Graph Neural Networks

Graph neural networks (GNNs) have emerged as a fundamental tool for learning from graph-structured data, achieving strong performance across a wide range of applications. However, understanding their generalization capabilities remains challenging due to the complex structural dependencies inherent in such data. Existing generalization analyses largely follow the classical machine learning paradigm, focusing primarily on model complexity while overlooking the fundamental role of graph structure. Therefore, in this work, we systematically investigate this role by asking: does the graph structure actually influence generalization, and if so, by how much? To answer the first question and validate our intuition, we theoretically prove that incorporating more edges into the prediction process transforms the input representations to be overly accommodating to the output model, thereby inducing overfitting. To address the second question, we formulate a structural complexity measure based on the number of effective edges and derive a Rademacher complexity-based generalization bound. In doing so, we demonstrate that GNN generalization depends explicitly on structural complexity, alongside traditional parameter-dependent factors. Motivated by these theoretical findings, we propose a structural entropy regularization method. This approach controls structural complexity by regulating effective edges to balance underfitting and overfitting, ultimately improving the generalization performance of GNNs.

Dynamic graphs are ubiquitous in real-world systems, and building generalizable dynamic Graph Foundation Models has become a frontier in graph learning. However, dynamic graphs from different domains pose fundamental challenges to unified modeling, as their semantic and temporal patterns are inherently inconsistent, making the multi-domain pre-training difficult. Consequently, the widely used "pretrain-then-finetune" paradigm often suffers from severe negative knowledge transfer. To the best of our knowledge, there exists no multi-domain dynamic GFM. In this work, we propose DyGFM, a Dynamic Graph Foundation Model over multiple domains based on decoupled and divergence-conditioned prompting. To disentangle transferable semantics from the domain-specific dynamics, we introduce a dual-branch pre-training strategy with semantic-temporal decoupling. To alleviate negative transfer during domain adaptation, we further develop a cross-domain routing mechanism with divergence-aware expert selection. To enable efficient downstream fine-tuning, we design a divergence-conditioned prompt generator that injects lightweight, learnable graph prompts tailored to semantic and temporal traits. Extensive experiments on continuous dynamic graph benchmarks demonstrate that DyGFM consistently outperforms 12 state-of-the-art baselines on both node classification and link prediction tasks, achieving superior effectiveness and efficiency.

Computing a minimum $s$-$t$ cut in a graph is a solution to a wide range of computer vision problems, and is often done using the Boykov-Kolmogorov (BK) algorithm. In this paper, we revisit the BK algorithm from both a theoretical and practical point of view. We improve the analysis of the time complexity of the BK algorithm to $O(mn|C|)$ and propose a new algorithm, the fast and compact BK (fcBK) algorithm, with a time complexity of $O(m|C|)$, where $m$, $n$, and $|C|$ are the number of edges, number of vertices, and the capacity of the cut, respectively. We additionally propose a compact graph representation that allows our implementation to find a minimum $s$-$t$ cut in a graph with upwards of $10^9$ vertices and $10^{10}$ edges on a machine with 128 GB of memory. We find our implementation of the BK algorithm to be the fastest available implementation of the BK algorithm when evaluating on a comprehensive set of benchmark datasets, highlighting the importance of memory-efficient implementations. We make our implementations publicly available for further research and implementation development within minimum $s$-$t$ cut algorithms.

Graph Neural Networks (GNNs) perform computations on graphs by routing the signal between graph regions using a graph shift operator or a message passing scheme. Often, the propagation of the signal leads to a loss of information, where the signal tends to diffuse across the graph instead of being deliberately routed between regions of interest. Two notions that depict this phenomenon are oversmoothing and oversquashing. In this paper, we propose an alternative approach for modeling signal propagation, inspired by quantum mechanics, using the notion of observables. Specifically, we model the place in the graph where the signal lies, how much the signal is concentrated there, and how much of the signal is propagated towards a location of interest when applying a GNN. Using these new concepts, we prove that standard spectral GNNs have poor signal propagation capabilities. We then propose a new type of spectral GNN, termed Schrödinger GNN, which we show has a superior capacity to route the signal across the graph.

Reference-based graph compression encodes each vertex's neighbor list as differences from a nearby encoded list. WebGraph's BVGraph fixes a single encoding pipeline and relies on a separately chosen vertex ordering -- typically URL-lexicographic or Layered Label Propagation (LLP). Their interaction is rarely measured. We propose a two-stage Leiden+LLP ordering: global LLP seeds labels, Leiden detects communities, and a final LLP pass reorders each community internally. We study how it interacts with reference-based compression, using BVGraph and three encoders we contribute -- BG, CS, and CG -- each picking, per vertex, the cheapest of up to 28 candidate decompositions. On graphs with poor initial vertex order, reordering with Leiden+LLP improves compression for every encoder measured, saving 0.9 to 4.6 bits per edge (bpe) over the original order on SNAP-style graphs delivered in vertex-ID order. The gain barely depends on the encoder: on four of five weakly ordered datasets, the four encoders agree on the Leiden+LLP-vs-plain-LLP gain within about +/- 0.04 bpe. On URL-ordered web crawls, where the ordering already encodes locality, BG and CS still benefit, while residual-sensitive configurations (BVGraph default, BV-HC, and CG relying on community contiguity) regress. The transfer holds across two encoder generations (Fibonacci-coded and fully context-adaptive range-coded) and three ordering seeds. With every structural bit entropy-coded, the best of our three encoders beats the strongest published baseline in each regime (Zuckerli, and the stronger of BV-HC / BVGraph default) on all seven datasets in every whole-graph and random-access comparison -- 28/28 cells, +0.3 to +35% over Zuckerli -- with the encoder-level gain consistently smaller than the ordering-level gain. All algorithms, the ordering pipeline, and generators are released as the Adjacently Julia library.

The Industry Foundation Classes (IFC) standard is central to building data exchange across the lifecycle, from design and construction to facility management and Digital Twin integration. In operational settings, stakeholders increasingly require access to building information without specialist knowledge of IFC's complex, deeply nested schema, motivating natural language interfaces. Existing LLM-based querying approaches typically rely on a single data representation, which is not equally suited to attribute retrieval and spatial reasoning. We present IfcLLM, a framework that combines complementary relational and graph representations, routing each query type to the more suitable backend. An LLM agent integrates both through iterative retry-and-refine reasoning, recovering from failures without user input. Evaluated across three IFC models on 30 query scenarios, our implementation achieves first-attempt accuracy between 93.3% and 100%, with all failed queries resolved via a fallback LLM. Built on an open-weight LLM, it supports local deployment in data-sensitive AEC settings.

Graph Neural Networks (GNNs) suffer from over-squashing in deep message passing, where information from exponentially growing neighborhoods is compressed into fixed-dimensional representations. We show that this issue becomes a distinct failure mode in multi-label graphs: neighboring nodes often share only limited labels while differing across many irrelevant ones, causing predictive signals to be diluted by noisy label information. To address this challenge, we propose the Multi-Label Graph Information Bottleneck (MLGIB), which formulates multi-label message passing as constrained information transmission under irrelevant label noise. MLGIB balances expressiveness and robustness by preserving predictive label signals while suppressing irrelevant noise. Specifically, it constructs a Markovian dependence space and derives tractable variational bounds, where the lower bound maximizes mutual information with target labels and the upper bound constrains redundant source information. These bounds lead to an end-to-end label-aware message-passing architecture. Extensive experiments on multiple benchmarks demonstrate consistent improvements over existing methods, validating the effectiveness and generality of the proposed framework.

