Graph neural networks (GNNs) have emerged as powerful tools for learning protein structures by capturing spatial relationships at the residue level. However, existing GNN-based methods often face challenges in learning multiscale representations and modeling long-range dependencies efficiently. In this work, we propose an efficient multiscale graph-based learning framework tailored to proteins. Our proposed framework contains two crucial components: (1) It constructs a hierarchical graph representation comprising a collection of fine-grained subgraphs, each corresponding to a secondary structure motif (e.g., α-helices, β-strands, loops), and a single coarse-grained graph that connects these motifs based on their spatial arrangement and relative orientation.

Understanding how individual edges influence the behavior of graph neural networks (GNNs) is essential for improving their interpretability and robustness. Graph influence functions have emerged as promising tools to efficiently estimate the effects of edge deletions without retraining. However, existing influence prediction methods rely on strict convexity assumptions, exclusively consider the influence of edge deletions while disregarding edge insertions, and fail to capture changes in message propagation caused by these modifications. In this work, we propose a proximal Bregman response function specifically tailored for GNNs, relaxing the convexity requirement and enabling accurate influence prediction for standard neural network architectures. Furthermore, our method explicitly accounts for message propagation effects and extends influence prediction to both edge deletions and insertions in a principled way. Experiments with real-world datasets demonstrate accurate influence predictions for different characteristics of GNNs. We further demonstrate that the influence function is versatile in applications such as graph rewiring and adversarial attacks.

Leveraging the lottery ticket hypothesis, novel training GMV pipeline, activates which diverse includes sub-net mix works ed-vie within w generation, a single GNN and multi-vie through w a decomposition and learning. This approach simultaneously broadens "views" from the data, model, and optimization perspectives during training to enhance the generalization additional prediction capabilities heads of into GNNs.

Dynamic GNNs, which integrate temporal and spatial features in Electroencephalography (EEG) data, have shown great potential in automating seizure detection. However, fully capturing the underlying dynamics necessary to represent brain states, such as seizure and non-seizure, remains a non-trivial task and presents two fundamental challenges. First, most existing dynamic GNN methods are built on temporally fixed static graphs, which fail to reflect the evolving nature of brain connectivity during seizure progression. Second, current efforts to jointly model temporal signals and graph structures and, more importantly, their interactions remain nascent, often resulting in inconsistent performance. To address these challenges, we present the first theoretical analysis of these two problems, demonstrating the effectiveness and necessity of explicit dynamic modeling and time-then-graph dynamic GNN method. Building on these insights, we propose EvoBrain, a novel seizure detection model that integrates a two-stream Mamba architecture with a GCN enhanced by Laplacian Positional Encoding, following neurological insights. Moreover, EvoBrainincorporates explicitly dynamic graph structures, allowing both nodes and edges to evolve over time. Our contributions include (a) a theoretical analysis proving the expressivity advantage of explicit dynamic modeling and time-then-graph over other approaches, (b) a novel and efficient model that significantly improves AUROC by 23% and F1 score by 30%, compared with the dynamic GNN baseline, and (c) broad evaluations of our method on the challenging early seizure prediction task.

Graph condensation (GC) aims to distill the original graph into a small-scale graph, mitigating redundancy and accelerating GNN training. However, conventional GC approaches heavily rely on rigid GNNs and task-specific supervision. Such a dependency severely restricts their reusability and generalization across various tasks and architectures. In this work, we revisit the goal of ideal GC from the perspective of GNN optimization consistency, and then a generalized GC optimization objective is derived, by which those traditional GC methods can be viewed nicely as special cases of this optimization paradigm. Based on this, Pre-trained Graph Condensation (PreGC) via optimal transport is proposed to transcend the limitations of task-and architecture-dependent GC methods. Specifically, a hybrid-interval graph diffusion augmentation is presented to suppress the weak generalization ability of the condensed graph on particular architectures by enhancing the uncertainty of node states. Meanwhile, the matching between optimal graph transport plan and representation transport plan is tactfully established to maintain semantic consistencies across source graph and condensed graph spaces, thereby freeing graph condensation from task dependencies. To further facilitate the adaptation of condensed graphs to various downstream tasks, a traceable semantic harmonizer from source nodes to condensed nodes is proposed to bridge semantic associations through the optimized representation transport plan in pre-training. Extensive experiments verify the superiority and versatility of PreGC, demonstrating its task-independent nature and seamless compatibility with arbitrary GNNs.

