Enhancing Imbalanced Node Classification via Curriculum-Guided Feature Learning and Three-Stage Attention Network

Imbalanced node classification in graph neural networks (GNNs) happens when some labels are much more common than others, which causes the model to learn unfairly and perform badly on the less common classes. To solve this problem, we propose a Curriculum-Guided Feature Learning and Three-Stage Attention Network (CL3AN-GNN), a learning network that uses a three-step attention system (Engage, Enact, Embed) similar to how humans learn. The model begins by engaging with structurally simpler features, defined as (1) local neighbourhood patterns (1-hop), (2) low-degree node attributes, and (3) class-separable node pairs identified via initial graph convolutional networks and graph attention networks (GCN and GAT) embeddings. This foundation enables stable early learning despite label skew. The Enact stage then addresses complicated aspects: (1) connections that require multiple steps, (2) edges that connect different types of nodes, and (3) nodes at the edges of minority classes by using adjustable attention weights. Finally, Embed consolidates these features via iterative message passing and curriculum-aligned loss weighting. We evaluate CL3AN-GNN on eight Open Graph Benchmark datasets spanning social, biological, and citation networks. Experiments show consistent improvements across all datasets in accuracy, F1-score, and AUC over recent state-of-the-art methods. The model's step-by-step method works well with different types of graph datasets, showing quicker results than training everything at once, better performance on new, imbalanced graphs, and clear explanations of each step using gradient stability and attention correlation learning curves. This work provides both a theoretically grounded framework for curriculum learning in GNNs and practical evidence of its effectiveness against imbalances, validated through metrics, convergence speeds, and generalisation tests.

Plain Transformers are Surprisingly Powerful Link Predictors

Link prediction is a core challenge in graph machine learning, demanding models that capture rich and complex topological dependencies. While Graph Neural Networks (GNNs) are the standard solution, state-of-the-art pipelines often rely on explicit structural heuristics or memory-intensive node embeddings -- approaches that struggle to generalize or scale to massive graphs. Emerging Graph Transformers (GTs) offer a potential alternative but often incur significant overhead due to complex structural encodings, hindering their applications to large-scale link prediction. We challenge these sophisticated paradigms with PENCIL, an encoder-only plain Transformer that replaces hand-crafted priors with attention over sampled local subgraphs, retaining the scalability and hardware efficiency of standard Transformers. Through experimental and theoretical analysis, we show that PENCIL extracts richer structural signals than GNNs, implicitly generalizing a broad class of heuristics and subgraph-based expressivity. Empirically, PENCIL outperforms heuristic-informed GNNs and is far more parameter-efficient than ID-embedding--based alternatives, while remaining competitive across diverse benchmarks -- even without node features. Our results challenge the prevailing reliance on complex engineering techniques, demonstrating that simple design choices are potentially sufficient to achieve the same capabilities.

Topology Matters: A Cautionary Case Study of Graph SSL on Neuro-Inspired Benchmarks

Understanding how local interactions give rise to global brain organization requires models that can represent information across multiple scales. We introduce a hierarchical self-supervised learning (SSL) framework that jointly learns node-, edge-, and graph-level embeddings, inspired by multimodal neuroimaging. We construct a controllable synthetic benchmark mimicking the topological properties of connectomes. Our four-stage evaluation protocol reveals a critical failure: the invariance-based SSL model is fundamentally misaligned with the benchmark's topological properties and is catastrophically outperformed by classical, topology-aware heuristics. Ablations confirm an objective mismatch: SSL objectives designed to be invariant to topological perturbations learn to ignore the very community structure that classical methods exploit. Our results expose a fundamental pitfall in applying generic graph SSL to connectome-like data. We present this framework as a cautionary case study, highlighting the need for new, topology-aware SSL objectives for neuro-AI research that explicitly reward the preservation of structure (e.g., modularity or motifs).

