Graph Neural Networks

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

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

The Zarankiewicz number $\textbf{Z}(m, n, s, t)$ is the maximum number of edges in a bipartite graph $G_{m, n}$ such that there is no complete $K_{s, t}$ bipartite subgraph. We determine for the first time the exact values of three Zarankiewicz numbers: $\textbf{Z}(11, 21, 3, 3)=116$, $\textbf{Z}(11, 22, 3, 3)=121$, and $\textbf{Z}(12, 22, 3, 3)=132$. We further establish lower bounds for 41 more Zarankiewicz numbers, including several that are within one edge of the best known upper bound, and we match the established value in four more closed cases. Our results are obtained using OpenEvolve, an open-source evolutionary algorithm based on Large Language Models (LLMs) that iteratively improves algorithms for generating mathematical constructions by optimizing a reward signal which we tailored for this specific problem. These findings provide new extremal graph constructions and demonstrate the potential of LLM-guided evolutionary search to contribute to mathematical research. In addition to presenting the resulting constructions, we report the generation algorithms produced, describe the relevant implementation details, and provide our computational costs. Our costs are remarkably low, at less than $30 for each Zarankiewicz parameter combination, showing that LLM-guided evolutionary search can be an inexpensive, reproducible, and accessible tool for discovering new combinatorial constructions.

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

While Graph Foundation Models (GFMs) have achieved remarkable success in homogeneous graphs, extending them to multi-domain heterogeneous graphs (MDHGs) remains a formidable challenge due to cross-type feature shifts and intra-domain relation gaps. Existing global feature alignment methods (PCA or SVD) enforce a shared feature space blindly, which distorts type-specific semantics and disrupts original topologies, inevitably leading to "Type Collapse" and "Relation Confusion". To address these fundamental limitations, we propose Decoupled relation Subspace Alignment (DRSA), a novel, plug-and-play relation-driven alignment framework. DRSA fundamentally shifts the paradigm by decoupling feature semantics from relation structures. Specifically, it introduces a dual-relation subspace projection mechanism to coordinate cross-type interactions within a shared low-rank relation subspace explicitly. Furthermore, a feature-structure decoupled representation is designed to decompose aligned features into a semantic projection component and a structural residual term, adaptively absorbing intra-domain variations. Optimized via a stable alternating minimization strategy based on Block Coordinate Descent, DRSA constructs a well-calibrated, structure-aware latent space. Extensive experiments on multiple real-world benchmark datasets demonstrate that DRSA can be seamlessly integrated as a universal preprocessing module, significantly and consistently enhancing the cross-domain and few-shot knowledge transfer capabilities of state-of-the-art GFMs. The code is available at: https://github.com/zhengziyu77/DSRA.

Representation learning is central to graph machine learning, powering tasks such as link prediction and node classification. However, most graph embeddings are hard to interpret, offering limited insight into how learned features relate to graph structure. Many networks naturally admit a role-mixture view, where nodes are best described as mixtures over latent archetypal factors. Motivated by this structure, we propose a compositional graph embedding framework grounded in Aitchison geometry, the canonical geometry for comparing mixtures. Nodes are represented as simplex-valued compositions and embedded via isometric log-ratio (ILR) coordinates, which preserve Aitchison distances while enabling unconstrained optimization in Euclidean space. This yields intrinsically interpretable embeddings whose geometry reflects relative trade-offs among archetypes and supports coherent behavior under component restriction; we consider both fixed and learnable ILR bases. Across node classification and link prediction, our method achieves competitive performance with strong baselines while providing explainability by construction rather than post-hoc. Finally, subcompositional coherence enables principled component restriction: removing and renormalizing subsets preserves a well-defined geometry, which we exploit via subcompositional dimensionality removal to probe how archetype groups influence representations and predictions.

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

We present \textit{CluProp}, a novel framework that reimagines varied-density clustering in high-dimensional spaces as a label propagation process over neighborhood graphs. Our approach formally bridges the gap between density-based clustering and graph connectivity, leveraging efficient propagation mechanisms from network science to mitigate the parameter sensitivity inherent in traditional density-based methods. Specifically, we introduce a deterministic density-based propagation strategy to ensure scalable neighborhood identification. The framework is agnostic to the choice of distance metric and exhibits superior performance on large-scale data, processing millions of points in minutes while consistently outperforming existing baselines in accuracy.

