Over-smoothing remains a fundamental challenge in deep Graph Neural Networks (GNNs), where repeated message passing causes node representations to become indistinguishable. While existing solutions, such as residual connections and skip layers, alleviate this issue to some extent, they fail to explicitly model how node representations evolve in a node-specific and progressive manner across layers. Moreover, these methods do not take global information into account, which is also crucial for mitigating the over-smoothing problem. To address the aforementioned issues, in this work, we propose a Dual Mamba-enhanced Graph Convolutional Network (DMbaGCN), which is a novel framework that integrates Mamba into GNNs to address over-smoothing from both local and global perspectives. DMbaGCN consists of two modules: the Local State-Evolution Mamba (LSEMba) for local neighborhood aggregation and utilizing Mamba’s selective state space modeling to capture node-specific representation dynamics across layers, and the Global Context-Aware Mamba (GCAMba) that leverages Mamba’s global attention capabilities to incorporate global context for each node. By combining these components, DMbaGCN enhances node discriminability in deep GNNs, thereby mitigating over-smoothing. Extensive experiments on multiple benchmarks demonstrate the effectiveness and efficiency of our method.

Accurate traffic forecasting plays a vital role in intelligent transportation systems, enabling applications such as congestion control, route planning, and urban mobility optimization. However, traffic forecasting remains challenging due to two key factors: (1) complex spatial dependencies arising from dynamic interactions between road segments and traffic sensors across the network, and (2) the coexistence of multi-scale periodic patterns (e.g., daily and weekly periodic patterns driven by human routines) with irregular fluctuations caused by unpredictable events (e.g., accidents, weather, or construction). To tackle these challenges, we propose HyperD (Hybrid Periodic Decoupling), a novel framework that decouples traffic data into periodic and residual components. The periodic component is handled by the Hybrid Periodic Representation Module, which extracts fine-grained daily and weekly patterns using learnable periodic embeddings and spatial-temporal attention. The residual component, which captures non-periodic, high-frequency fluctuations, is modeled by the Frequency-Aware Residual Representation Module, leveraging complex-valued MLP in frequency domain. To enforce semantic separation between the two components, we further introduce a Dual-View Alignment Loss, which aligns low-frequency information with the periodic branch and high-frequency information with the residual branch. Extensive experiments on four real-world traffic datasets demonstrate that HyperD achieves state-of-the-art prediction accuracy, while offering superior robustness under disturbances and improved computational efficiency compared to existing methods.

Rui Miao, Yixin Liu, Yili Wang, Xu Shen, Yue Tan, Yiwei Dai, Shirui Pan, Xin Wang. Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). 2026.

Graph Neural Networks (GNNs) are highly vulnerable to adversarial attacks, which can greatly degrade their performance. Existing graph purification methods attempt to address this issue by filtering attacked graphs. However, they struggle to defend effectively against multiple types of adversarial attacks (e.g., targeted attacks and non-targeted attacks) simultaneously due to limited flexibility. Additionally, these methods lack comprehensive modeling of graph data, relying heavily on heuristic prior knowledge. To overcome these challenges, we introduce the Graph Defense Diffusion Model (GDDM), a flexible purification method that leverages the denoising and modeling capabilities of diffusion models. The iterative nature of diffusion models aligns well with the stepwise process of adversarial attacks, making them particularly suitable for defense. By iteratively adding and removing noises (edges), GDDM effectively purifies attacked graphs, restoring their original structures and features. Our GDDM consists of two key components: (1) Graph Structure-Driven Refiner, which preserves the basic fidelity of the graph during the denoising process, and ensures that the generated graph remains consistent with the original scope; and (2) Node Feature-Constrained Regularizer, which removes residual impurities from the denoised graph, further enhancing the purification effect. By designing tailored denoising strategies to handle different types of adversarial attacks, we improve the GDDM's adaptability to various attack scenarios. Furthermore, GDDM demonstrates strong scalability, leveraging its structural properties to seamlessly transfer across similar datasets without retraining. Extensive experiments on three real-world datasets demonstrate that GDDM outperforms state-of-the-art methods in defending against various adversarial attacks, showcasing its robustness and effectiveness.