Graph neural networks are widely used for node classification, but they remain vulnerable to out-of-distribution (OOD) shifts in node features and graph structure. Prior work established that methods trained with standard supervised learning (SL) objectives tend to capture spurious signals from either features and/or structure, leaving the model fragile under distributional changes. To address this, we propose TIDE, a novel and effective Tri-Component Information Decomposition framework that explicitly decomposes information into feature-specific, structure-specific and joint components. TIDE aims to preserve only the label-relevant part of the joint information while filtering out spurious feature- and structure-specific information, thereby enhancing the separation between in-distribution (ID) and OOD nodes. Beyond the framework, we provide theoretical and empirical analyses showing that an information bottleneck objective is preferable to standard SL for graph OOD detection, with higher ID confidence and a greater entropy gap between ID and OOD data. Extensive experiments across seven datasets confirm the efficacy of TIDE, achieving up to a 34% improvement in FPR95 over strong baselines while maintaining competitive ID accuracy.

Graph coarsening is a graph dimensionality reduction technique that aims to construct a smaller and more tractable graph while preserving the essential structural and semantic properties of the original graph. However, most existing methods rely on pair-wise similarity matching, where each node independently searches for its best partner based on global information. This selfishness matching paradigm incurs substantial computational and memory overhead. To address this problem, we shift to a non-selfishness principle that prioritizes the collective interference of neighborhood in coarsening, and propose an efficient method named NOPE, which achieves linear memory consumption and near-linear computational complexity in the number of nodes. Furthermore, we derive a faster variant NOPE*, which reduces O(δ\dot d) interference evaluation to O(d) based on the local isotropy assumption, and consequently alleviates the computational bottleneck for high-degree nodes. Experimental results show that NOPE* achieves 1.8-10\times speedup over NOPE and surpass almost all baselines with 1-3 orders of magnitude acceleration. Meanwhile, learning on coarsened graphs yields comparable performance to original graphs, and can even show superior performance over LLM-based graph reasoning owing to compact graph information. The code can be available at https://github.com/dazonglian/NOPE-main.

Continual graph learning (CGL) aims to learn from dynamically evolving graphs while mitigating catastrophic forgetting. Existing CGL approaches typically adopt a task-based formulation, where the data stream is partitioned into a sequence of discrete tasks with pre-defined boundaries. However, such assumptions rarely hold in real-world environments, where data distributions evolve continuously and task identity is often unavailable. To better reflect realistic non-stationary environments, we revisit continual graph learning from a task-free perspective. We propose a unified formulation that models the data stream as a time-varying mixture of latent task distributions, enabling continuous modeling of distribution drift. Based on this formulation, we construct \emph{DRIFT}, a benchmark that spans a spectrum of transition dynamics ranging from hard task switches to smooth distributional drift through a Gaussian parameterization. We evaluate representative continual learning methods under this task-free setting and observe substantial performance degradation compared to traditional task-based protocols. Our findings indicate that many existing approaches implicitly rely on task boundary information and struggle under realistic task-free graph streams. This work highlights the importance of studying continual graph learning under realistic non-stationary conditions and provides a benchmark for future research in this direction. Our code is available at https://github.com/UConn-DSIS/DRIFT.

Graph neural networks (GNNs) deployed as cloud services can be stolen through model-extraction attacks, which train a surrogate from query responses to reproduce the target's behavior, and a growing line of ownership defenses tries to prevent or trace such theft. This paper asks two questions: how hard is it to steal a GNN, and can we stop it? Prior work cannot answer either, because experiments use inconsistent datasets, threat models, and metrics. We introduce GraphIP-Bench, a unified benchmark that evaluates both sides under a single black-box protocol. GraphIP-Bench integrates twelve extraction attacks, twelve defenses spanning watermarking, output perturbation, and query-pattern detection, ten public graphs covering homophilic, heterophilic, and large-scale regimes, three GNN backbones, and three graph-learning tasks. It reports fidelity, task utility, ownership verification, and computational cost on shared splits, queries, and budgets. We further add a joint attack-and-defense track that runs every attack on every defended target and measures watermark verification on the resulting surrogate, exposing how much protection a defense retains after extraction. The empirical picture is clear: stealing a GNN is easy at medium query budgets and most defenses do not change this; several watermarks verify reliably on the protected model but lose most of their verification signal on the extracted surrogate, exposing a gap that single-model evaluations miss; and heterophilic graphs are systematically harder to steal, while a cross-architecture mismatch between target and surrogate reduces but does not prevent extraction. We release GraphIP-Bench with reproducible scripts and configurations, and integrate the attacks and defenses into the PyGIP library. Code: https://github.com/LabRAI/GraphIP-Bench. Library: https://labrai.github.io/PyGIP/index.html.

Financial transaction fraud prevention faces challenges such as complex relationship structures, concealed behavioral patterns, and dynamically changing data distribution. Discrimination models relying solely on independent sample features are insufficient to fully characterize the risks of group collaboration and chain transfers within transaction networks. This paper proposes a graph neural network representation learning and risk discrimination framework for financial transaction fraud prevention. It integrates transaction records and identity information into node attributes and constructs a transaction graph based on shared attributes and interaction consistency to explicitly model inter-transaction relationships. In model design, a multi-layer message passing mechanism is employed to aggregate neighborhood information, learn node embedding representations containing structural context semantics, and output transaction-level fraud probability and risk scores through a lightweight risk discrimination head. A weighted supervision objective is introduced to mitigate training bias caused by class imbalance, and structural consistency regularization constraints are combined to suppress the impact of noisy edges on representation drift, thereby improving the stability and usability of risk characterization. Experiments are conducted on a publicly available financial transaction dataset, comparing various methods in the same direction and comprehensively evaluating them under a unified evaluation protocol. The results show that the proposed method outperforms other methods in risk ranking and probability calibration quality, validating the effectiveness of graph structure modeling and representation learning collaboration in financial transaction fraud prevention.

Existing multiplex graph models often assume homophily, where connected nodes tend to belong to the same class or share similar attributes. Consequently, these models may struggle with graphs exhibiting heterophily, where connected nodes typically belong to different classes and have dissimilar attributes. While recent methods have been developed to learn reliable node representations from unidimensional graphs with heterophily, they do not fully address the complexities of multiplex graphs. In a multiplex graph, nodes are linked through multiple types of edges (referred to as dimensions), which can simultaneously exhibit homophilic and heterophilic interactions. To address this gap, we propose \methodname, a novel method for node classification in multiplex graphs that adapts to both homophilic and heterophilic dimensions. \methodname introduces dimension-specific compatibility matrices to model varying degrees of homophily and heterophily across dimensions. A key innovation is its use of a product of trainable low-pass and high-pass filters, approximated via Chebyshev polynomials, to capture both smooth and abrupt changes in the graph signal. By composing these filters and optimizing label predictions using a proximal-gradient method, \methodname dynamically adjusts to the heterophilic characteristics of each dimension. Extensive experiments on synthetic and real-world datasets provide evidence that \methodname captures the complex interplay of homophilic and heterophilic interactions in multiplex graphs, and tends to yield improved node classification performance compared to state-of-the-art methods.