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

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

Gene Regulatory Network (GRN) inference is essential for understanding complex cellular mechanisms, rendered tractable through single-cell transcriptomic data. With the emergence of single-cell Foundation Models (scFMs), enhanced transcriptomic encoding is widely expected to revolutionize GRN inference. However, we observe that their performance remains far from satisfactory. The primary reason is that the standard reconstruction-based pre-training objectives often fail to explicitly capture latent regulatory signals. To bridge this gap, we first introduce a GRN generalization benchmark designed to evaluate regulatory predictions on unseen genes and datasets, which relies on the zero-shot capabilities of scFMs and is inherently challenging for traditional methods. Furthermore, to unlock the regulatory knowledge within the foundation models, we propose two novel methods, Virtual Value Perturbation and Gradient Trajectory, to distill implicit regulatory information from scFMs into highly generalizable inter-gene features. Extensive experiments demonstrate that our approach significantly outperforms existing methods, establishing a new paradigm for leveraging the potential of scFMs in universal GRN inference.

Standard diffusion models for graph generation typically rely on uniform time-stepping, an approach that overlooks the non-homogeneous dynamics of distributional evolution on complex manifolds. In this paper, we present an information-geometric framework that reinterprets the diffusion sampling trajectory as a parametric curve on a Riemannian manifold. Our key observation is that the Fisher-Rao metric provides a principled measure of the intrinsic distance. By analyzing this metric, we derive the Drift Variation Score (DVS), a geometry-aware indicator that quantifies the instantaneous rate of distributional change. Unlike prior heuristic-based adaptive samplers, our DVS solver enforces a constant informational speed on the statistical manifold, automatically maintaining a uniform rate of distributional change along the sampling trajectory. This equal arc-length strategy ensures that each discretization step contributes equally to the information speed. Theoretical analysis verifies that DVS characterizes the local stiffness of the sampling dynamics in the Fisher-Rao sense. Experimental results on molecule and social network generation show that DVS significantly improves structural fidelity and sampling efficiency. Code is at https://github.com/kunzhan/DVS

LLM routing is increasingly important for selecting suitable models under diverse user needs and deployment constraints, but its practical effectiveness depends on continual adaptation to emerging queries and newly released models. New-LLM integration is particularly challenging, as newly released models lack the query-response-reward interactions required for router training and cannot be profiled as directly as new queries via semantic embeddings. Existing profiles are limited: LLM-generated descriptions are often coarse, while interaction-based embeddings are costly to construct. To address this problem, we propose RouteProfile, a graph-based profiling framework that constructs LLM profiles from public signals in technical reports or model cards, including model family, model description, reported benchmark scores, and benchmark domains. RouteProfile organizes these heterogeneous signals into a graph and studies profile construction along four dimensions: organizational form, representation type, aggregation depth, and learning configuration. We evaluate RouteProfile in training-free cold-start routing and new-LLM integration settings. Experiments show that: (1) structured profiles outperform flat baselines in training-free cold-start routing; (2) model family metadata is more reliable than benchmark domain information; and (3) effective new-LLM integration requires profile-router co-design. Overall, our findings highlight the importance of profile design for enabling routing systems to adapt to the evolving model ecosystem.

Electroencephalogram (EEG) signals are vital for automated seizure detection, but their inherent noise makes robust representation learning challenging. Existing graph construction methods, whether correlation-based or learning-based, often generate redundant or irrelevant edges due to the noisy nature of EEG data. This significantly impairs the quality of graph representation and limits downstream task performance. Motivated by the remarkable reasoning and contextual understanding capabilities of large language models (LLMs), we explore the idea of using LLMs as graph edge refiners. Specifically, we propose a two-stage framework: we first verify that LLM-based edge refinement can effectively identify and remove redundant connections, leading to significant improvements in seizure detection accuracy and more meaningful graph structures. Building on this insight, we further develop a robust solution where the initial graph is constructed using a Transformer-based edge predictor and multilayer perceptron, assigning probability scores to potential edges and applying a threshold to determine their existence. The LLM then acts as an edge set refiner, making informed decisions based on both textual and statistical features of node pairs to validate the remaining connections. Extensive experiments on TUSZ dataset demonstrate that our LLM-refined graph learning framework not only enhances task performance but also yields cleaner and more interpretable graph representations.

Hyperbolic geometry has emerged as an effective latent space for representing complex networks, owing to its ability to capture hierarchical organization and heterogeneous connectivity patterns using low-dimensional embeddings. As a result, numerous hyperbolic graph representation learning methods have been proposed in recent years. However, their practical adoption and systematic comparison remain challenging, as implementations are fragmented and shared tools for reproducible and fair evaluation are lacking. In this work, we introduce a unified open-source framework for hyperbolic graph representation learning that integrates several widely used embedding methods under a common optimization interface. The novel framework enables consistent training, visualization, and evaluation of hyperbolic embeddings, and interfaces seamlessly with standard network analysis tools. Leveraging this unified setup, we conduct an experimental study of hyperbolic embedding methods on real-world networks, focusing on two canonical downstream tasks: link prediction and node classification. Beyond predictive accuracy, the study offers practical insights into the strengths and limitations of existing approaches, thereby facilitating informed method selection and fostering reproducible research in hyperbolic graph representation learning.