The communication topology in large language model-based multi-agent systems fundamentally governs inter-agent collaboration patterns, critically shaping both the efficiency and effectiveness of collective decision-making.While recent studies for communication topology automated design tend to construct sparse structures for efficiency, they often overlook why and when sparse and dense topologies help or hinder collaboration.In this paper, we present a causal framework to analyze how agent outputs, whether correct or erroneous, propagate under topologies with varying sparsity.Our empirical studies reveal that moderately sparse topologies, which effectively suppress error propagation while preserving beneficial information diffusion, typically achieve optimal task performance.Guided by this insight, we propose a novel topology design approach, EIB-LEARNER, that balances error suppression and beneficial information propagation by fusing connectivity patterns from both dense and sparse graphs.Extensive experiments show the superior effectiveness, communication cost, and robustness of EIB-LEARNER.The code is in

Designing crystal materials with desired physicochemical properties remains a fundamental challenge in materials science. While large language models (LLMs) have demonstrated strong in-context learning (ICL) capabilities, existing LLM-based crystal generation approaches are limited to zero-shot scenarios and are unable to benefit from few-shot scenarios. In contrast, human experts typically design new materials by modifying relevant known structures which aligns closely with the few-shot ICL paradigm. Motivated by this, we propose CrystalICL, a novel model designed for few-shot crystal generation. Specifically, we introduce a space-group based crystal tokenization method, which effectively reduces the complexity of modeling crystal symmetry in LLMs. We further introduce a condition-structure aware hybrid instruction tuning framework and a multi-task instruction tuning strategy, enabling the model to better exploit ICL by capturing structure-property relationships from limited data. Extensive experiments on four crystal generation benchmarks demonstrate the superiority of CrystalICL over the leading baseline methods on conditional and unconditional generation tasks.

To build safe and reliable graph machine learning systems, unsupervised graph-level anomaly detection (GLAD) and unsupervised graph-level out-of-distribution (OOD) detection (GLOD) have received significant attention in recent years. Though these two lines of research share the same objective, they have been studied independently in the community due to distinct evaluation setups, creating a gap that hinders the application and evaluation of methods from one to the other. To bridge the gap, in this work, we present a Unified Benchmark for unsupervised Graph-level OOD and anomaly Detection (UB-GOLD), a comprehensive evaluation framework that unifies GLAD and GLOD under the concept of generalized graph-level OOD detection. Our benchmark encompasses 35 datasets spanning four practical anomaly and OOD detection scenarios, facilitating the comparison of 18 representative GLAD/GLOD methods. We conduct multi-dimensional analyses to explore the effectiveness, generalizability, robustness, and efficiency of existing methods, shedding light on their strengths and limitations. Furthermore, we provide an open-source codebase of UB-GOLD to foster reproducible research and outline potential directions for future investigations based on our insights.

Graph Neural Networks (GNNs) have shown great success in various graph-based learning tasks. However, it often faces the issue of over-smoothing as the model depth increases, which causes all node representations to converge to a single value and become indistinguishable. This issue stems from the inherent limitations of GNNs, which struggle to distinguish the importance of information from different neighborhoods. In this paper, we introduce MbaGCN, a novel graph convolutional architecture that draws inspiration from the Mamba paradigm—originally designed for sequence modeling. MbaGCN presents a new backbone for GNNs, consisting of three key components: the Message Aggregation Layer, the Selective State Space Transition Layer, and the Node State Prediction Layer. These components work in tandem to adaptively aggregate neighborhood information, providing greater flexibility and scalability for deep GNN models. While MbaGCN may not consistently outperform all existing methods on each dataset, it provides a foundational framework that demonstrates the effective integration of the Mamba paradigm into graph representation learning. Through extensive experiments on benchmark datasets, we demonstrate that MbaGCN paves the way for future advancements in graph neural network research. Our code is in https://github.com/hexin5515/MbaGCN.