Graph Self-Supervised Learning (GSSL) has emerged as a powerful paradigm for generating high-quality representations for graph-structured data. While multi-scale graph contrastive learning has received increasing attention, many existing methods still predominantly focus on a single graph abstraction level. To address this limitation, we propose a unified contrastive framework that can target node-level, proximity-level, cluster-level, and graph-level information and integrate them through a linear combination of similarity scores on positive pairs and dissimilarity scores (i.e., similarity scores on negative pairs). Furthermore, current approaches typically assign uniform penalty strengths to all examples, which reduces optimization flexibility and leads to ambiguous convergence status. To overcome this, we introduce a novel parameter-free fine-grained self-weighting mechanism that adaptively assigns weights to individual similarity and dissimilarity scores. The proposed mechanism emphasizes the scores that deviate significantly from their target values. Our approach not only enhances optimization flexibility but also eliminates the computational overhead of hyperparameter tuning in conventional multi-task GSSL methods. Comprehensive experiments on real-world datasets show that our methods consistently outperform state-of-the-art approaches across downstream tasks, including classification, clustering, and link prediction, in both single-level and multi-level scenarios.

For minimally rigid graphs, the same edge-length data can admit multiple realizations (up to translations and rotations). Finding graphs with exceptionally many realizations is an extremal problem in rigidity theory, but exhaustive search quickly becomes infeasible due to the super-exponential growth of the number of candidate graphs and the high cost of realization-count evaluation. We propose a reinforcement-learning approach that constructs minimally rigid graphs via 0- and 1-extensions, also known as Henneberg moves. We optimize realization-count invariants using the Deep Cross-Entropy Method with a policy parameterized by a Graph Isomorphism Network encoder and a permutation-equivariant extension-level action head. Empirically, our method matches the known optima for planar realization counts and improves the best known bounds for spherical realization counts, yielding new record graphs.

Segmenting small and sparse structures in large-scale images is fundamentally constrained by voxel-level, lattice-bound computation and extreme class imbalance -- dense, full-resolution inference scales poorly and forces most pipelines to rely on fixed regionization or downsampling, coupling computational cost to image resolution and attenuating boundary evidence precisely where minority structures are most informative. We introduce SEMIR (Semantic Minor-Induced Representation Learning), a representation framework that decouples inference from the native grid by learning a task-adapted, topology-preserving latent graph representation with exact decoding. SEMIR transforms the underlying grid graph into a compact, boundary-aligned graph minor through parameterized edge contraction, node deletion, and edge deletion, while preserving an exact lifting map from minor predictions to lattice labels. Minor construction is formalized as a few-shot structure learning problem that replaces hand-tuned preprocessing with a boundary-alignment objective: minor parameters are learned by maximizing agreement between predicted boundary elements and target-specific semantic edges under a boundary Dice criterion, and the induced minor is annotated with scale- and rotation-robust geometric and intensity descriptors and supports efficient region-level inference via message passing on a graph neural network (GNN) with relational edge features. We benchmark SEMIR on three tumor segmentation datasets -- BraTS 2021, KiTS23, and LiTS -- where targets exhibit high structural variability and distributional uncertainty. SEMIR yields consistent improvements in minority-structure Dice at practical runtime. More broadly, SEMIR establishes a framework for learning task-adapted, topology-preserving latent representations with exact decoding for high-resolution structured visual data.

Message-passing based approaches form the default backbone of most learning architectures on graph-structured data. However, the rapid progress of modern deep learning architectures in other domains, particularly sequence modeling, raises the question of how graph learning can benefit from these advances. We introduce Linearized Graph Sequence Models, a framework that recasts message-passing graph computation from the perspective of sequence modeling to simplify architectural choices. Our approach systematically separates the computational processing depth from the information propagation depth, allowing core graph architectural decisions to be treated as sequence modeling choices. Specifically, we analyze, both empirically and theoretically, what sequence properties make methods effective for learning and preserving the graph inductive bias. In particular, we validate our findings, demonstrating improved performance on long-range information tasks in graphs. Our findings provide a principled way to integrate modern sequence modeling advances into message-passing based graph learning. Beyond this, our work demonstrates how the separation of processing and information depth can recast central architectural questions as input modeling choices.

Graph-based machine learning has emerged as a promising approach for manufacturability analysis by learning directly from CAD models represented as Boundary Representations (B-reps), exploiting both surface geometry and topological connectivity. However, purely geometric representations often lack the process-specific semantics required for accurate manufacturability prediction: many manufacturing factors, such as surface roles or bend intent, are not explicitly encoded in shape alone and are difficult for data-driven models to infer reliably. We propose a hybrid approach that addresses this challenge by enriching B-rep attributed adjacency graphs with manufacturing features recognized through a rule-based module. Applied to sheet metal bending, recognized features, such as bend characteristics, flange lengths, and surface roles are integrated as node attributes, concentrating the learning signal on process-relevant geometric patterns. Experiments on both a large-scale synthetic manufacturability benchmark and a real-world industrial dataset with measured bending times, one of the first such validations on genuine production data, demonstrate that combining domain knowledge with graph-based learning improves prediction accuracy across both tasks. The results demonstrate that hybrid modeling offers a feasible and effective path toward deployable tools for manufacturability assessment and effort estimation in industrial CAD environments.

Leveraging Graph Neural Networks (GNNs) as graph encoders and aligning the resulting representations with Large Language Models (LLMs) through alignment instruction tuning has become a mainstream paradigm for constructing Graph Language Models (GLMs), combining the generalization ability of LLMs with the structural modeling capacity of GNNs. However, existing GLMs that adopt GNNs as graph encoders largely overlook the problem of aligning GNN-encoded representations across domains and tasks with the LLM token space to obtain unified graph tokens, thereby limiting their ability to generalize across diverse graph data. To bridge this gap, we aim to incorporate a multi-domain, multi-task GNN encoder into GLMs and align its representations with LLMs to enable multi-domain, multi-task graph alignment instruction tuning. This alignment problem remains underexplored and poses two key challenges: 1) learning GNN-encoded representations that are simultaneously generalizable across domains and tasks and well aligned with textual semantics is difficult, due to substantial variations in graph structures, feature distributions, and supervision signals, together with the lack of textual-semantic alignment guidance in task-specific GNN training; 2) diverse graph data and task-specific instructions can exhibit different degrees of compatibility with the LLM token space during instruction tuning, leading to varying alignment difficulty and rendering a fixed alignment strategy suboptimal. To tackle these challenges, we propose UniGraphLM, a Unified Graph Language Model that incorporates a multi-domain, multi-task GNN encoder to learn generalizable graph representations aligned with textual semantics, and then adaptively aligns these representations with the LLM.

Long-term memory is becoming a central bottleneck for language agents. Exsting RAG and GraphRAG systems largely treat memory graphs as static retrieval middleware, which limits their ability to recover complete evidence chains from partial cues, exploit reusable graph-structrual roles, and improve the memory itself through downstream feedback. We introduce SAGE, a Self-evolving Agentic Graph-memory Engine that models graph memory as a dynamic long-term memory substrate. SAGE couples two roles: a memory writer that incrementally constucts structured graph memory from interaction histories, and a Graph Foundation Model-based memory reader to perform retrieval and provide feedback to the memory writer. We provide rigorooous theoretical annalyses supporting the framework. Across multi-hop QA, open-domain retireval, domain-specific review QA, and long-term agent-memory benchmarks, SAGE improves evidence recovery, answer grounding, and retrieval efficiency: after two self-evolution rounds, it achieves the best average rank on multi-hop QA; in zero-shot open-domain transfer, it reaches 82.5/91.6 Recall@2/5 on NQ. Further results on LongMemEval and HaluMem show that traning and reader-writer feedback improve multiple long-term memory and hallucination-diagnostic metrics, suggesting that self-evolving, structure-aware graph memory is a promising foundation for robust long-horizon language agents.

