Zhiyang Qiu, Yangtao Wang, Xiaocui Li +3cs.LG cs.AI
Graph prompt learning is an effective paradigm to adapt pre-trained graph models to downstream tasks in low-resource scenarios. However, existing multi-task graph pre-training frameworks generally use randomly initialized prompts, leading to poor alignment between the prompt space, pretext objectives and graph structural characteristics. This greatly weakens the task relevance, structural awareness and transferability of prompt representations. To address this challenge, we propose TPGC, a dual-prior prompt initialization solution that explicitly models the synergy between task prior and structural prior. Specifically, the Task-Prior Injection Module first conducts a short homologous multi-task pre-training on an auxiliary graph, enabling prompt initialization to inherit optimization preferences associated with multiple pretext tasks. Built on the task-aware representations, the Structure-Prior Injection Module further extracts transferable global structural context from the auxiliary graph, converting it into layer-wise prompt vectors by aggregating structurally informative node embeddings. Extensive experiments on 6 mainstream benchmarks covering node and graph classification show that TPGC achieves consistently better performance under few-shot settings than state-of-the-art baselines, with fewer downstream tunable parameters and lower runtime. The code is available at https://github.com/Virgilqiu/TPGC
Noisy node classification problem is a fundamental yet challenging task for real-world graph-related web services, where node labels are often corrupted or unreliable due to weak supervision or automatic annotation. However, existing methods typically train models based on one-hot labels, which not only makes models susceptible to overfitting on noisy labels, but also leads to error accumulation after pseudo-label-guided enhancement. In this paper, we propose a novel Partial label-based Self-training framework (PaSta for short) that leverages partial label learning technique to overcome the limitations of existing methods. Specifically, PaSta first trains multiple annotators to comprehensively capture the class distribution of nodes and aggregates their predictions to construct high-quality partial labels. Subsequently, we design a partial label-based classification model with two well-crafted loss functions to guide the model learning at both label and representation spaces. To further enhance the robustness against noisy labels, we introduce a self-training strategy where the labels refined by partial label learning are then used to further optimize the annotators in a closed-loop iterative manner. Extensive experiments on five datasets demonstrate that, compared with existing state-of-the-art methods, PaSta achieves an average improvement of 1.1% in classification performance under various noise settings.
Class-imbalanced node classification on temporal graphs is challenging because majority-dominated temporal propagation progressively assimilates minority representations, while conventional node and neighborhood information provides insufficient discriminative evidence for minority classes. To address these issues, we propose MDTE, a minority-aware diffusion framework that reconstructs stable and discriminative temporal edge-event representations through conditional diffusion denoising. Specifically, MDTE introduces Distribution-Aware Selective Propagation, which combines Local Outlier Factor (LOF)-based propagation filtering with cluster-aware low-frequency propagation. The module preserves informative neighborhood dependencies while mitigating harmful propagation and majority-class information assimilation. It further develops Multi-View Discriminative Fusion, which exploits feature reconstruction and topology prediction to characterize class-wise differences in distribution learning and extracts complementary discriminability signals to guide denoising. Experiments on five real-world datasets demonstrate that MDTE consistently achieves the best performance on minority-class-oriented metrics, improving minority-class recall by up to 23.53 percentage points, minority-class F1 by 8.68 percentage points, and AUPRC by 2.67 percentage points over the strongest baselines.
Multimodal graph learning requires jointly training over graph structure and heterogeneous node attributes, yet existing methods largely decouple these processes: prior multimodal graph neural networks (GNNs) focus on aligning modalities in a shared embedding space while operating on fixed or weakly adapted graph structures, and graph structure learning approaches infer topology from unimodal node representations without accounting for multimodal interactions. This separation fundamentally limits the ability of GNNs to capture semantically meaningful relationships in multimodal settings, where observed edges are often noisy, incomplete, or misaligned with underlying semantics. We propose ReCoG (Reciprocal Co-Evolution for Multimodal Graph Learning), a new learning paradigm that tightly couples graph structure learning and multimodal representation learning through end-to-end reciprocal interaction. Concretely, ReCoG integrates (i) a multimodal graph refiner that infers and corrects edges using cross-modal semantic evidence, and (ii) a coupled cross-modal message passing mechanism that performs joint intra- and inter-modality propagation over the refined graph. This unified design yields greater expressiveness than decoupled or two-stage formulations and allows dynamic interaction between topology and representation learning. Across diverse benchmarks for node classification and link prediction, ReCoG consistently outperforms strong multimodal graph structure learning baselines, including graph foundation models. Our results demonstrate that reciprocal co-evolution of structure and semantics is important for effective multimodal graph learning, challenging the prevailing separation between topology and representation learning.