In modern parametric model training, full-batch gradient descent (and its variants) suffers due to progressively stronger biasing towards the exact realization of training data; this drives the systematic ``generalization gap'', where the train error becomes an unreliable proxy for test error. Existing approaches either argue this gap is benign through complex analysis or sacrifice data to a validation set. In contrast, we introduce decoupled descent (DD), a novel theory-based training algorithm that satisfies a train-test identity -- enforcing the train error to asymptotically track the test error for stylized Gaussian mixture models. Within this specific regime, leveraging approximate message passing theory, DD iteratively cancels the biases due to data reuse, rigorously demonstrating the feasibility of zero-cost validation and $100\%$ data utilization. Moreover, DD is governed by a low-dimensional state evolution recursion, rendering the dynamics of the algorithm transparent and tractable. We validate DD on XOR classification, yielding superior performance compared to GD; additionally, we implement noisy MNIST and non-linear probing of CIFAR-10, demonstrating that even when our stylized assumptions are relaxed, DD narrows the generalization gap compared to GD.

Every document format in existence was designed for a human reader moving linearly through text. Autonomous LLM agents do not read - they retrieve. This fundamental mismatch forces agents to inject entire documents into their context window, wasting tokens on irrelevant content, compounding state across multi-turn loops, and broadcasting information indiscriminately across agent roles. We argue this is not a prompt engineering problem, not a retrieval problem, and not a compression problem: it is a format problem. We introduce OBJECTGRAPH (.og), a file format that reconceives the document as a typed, directed knowledge graph to be traversed rather than a string to be injected. OBJECTGRAPH is a strict superset of Markdown - every .md file is a valid .og file - requires no infrastructure beyond a two-primitive query protocol, and is readable by both humans and agents without tooling. We formalize the Document Consumption Problem, characterise six structural properties no existing format satisfies simultaneously, and prove OBJECTGRAPH satisfies all six. We further introduce the Progressive Disclosure Model, the Role-Scoped Access Protocol, and Executable Assertion Nodes as native format primitives. Empirical evaluation across five document classes and eight agent task types demonstrates up to 95.3 percent token reduction with no statistically significant degradation in task accuracy (p > 0.05). Transpiler fidelity reaches 98.7 percent content preservation on a held-out document benchmark.

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

Terrestrial network limitations drive the integration of non-terrestrial networks (NTNs), notably mega-constellations comprising thousands of low Earth orbit (LEO) satellites. While these satellites act as interconnected network switches via inter-satellite links (ISLs), their massive scale creates severe bottlenecks for network management. To address this, we propose a scalable, hierarchical software-defined networking (SDN) framework. Our architecture leverages graph neural networks (GNNs) to compactly represent the constellation topology, and Koopman theory to linearize nonlinear dynamics. Specifically, a Graph Koopman Autoencoder (GKAE) forecasts spatio-temporal behavior within a linear subspace for each orbital shell. A central SDN controller then aggregates these shell-level predictions for globally coordinated control. Simulations on the Starlink constellation demonstrate that our approach achieves at least a 42.8% improvement in spatial compression and a 10.81% improvement in temporal forecasting compared to established baselines, all while utilizing a significantly smaller model footprint.

Graph few-shot learning, which focuses on effectively learning from only a small number of labeled nodes to quickly adapt to new tasks, has garnered significant research attention. Despite recent advances in graph few-shot learning that have demonstrated promising performance, existing methods still suffer from several key limitations. First, during the meta-training phase, these methods typically perform node representation learning in Euclidean space, which often fails to capture the inherently hierarchical structure existing in real-world graph data. Second, during the meta-testing phase, they usually fit an empirical target distribution derived from only a few support samples, even when this distribution significantly deviates from the true underlying distribution. To address these issues, we propose IMPRESS, a novel framework that IMproves graPh few-shot learning with hypeRbolic spacE and denoiSing diffuSion. Specifically, our model learns node representations in a hyperbolic space and enriches the support distribution through denoising diffusion mechanisms. Theoretically, IMPRESS achieves a tighter generalization bound. Empirically, IMPRESS consistently outperforms competitive baselines across multiple benchmark datasets.