Skill libraries enable large language model agents to reuse experience from past interactions, but most existing libraries store skills as isolated entries and retrieve them only by semantic similarity. This leads to two key challenges for compositional tasks. Firstly, an agent must identify not only relevant skills but also how they depend on and build upon each other. Secondly, it also makes library maintenance difficult, since the system lacks structural cues for deciding when skills should be merged, split, or removed. We propose SKILLGRAPH, a framework that represents reusable skills as nodes in a directed graph, with typed edges encoding prerequisite, enhancement, and co-occurrence relations. Given a new task, SKILLGRAPH retrieves not just individual skills, but an ordered skill subgraph that can guide multi-step decision making. The graph is continuously updated from agent trajectories and reinforcement learning feedback, allowing both the skill library and the agent policy to improve together. Experiments on ALFWorld, WebShop, and seven search-augmented QA tasks show that SKILLGRAPH achieves state-of-the-art performance against memory-augmented RL methods, with especially large gains on complex tasks that require composing multiple skills.

We propose a subgraph importance estimation method for pretrained Graph Neural Networks (GNNs) on graph-level tasks, formulated as a linear Group Lasso regression problem in the embedding space. Our method effectively leverages prior domain knowledge of graph substructures, while remaining independent of the specific form of the output layer or readout function used in the GNN architecture, and it does not require access to ground-truth target labels. Experiments on real-world graph datasets demonstrate that our method consistently outperforms existing baselines in subgraph importance estimation. Furthermore, we extend our method to identify important nodes within the graph.

Uncertainty quantification has become an important factor in understanding the data representations produced by Graph Neural Networks (GNNs). Despite their predictive capabilities being ever useful across industrial workspaces, the inherent uncertainty induced by the nature of the data is a huge mitigating factor to GNN performance. While aleatoric uncertainty is the result of noisy and incomplete stochastic data such as missing edges or over-smoothing, epistemic uncertainty arises from lack of knowledge about a system or model (e.g., a graph's topology or node feature representation), which can be reduced by gathering more data and information. In this paper, we propose an original new framework in which node-level epistemic uncertainty is modelled in a belief function (finite random set) formalism. The resulting Random-Set Graph Neural Networks have a belief-function head predicting a random set over the list of classes, from which both a precise probability prediction and a measure of epistemic uncertainty can be obtained. Extensive experiments on 9 different graph learning datasets, including real-world autonomous driving benchmarks as such Nuscene and ROAD, demonstrate RS-GNN's superior uncertainty quantification capabilities

Federated graph learning (FGL) enables collaborative training on graph data across multiple clients. As graph data increasingly contain multimodal node attributes such as text and images, multimodal federated graph learning (MM-FGL) has become an important yet substantially harder setting. The key challenge is that clients from different modality domains may not share a common semantic space: even for the same concept, their local encoders can produce inconsistent representations before collaboration begins. This makes direct parameter coordination unreliable and further causes two downstream problems: forcing heterogeneous client representations into a naively shared semantic space may create false semantic agreement, and graph message passing may amplify residual inconsistency across neighborhoods. To address this issue, we propose \textbf{STAGE}, a protocol-first framework for MM-FGL. Instead of relying on direct parameter averaging, STAGE builds a shared semantic space that first translates heterogeneous multimodal features into comparable representations and then regulates how these representations propagate over local graph structures. In this way, STAGE not only improves cross-client semantic calibration, but also reduces the risk of inconsistency amplification during graph learning. Extensive experiments on 8 multimodal-attributed graphs across 5 graph-centric and modality-centric tasks show that STAGE consistently achieves state-of-the-art performance while reducing per-round communication payload.

Automated analysis of building facades from street-level imagery has great potential for urban analytics, energy assessment, and emergency planning. However, it requires reasoning over spatially arranged elements rather than solely isolated detections. In this work, we model each facade as a graph over window/door detections with a vertical prior on edges. Additionally, we introduce GATA2Floor, a multi-head Graph Attention v2 (GATv2) based model that predicts the global floor count of a building and, via learnable cross-attention queries, softly assigns elements to latent floor slots, yielding interpretable outputs and robustness to irregular designs. To mitigate the lack of labeled datasets, we demonstrate that the proposed graph-based reasoning can be applied without annotations by leveraging a lightweight label-free proposal mechanism based on self-supervised features and vision-language scoring. Our approach demonstrates the value of graph-attention-based relational reasoning for facade understanding.

Weakly supervised graph anomaly detection aims to unveil unusual graph instances, e.g., nodes, whose behaviors significantly differ from normal ones, given only a limited number of annotated anomalies and abundant unlabeled samples. A major challenge is to learn a meaningful latent feature representation that reduces intra-class variance among normal data while remaining highly sensitive to anomalies. Although recent works have applied self-supervised feature learning for graph anomaly detection, their strategies are not specifically tailored to its unique requirements, motivating our exploration of a more domain-specific approach. In this paper, we introduce a weakly supervised graph anomaly detection method that leverages a feature learning strategy tailored for graph anomalies. Our approach is built upon a multi-task learning scheme that extracts robust feature representations through synthesized anomalies. We generate synthetic anomalies by perturbing the normal graph in various ways and assign a dedicated detection head to each anomaly type, ensuring that learned features are sensitive to potential deviations from normal patterns. Although synthetic anomalies may not perfectly replicate real-world patterns, they provide valuable auxiliary data for effective feature learnin, much like features learned from ImageNet classification transfer to downstream vision tasks. Additionally, we adopt a two-phase learning strategy: an initial warm-up phase using only synthetic samples, followed by a full-training phase integrating both tasks, to balance the influence of synthetic and real data. Extensive experiments on public datasets demonstrate the superior performance of our method over its competitors. Code is available at https://github.com/yj-zhou/SAWGAD.

We study a graph pathfinding problem Distance-$r$ Independent Unlabeled Multi-Agent Pathfinding, finding a set of collision-free paths between two sets where agents must stay at pairwise distance at least $r+1$ at all times. This additional constraint, generalizing collision modeling for classical MAPF, targets aspects of real-world multi-agent coordination. This additional distance constraint makes feasibility (i.e., whether a solution exists) PSPACE-complete, in contrast to standard (unlabeled) MAPF, where it can be decided in polynomial time. We address the challenge via two complementary approaches: (i) reduction-based optimal algorithms with a feasibility-preserving compression procedure, and (ii) a configuration generator-based search. Despite the hardness, empirical results show that our algorithm can handle hundreds of agents in a practical timeframe.