Text-Attributed Graphs (TAGs) integrate graph structures and node-associated textual attributes, and recent studies have increasingly leveraged Large Language Models (LLMs) to improve TAG learning in few-shot settings. However, existing approaches typically utilize LLM-derived information uniformly across all nodes, despite substantial variations in its reliability, while also incurring considerable monetary costs. We argue that the most appropriate source of supervision may differ across nodes, as Graph Neural Networks (GNNs) and LLMs exhibit complementary strengths in exploiting structural and semantic information, respectively. To this end, we propose CoTeach, a Confidence-aware dual-teacher learning framework that dynamically selects the more reliable teacher for each node. Experimental results demonstrate that CoTeach consistently improves few-shot node classification performance while reducing unnecessary LLM utilization and associated monetary costs.
A composite structural index summarises a network in one number; for a triangle-based index it is spectrally redundant: Tr(A^3) is the third moment of the adjacency spectrum. The non-redundant content sits one level down, in diag(A^3), which depends on eigenvectors and is not spectrally determined. A corollary in the theory paper for this index family stated that, and predicted: the global scalar should tie sharpened spectral baselines rather than beat them, while the node-wise attribution should do better where the number of structural epicentres is unknown. This paper tests it. We construct Omega-N by localizing each of the four factors. The direct localization is badly conditioned; two corrections from published practice fix it, a configuration-null excess for every local factor and a personalized-PageRank neighbourhood at several scales, giving ten interpretable features per node from the graph alone, with no attributes, training or embeddings. Against a recursive feature engine at five levels of recursion, Omega-N wins on one and ties on four of six in-domain node-classification evaluations, with ten features against up to 252. Two statistics computed from the graph and labels, not from performance, partition the eight benchmarks without error, and the two they exclude are the two it loses. The strongest application is drug-target prioritisation on protein interaction networks: +0.073 to +0.144 AUPRC over a centrality battery across four constructions, replicated on an independent AP-MS network and label source, surviving three bias controls (degree-matched, ten repetitions: +0.1047 and +0.1030, both 10/10, p=0.00195). The clearest negative sits in the same application: adding Omega-N to centralities plus Node2Vec changes nothing (+0.0014, p=0.31). The claim is narrow: ten interpretable features
Bryan Lima Cavalcante, Thiago Alves Rochacs.LG cs.AI cs.LO
Graph Neural Networks (GNNs) have achieved remarkable performance in node classification tasks, motivating growing interest in methods capable of explaining their predictions. Recent logic-based approaches, such as LogicXGNN, derive global logical rules for Graph Neural Networks (GNNs) from collections of explanatory subgraphs. While informative, these subgraphs may contain redundant structural information that is specific to individual nodes, potentially limiting the generality of the extracted rules. In this work, we propose a logic-based framework for node classification in Simple Graph Convolution (SGC) networks that uses minimal abductive explanations as an intermediate representation for rule extraction. For each node, we compute a minimal set of node-feature pairs sufficient to preserve the predicted class. These explanations are then used to train decision trees from which global logical rules are extracted. Experiments on benchmark datasets show that the proposed framework produces compact global rules while maintaining high fidelity to the original SGC model.
Preben M. Ness, Fariz Ikhwantri, Dusica Marijancs.LG
Are heterophilic nodes in a graph harder to classify because they are heterophilic or because they are rare? Some existing work frames classification of such nodes as a subgroup generalisation problem, where a model performs well on the majority group at the expense of the rare group. Others explain this as a problem of neighbourhood aggregation in graph neural networks (GNNs). We assess these two viewpoints through a detailed evaluation of six GNNs on five datasets of varying homophily, and find that homophilic nodes tend to be easier to classify, even when they are rare---challenging the subgroup framing. However, our findings also nuance existing beliefs about how GNNs misrepresent heterophilic nodes. We demonstrate that the information needed to classify heterophilic nodes correctly is often recoverable by retraining the classification head of a model, or even just the final linear classification layer.
