAGs requires jointly modeling text semantics and graph structure. A standard approach for modeling TAGs is to combine a language model (LM) and a graph neural network (GNN), but joint training is computationally expensive and difficult to scale. Dataset distillation is a promising way to reduce training costs, but existing methods are not well suited to TAGs because they are typically designed for a single modality or still require repeatedly training expensive LM-GNN models on the full dataset during distillation. To address this, we propose TaLK, an effective dataset distillation method for TAGs that couples an LM with a graph-aware neural tangent kernel. This design enables efficient dataset distillation, avoiding repeated joint training on the full dataset while reflecting both textual and structural information for effective TAG learning. Experiments on multiple TAG benchmarks show that TaLK consistently outperforms existing baselines and achieves up to 97% of full-dataset performance with only 1% synthetic data.

Graph theory is inherently descriptive, capturing what relationships exist but not why they arise, because it treats edges as primitive constructs. This paper proposes a new explanatory framework for graph learning, where relationships emerge from latent continuous information entropy fields, and a graph becomes a discrete instantiation of an underlying field. To formalize this field, we introduce the Field-informed Graph Network (FGN). It learns a scalar field from node features and leverages it to modulate message passing. The information-theoretic objective balances structural fidelity with field smoothness, forming a self-reinforcing loop. In this loop, the field modulates information diffusion through field-modulated weighting, and the updated node representations iteratively refine the field. As a result, FGN learns by simulating its own co-evolution. Extensive experiments on node classification and graph classification benchmarks demonstrate superior performance, robustness to perturbations, and structurally coherent field representations.

We present an exploratory benchmark and quantum-inspired modeling prototype for fraud screening in dynamic financial transaction graphs. Coordinated fraud may not be visible from individual transactions alone, but may emerge as a multi-period relational pattern. We focus on sparse-ring fraud, a stylized pattern in which a completed directed cycle is distributed across several days, requiring models to integrate evidence across both time and graph structure. We study this problem using a synthetic transaction simulator with completed sparse-ring injections and broken-ring decoys. Daily directed transaction graphs are aggregated into rolling windows and represented using raw graph features, persistent-homology summaries, or hybrid feature vectors that combine both. We compare a gated recurrent unit (GRU) baseline with quantum-inspired Contextual Machine Learning (CML) as sequence-level classifiers. Because the benchmark uses synthetic data, a modest sample size, and sequence-level labels, the results are exploratory. Within this scope, topology-only summaries are too compressed to solve the supervised ring-completion task by themselves, largely because they remove account-pair identity and edge direction. The strongest results come from hybrid representations that combine identity-preserving graph features with topological summaries. These findings suggest that topology is most useful as a contextual layer over dynamic graph features, and that CML is a promising candidate model for fraud patterns whose evidence is distributed across temporal and relational context.

This paper studies learning-augmented online weighted vertex cover with advice and a parameter $λ\in (0,1)$. We consider two graph cases: bipartite graphs and general graphs. In both settings, the online algorithm must maintain a feasible vertex cover under irrevocable decisions. We show that these problems admit the same robustness--consistency tradeoffs as learning-augmented ski rental. For the bipartite graph model, we give a randomized algorithm that is $\frac{1}{1-e^{-λ}}$-robust and $\fracλ{1-e^{-λ}}$-consistent. For the general graph model, we give a deterministic algorithm that is $(1+\frac{1}λ)$-robust and $(1+λ)$-consistent. We prove that the tradeoffs above are optimal in both settings. We also validate the proposed algorithms through experiments on synthetic and real-world datasets.

Can one graph represent every kind of LLM agent's run? A trace records what each step did, never what it relied on, the state it read, and the results it reused. GRADE recovers that missing layer: it models any run as one graph over its step nodes with two edge layers, execution edges (what ran in what order) read from the trace for free, and dependency edges (what each step relied on) rarely logged, so each is graded by how it is known, observed, declared, or inferred. One representation, and each layer earns its place. Across six corpora of LLM agents spanning tool use, coding, and the web, the dependency layer can predict failure where run size is weak and, under leave-one-corpus-out transfer, stays above chance on every held-out class while run size fails. Meanwhile, the execution layer localizes the faulting step in a failed multi-agent run. This work also provides a more in-depth analysis of why generic graph neural networks may misread the dependency layer, unlike our feature-based alternative. The same graph representation opens further uses, carrying from failure diagnosis in a single run to efficiency and robustness optimization at scale.