Multimodal Graph Neural Networks (MGNNs) have shown strong potential for learning from multimodal attributed graphs, yet most existing approaches rely on tightly coupled architectures that suffer from prohibitive computational overhead. In this paper, we present a systematic empirical analysis showing that decoupled MGNNs are substantially more efficient and scalable for large-scale graph learning. However, we identify a critical bottleneck in existing decoupled pipelines, namely modal conflict, which arises in both the propagation and aggregation stages. Specifically, independent multi-hop diffusion causes cross-modal semantic divergence during propagation, while naive fusion fails to align multi-hop feature trajectories during aggregation, jointly limiting effective representation learning. To address this challenge, we propose CAMPA, a Cross-modal Aligned Multimodal Propagation & Aggregation framework for decoupled multimodal graph learning. Concretely, CAMPA introduces a two-stage alignment mechanism: (1) cross-modal aligned propagation, which injects cross-modal similarity priors into message passing to preserve semantic consistency without additional parameter overhead; (2) trajectory aligned aggregation, which leverages trajectory-level self-attention and cross-attention to capture and align long-range dependencies across modalities and hops. Extensive experiments on diverse benchmark datasets and tasks demonstrate that CAMPA consistently outperforms strong coupled and decoupled baselines while preserving the efficiency advantages of the decoupled paradigm.

Graph Neural Networks (GNNs) have emerged as a powerful paradigm in Knowledge Graphs (KGs) due to their intrinsic ability to model graph-structured data. However, there remains a lack of a systematic review about GNN-based methodologies across the entire knowledge graph technologies pipeline. To address this gap, we first propose a novel two-level taxonomy framework for GNN-based knowledge graph technologies: the KG technologies pipeline and GNN-based perspective. Specifically, the knowledge graph technologies pipeline covers knowledge graph construction, knowledge graph embedding, knowledge reasoning and knowledge graph applications. Meanwhile, the GNN-based perspective provides a new categorization of knowledge graph technologies with GNN models, such as GCN, GAT, and HGNN. Then, we analyze the advantages of GNN technology based on the characteristics of different tasks in the knowledge graph lifecycle. Furthermore, we detailed review various GNN-based models for knowledge graph following the proposed taxonomy, and summarize strengths and limitations. Finally, we discuss unresolved challenges and outline promising directions for future research.

Treating and preventing Human Immunodeficiency Virus (HIV) remains a critical global health challenge. While antiretroviral therapy provides a path toward viral suppression -- effectively eliminating an individual's transmission risk -- systemic resource constraints limit the reach of intervention efforts. This work addresses the strategic distribution of intensive resources among virally unsuppressed individuals to minimize the expected cascade of new infections within a transmission network. We formalize this challenge as a novel constrained optimization problem where we have resources to "treat" $k$ out of a set $\mathbf{P}$ of virally unsuppressed individuals, and establish its theoretical connections to existing computational literature. We then propose Cascade-Aware Suppression of Transmission (CAST), a polynomial-time $(δ, ε)$-approximation algorithm that achieves a $2\sqrt{|\mathbf{P}|}$ approximation ratio by leveraging connections to the Minimum-$k$-Union (MkU) problem and Hoeffding-style concentration bounds. Extensive evaluations on real-world HIV networks demonstrate that CAST outperforms standard public health and computer science baselines. Furthermore, we show that CAST is empirically robust across diverse infectious disease networks, varied edge probability initializations, and settings involving imperfect network data.

Collaborative filtering (CF) models based on graph neural networks (GNNs) achieve strong performance in recommender systems by propagating user-item signals over interaction graphs. However, they are highly susceptible to popularity bias, since skewed interaction distributions and repeated message passing across high-order neighborhoods amplify the influence of popular items while suppressing long-tail ones. Existing debiasing approaches, including re-weighting objectives, regularization, causal methods, and post-processing, are less effective in GNN-based settings because they do not directly counteract bias propagated through the aggregation process, and recent in-aggregation weighting methods often rely on static heuristics or unstable embedding estimates. We propose Debiasing Popularity Amplification in Aggregation (DPAA), a popularity debiasing framework for GNN-based CF that integrates adaptive, embedding-aware interaction weighting and layer-wise weighting directly into message passing. DPAA assigns interaction-level weights from a representation-aware popularity signal, stabilized by a smooth transition from pre-trained to evolving model embeddings during training. It further introduces a layer-wise weighting that amplifies higher-order neighborhoods, surfacing long-range interactions with diverse and underexposed items. Experiments on real-world and semi-synthetic datasets show that DPAA outperforms state-of-the-art popularity-bias correction methods for GNN-based CF.

Graph representation learning has become a standard approach for analyzing networked data, with latent embeddings widely used for link prediction, community detection, and related tasks. Yet a basic design choice, the latent dimension, is still treated as a brittle hyperparameter, fixed before training and tuned by held-out performance. Learned factors are also identifiable only up to rotation and rescaling, so the nominal rank rarely coincides with the quantity that governs model behavior. We propose Spectral Prefix Extraction and Capacity-Targeted Representation Analysis (Spectra), which replaces rank as the unit of analysis with the spectrum of a learned positive semidefinite kernel, trace-normalized so that spectra are comparable across fits. The normalized eigenvalues form a distribution on the simplex, and their Shannon effective rank acts both as a summary of learned capacity and as a controllable training-time coordinate: a single scalar shapes this realized dimension during training, and bisection targets any desired value within the rank cap. To theoretically support that, we show local regularity and monotonicity of the realized-dimension profile. Across collaboration, social, biological, and infrastructure networks, Spectra traces performance--capacity frontiers that make the trade-off between predictive accuracy and realized dimension visible. It performs competitively with strong link-prediction baselines, yields aligned lower-capacity views of the same fitted model through spectral prefixes, and provides a principled handle on capacity in the overparameterized regime. Capacity thus becomes a property of the fitted model rather than a hyperparameter of the training.

Molecular Graph Neural Networks (GNNs) are increasingly common in drug discovery, particularly for Quantitative Structure-Activity Relationship (QSAR) studies; yet, their superiority compared to classical molecular featurisation approaches is disputed. We report a general strategy for improving GNNs for QSAR by pre-training to predict Extended-Connectivity Fingerprints (ECFP). We validate our approach with statistical tests and challenging out-of-distribution (OOD) splits. Across five out of six Biogen benchmarks, we observed a statistically significant improvement in standard performance metrics over all evaluated baselines when using ECFP pre-trained GNNs. However, for more heterogeneous datasets and more complex endpoints, such as binding affinity prediction, pre-trained GNNs underperformed in OOD settings. Importantly, we investigated the impact of substructure-level data leakage during pre-training on downstream performance. While we identified scenarios where pre-training on ECFPs was less effective, our findings show that ECFP-based pre-training can enhance downstream OOD performance on a diverse set of practically relevant QSAR tasks.

Forward error correction is essential for reliable communication over noisy channels. Attention-based model-free neural decoders have shown strong performance for short codes, but their scalability to longer codes is limited by the quadratic memory and computational cost of attention. In this paper, we introduce the Mamba message-passing decoder (MMPD), an attention-free syndrome-based neural decoder for binary linear codes. MMPD retains the Tanner-graph structure of a message-passing decoder by performing local pairwise aggregation along variable-check edges. To enable efficient long-range information propagation, these local updates are combined with bidirectional Mamba state-space blocks. By avoiding dense attention matrices, MMPD scales more favorably for long codes in both memory and computation. Experiments on the (1056, 880) LDPC code show that MMPD achieves a 0.45 dB gain over the state-of-the-art CrossMPT decoder at a specified target bit error rate, while reducing memory consumption by a factor of 1.5. This reduction factor increases substantially for longer codes, demonstrating the applicability of MMPD to scalable neural decoding of practical long codes.