Self-supervised learning on graphs is largely shaped by contrastive methods that depend on carefully designed augmentations, and by generative methods that reconstruct node attributes in the input space. Both paradigms can entangle representations with low-level input statistics rather than with relational structure. Joint-embedding predictive architectures (JEPA) instead learn by predicting latent targets rather than reconstructing inputs. Recent work has explored this idea for graph-level representation learning, but how to design JEPA-style objectives for node-level tasks, and which structural signals the predictor should condition on, remains less clear. We present NodeJEPA, a joint-embedding predictive architecture for node-level graph self-supervised learning. NodeJEPA masks structure-aware k-hop ego-subgraphs and trains a context encoder to predict the latent representations of the masked nodes. These targets come from an EMA-updated target encoder with stop-gradient. A structure-conditioned predictor integrates spectral and centrality descriptors through cross-attention. Variance, covariance, and Laplacian spectral regularizers help stabilize the embedding geometry, and an optional curriculum gradually increases masking difficulty during training. Because prediction occurs in latent space, NodeJEPA does not rely on input reconstruction or hand-crafted graph augmentations. We evaluate NodeJEPA on standard node classification benchmarks under linear probing and fine-tuning protocols, and conduct ablations on masking, prediction, and regularization design choices. Our study offers a practical recipe for node-level JEPA-style latent prediction on graphs, and clarifies when structural conditioning helps representation learning. Code, configurations, and evaluation scripts are publicly available at https://github.com/OliverZ-dot/Node-Jepa.
Mengyao Zhou, Zhiheng Zhou, Xiao Han +1cs.LG cs.AI
Hypergraph neural networks (HGNNs) have demonstrated remarkable capabilities in processing complex higher-order relationships. However, their performance is highly dependent on labeled data, making them vulnerable to label noise. Despite advances in learning with label noise (LLN) and graph learning with label noise (GLN), noisy-label learning on hypergraphs remains underexplored. In this paper, we present a systematic study of hypergraph node classification under label noise. First, we adapt representative LLN and GLN methods to hypergraphs and evaluate them under a unified benchmark, revealing the limitations of existing robust learning strategies for hypergraphs. Building on this, we propose a new hypergraph robust framework, HyperTrust, which first estimates hyperedge trustworthiness through a pretraining-based, entropy-aware strategy, and then incorporates the HyperedgeBoost module to enhance reliable supervision by connecting unlabeled nodes to trustworthy hyperedges, as well as the HyperedgePrune module to suppress noisy propagation by removing untrustworthy node-hyperedge incidences. Finally, two modules work collaboratively to adjust the hypergraph structure and generate final predictions. Extensive experiments and theoretical analysis demonstrate the effectiveness and robustness of HyperTrust on multiple hypergraph datasets under various noisy settings. Our work provides a unified benchmark and an effective solution for hypergraph learning with label noise and lays a foundation for future research in this direction.
Training Graph Neural Networks on large graphs is challenged by the memory cost of storing all node representations across layers. We show that several existing scalable approaches can be written as structured modifications of the GNN propagation matrix, providing a unified perspective that exposes their respective limitations. In particular, graph coarsening replaces it by a low-rank approximation that enables spectral guarantees but assigns uniform representations to clustered nodes, while Cluster-GCN restricts the propagation matrix to intra-cluster connections that allow efficient batching but sever long-range information. These are complementary failures of the \emph{same} decomposition of the graph into groups of nodes. To obtain the best of both worlds, we propose \textbf{CoRe-GNN}, which performs both propagations in parallel at each layer: a coarsened inter-cluster term capturing long-range structure, and a local intra-cluster term preserving per-node discriminability. We prove that CoRe-GNN inherits analogous approximation guarantees to those of graph coarsening, and introduce a natural cluster-based \emph{batching scheme} that scales to graphs with millions of nodes. On node classification benchmarks spanning homophilic, heterophilic, large-scale, and long-range graphs, CoRe-GNN outperforms both graph coarsening and Cluster-GCN baselines. Notably, CoRe-GNN reaches competitive accuracy on \emph{long-range} tasks, while remaining memory-efficient through batching.
Jorge Luiz Franco, Gabriel Duarte, Alexander Nikitin +3cs.LG cs.SI
Topological neural networks (TNNs) enable leveraging high-order structures on graphs (e.g., cycles and cliques) to boost the expressive power of message-passing neural networks. In turn, however, these structures are typically identified a priori through an unsupervised graph lifting operation. Notwithstanding, this choice is crucial and may have a drastic impact on a TNN's performance on downstream tasks. To circumvent this issue, we propose $\partial$lift (DiffLift), a general framework for learning graph liftings to hypergraphs and cellular- and simplicial complexes in an end-to-end fashion. In particular, our approach leverages learned vertex-level latent representations to identify and parameterize distributions over candidate higher-order cells for inclusion. This results in a scalable model which can be readily integrated into any TNN. Our experiments show that $\partial$lift outperforms existing lifting methods on multiple benchmarks for graph and node classification across different TNN architectures. Notably, our approach leads to gains of up to 45% over static liftings, including both connectivity- and feature-based ones.