Entity search, i.e., finding the most similar entities to a query entity, faces unique challenges in e-commerce, where product similarity varies across categories and contexts. Traditional embedding-based approaches often struggle to capture nuanced context-specific attribute relevance. In this paper, we present a two-stage approach combining Large Language Model (LLM)-driven attribute graph construction with graph-aware LLM ranking. In the offline stage, we extract structured product attributes from unstructured text, and construct a reusable attribute graph with category-aware schemas. In the online stage, we rank retrieved candidates by reasoning over this structured representation rather than raw text, reducing per-product token usage by 57% while improving ranking precision. Experiments show that our approach outperforms multiple baselines under zero-shot scenarios, achieving a over 5% improvement in average precision without requiring training data, generalizes robustly across diverse product categories, and shows immense potential for real-world deployment.

Heterogeneous graphs with heterophily have emerged as a powerful abstraction for modeling complex real-world systems, where nodes of different types and labels interact in diverse and often non-homophilous ways. Despite recent advances, robust representation learning for such graphs remains largely unexplored, particularly in the presence of noisy or misleading connectivity. In this work, we investigate this problem and identify structural noise as a critical challenge that significantly degrades model performance. To address this issue, we propose a unified framework, Heterogeneous Graph Unified Learning (HGUL), which jointly handles heterophily and noisy graph structures. The framework consists of three complementary modules: a kNN-based graph construction module that recovers reliable local neighborhoods, a graph structure learning module that adaptively refines the adjacency by filtering noisy edges, and a heterogeneous affinity learning module that captures class-level relationships via an extended affinity matrix derived from a polynomial graph kernel. Extensive experiments on multiple datasets demonstrate that HGUL consistently outperforms existing methods on clean graphs and maintains strong robustness under varying levels of structural noise. The results further underscore the importance of jointly modeling heterophily and noise in heterogeneous graph learning.

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

Biomedical knowledge graphs (KGs) are widely used in the life sciences, yet many are derived from unstructured documents and therefore lack schema-level constraints, whereas graphs assembled from structured resources are difficult to harmonize into a unified representation. We present OptimusKG, a multimodal biomedical labeled property graph (LPG) built from structured and semi-structured resources to preserve factual, type-specific metadata across molecular, anatomical, clinical, and environmental domains. OptimusKG contains 190,939 nodes across 10 entity types, 21,818,752 edges across 27 edge types, and 67,070,490 property instances encoding 109,665,797 values across 145 distinct property keys, derived from 18 ontologies and controlled vocabularies. The graph enforces a top-level schema for nodes and edges and retains granular, type-specific properties, cross-references, and provenance. We assessed the validity of OptimusKG by evaluating whether graph relationships are supported by evidence from the scientific literature using a multimodal agent, PaperQA3. PaperQA3 identified supporting evidence for 70.0% of sampled edges, whereas 83.4% of sampled false edges received no supporting evidence. Edges without literature support were concentrated in associations derived from experimental and functional genomics resources, suggesting that OptimusKG captures biomedical knowledge that may precede synthesis in the scientific literature. OptimusKG is distributed as Apache Parquet files, providing a standardized resource for graph-based machine learning, knowledge-grounded retrieval with large language models, and biomedical discovery use cases such as hypothesis generation.

We propose C-MTAD-GAT, an \emph{unsupervised}, \emph{context-aware} graph-attention model for anomaly detection in multivariate time series from mobile networks. C-MTAD-GAT combines graph attention with lightweight context embeddings, and uses a deterministic reconstruction head and multi-step forecaster to produce anomaly scores. Detection thresholds are calibrated \emph{without labels} from validation residuals, keeping the pipeline fully unsupervised. On the public TELCO dataset, C-MTAD-GAT consistently outperforms MTAD-GAT and the Telco-specific DC-VAE, two state-of-the-art baselines, in both event-level and pointwise F1, while triggering substantially fewer alarms. C-MTAD-GAT is also deployed in the Core network of a national mobile operator, demonstrating its resilience in real industrial settings.

This paper proposes a novel algorithm for semisupervised learning. This algorithm learns graph cuts that maximize the margin with respect to the labels induced by the harmonic function solution. We motivate the approach, compare it to existing work, and prove a bound on its generalization error. The quality of our solutions is evaluated on a synthetic problem and three UCI ML repository datasets. In most cases, we outperform manifold regularization of support vector machines, which is a state-of-the-art approach to semi-supervised max-margin learning.