Graph neural networks are increasingly adopted in trigger systems for collider experiments, where strict latency and throughput constraints render deployment on embedded platforms challenging. As detectors move towards higher granularity, the number of inputs per inference increase and FPGA-only solutions face resource bottlenecks. This work presents an end-to-end demonstrator for the real-time deployment of a dynamic Graph Neural Network for the Belle II electromagnetic calorimeter hardware trigger on the AMD Versal VCK190, leveraging both FPGA fabric and AI Engine tiles. We develop a Python-based semi-automated design flow covering operator fusion, partitioning, mapping, spatial parallelization, and kernel-level optimization. Our design achieves a throughput of 2.94 million events per second at an end-to-end latency of 7.15 microseconds. Compared to the FPGA-only baseline, this represents a 53% throughput improvement while reducing DSP utilization from 99% to 19% at 29% AI Engine tile utilization. To validate the deployment, an interactive visualization pipeline enables real-time monitoring of inference results on the physical demonstrator.

Graph Neural Networks (GNNs) have achieved strong results in molecular property prediction, but polymers present distinct challenges: labeled datasets are scarce and small (typically in the order of hundreds of polymers) due to the need for expensive experimentation, and complex polymer chain distributions influence polymer properties. Established practice in polymer prediction represents polymers solely by graphs of their repeat units, discarding the chain-scale morphology that governs key properties such as the glass transition temperature ($T_g$). In this work, we propose a principled graph construction that addresses this gap. Given a polymer's molecular mass distribution (MMD), we sample representative chains from the Schulz-Zimm distribution and construct representative sets of large graphs encoding chain-scale topology directly, with atoms and bonds featurized using rich chemical descriptors. We further pretrain GNN encoders via masked graph modeling on 100,000 unlabeled PSMILES strings before fine-tuning on labeled data. On a dataset of 381 polymers (180 homopolymers and 201 copolymers), we show that graph construction and self-supervised pretraining are jointly necessary: without pretraining, the large graph method matches the repeat-unit baseline (28.40 K vs. 28.36 K RMSE); with pretraining, it achieves 24.76 K +/- 3.30 K, a 5.1% reduction in mean error over the pretrained repeat-unit baseline (26.08 K +/- 4.20 K, p < 0.001, 30 runs). An ablation removing chemical features degrades performance to 36.65 K, confirming both components are essential. Results are architecture-agnostic, holding for both GINE and GATv2 encoders.

Biomedical knowledge graphs underwrite drug repurposing and clinical decision support, yet the upstream ontologies they depend on update on independent cycles that add millions of edges and deprecate hundreds of thousands more between releases. Yet existing continual graph learning has been studied almost exclusively on synthetic random splits of static, generic KGs, a regime that cannot reproduce the asynchronous, structured evolution real biomedical KGs undergo. To this end, we introduce PrimeKG-CL, a CGL benchmark built from nine authoritative biomedical databases (129K+ nodes, 8.1M+ edges, 10 node types, 30 relation types) with two genuine temporal snapshots (June 2021, July 2023; 5.83M edges added, 889K removed, 7.21M persistent), 10 entity-type-grouped tasks, multimodal node features, and a per-task persistent/added/removed test stratification. On three tasks (biomedical relationship prediction, entity classification, KGQA), we evaluate six CL strategies across four KGE decoders, plus LKGE, an LLM-RAG agent, and CMKL. We find that decoder choice and continual learning strategy interact strongly: no single strategy performs best across all decoders, and mismatched combinations can significantly degrade performance. Moreover, only DistMult exhibits a clear separation between persistent and deprecated knowledge, indicating that standard metrics conflate retention of still-valid facts with failure to forget outdated ones; this effect is absent under RotatE. In addition, multimodal features improve entity-level tasks by up to 60%, and a recent CKGE framework (IncDE) failed to scale to our 5.67M-triple base task across five attempts up to 350GB RAM. Data, pipeline, baselines, and the stratified split are released openly. Dataset:huggingface.co/datasets/yradwan147/PrimeKGCL|Code:github.com/yradwan147/primekg-cl-neurips2026

The counting power of Message Passing Neural Networks (MPNN) has been the subject of many recent papers, showing that they can express logic that involves counting up to a threshold or more generally satisfy a linear arithmetic constraint. In this paper, we study the counting capabilities of MPNN beyond linear arithmetic, primarily utilising local and global mean aggregations. In particular, our goal is to tease out conditions required to express extensions of graded modal logic with polynomial counting constraints. We show that global polynomial counting constraints in node-labelled graphs can be checked using mean MPNN under mild assumptions. Checking local constraints is also possible, if we consider formulas with no nested modalities and additionally either (i) permit sum/max aggregations, or (ii) only restrict to regular graphs. We also show how formulas with nested modalities can be captured by mean MPNN over graphs with tree-like structures and similar assumptions.

Pre-trained language models advance patent classification and retrieval by encoding claims as flat token sequences, but they overlook the dependency hierarchy among claims. Incorporating this hierarchy into self-attention poses two challenges. First, claim dependencies include relation types with different levels of reliability, so treating them uniformly may allow noisy technical relations to interfere with more reliable legal citations. Second, claim dependencies are defined at the claim level, whereas Transformer attention operates over tokens, making direct structural injection nontrivial. We propose the Patent Heterogeneous Attention-Guided Graph Encoder (PHAGE), which constructs a typed claim graph that distinguishes legal citations from technical relations. PHAGE projects this claim-level topology into token-level attention through a connectivity mask and learnable relation-aware biases, and fine-tunes the encoder using a dual-granularity contrastive objective that combines inter-patent taxonomy with intra-patent topology. At inference, the graph-specific attention components are removed, allowing representations to be generated through a standard encoder forward pass without CDG construction. Experiments on patent classification, retrieval, and clustering show that PHAGE consistently outperforms domain-adapted and citation-aware baselines, demonstrating the value of claim-level structural guidance for graph-free patent representation learning.

Graph foundation models (GFMs), pretrained on massive graph data, have transformed graph machine learning by supporting general-purpose reasoning across diverse graph tasks and domains. Existing GFMs pretrained with fixed-hop subgraph sampling impose a fixed receptive field, causing scale mismatch on diverse tasks, which often require heterogeneous and unknown structural contexts beyond a fixed sampling scale. We propose R-GFM, a Riemannian Graph-of-Graphs (GoG) based foundation model, that treats structural scale as a first-class citizen in modeling. R-GFM constructs a multi-scale GoG over-sampled subgraphs at different hop distances and learns geometry-adaptive representations from Riemannian manifolds. Theoretical analysis shows that R-GFM reduces structural domain generalization error compared to fixed-scale GFMs. Experiments on various datasets demonstrate that R-GFM achieves state-of-the-art performance, with up to a 49% relative improvement on downstream tasks. Our code is available at https://github.com/USTC-DataDarknessLab/R-GFM.

Protein-protein interactions (PPIs) are fundamental to cellular function and disease mechanisms. Current learning-based PPI predictors focus on learning powerful protein representations but neglect designing specialized classification heads. They mainly rely on generic aggregating methods like concatenation or dot products, which lack biological insight. Motivated by the biological "L3 rule", where multiple length-3 paths between a pair of proteins indicate their interaction likelihood, our study addresses this gap by designing a biologically informed PPI classifier. In this paper, we provide empirical evidence that popular PPI datasets strongly support the L3 rule. We propose an L3-path-regularized graph prompt learning method called L3-PPI, which can generate a prompt graph with virtual L3 paths based on protein representations and controls the number of paths. L3-PPI reformulates the classification of protein embedding pairs into a graph-level classification task over the generated prompt graph. This lightweight module seamlessly integrates with PPI predictors as a plug-and-play component, injecting the interaction prior of complementarity to enhance performance. Extensive experiments show that L3-PPI achieves superior performance enhancements over advanced competitors.