While signed-directed graphs have been studied using linear Laplacians in the design of graph neural networks, relatively little research has focused on developing non-linear Laplacian operators for such networks. We introduce a non-linear Laplacian operator specific to signed and directed networks (NLSD). This non-linear operator extends the concepts of the signed Laplacian for signed graphs and the Laplacian for directed graphs. The NLSD calculates node-specific potentials based on features More precisely, if the potential discrepancy is not aligned with the edge direction, we ignore it (and vice versa) leveraging message-passing techniques only across edges where potential discrepancies align with the edge's direction. Utilizing this novel operator, we propose an efficient spectral GNN framework (NLSD-GNN). We conducted comprehensive evaluations focusing on node classification and link prediction, examining scenarios involving signed, directional, or both types of information. Our findings reveal that this spectral GNN framework not only integrates signed and directional data effectively but also achieves superior performance across diverse datasets.
Multi-label node classification is an important yet challenging task in graph learning, where nodes exhibit multiple semantics simultaneously. Existing methods for multi-label node classification can effectively model multiple labels, while only considering in-domain scenarios where the model needs to be trained and tested within the same graph domain, resulting in limited cross-domain generalization. Recently, Graph Foundation Models (GFMs) have emerged as a promising paradigm for learning transferable graph representations across diverse graph domains and downstream tasks. However, existing GFMs are built upon single-label assumption, where all nodes are arbitrarily regarded as containing only one class of semantic and embedded into a single representation. For multi-label nodes, such a representation essentially approximates multiple semantics with a single point in the representation space, inevitably leading to semantic entanglement and making simultaneous discrimination of multiple labels difficult. To address these limitations, we propose a Multi-Semantic Basis Graph Foundation Model (MSB-GFM), a framework for cross-domain multi-label node classification. Specifically, we introduce a multi-semantic basis representation learning paradigm that models each multi-label node as an adaptive composition of semantic bases, thereby enabling flexible representational capacity for modeling multiple semantics. Furthermore, we develop a semantic-structure dual-channel architecture with domain adversarial training for effective cross-domain knowledge transfer. Extensive experiments demonstrate the effectiveness of our model.
Neelam Akula, Surbhi Kumar, Murat Kantarcioglu +1cs.LG cs.SI
Many real-world graphs support multiple predictive tasks over the same underlying structure, creating an opportunity to reuse supervision across node classification (NC) and link prediction (LP). However, existing evaluations often rely on incompatible splits, observed-graph assumptions, and negative sampling rules, making conclusions about same-graph cross-task transfer unreliable. We formalize same-graph NC-LP transfer and propose a leakage-free protocol that fixes node and edge splits, uses a shared message-passing graph that excludes evaluated edges, and employs fixed negatives for LP. Across three backbones (GCN, GraphSAGE, GPS), we find that transfer is strongly directional and predictable: NC $\to$ LP is consistently beneficial on homophilic graphs, while LP $\to$ NC is fragile and can even degrade accuracy under naive representation reuse. LP $\to$ NC becomes reliably positive mainly in a structure-dominant regime where LP is easy but NC is unsaturated, suggesting that LP acts as structural pretraining. Finally, we introduce the CoTask Score (CTS) to summarize joint NC+LP utility when a shared encoder must serve both tasks, and show that simple dataset statistics, especially homophily, can guide mechanism choice and help avoid negative transfer.