PIMPC-GNN: Physics-Informed Multi-Phase Consensus Learning for Enhancing Imbalanced Node Classification in Graph Neural Networks

Graph neural networks (GNNs) often struggle in class-imbalanced settings, where minority classes are under-represented and predictions are biased toward majorities. We propose \textbf{PIMPC-GNN}, a physics-informed multi-phase consensus framework for imbalanced node classification. Our method integrates three complementary dynamics: (i) thermodynamic diffusion, which spreads minority labels to capture long-range dependencies, (ii) Kuramoto synchronisation, which aligns minority nodes through oscillatory consensus, and (iii) spectral embedding, which separates classes via structural regularisation. These perspectives are combined through class-adaptive ensemble weighting and trained with an imbalance-aware loss that couples balanced cross-entropy with physics-based constraints. Across five benchmark datasets and imbalance ratios from 5-100, PIMPC-GNN outperforms 16 state-of-the-art baselines, achieving notable gains in minority-class recall (up to +12.7\%) and balanced accuracy (up to +8.3\%). Beyond empirical improvements, the framework also provides interpretable insights into consensus dynamics in graph learning. The code is available at \texttt{https://github.com/afofanah/PIMPC-GNN}.

Hyperbolic Graph Neural Networks Under the Microscope: The Role of Geometry-Task Alignment

Many complex networks exhibit hyperbolic structural properties, making hyperbolic space a natural candidate for representing hierarchical and tree-like graphs with low distortion. Based on this observation, Hyperbolic Graph Neural Networks (HGNNs) have been widely adopted as a principled choice for representation learning on tree-like graphs. In this work, we question this paradigm by proposing an additional condition of geometry-task alignment, i.e., whether the metric structure of the target follows that of the input graph. We theoretically and empirically demonstrate the capability of HGNNs to recover low-distortion representations on two synthetic regression problems, and show that their geometric inductive bias becomes helpful when the problem requires preserving metric structure. Additionally, we evaluate HGNNs on the tasks of link prediction and node classification by jointly analyzing predictive performance and embedding distortion, revealing that only link prediction is geometry-aligned. Overall, our findings shift the focus from only asking "Is the graph hyperbolic?" to also questioning "Is the task aligned with hyperbolic geometry?", showing that HGNNs consistently outperform Euclidean models under such alignment, while their advantage vanishes otherwise.

Learning Consistent Causal Abstraction Networks

Causal artificial intelligence aims to enhance explainability, trustworthiness, and robustness in AI by leveraging structural causal models (SCMs). In this pursuit, recent advances formalize network sheaves and cosheaves of causal knowledge. Pushing in the same direction, we tackle the learning of consistent causal abstraction network (CAN), a sheaf-theoretic framework where (i) SCMs are Gaussian, (ii) restriction maps are transposes of constructive linear causal abstractions (CAs) adhering to the semantic embedding principle, and (iii) edge stalks correspond--up to permutation--to the node stalks of more detailed SCMs. Our problem formulation separates into edge-specific local Riemannian problems and avoids nonconvex objectives. We propose an efficient search procedure, solving the local problems with SPECTRAL, our iterative method with closed-form updates and suitable for positive definite and semidefinite covariance matrices. Experiments on synthetic data show competitive performance in the CA learning task, and successful recovery of diverse CAN structures.

<SOG_k>: One LLM Token for Explicit Graph Structural Understanding

Large language models show great potential in unstructured data understanding, but still face significant challenges with graphs due to their structural hallucination. Existing approaches mainly either verbalize graphs into natural language, which leads to excessive token consumption and scattered attention, or transform graphs into trainable continuous embeddings (i.e., soft prompt), but exhibit severe misalignment with original text tokens. To solve this problem, we propose to incorporate one special token <SOG_k> to fully represent the Structure Of Graph within a unified token space, facilitating explicit topology input and structural information sharing. Specifically, we propose a topology-aware structural tokenizer that maps each graph topology into a highly selective single token. Afterwards, we construct a set of hybrid structure Question-Answering corpora to align new structural tokens with existing text tokens. With this approach, <SOG_k> empowers LLMs to understand, generate, and reason in a concise and accurate manner. Extensive experiments on five graph-level benchmarks demonstrate the superiority of our method, achieving a performance improvement of 9.9% to 41.4% compared to the baselines while exhibiting interpretability and consistency. Furthermore, our method provides a flexible extension to node-level tasks, enabling both global and local structural understanding. The codebase is publicly available at https://github.com/Jingyao-Wu/SOG.