Graph learning research has increasingly shifted toward continual graph learning (CGL), which better reflects real-world scenarios where graphs evolve over time. However, existing CGL methods largely assume clean supervision and overlook a critical challenge: the newly arriving portions of the graph are often noisy, due to annotation errors or adversarial corruption. This mismatch limits their applicability in practice. In this work, we study robust continual graph learning, where models must simultaneously handle catastrophic forgetting and noisy supervision in evolving graph data. We show that label noise introduces a new failure mode, catastrophic remembering, where models persistently reinforce corrupted knowledge across tasks. To address these challenges, we propose a Unified Flow-Oriented framework (UFO). First, UFO models conditional feature distributions via flow-based generative modeling and produces replay representations, mitigating forgetting without storing historical data. Second, UFO estimates instance-level reliability scores to distinguish clean from noisy nodes, reducing the impact of corrupted supervision and alleviating catastrophic remembering. Extensive experiments on four benchmark graph datasets under varying noise ratios demonstrate that UFO consistently outperforms existing methods in both accuracy and forgetting metrics. Code is available at: https://anonymous.4open.science/r/UFO.

With the rapid growth of mobile robotics and embedded intelligence, there is an increasing demand for efficient on-device data processing on edge platforms. A promising research direction is the use of neuromorphic sensors inspired by human sensory systems, which generate sparse, event-based data encoding changes in the environment. In this work, we present the first end-to-end FPGA implementation of a keyword spotting system that integrates a Neuromorphic Auditory Sensor (NAS) and a graph neural network (GNN) on a single FPGA device, enabling real-time processing of raw audio data. The proposed architecture eliminates conventional signal preprocessing and operates directly on event-based audio streams. Leveraging a compute-near-memory network architecture, the system achieves efficient inference with low latency and low power consumption. Experimental results demonstrate an accuracy of 87.43% after quantization on the Google Speech Commands v2 dataset processed through the neuromorphic sensor, with end-to-end latency below 35 us and average power consumption of 1.12 W. The processed datasets, software models, and hardware modules are available at https://github.com/vision-agh/NAS-GNN-KWS.

Graph Neural Networks (GNN) and Transformer-based architectures have achieved remarkable progress in graph learning, yet they still struggle to capture both global structural dependencies and model the dynamic information propagation. In this paper, we propose CTQWformer, a hybrid graph learning framework that integrates continuous-time quantum walks (CTQW) with GNN. CTQWformer employs a trainable Hamiltonian that fuses graph topology and node features, enabling physically grounded modeling of quantum walk dynamics that captures rich and intricate graph structure information. The extracted CTQW-based representations are incorporated into two complementary modules:(i) a Graph Transformer module that embeds final-time propagation probabilities as structural biases in the self-attention mechanism, and (ii) a Graph Recurrent Module that captures temporal evolution patterns with bidirectional recurrent networks. Extensive experiments on benchmark graph classification datasets demonstrate that CTQWformer outperforms graph kernel and GNN-based methods, demonstrating the potential of integrating quantum dynamics into trainable deep learning frameworks for graph representation learning. To the best of our knowledge, CTQWformer is the first hybrid CTQW-based Transformer, integrating CTQW-derived structural bias with temporal evolution modeling to advance graph learning.

While Graph Neural Networks (GNNs) have demonstrated significant efficacy in node classification tasks, where predictions rely on local neighborhood information, the performance of GNNs often drops when prediction tasks depend on long-range interactions. These limitations are attributed to phenomena such as oversquashing, where structural bottlenecks restrict signal propagation across the network topology. To address this challenge, we introduce RAwR, a computationally efficient rewiring framework that augments the input graph with a quotient graph derived from equitable partitions. This approach facilitates accelerated communication between nodes that share identical structural roles, as identified by the Weisfeiler-Leman graph coloring, and thereby reduces the total effective resistance of the system. Furthermore, by employing an approximate definition of the equitable partition, RAwR enables a controllable reduction of the quotient graph, which, in its most condensed state, recovers the conventional Master Node rewiring technique. Empirical evaluations across a diverse suite of benchmarks -- including homophilic, heterophilic, and synthetic long-range datasets -- demonstrate that RAwR achieves state-of-the-art results. Our contribution is further supported by an analytical investigation using a teacher-student model of linear GNNs, which elucidates the theoretical foundations of role-based rewiring. This analysis leads to the formulation of Spectral Role Lift (SRL), a metric designed to identify the optimal approximate equitable partition for maximizing predictive performance.

Graph-level anomaly detection (GLAD) is crucial for ensuring the reliability of graph-driven applications by identifying abnormal graphs that deviate from the majority. Considering the privacy concerns in distributed scenarios, federated graph-level anomaly detection (FedGLAD) has emerged as a promising solution to enable collaborative detection without sharing raw data. However, existing methods suffer from poor generalization due to the reliance on unrealistic synthetic anomalies and insufficient personalization capabilities under data heterogeneity. To address these challenges, we propose a novel Federated graph-level anomaly detection approach with Cluster-adaptIve GAted Reconstruction (FedCIGAR). Specifically, we design a reconstruction-based paradigm trained on normal graphs to avoid synthetic data. Furthermore, we introduce a client-side node contribution gating mechanism and a server-side sliding window-based clustering strategy to tackle data heterogeneity. Extensive experiments demonstrate that FedCIGAR achieves superior performance and robustness in contrast to state-of-the-art methods.

Graph Neural Networks (GNNs) excel at relational reasoning but face two persistent challenges: the lack of interpretable attribution for heterogeneous node types, and the computational overhead of message passing over large, noisy graphs. We propose the Hierarchical Attention-based Heterogeneous GNN (HA-HeteroGNN), a framework that addresses both issues through a unied explainability-to-pruning pipeline. A two-tier attention mechanism separates sensor-level and context-level computation across 16 node types and 18 edge types, producing per-node relevance scores via an attention-based GNN Explainer without requiring gradient backpropagation. These relevance scores then serve as a principled pruning criterion: removing nodes identied as consistently uninformative yields a 27% reduction in graph edges while simultaneously improving classication accuracy by 2.46.1% across all model variants, challenging the conventional assumption that pruning necessarily trades accuracy for eciency. Experiments on a 50,000-record synthetic dataset spanning 11 report categories demonstrate 97.5% cross-strategy explanation stability and domain consistent sensor attribution, with training-time reductions of up to 43.9% and real-time inference latency of approximately 5860 ms per sample.