Tsuyoshi Iwata, Johannes Laurmaa, Ryohei Hisanoq-fin.RM cs.LG
The monitoring of business conduct risk is hindered by sparse, uneven, and visibility-biased data. Prior studies show that business conduct risk information and media coverage propagate through supply chain, peer, and corporate structure networks, yet incident records remain incomplete for many firms. As a result, the absence of reported events could reflect limited coverage rather than the absence of underlying business conduct risk. This paper examines whether inter-firm relationships can improve the prediction of future recorded conduct related incidents, particularly among firms with limited prior visibility. We formulate the task as Positive--Unlabeled node classification on a corporate ownership graph, where firms with recorded incidents are treated as labeled positives and firms without recorded incidents remain unlabeled. We then propose a visibility- and relation-aware GCNII framework that combines relation specific message passing with non-negative Positive--Unlabeled learning to account for positive contamination in the unlabeled set. In a forward-looking evaluation, the proposed approach achieved the strongest observed ranking performance relative to non-graph- and simple graph-based benchmarks. The results further show that graph-based inference retains its predictive value among firms without prior recorded incidents. These findings demonstrate the value of inter-firm relational structure as a complementary source of information for extending risk prioritization
Unsupervised graph representation learning aims to derive meaningful node embeddings by capturing both structural and attribute information without relying on labeled data. Existing methods, such as GAEs, have demonstrated effectiveness but typically rely on message-passing mechanisms that assume homophily, leading to performance degradation on heterophilous graphs, where connected nodes exhibit dissimilar features. This homophily bias results in the loss of critical high-frequency components that are essential for identifying heterophilous patterns. To address these challenges, we propose \textsc{AlignGAE}, a novel extension of \textit{MaskGAE} that preserves the full frequency spectrum through complementary view alignment. Our framework introduces a dual-encoder architecture that separately processes structural and attribute information, incorporates node positional encoding to approximate Neighborhood Identity Distribution (NID), and employs dual reconstruction tasks for both edges and node attributes. We further propose theoretically grounded NID alignment strategies that ensure semantic consistency across views while preserving their distinct characteristics. Through comprehensive spectral analysis, we demonstrate that \textsc{AlignGAE} achieves optimal representation properties when the alignment loss converges. Extensive experiments across 12 benchmark datasets validate our approach, showing that \textsc{AlignGAE} outperforms state-of-the-art methods by up to 18.7\% on heterophilous graphs in node classification, while maintaining competitive performance on homophilous graphs. Our results establish a new paradigm for frequency-aware graph representation learning.
Vision-language models (VLMs) provide a unified representation space for textual and visual information, yet their potential as general-purpose backbones for graph-structured data remains largely unexplored. In practice, attributed graphs exhibit substantial modality heterogeneity: some graphs contain only textual node attributes, others only visual attributes, while still others provide both. Existing graph learning approaches are typically designed for fixed modality schemas, requiring separate models for different settings and limiting scalability and cross-graph generalization. To bridge this gap, we present OMG-VLM (One Model, Many Graphs with Vision-Language Models), a unified framework for learning over attributed graphs across heterogeneous modality schemas. OMG-VLM leverages a pretrained VLM as a shared backbone and introduces structure-aware graph adapters that integrate neighborhood information while remaining compatible with the VLM's native embedding space. This design enables effective learning over text-attributed, image-attributed, and multi-attributed graphs within a single model. Extensive experiments across diverse domains show that OMG-VLM consistently outperforms state-of-the-art GNN- and LLM-based baselines on attributed graph learning tasks such as node classification and link prediction, while exhibiting strong generalization to unseen graphs and varying modality schemas. The source code is available at https://github.com/Jo-eyang/OMG-VLM.
Dynamic graph learning aims to capture evolving structural and semantic patterns in real-world systems, such as fraud detection and recommender systems. Due to the scarcity of labeled data in real-world dynamic graphs, recent studies have introduced generative or contrastive paradigms (e.g., masked graph autoencoders or graph contrastive learning) to generate task-agnostic graph embeddings. However, these methods typically rely on complex edge-level reconstruction objectives and tailored graph augmentation strategies. This incurs substantial computational overhead when scaling to large-scale dynamic graphs. In this paper, we propose SG-JEPA, a joint spiking embedding predictive architecture for large-scale dynamic graphs. In contrast to existing self-supervised methods, SG-JEPA partitions nodes into context and target sets along the temporal dimension to learn embeddings that are predictive of each other via additional spatial-temporal information. Furthermore, through encoding sequential inputs into coarse-to-fine spike count embeddings, spiking neurons enable SG-JEPA to adapt to the varying computational constraints of downstream tasks. Extensive experiments demonstrate that SG-JEPA achieves competitive or even superior performance over discriminative baselines on node classification, while effectively scaling to the dynamic graph with 13 million edges. SG-JEPA avoids the complex machinery (negative sampling, graph augmentations, edge-level reconstruction, etc.), resulting in superior training efficiency and memory scalability compared with prior self-supervised dynamic graph baselines.