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

Reusing verification artefacts requires identifying structural and semantic similarities across programs and their specifications. In this paper, we focus on graph construction as a foundational step toward this goal. We present a pipeline that converts imperative programs and their annotations into typed, attributed graphs. Our experiments cover datasets including C with ACSL, Java with JML, and Dafny programs. The pipeline integrates abstract syntax tree parsing with semantic embeddings derived from models such as SentenceTransformer and CodeBERT. This enables the generation of graph representations that capture both structural relationships and semantic context. Our results show that consistent graph representations can be constructed across different languages and annotation styles. This work provides a practical basis for future steps in semantic enrichment and approximate graph matching for scalable verification artefact reuse.

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

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

Accurate end-to-end tail-latency forecasting is critical for proactive SLO management in microservice systems. However, modeling long-range dependency propagation and non-stationary, bursty workloads while maintaining inference efficiency at scale remains challenging. We present STLGT (Scalable Trace-based Linear Graph Transformer), a per-API predictor that encodes traces as span graphs for multi-step p95 tail-latency forecasting. STLGT uses a structure-aware linear graph Transformer to propagate cross-service dependencies with inference time linear in span graph size, and a decoupled temporal module to capture workload dynamics. Across a personalized education microservice application, DeathStarBench, and Alibaba traces, STLGT improves forecasting accuracy over PERT-GNN by 8.5% MAPE on average and achieves up to 12x faster CPU inference at N=32, matching the maximum span graph size after preprocessing the Alibaba traces. Ablation studies further demonstrate the effectiveness of each component, especially under bursty traffic.

Graph Contrastive Learning (GCL) has emerged as a prominent framework for unsupervised graph representation learning. However, relying on augmentation design alone to define the invariances learned by GCL can be brittle under structural perturbations. To address this issue, we propose Cheeger--Hodge Contrastive Learning (CHCL), a framework that aligns a perturbation-stable Cheeger--Hodge joint signature across augmented views for robust graph representation learning. The proposed signature combines a Cheeger-inspired connectivity signature derived from the algebraic connectivity $λ_2$ with the low-frequency spectrum of the 1-Hodge Laplacian, thereby capturing both global connectivity and higher-order structural information. By aligning encoder representations with the proposed Cheeger--Hodge joint signature across augmented views, CHCL learns graph embeddings that are robust to local structural perturbations. Extensive experiments on standard benchmarks, transfer settings demonstrate that CHCL consistently improves performance, robustness, and generalization.

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

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

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

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

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

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

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

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

Smooth functions on graphs have wide applications in manifold and semi-supervised learning. In this work, we study a bandit problem where the payoffs of arms are smooth on a graph. This framework is suitable for solving online learning problems that involve graphs, such as content-based recommendation. In this problem, each item we can recommend is a node of an undirected graph and its expected rating is similar to the one of its neighbors. The goal is to recommend items that have high expected ratings. We aim for the algorithms where the cumulative regret with respect to the optimal policy would not scale poorly with the number of nodes. In particular, we introduce the notion of an effective dimension, which is small in real-world graphs, and propose three algorithms for solving our problem that scale linearly and sublinearly in this dimension. Our experiments on content recommendation problem show that a good estimator of user preferences for thousands of items can be learned from just tens of node evaluations.

We consider adversarial multi-armed bandit problems where the learner is allowed to observe losses of a number of arms beside the arm that it actually chose. We study the case where all non-chosen arms reveal their loss with a fixed but unknown probability $r$, independently of each other and the action of the learner. We propose two algorithms that work for different ranges of $r$. We show that after $T$ rounds in a bandit problem with $N$ arms, the expected regret of our first algorithm is $O(\sqrt{(T /r) \log N })$ whenever $r\ge(\log T)/(2N)$, while our second algorithm achieves a regret of $O(\sqrt{(T/r) \log (N+T)})$ for smaller values of $r$. We also give a quick estimation procedure that decides the range of~$r$. All our bounds are within logarithmic factors of the best achievable performance of any algorithm that is even allowed to know~$r$.

Graph neural Ordinary Differential Equations (ODE) combine neural ODE with the message passing mechanism of Graph Neural Networks (GNN), providing a continuous-time modeling method for graph representation learning. However, in dynamic graph scenarios, existing graph neural ODEs typically employ a unified message passing mechanism, assuming that inter-node interactions share the same message passing function at any time, which makes it challenging to capture the diversity and time-varying nature of inter-node interaction patterns. To address this, we propose Time-varying Interaction Graph Ordinary Differential Equations (TI-ODE). The core idea of TI-ODE is to decompose the evolution function of a graph ODE into a set of learnable interaction basis functions, where each basis function corresponds to a distinct type of inter-node interaction. These basis functions are dynamically combined through time-dependent learnable weights, enabling inter-node interaction patterns to adaptively evolve over time. Experimental results on six dynamic graph datasets demonstrate that TI-ODE consistently outperforms existing methods and achieves state-of-the-art performance on attribute prediction tasks, and experiments on the \textit{Covid} dataset further verify the interpretability and generalizability of our TI-ODE. Furthermore, we demonstrate both theoretically and empirically that TI-ODE exhibits superior robustness compared to models utilizing a unified message-passing mechanism.