Autonomous mobile robots are expected to exhibit socially compliant navigation for minimizing pedestrian disturbance. While capturing social interactions and incorporating pedestrian motion estimations into decision-making are beneficial for compliance, prior methods fail to address both spatial and temporal characteristics present in real-world data. Reinforcement Learning offers high capability, but it requires hand-crafted reward functions that reduce social behavior to static criteria, limiting its ability to reproduce patterns that exist in real pedestrian behavior. Imitation Learning offers direct training from real-world data but lacks modeling of social interactions and suffers from error accumulation. To this end, we propose an imitation learning framework that leverages spatiotemporal dynamics for socially compliant navigation. To represent social context based on interactions, we introduce a graph-based auxiliary network that encodes crowd states by attending to pedestrians. In addition, we present a navigation module that captures temporal dynamics and mitigates error accumulations by incorporating encoded state predictions and employing a trajectory-level learning objective. Our framework outperforms established data-driven baselines on simulation and a real-world dataset across diverse social metrics.

Pre-trained foundation models have demonstrated remarkable success in many domains, enabling a unified backbone to generalize across diverse downstream tasks. However, extending this paradigm to graph learning remains challenging due to the intrinsic mismatch between graph data and fixed architectural designs. In this work, we show that this limitation can be overcome via recurrent graph models. To achieve this, we conduct a systematic theoretical analysis, rigorously deriving step dependence as a necessary and sufficient condition for an adaptively convergent recurrent process. Building on this foundation, we propose AdaR, an Adaptive Recurrent graph model, empowering flexible test-time computing on various downstream tasks without changing model parameters. To enable adaptive inference, AdaR explicitly encodes normalized step information and representation-target relations into the recurrent updates. To ensure convergence of the recurrent process, AdaR employs gradient-based supervision signals that guide representation updates throughout the recurrence. Empirical results demonstrate that AdaR consistently outperforms strong baselines in both inductive and transductive settings.

Graph neural networks (GNNs) tightly couple their input-output parameters to dataset-specific feature spaces and target sets, exhibiting limited transferability across different datasets. In contrast, language models (LMs) generalize flexibly via a unified input-output interface, motivating recent attempts to adapt LMs to graph tasks. However, existing methods struggle to encode whole-graph information, leading to potential information loss and suboptimal graph understanding. In this work, we propose a novel weight-level information injection paradigm for adapting LMs to graph tasks. This paradigm injects whole-graph information by generating task-specific weight updates that interact directly with hidden representations. Instantiating this paradigm following low-rank adaptation (LoRA), we introduce GaRA, a Graph-aware LoRA generation model. GaRA constructs low-rank weight updates conditioned on the original graph structures and constrains the norm of the generated updates, thus injecting whole-graph information and avoiding the optimization bias in the weight generation. Empirical studies demonstrate that GaRA consistently outperforms baselines on zero-shot graph learning tasks.

Deep learning has demonstrated significant success for modeling biochemical molecular systems, where inputs are commonly represented as graphs or 3D grids. A major challenge is that computational cost scales with resolution, making full graph/grid computation of molecular densities expensive and often unstable. We introduce a multigrid training strategy that leverages low-resolution optimization to accelerate learning at higher resolution through parameter transfer across discretizations. For graph molecular representations, we progressively transfer parameters learned from a coarse graph to a sequence of increasingly finer graphs via biased random walk upsampling. For 3D molecular generation, we voxelize the molecular structures at multiple resolutions, pretrain a coarse-resolution conditional Variational Autoencoder (CVAE), and initialize a fine-resolution CVAE by transferring shape compatible convolutional parameters from the coarse model. Numerical experiments on receptor-conditioned 3D Ligand generation show that multigrid training accelerates convergence and improves generalization compared to training from scratch.