How deep does a graph neural network need to be on a sparse graph? We study its purest statistical form: node classification on the sparse contextual stochastic block model (CSBM) with average degree $Δ=O(1)$, whose local weak limit is a broadcast-labelled Poisson Galton-Watson tree. Prior work derived a message-passing classifier $h_\ell$ that aggregates from each vertex at distance $k\le\ell$ the attenuated evidence $2\operatorname{artanh}(γ^k t(X_v))$, with $γ$ the edge signal and $t$ a bounded likelihood-ratio transform of the feature. We prove that the value of depth is governed by a single number, the Kesten-Stigum ratio $κ=γ^2Δ$. Below the threshold ($κ<1$), the error sequence is Cauchy at a geometric rate, $|\mathcal{E}(\ell)-\mathcal{E}(\ell')|\le Cκ^{(\ell+1)/3}$ for all $\ell'>\ell$, so all layers beyond depth $O(\log(1/ε))$ change the error by less than $ε$; conversely, under mild regularity each sufficiently deep layer still flips the decision with probability at least $cκ^{\ell/2}$, the empirically sharp exponent. Above the threshold ($κ>1$), depth is geometrically productive: $\mathcal{E}(\ell)$ is driven to a branching-process floor of order at most $1/(κ-1)$ at any geometric rate $κ^{-s\ell}$, $s<1$ (this bound has content only for $κ>17$). No local classifier of any depth beats the universal floor $e^{-Δ}Φ(-ζ)$ set by isolated roots ($ζ$ the feature signal-to-noise ratio), while the first layer provably helps by an explicit total-variation amount. Simulations with an exact belief-propagation baseline on the same trees show that the pairwise rule's error curve is mildly non-monotone in $\ell$, so an optimal finite depth exists (an exact instance is certified in the appendix), while BP saturates strictly faster, at an effective per-layer ratio below $κ$ that we identify.
In real-world applications, node classification on graphs often faces the challenge of class imbalance, where majority classes dominate training, resulting in biased model performance. Traditional GNNs often struggle in such scenarios, as they tend to overfit to majority classes while underrepresenting minority classes. Existing solutions, which either prioritize nodes based on class size or synthesize new nodes for minority classes, often fall short of effectively addressing this imbalance issue. This paper introduces an approach to class-imbalanced node classification by utilizing a balanced meta-set for importance measurement, where a training node is considered significant if it enhances model performance under an unbiased setting. Our method identifies important nodes that can counteract class imbalance and utilizes them for model training, allowing for fine-grained and dynamic node selection throughout the training process. We theoretically derive a formula to directly assess node importance, reducing computational overhead and providing an intuitive threshold for node selection. Guided by this metric, we develop a novel framework that filters valuable labeled, unlabeled, and synthetic nodes that enhance model performance in an unbiased context. A key advantage of this framework is its separation of the synthetic node generation process from the filtering process, ensuring compatibility with various node generation methods. Furthermore, we introduce a strategy to construct a high-quality meta-set that closely approximates the overall feature distribution, ensuring robust representation of each class. We evaluate our framework, NodeImport, across multiple datasets using popular GNN architectures, demonstrating its superiority over existing baselines. Our results highlight the flexibility and effectiveness of the framework in mitigating class imbalance, leading to improved outcomes.
We introduce a constrained two-view framework for node prediction that aligns structure-conditioned GNN embeddings with a structure-free feature prior learned by an anchor model. Conventional Graph Neural Networks (GNNs) couple feature transformation and neighborhood aggregation, which renders them vulnerable to topology noise and heterophilous connections. To decouple this dependency, our framework utilizes an independent anchor network to capture intrinsic attribute features via a self-supervised reconstruction objective. Furthermore, we propose a Channel-Split Adaptive Gated GNN (CSAG-GNN) that dynamically routes representations between global spectral smoothing and local spatial discrimination through a node-wise gating mechanism. We propose a stable cyclic alternating optimization strategy to solve the resulting coupled bi-level objective, preventing mutual representation drift during training. Empirical results on both homophilous and heterophilous benchmarks show balanced performance gains and structural robustness over competitive baselines.