Motivation: Multi-omics integration can improve cancer subtyping, but modality informativeness and noise vary across cancer types and patients. Existing graph-based methods optimize modality weights jointly with the classification objective and therefore lack independent reliability estimates, so low-quality omics distort patient similarity graphs and amplify noise through message passing. Results: We propose CMGL, a two-stage framework that estimates per-sample modality reliability through evidential deep learning and uses the frozen confidence scores to guide cross-omics fusion and graph construction. On four MLOmics cancer-subtype tasks and the 32-class pan-cancer task, CMGL consistently improves over the strongest baseline, surpassing it by 4.03% in average accuracy on the four single-cancer tasks. Its representations recover the PAM50 intrinsic subtypes of breast invasive carcinoma (BRCA), and the BRCA-trained model transfers without fine-tuning to kidney renal clear cell carcinoma (KIRC), stratifying patients into prognostically distinct groups.

Automatic depression detection from conversational interactions holds significant promise for scalable screening but remains hindered by severe data scarcity and a lack of clinical interpretability. Existing approaches typically rely on black-box deep learning architectures that struggle to model the subtle, temporal evolution of depressive symptoms or account for participant-specific heterogeneity. In this work, we propose PsyGAT (Psychological Graph Attention Network), a psychologically grounded framework that models conversational sessions as dynamic temporal graphs. We introduce Psychological Expression Units (PEUs) to explicitly encode utterance-level clinical evidence, structuring the session graph to capture transitions in psychological states rather than mere semantic dependencies. To address the critical class imbalance in depression datasets, we employ clinically approved persona-based data augmentation, enable robust model learning. Additionally, we integrate session-level personality context directly into the graph structure to disentangle trait-based behavior from acute depressive symptoms. PsyGAT achieves state-of-the-art performance, surpassing both strong graph-based baselines and closed-source LLMs like GPT-5, achieving 89.99 and 71.37 Macro F1 scores in DAIC-WoZ and E-DAIC, respectively. We further introduce Causal-PsyGAT, an interpretability module that identifies symptom triggers. Experiments show a 20% improvement in MRR for identifying causal indicators, effectively bridging the gap between depression monitoring and clinical explainability. The full augmented dataset is publicly available at https://doi.org/10.6084/m9.figshare.31801921.

Post-Training Quantization (PTQ) compresses large language models to low bit-widths using a small calibration set, and its quality depends strongly on which samples are chosen. We identify a failure mode in which calibration samples fail to activate outlier channels, hidden dimensions with unusually large activations, causing the quantizer to underestimate their dynamic range and producing per-channel reconstruction errors that dominate layer-wise loss. Motivated by this observation, we argue that PTQ calibration quality is governed more by weighted outlier-channel coverage than by generic sample representativeness, and formulate calibration selection as a weighted set cover problem over outlier channels. The objective is monotone submodular, and the greedy algorithm, COVERCAL, operates on pre-computed activation statistics and requires no GPU time at selection. We further show that the weight choice is internally consistent: under a stylized clipping model, missed weighted coverage upper-bounds surrogate loss, justifying the weighted coverage objective as principled rather than purely empirical. Across LLaMA-2, LLaMA-3, and Mistral, under AWQ and GPTQ backends and five downstream evaluations, COVERCAL improves over random, max-perplexity, max-activation-variance, and stratified baselines, with the largest gains at small calibration budgets. At INT4 with 128 samples, COVERCAL improves MMLU by 1.2 to 1.5 points over random calibration and reduces perplexity degradation by 15 to 30%; with 64 samples, it matches or exceeds random calibration at 256. The contribution is not a new PTQ backend but a formulation of calibration selection as weighted outlier coverage, with a simple, efficient algorithm and a surrogate-based justification.