Kernelized Edge Attention: Addressing Semantic Attention Blurring in Temporal Graph Neural Networks

Temporal Graph Neural Networks (TGNNs) aim to capture the evolving structure and timing of interactions in dynamic graphs. Although many models incorporate time through encodings or architectural design, they often compute attention over entangled node and edge representations, failing to reflect their distinct temporal behaviors. Node embeddings evolve slowly as they aggregate long-term structural context, while edge features reflect transient, timestamped interactions (e.g. messages, trades, or transactions). This mismatch results in semantic attention blurring, where attention weights cannot distinguish between slowly drifting node states and rapidly changing, information-rich edge interactions. As a result, models struggle to capture fine-grained temporal dependencies and provide limited transparency into how temporal relevance is computed. This paper introduces KEAT (Kernelized Edge Attention for Temporal Graphs), a novel attention formulation that modulates edge features using a family of continuous-time kernels, including Laplacian, RBF, and learnable MLP variant. KEAT preserves the distinct roles of nodes and edges, and integrates seamlessly with both Transformer-style (e.g., DyGFormer) and message-passing (e.g., TGN) architectures. It achieves up to 18% MRR improvement over the recent DyGFormer and 7% over TGN on link prediction tasks, enabling more accurate, interpretable and temporally aware message passing in TGNNs.

OptiMAG: Structure-Semantic Alignment via Unbalanced Optimal Transport

Multimodal Attributed Graphs (MAGs) have been widely adopted for modeling complex systems by integrating multi-modal information, such as text and images, on nodes. However, we identify a discrepancy between the implicit semantic structure induced by different modality embeddings and the explicit graph structure. For instance, neighbors in the explicit graph structure may be close in one modality but distant in another. Since existing methods typically perform message passing over the fixed explicit graph structure, they inadvertently aggregate dissimilar features, introducing modality-specific noise and impeding effective node representation learning. To address this, we propose OptiMAG, an Unbalanced Optimal Transport-based regularization framework. OptiMAG employs the Fused Gromov-Wasserstein distance to explicitly guide cross-modal structural consistency within local neighborhoods, effectively mitigating structural-semantic conflicts. Moreover, a KL divergence penalty enables adaptive handling of cross-modal inconsistencies. This framework can be seamlessly integrated into existing multimodal graph models, acting as an effective drop-in regularizer. Experiments demonstrate that OptiMAG consistently outperforms baselines across multiple tasks, ranging from graph-centric tasks (e.g., node classification, link prediction) to multimodal-centric generation tasks (e.g., graph2text, graph2image). The source code will be available upon acceptance.

NAG: A Unified Native Architecture for Encoder-free Text-Graph Modeling in Language Models

Prevailing methods for integrating graphs into Language Models (LMs) typically rely on a segregated architecture: external Graph Neural Networks (GNNs) encode structural topology, while LMs process textual semantics. We argue this approach is suboptimal for text-graphs: it creates a conceptually disjointed interaction paradigm. By segregating structural encoding from semantic processing, these systems must perform a complex implicit alignment between abstract graph tokens and concrete textual elements. Challenging the necessity of external encoders, we propose NAG (Native Architecture for Graphs), a unified framework that internalizes graph processing within the LM's native manifold. Instead of bridging disparate embedding spaces, NAG repurposes the self-attention mechanism to enforce topological dependencies and recalibrates positional IDs to ensure structural equivalence. This allows the model to harness its intrinsic linguistic capability to simultaneously comprehend node and edge content alongside structural topology. We introduce two efficient implementations: NAG-Zero for absolute preservation of the base model's linguistic capabilities, and NAG-LoRA for enhanced structural adaptation. Experiments across diverse graph tasks validate that NAG achieves robust graph comprehension without the overhead of external encoders, offering a simpler, more coherent paradigm for text-graph modeling.