Mesh-based simulations provide high-fidelity solutions to partial differential equations (PDEs), but achieving such accuracy typically requires fine meshes, leading to substantial computational overhead. Super-resolution techniques aim to mitigate this cost by reconstructing high-resolution (HR), high-fidelity solutions from low-cost, low-resolution (LR) counterparts. However, training neural networks for super-resolution often demands large amounts of expensive HR supervision data. To address this challenge, we propose SuperMeshNet, an HR data-efficient super-resolution framework for mesh-based simulations aided by message passing neural networks (MPNNs). At its core, SuperMeshNet introduces complementary learning, a semi-supervised approach that effectively leverages both 1) a small amount of paired LR-HR data and 2) abundant unpaired LR data via two jointly trained, complementary MPNN-based models. Additionally, our model is enriched by inductive biases, which are empirically shown to further improve super-resolution performance. Extensive experiments demonstrate that SuperMeshNet requires 90% less HR data to achieve even lower root mean square error (RMSE) than that of the fully supervised benchmark without the inductive biases. The source code and datasets are available at https://github.com/jykim-git/SuperMeshNet.git.

We introduce a use of the $M$-cover (or $M$-layer) transform for machine learning. The method replicates a model $M$ times, but instead of coupling the copies through parameter averaging or an explicit attractive force, as in replicated SGD or Elastic SGD, it rewires the contexts in which local learning messages are computed. Each local loss is evaluated on a routed model whose parameters are drawn from different copies according to permutations sampled from a structured mixing kernel $Q$. Training then uses the original local update rule, while the resulting learning messages are redistributed across the copies through these routed computational paths. Thus $Q$ defines a topology for message transport and controls the long-loop structure of the lifted factor graph. We formulate this construction for perceptrons, committee machines, and multilayer perceptrons, showing that the same principle applies from discrete models to differentiable neural networks. The resulting framework provides a mechanism for improving generalization through structured message sharing rather than replica collapse or parameter-space coupling.

Scene graphs (SGs) represent objects and their relationships as structured graphs, enabling applications in image generation, robotics, and 3D understanding. Recent work suggests that conditioning image generation on scene graphs improves compositional fidelity compared to text-only prompting. However, since users typically provide text rather than structured graphs, a key challenge is to generate scene graphs from natural language. Prior work on discrete diffusion has demonstrated success in generating generic graphs such as molecules and circuits, but fails to account for the hierarchical structure and strong dependencies between objects, edges, and relations in scene graphs. We address this limitation by introducing a dependency-aware, hierarchically constrained discrete diffusion model for scene graph generation. Our approach decouples structure and semantics across the forward and reverse processes, enabling the model to capture conditional dependencies. At inference time, we perform training-free conditioning to sample text-aligned scene graphs. We evaluate our method on standard SG benchmarks and demonstrate improvements over both continuous and discrete graph generation baselines across graph and layout metrics. When fed to downstream image generation, our approach yields improved compositional alignment compared to text-to-image models, particularly in multi-object scenarios.

Accurate and efficient storm-surge emulation is essential for coastal hazard assessment, yet high-fidelity hydrodynamic models remain too expensive for large scenario ensembles and rapid evaluation under heterogeneous climate forcings. We present PACT, a peak-aware cross-attention graph transformer for efficient station-level storm-surge prediction from atmospheric forcing fields. PACT represents each forcing patch as a graph, encodes spatial structure with GraphSAGE, and uses a learned station query to aggregate node information through cross-attention rather than uniform pooling. A Transformer encoder models temporal dependence across the forcing history, and a horizon-query decoder generates lead-specific forecasts from a shared temporal memory. To better capture extreme events, we introduce a peak-aware learning strategy that couples a lightweight auxiliary peak-aware head with a tailored training objective, including a tail-focused loss on peak-dominated samples and a horizon-wise slope regularizer to encourage coherent multi-step evolution. Across multiple tide-gauge stations along the US Northeast coast, PACT outperforms a strong spatio-temporal graph neural network baseline in both RMSE and MAE. Diagnostics show improved peak fidelity and tail preservation for reanalysis and most CMIP6 datasets. PACT is also computationally efficient, requiring about 3.5~s to generate a full winter-season surge trajectory for one year after training. Under distribution shift across five CMIP6 forcings, PACT transfers well within the CMIP6 family but degrades markedly when transferring from reanalysis to climate-model forcings, highlighting a persistent reanalysis--GCM gap.

Graph-based agent memory is increasingly used in LLM agents to support structured long-term recall and multi-hop reasoning, but it also creates a new poisoning surface: an attacker can inject a crafted relation into graph memory so that it is later retrieved and influences agent behavior. Existing agent-memory poisoning attacks mainly target flat textual records and are ineffective in graph-based memory because malicious relations often fail to be extracted, merged into the target anchor neighborhood, or retrieved for the victim query. We present SHADOWMERGE, a poisoning attack against graph-based agent memory that exploits relation-channel conflicts. Its key insight is that a poisoned relation can share the same query-activated anchor and canonicalized relation channel as benign evidence while carrying a conflicting value. To realize this, we design AIR, a pipeline that converts the conflict into an ordinary interaction that can be extracted, merged, and retrieved by the graph-memory system. We evaluate SHADOWMERGE on Mem0 and three public real-world datasets: PubMedQA, WebShop, and ToolEmu. SHADOWMERGE achieves 93.8% average attack success rate, improving the best baseline by 50.3 absolute points, while having negligible impact on unrelated benign tasks. Mechanism studies show that SHADOWMERGE overcomes the three key limitations of existing agent-memory poisoning attacks, and defense analysis shows that representative input-side defenses are insufficient to mitigate it. We have responsibly disclosed our findings to affected graph-memory vendors and open sourced SHADOWMERGE.

SO(3) equivariant graph neural networks have become the dominant paradigm for atomistic foundation models, achieving high accuracy and data efficiency by building rotational symmetry directly into the architecture. Yet the computational cost of their higher-order tensor operations creates a tough trade-off between model accuracy and inference efficiency. In this paper, we propose a structural pruning method for SO(3) equivariant atomistic foundation models to bridge this accuracy-efficiency gap. The pruning is applied along the channel and order dimensions, with each irreducible representation kept or removed as a complete block, thereby retaining SO(3) equivariance. Starting from a large checkpoint, the pruned model substantially reduces the inference cost while retaining higher accuracy than an independently trained small model. The pruned MACE-MP model outperforms the official from-scratch trained small model on 7 of 9 metrics on the Matbench Discovery leaderboard. In terms of efficiency, compressed MACE-MP and MACE-OFF models contain 1.5$\times$ to 4$\times$ fewer parameters and require 2.5$\times$ to 4$\times$ less pre-training compute than training a small model from scratch. For downstream applications, fine-tuning the pruned model reduces energy and force errors by 70.1% and 34.4% compared to training task-specific models from scratch across eight representative downstream datasets. We demonstrate that the method generalizes to other SO(3) equivariant architectures (SevenNet, eSCN) and can be combined with quantization and knowledge distillation for further gains.

Graph foundation models (GFMs) seek transferable representations across graph domains but are limited by structural heterogeneity and incompatible node feature spaces. We propose Structure-Centric Graph Foundation Models (SCGFM), which treat graph topology as the primary source of transferable knowledge. Modeling graphs as metric measure spaces, SCGFM introduces learnable geometric bases that define a shared structural coordinate system. Graphs are aligned to these bases via Gromov-Wasserstein distances, yielding structure-aligned latent representations that accommodate heterogeneous graph topologies. To address feature incompatibility, SCGFM employs a structure-aware feature re-encoding mechanism that unifies node representations without assuming a fixed feature dimensionality or requiring dataset-specific preprocessing. Experiments on graph- and node-level tasks demonstrate strong in-domain and cross-domain generalization, outperforming existing GFM approaches.

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

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

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

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

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

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