We investigate whether the Feed-Forward Network (FFN) sublayer in a decoder-only transformer can be replaced by an explicit learned memory graph while preserving the surrounding autoregressive architecture. The proposed Graph Memory Transformer (GMT) keeps causal self-attention intact, but replaces the usual per-token FFN transformation with a memory cell that routes token representations over a learned bank of centroids connected by a learned directed transition matrix. In the base GMT v7 instantiation studied here, each of 16 transformer blocks contains 128 centroids, a 128 * 128 edge matrix, gravitational source routing, token-conditioned target selection, and a gated displacement readout. The cell therefore returns movement from an estimated source memory state toward a target memory state, rather than a retrieved value. The resulting model is a fully decoder-only language model with 82.2M trainable parameters and no dense FFN sublayers, compared with a 103.0M-parameter dense GPT-style baseline used in the evaluation. The base v7 model trains stably and exposes centroid usage, transition structure, and source-to-target movement as directly inspectable quantities of the forward computation. It remains behind the larger dense baseline in validation loss and perplexity (3.5995/36.58 vs. 3.2903/26.85), while showing close zero-shot benchmark behavior under the evaluated setting. These results are not intended as a state-of-the-art claim; they support the viability and structural interpretability of replacing dense within-token transformation with graph-mediated memory navigation. Broader scaling, optimized kernels, and more extensive benchmark evaluation are left for subsequent work.

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

Hierarchical clustering is a fundamental task in data analysis, but classical methods have long lacked a principled objective function. Dasgupta [STOC 2016] took an important step toward addressing this gap by proposing a well-motivated objective function for cluster trees. Cohen-Addad et al. [J. ACM 2019] subsequently introduced the notion of admissibility: an objective function is admissible if, whenever the input similarity matrix admits generating trees, its minimizers are precisely those generating trees. They also gave a necessary and sufficient condition for admissibility within a family of objective functions based on aggregate intercluster similarity. We refer to this family as sum-type objective functions. However, apart from Dasgupta's original objective function, no explicit admissible objective functions in this family were provided. In this paper, we study admissible objective functions for hierarchical clustering in two directions. For sum-type objective functions, we give a complete characterization when the scaling function is a symmetric polynomial of degree at most two, and we derive sufficient conditions for degree-three polynomials. We also show that the recursive sparsest cut algorithm achieves an O$(φ)$-approximation ratio for the admissible objective functions covered by our characterization, where $φ$ is the approximation factor of the sparsest cut subroutine. We then introduce max-type objective functions, where cluster interaction is measured by maximum, rather than aggregate, intercluster similarity. For this class, we characterize which objective functions are admissible for arbitrary symmetric scaling functions and give a complete characterization when the scaling function is a symmetric polynomial of degree at most two.

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

We propose PathBoost, a gradient tree boosting method for graph-level classification and regression that learns discriminative path-based features directly from the input graph structure. Building on a previous work, which was tailored to a specific chemistry application, PathBoost introduces three key extensions: (i) adaptation to binary classification through gradient boosting with a logistic loss, (ii) incorporation of multiple node and edge attributes into the path feature space via a prefix-based decomposition, and (iii) automatic anchor node selection based on categorical attribute diversity, eliminating the need for the user to specify the starting point of the considered path features. We compared PathBoost to graph neural networks and graph kernel approaches on several benchmark datasets, obtaining better results in half of them, and comparable results in the rest. PathBoost shows better performances on graphs with larger average node counts. Overall, the results demonstrate that path-based boosting methods can be competitive with more complex black-box approaches.

Semi-supervised classification, where unlabeled data are massive but labeled data are limited, often arises in machine learning applications. We address this challenge under high-dimensional data by leveraging the manifold and cluster assumptions. Based on the Fermat distance, a density-sensitive metric that naturally encodes the cluster assumption, we propose the weighted $k$-nearest neighbors (NN) classifier and multidimensional scaling (MDS)-induced classifiers. The use of MDS with a large target dimension allows the effective application of linear classifiers to complex manifold data. Theoretically, we derive a sharp lower bound for the expected excess risk within clusters and prove that the weighted $k$-NN classifier utilizing the true Fermat distance is minimax optimal. Furthermore, we explicitly quantify the utility of unlabeled data by showing that the error arising from estimating the Fermat distance decays exponentially with the pooled sample size. Such a rate is much faster than the related rates in the literature. Extensive experiments on synthetic and real datasets demonstrate competitive or superior performance of our approaches compared to state-of-the-art graph-based semi-supervised classifiers.