Graph Foundation Models (GFMs) have emerged as a promising paradigm for learning transferable representations across diverse graph domains. Recent advancements in GFMs have been largely dominated by two paradigms: Graph Neural Network and Large Language Model (LLM) based methods. However, these methods often face a fundamental dilemma between training with limited data and a heavy reliance on textual attributes. Tabular foundation models (TFMs) offer a potential alternative, as node features and representations can be naturally organized in a tabular form. However, how to enable TFMs to effectively capture structural information of graphs remains largely unexplored. The key challenge is to learn a graph-to-table alignment mechanism that enables graph structural understanding for TFMs. To address this, we propose GTAlign, a surprisingly simple yet effective Graph-to-Table Alignment framework for text-free Graph Foundation Model. Specifically, we first pretrain a graph encoder that maps diverse graphs into a unified latent space to capture domain-agnostic graph representations. To further bridge the gap between graph topology and the tabular representation space, we propose community-guided continual pre-training, where pseudo-labels derived from graph community are used to construct few-shot prediction episodes. Lastly, we adapt the graph encoder for an unseen target domain and perform in-context inference. Extensive experiments on five benchmark datasets demonstrate that GTAlign significantly outperforms state-of-the-art baselines on both node and graph classification, offering a simple, effective, and text-free GFM model. Code will be released upon acceptance.
Lidia Losavio, Francesco Sovrano, Dario Fenoglio +2cs.LG cs.AI
Money laundering threatens financial stability and exposes institutions to penalties, motivating automated detection. Because laundering schemes often emerge through relational patterns, graph neural networks (GNNs) are increasingly used for anti-money laundering (AML). Yet AML GNNs are typically evaluated with aggregate metrics such as overall F1 score, which hide an operational issue: high-activity recipient accounts concentrate many incoming transactions, making suspicious signals harder to isolate and costlier to investigate. We introduce a recipient-degree stratified evaluation that reports standard AML metrics across recipient-context density. Across three datasets (HI-Small, HI-Medium, and AMLSim-32k-5%), it reveals consistent degradation in dense recipient contexts, which we trace to three GNN characteristics: two known limitations that AML amplifies, i.e., (1) multiset non-discriminability and (2) cardinality blindness, and (3) an attention-specific effect: in dense neighborhoods, normalized attention attenuates weak but pattern-relevant multi-hop signals. Guided by this diagnosis, we propose SALT-GNN, a lightweight statistics-aware architecture that fuses degree-aware statistical aggregation with attention at each message-passing layer, so distributional and cardinality information shapes the node states used by subsequent attention steps. Ablations support fusion placement as a key factor in dense-context performance. On HI-Small and HI-Medium, SALT-GNN uses up to 77% fewer parameters than task-specific graph-transformer baselines while improving dense-context F1 score by 3-6 points; on AMLSim-32k-5%, it improves highest-degree F1 score by 16-20 points. The gains hold for both Transformer- and GAT-style attention, indicating that the benefit comes from where statistical and attentional evidence is fused rather than from a specific attention operator.
Text-attributed graphs (TAGs), where each node carries a natural language description, require models to jointly reason over text and graph topology. Existing approaches often handle the two modalities separately: graph neural networks operate on shallow text features, while hybrids of LLMs and graphs use the language model mainly as a text encoder and delegate structure learning to a separate graph module. We propose method that unifies textual reasoning and graph message passing within a masked diffusion language model, a language model with bidirectional attention and generative decoding. For each graph instance, method linearises a sampled local neighbourhood into a token sequence and injects graph structure through a topology attention mask, which realises message passing over the graph. Because the diffusion language model can both interpret and generate text, the method adapts to different tasks simply by changing the prompt, supporting node classification, link prediction, and cross-dataset transfer with no target-specific fine-tuning. Experiments show that method outperforms graph neural networks, graph transformers, and LLM-based baselines on all three TAG benchmarks across two tasks, improving over the strongest baseline by up to 3.9 points.
We develop a spectral theory for \emph{normalized corrected GNN propagation}. The object of study is the symmetric normalized adjacency with its degree-stationary component removed, matching the normalization used by standard GCN-style models while isolating the stationary direction most directly tied to oversmoothing. The central theoretical question is whether this corrected normalized operator preserves class-discriminative signal after many propagation layers. Our main result is a high-probability exact-recovery theorem for the binary Contextual Stochastic Block Model after \(k=O(\log n)\) propagation steps in the dense polylogarithmic regime \(p\ge C\log^B n/n\), for any fixed \(B>4\), under explicit graph-signal and feature-SNR conditions. We also establish a multi-class partial recovery theorem showing contraction toward class centers for most nodes. Synthetic and real node-classification experiments are included as empirical checks of the theory's predicted dependence on depth, graph signal, and feature noise.