Graph embedding maps graph nodes into low-dimensional vectors to support applications such as recommendation, fraud detection, and graph-based retrieval-augmented generation (GraphRAG). As graphs scale to billions of edges, scalable and efficient graph embedding has become increasingly important. Existing frameworks commonly adopt a sampling-training paradigm, in which mini-batches are constructed by sampling nodes and their neighbors. However, sampling is typically decoupled from evolving embedding quality, causing redundant exploration of well-trained regions while under-sampling undertrained nodes. At the system level, such decoupling further leads to excessive communication, serialized execution, and low resource utilization in distributed environments. We present FeLoG, a feedback loop-driven system for scalable distributed graph embedding. (1) FeLoG introduces feedback-coupled sampling and training, dynamically prioritizing undertrained nodes according to real-time embedding-quality feedback, thereby reducing redundant computation and accelerating convergence. (2) It employs activity-aware communication that compresses frequently occurring node sequences to reduce intra-machine PCIe traffic and selectively synchronizes frequently updated embeddings to reduce inter-machine communication. (3) It adopts a round-interleaved pipeline that overlaps next-round sampling with current-round training to improve CPU-GPU utilization. Experiments against six state-of-the-art baselines on large-scale graphs show that FeLoG achieves an average speedup of 27.9x, reduces communication cost by more than 53.1%, and sustains over 80% CPU-GPU utilization.

Graph Neural Networks are great for link prediction in various network-like structures; however, the question of their speed/quality tradeoff has been barely studied. While in practice the time it takes to do inference matters little for small benchmarks, the latency does limit applicability in large-scale domains. In this work, we explore early-exiting strategies that can be applied to Graph Neural Networks to solve the problem of link-prediction faster. We use no auxiliary losses to enforce early exiting, allowing it to emerge as an implicit property of the architecture. We show that our method enables early exiting in several setups, moving the Pareto frontier on the HeaRT benchmark for GCN and SAS-GNN backbones. Our findings show that inference speed of GNNs on many link-prediction problems can be improved, while losing little, or even winning in terms of prediction quality. The code is available in our repository: https://github.com/knyazer/link_prediction.

In this study, we propose a novel pipeline for generic, model-agnostic, local-level counterfactual explainability in graph neural networks (GNNs). Although counterfactual explainers capable of both adding and removing edges have emerged in recent years, the need for generic and efficient solutions remains unmet, particularly concerning qualitative explanation generation. Our approach couples progress in factual explainability with missing edge prediction models rooted in link prediction research, in order to enhance the quality, robustness and intuitiveness of explanations. A multi-faceted experimental analysis conducted on real-world and synthetic graph classification benchmarks, both binary and multi-label, demonstrates the advancements in comparison to state-of-the-art baselines across diverse metrics.

Training medical image classifiers on entire datasets is wasteful when annotation budgets are limited: not all samples contribute equally, yet acquiring expert labels is expensive. Active learning reduces annotation cost through iterative querying, but assumes repeated access to an oracle and requires multiple rounds of model training. One-shot geometry-based methods such as facility location avoid retraining but operate on pairwise distances that ignore the local structure of the data manifold. We propose a graph-based one-shot selection method that operates entirely on frozen foundation model embeddings. Given embeddings from a pretrained encoder, we construct a k-nearest neighbor graph over all training samples and derive a two-term coverage kernel from the heat diffusion kernel, capturing both direct and two-hop neighborhood relationships. Greedy facility location on this kernel selects class-balanced subsets that maximize coverage of the data manifold. The two-term kernel matches the full spectral heat kernel in selection behavior while reducing computation to sparse matrix operations with a single hyperparameter. We evaluate on five MedMNIST datasets spanning histopathology, radiology, and microscopy, comparing against both training-dynamics and geometry-based baselines. Our method achieves the highest balanced accuracy on nine of ten dataset-ratio conditions, with the largest gains on class-imbalanced datasets where global graph construction captures cross-class structure that per-class methods miss, all without any model training during selection. Code is available at https://github.com/zahiriddin-rustamov/graph-coverage-selection.