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

Active perception is a fundamental problem in autonomous robotics in which the robot must decide where to move and what to sense in order to obtain the most informative observations for accomplishing its mission. Existing approaches either solve a computationally expensive traveling salesman problem over heuristically selected informative nodes, or adopt a more efficient but overly constrained shortest path tree formulation. To address these limitations, we explore beam search algorithms as scalable alternatives. While the standard beam search provides scalability by preserving the top-B paths at each depth level, it is prone to local optima and exhibits parameter sensitivity. Our first contribution is a node-wise beam search (NBS) algorithm, which maintains top-B candidates per node to enable more effective exploration of the solution space. Systematic benchmarking on graphs shows that NBS consistently outperforms other baselines and maintains strong performance even at low beam widths. As a second contribution, we integrate the concept of frontiers into the path selection criterion, introducing the expected gain metric, which better balances exploration and exploitation compared to existing alternatives. Our third contribution proposes the rapidly-exploring random annulus graph (RRAG), a novel graph construction method that preserves full orientation sampling and ensures connectivity in cluttered environments through a fallback local sampling-based planner. Extensive experiments demonstrate that NBS combined with RRAG achieves the highest performance across all three representative active perception tasks, outperforming state-of-the-art algorithms by at least 20% in one or more tasks. We further validate the approach on real robotic platforms in different scenarios.

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

This book presents a comprehensive and systematic survey of graph theory under uncertainty, with particular emphasis on the unifying role of the uncertain graph framework. It reviews fundamental concepts, structural properties, graph classes, and graph parameters within fuzzy, neutrosophic, and related models, while also introducing a wide range of extensions such as uncertain digraphs, hypergraphs, superhypergraphs, and dynamic graphs. In addition to theoretical developments, the book explores practical applications, including uncertain molecular graphs, decision-making systems, graph neural networks, knowledge graphs, and cognitive maps. By organizing diverse uncertainty-aware graph models within a common perspective, this work provides a coherent framework for understanding their relationships, capabilities, and applications in complex systems.

Accurate prediction of drug-target binding affinity accelerates drug discovery by prioritizing compounds for experimental validation. Current methods face three limitations: sequence-based approaches discard spatial geometric constraints, structure-based methods fail to exploit hydrogen bond features, and conventional loss functions neglect prediction-target correlation, a key factor for identifying high-affinity compounds in virtual screening. We developed HBGSA (Hydrogen Bond Graph with Self-Attention), a 3.06M-parameter model that encodes hydrogen bond spatial features. HBGSA uses graph neural networks to model hydrogen bond spatial topology with self-attention enhancement and Pearson correlation loss. Experimental results on PDBbind Core Set and CSAR-HiQ dataset demonstrate that HBGSA outperforms baseline methods with strong generalization capability. Ablation studies confirm the effectiveness of hydrogen bond modeling and Pearson correlation loss.

Graph neural networks achieve strong node-classification accuracy, but learned message passing entangles ego attributes, neighborhood smoothing, high-pass graph differences, class geometry, and classifier-boundary effects inside opaque representations. This obscures why nodes are classified as they are and which graph-learning mechanisms a dataset requires. We propose WG-SRC, a white-box signal-subspace probe for prediction and graph dataset diagnosis. WG-SRC replaces learned message passing with a fixed, named graph-signal dictionary containing raw features, row- and symmetric-normalized low-pass propagation, and high-pass graph differences. It combines Fisher coordinate selection, class-wise PCA subspaces, closed-form multi-alpha ridge classification, and validation-based score fusion, so prediction and analysis rely on explicit class subspaces, energy-controlled dimensions, and closed-form linear decisions. As a white-box graph-learning instrument, WG-SRC uses predictive performance to validate its diagnostics. Across six node-classification datasets, it remains competitive with reproduced baselines and achieves positive average gain under aligned splits. Its atlas decomposes behavior into raw-feature, low-pass, high-pass, class-geometric, and ridge-boundary components. The resulting fingerprints distinguish low-pass-dominated Amazon graphs, mixed high-pass and class-geometrically complex Chameleon behavior, and raw- or boundary-sensitive WebKB graphs. Aligned interventions show when high-pass blocks act as removable noise, when raw or graph-derived signals should be preserved, and when ridge correction matters. WG-SRC therefore serves both as a functioning white-box classifier and as a dataset-fingerprinting probe, enabling fingerprint-conditioned analysis of how black-box model components behave under different graph-signal conditions.

We propose Mochi, a Graph Foundation Model that addresses task unification and training efficiency by adopting a meta-learning based training framework. Prior models pre-train with reconstruction-based objectives such as link prediction, and assume that the resulting representations can be aligned with downstream tasks through a separate unification step such as class prototypes. We demonstrate through synthetic and real-world experiments that this procedure, while simple and intuitive, has limitations that directly affect downstream task performance. To address these limitations, Mochi pre-trains on few-shot episodes that mirror the downstream evaluation protocol, aligning the training objective with inference rather than relying on a post-hoc unification step. We show that Mochi, along with its more powerful variant Mochi++, achieves competitive or superior performance compared to existing Graph Foundation Models across 25 real-world graph datasets spanning node classification, link prediction, and graph classification, while requiring 8$\sim$27 times less training time than the strongest baseline.

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