Graph theory is inherently descriptive, capturing what relationships exist but not why they arise, because it treats edges as primitive constructs. This paper proposes a new explanatory framework for graph learning, where relationships emerge from latent continuous information entropy fields, and a graph becomes a discrete instantiation of an underlying field. To formalize this field, we introduce the Field-informed Graph Network (FGN). It learns a scalar field from node features and leverages it to modulate message passing. The information-theoretic objective balances structural fidelity with field smoothness, forming a self-reinforcing loop. In this loop, the field modulates information diffusion through field-modulated weighting, and the updated node representations iteratively refine the field. As a result, FGN learns by simulating its own co-evolution. Extensive experiments on node classification and graph classification benchmarks demonstrate superior performance, robustness to perturbations, and structurally coherent field representations.
Graph neural networks (GNNs) excel at aggregating neighbor information for classification, yet their performance is hindered by graph structural entanglement, where spurious correlations from semantically irrelevant neighbors contaminate node embeddings. This challenge is most acute for nodes near class boundaries in the embedding space, where amplified structural noise blurs decision boundaries and destabilizes predictions. Existing robust GNN methods largely treat all nodes uniformly, ignoring boundary vulnerabilities. In this paper, to improve classification performance, we tackle graph structural disentanglement by identifying boundary-region entanglement as the primary bottleneck and propose Boundary Embedding Shaping (BES), an adaptive contrastive learning GNN plug-in module that selectively suppresses spurious structural noise at decision boundaries with minimal model parameter perturbation. Extensive experiments demonstrate that BES consistently improves boundary discrimination and outperforms existing leading methods. Notably, BES boosts GCN performance by an average of 3.3% in node classification (up to 5.0% on WikiCS) and achieves superior accuracy in link prediction.
Graph neural networks (GNNs) offer a flexible framework for learning from scientific data with physical, biological, or functional associations. One promising domain is plant physiology, where observed responses result from several interacting processes that are difficult to isolate, even with human intervention. A key example is the A-Ci curve, which relates the net CO2 assimilation rate (Anet) to leaf intercellular CO2 concentration (Ci) and is also used to estimate photosynthetic parameters in biophysical models. However, accurate estimation requires accurate identification of the active biochemical limiting state at each curve point, which is a major source of uncertainty. Here, we express the limitation-state identification in A-Ci curves as a graph-based node classification problem. A graph representation of the A-Ci curve is created using distance-based k-nearest-neighbor (kNN) and auxiliary-signal-guided (ASG) connectivity. The methodology was evaluated against the conventional machine learning baselines, graph-based architectures, and an automated fitting-based benchmark. Results on a large synthetic dataset with known ground-truth limitation states show that graph-based models improve classification, especially near biochemical transition areas. The top-performing configuration, SEAGAN (domain-Specific and Edge-Aware Graph Attention Network for Dynamic Plant Processes), integrates process-aware node features, edge attributes, kNN connectivity, and graph attention with a weighted cross-entropy loss, obtaining an F1-score of 0.857 and accuracy of 0.882. The results suggest that using A-Ci curves as graphs enables better identification of the biochemical limiting condition and reduces the uncertainty associated with both human and automated methods.
Multimodal attributed graphs (MAGs) integrate graph topology with heterogeneous modality attributes, such as text and images, thereby enabling richer modeling of complex relational systems. However, such expressiveness also makes learning on MAGs depend on multiple semantic sources, including structural topology, textual and visual attributes, each of which can be regarded as a branch for node representation. Node-level branch semantic imbalance arises when these branches differ across nodes in semantic informativeness and reliability: a branch that provides discriminative semantics for one node may mislead another due to bias in modality quality or structural context. Existing methods often mitigate such heterogeneity through cross-branch agreement or alignment, implicitly treating the dominant prediction as reliable supervision. When the dominant branch is biased, forced imitation may propagate its bias to other branches and suppress original semantics that are useful for classification. We propose GraphMNL, a graph-aware multimodal negative learning framework that addresses this issue by using Negative Learning as cross-branch guidance. Instead of forcing inferior branches to imitate a teacher prediction, the model teaches them which classes a node is unlikely to belong to. GraphMNL builds a branch library, identifies dominant and inferior branches via graph-aware reliability arbitration, gates unstable transfer, and applies target-preserving negative learning over non-target classes. This design decouples target supervision from branch guidance so that supervised losses learn the correct class, while Negative Learning suppresses unlikely alternatives when branch agreement is unreliable. Through the comprehensive experimental evaluation, GraphMNL achieves the best performance on Grocery datasets with 72.47% accuracy and 76.60 F1 score on Reddit M datasets.