Verification of multi-agent systems requires the ability to check meticulous topological properties when it comes to agents that can move through space in continuous time. This demands a logic with sufficient expressiveness to capture these dynamics. MuTGL logic has interesting properties for expressing entangled space-time properties. However, this logic lacks the expressivity needed to analyse reachability within specific distance bounds, or to track the length or the cost of communication chains: these are fundamental for decentralized monitoring, or graph-theoretic analysis of distributed protocols, where algorithmic complexities often relates with the system's communication graph diameter. We then introduce an extension of muTGL, including a new operator called the space horizon. This addition allows us to bound the distance of communication chains, hence enhancing the logic's expressiveness. We show that this operator allows to encode modalities from other logics, such as reachability or escaping which were not available in vanilla muTGL, while allowing a deeper entanglement of spatial and temporal properties. We provide a centralized offline monitoring algorithm for this logic and illustrate it on several examples on simulations of Consensus-Based Bundle Algorithms, distributed protocols for task allocation.

Medical image re-identification (MedReID) enables longitudinal patient linkage but remains vulnerable to shortcut learning and often produces decisions that clinicians cannot audit against named anatomy. We propose Graph-of-Differences (GoD), which grounds identity comparisons in explicit anatomical structure. Each image is represented as an anatomy graph whose nodes correspond to named anatomical regions; given an image pair, soft node correspondence is established, and differences are computed over matched anatomy. A graph-level difference alignment objective ties these anatomy-matched differences to the global backbone difference, ensuring the retrieval signal is anchored in homologous structures rather than arbitrary spatial tokens. Explanations are defined over named graph nodes and quantitatively audited via node insertion/deletion tests, replacing unstable pixel heatmaps with verifiable structure-level evidence. On internal benchmarks, GoD improves Rank-1 by +7.1 pp on fundus and +3.1 pp on CXR over a strong frozen-backbone baseline, with further gains on zero-shot external transfers confirming that anatomy grounding improves both accuracy and generalization. Code is available at https://github.com/GenMI-Lab/GoD.git.

Graph Neural Networks (GNNs) have emerged as a powerful paradigm for learning on graph-structured data by iteratively propagating and aggregating information across edges. However, conventional message passing schemes often suffer from over-squashing, whereby exponentially large neighborhoods are compressed into fixed-dimensional embeddings, impeding effective long-range dependency learning. In this work, we introduce Ramanujan Propagation, a graph rewiring strategy that leverages Ramanujan graphs to alleviate topological bottlenecks in GNNs. We first establish that suitably chosen Ramanujan graphs guarantee non-negative resistance curvature, which mitigates over-squashing and facilitates efficient information flow. We then propose an algorithmic framework to construct a Ramanujan rewired graph that preserves the local connectivity of the original graph. Our experiments demonstrate that our method outperforms nine state-of-the-art rewiring techniques. These results establish Ramanujan graphs as a rigorous structural prior for scalable, topology-aware message passing in GNNs.

Semi-supervised learning (SSL) on data streams is challenging due to the continuous evolution of high-volume data and the scarcity of labels. Existing methods are limited in leveraging the intrinsic relationships among samples because they typically rely on fixed similarity measures or static graph structures, which cannot capture how relationships evolve over time. We propose SLeDGe, an SSL method for data streams that jointly learns a predictive model and an adaptive graph structure under strict memory and label constraints. SLeDGe maintains compact labeled and unlabeled memories using distinct update strategies, balancing rapid adaptation to novel features with the retention of historical consistency. In addition, by encouraging sparsity in the relational graph, SLeDGe filters out spurious connections and enables effective propagation of label supervision. Across 12 datasets, SLeDGe outperforms state-of-the-art competitors, achieving average relative accuracy gains of 31.7% with 0.1% labels and 14.8% with 1% labels.