Graph neural networks (GNNs) can efficiently process text-attributed graphs (TAGs) due to their message-passing mechanisms, but their training heavily relies on the human-annotated labels. Moreover, the complex and diverse local topologies of nodes of real-world TAGs make it challenging for a single mechanism to handle. Large language models (LLMs) perform well in zero-/few-shot learning on TAGs but suffer from a scalability challenge. Therefore, we propose a preference-driven knowledge distillation (PKD) framework to synergize the complementary strengths of LLMs and various GNNs for few-shot node classification. Specifically, we develop a GNN-preference-driven node selector that effectively promotes prediction distillation from LLMs to teacher GNNs. To further tackle nodes' intricate local topologies, we develop a node-preferencedriven GNN selector that identifies the most suitable teacher GNN for each node, thereby facilitating tailored knowledge distillation from teacher GNNs to the student GNN. Extensive experiments validate the efficacy of our proposed framework in few-shot node classification on real-world TAGs.

Graph Neural Networks (GNNs) have achieved great success but are often considered to be challenged by varying levels of homophily in graphs. Recent empirical studies have surprisingly shown that homophilic GNNs can perform well across datasets of different homophily levels with proper hyperparameter tuning, but the underlying theory and effective architectures remain unclear. To advance GNN universality across varying homophily, we theoretically revisit GNN message passing and uncover a novel smoothness-generalization dilemma, where increasing hops inevitably enhances smoothness at the cost of generalization. This dilemma hinders learning in high-order homophilic neighborhoods and all heterophilic ones, where generalization is critical due to complex neighborhood class distributions that are sensitive to shifts induced by noise or sparsity. To address this, we introduce the Inceptive Graph Neural Network (IGNN) built on three simple yet effective design principles, which alleviate the dilemma by enabling distinct hop-wise generalization alongside improved overall generalization with adaptive smoothness. Benchmarking against 30 baselines demonstrates IGNN's superiority and reveals notable universality in certain homophilic GNN variants. Our code and datasets are available at https://github.com/galogm/IGNN.

Heterophilous graphs, where dissimilar nodes tend to connect, pose a challenge for graph neural networks (GNNs). Increasing the GNN depth can expand the scope (i.e., receptive field), potentially finding homophily from the higher-order neighborhoods. However, GNNs suffer from performance degradation as depth increases. Despite having better expressivity, state-of-the-art deeper GNNs achieve only marginal improvements compared to their shallow variants. Through theoretical and empirical analysis, we systematically demonstrate a shift in GNN generalization preferences across nodes with different homophily levels as depth increases. This creates a disparity in generalization patterns between GNN models with varying depth. Based on these findings, we propose to improve deeper GNN generalization while maintaining high expressivity by Mixture of scope experts at test (Moscat). Experimental results show that Moscat works flexibly with various GNNs across a wide range of datasets while significantly improving accuracy. Our code is available at https://github.com/Hydrapse/moscat.

Deep neural networks (DNNs) have been shown to memorize their training data, but similar analyses for graph neural networks (GNNs) remain under-explored. We introduce NCMemo(Node Classification Memorization), the first framework to quantify label memorization in semi-supervised node classification. We establish an inverse relationship between memorization and graph homophily, i.e., the tendency of connected nodes to share labels or features. Lower homophily significantly increases memorization, indicating that GNNs rely on label memorization when learning less homophilic graphs. We then analyze GNN training dynamics and find that increased memorization in low-homophily graphs is tightly coupled to GNNs' implicit bias toward using graph structure.

Graph condensation, which reduces the size of a large-scale graph by synthesizing a small-scale condensed graph as its substitution, has immediate benefits for various graph learning tasks. However, existing graph condensation methods rely on the joint optimization of nodes and structures in the condensed graph, and overlook critical issues in effectiveness and generalization ability. In this paper, we advocate a new Structure-Free Graph Condensation paradigm, named SFGC, to distill a largescale graph into a small-scale graph node set without explicit graph structures, i.e., graph-free data. Our idea is to implicitly encode topology structure information into the node attributes in the synthesized graph-free data, whose topology is reduced to an identity matrix.