Large-scale graph data poses a training scalability challenge, which is generally treated by employing batch sampling methods to divide the graph into smaller subgraphs and train them in batches. However, such an approach introduces a topological bias in the local batches compared with the complete graph structure, missing either node features or edges. This topological bias is empirically shown to affect the generalization capabilities of graph neural networks (GNNs). To address this issue, we propose adaptive subgraph contrastive learning (AdaGCL) that bridges the gap between large-scale batch sampling and its generalization poorness. Specifically, AdaGCL augments graphs depending on the sampled batches and leverages a subgraph-granularity contrastive loss to learn the node embeddings invariant among the augmented imperfect graphs. To optimize the augmentation strategy for each downstream application, we introduce a node-centric information bottleneck (Node-IB) to control the trade-off regarding the similarity and diversity between the original and augmented graphs. This enhanced version of AdaGCL referred to as AdaGCL+, automates the graph augmentation process by dynamically adjusting graph perturbation parameters (e.g., edge dropping rate) to minimize the downstream loss. Extensive experimental results showcase the scalability of AdaGCL+ to graphs with millions of nodes using batch sampling methods. AdaGCL+ consistently outperforms existing methods on numerous benchmark datasets in terms of node classification accuracy and runtime efficiency.

Sharpness-aware minimization (SAM) has received increasing attention in computer vision since it can effectively eliminate the sharp local minima from the training trajectory and mitigate generalization degradation. However, SAM requires two sequential gradient computations during the optimization of each step: one to obtain the perturbation gradient and the other to obtain the updating gradient. Compared with the base optimizer (e.g., Adam), SAM doubles the time overhead due to the additional perturbation gradient. By dissecting the theory of SAM and observing the training gradient of the molecular graph transformer, we propose a new algorithm named GraphSAM, which reduces the training cost of SAM and improves the generalization performance of graph transformer models. There are two key factors that contribute to this result: (i) \textit{gradient approximation}: we use the updating gradient of the previous step to approximate the perturbation gradient at the intermediate steps smoothly (\textbf{increases efficiency}); (ii) \textit{loss landscape approximation}: we theoretically prove that the loss landscape of GraphSAM is limited to a small range centered on the expected loss of SAM (\textbf{guarantees generalization performance}). The extensive experiments on six datasets with different tasks demonstrate the superiority of GraphSAM, especially in optimizing the model update process.

Graph neural networks (GNNs) have exhibited prominent performance in learning graph-structured data. Considering node classification task, based on the i.i.d assumption among node labels, the traditional supervised learning simply sums up cross-entropy losses of the independent training nodes and applies the average loss to optimize GNNs’ weights. But different from other data formats, the nodes are naturally connected. It is found that the independent distribution modeling of node labels restricts GNNs’ capability to generalize over the entire graph and defend adversarial attacks. In this work, we propose a new framework, termed joint-cluster supervised learning, to model the joint distribution of each node with its corresponding cluster. We learn the joint distribution of node and cluster labels conditioned on their representations, and train GNNs with the obtained joint loss. In this way, the data-label reference signals extracted from the local cluster explicitly strengthen the discrimination ability on the target node. The extensive experiments demonstrate that our joint-cluster supervised learning can effectively bolster GNNs’ node classification accuracy. Furthermore, being benefited from the reference signals which may be free from spiteful interference, our learning paradigm significantly protects the node classification from being affected by the adversarial attack.

Despite the recent progress of molecular representation learning, its effectiveness is assumed on the close-world assumptions that training and testing graphs are from identical distribution. The open-world test dataset is often mixed with out-of-distribution (OOD) samples, where the deployed models will struggle to make accurate predictions. The misleading estimations of molecules' properties in drug screening or design can result in the tremendous waste of wet-lab resources and delay the discovery of novel therapies. Traditional detection methods need to trade off OOD detection and in-distribution (ID) classification performance since they share the same representation learning model. In this work, we propose to detect OOD molecules by adopting an auxiliary diffusion model-based framework, which compares similarities between input molecules and reconstructed graphs. Due to the generative bias towards reconstructing ID training samples, the similarity scores of OOD molecules will be much lower to facilitate detection. Although it is conceptually simple, extending this vanilla framework to practical detection applications is still limited by two significant challenges. First, the popular similarity metrics based on Euclidian distance fail to consider the complex graph structure. Second, the generative model involving iterative denoising steps is notoriously time-consuming especially when it runs on the enormous pool of drugs. To address these challenges, our research pioneers an approach of Prototypical Graph Reconstruction for Molecular OOd Detection, dubbed as PGR-MOOD. Specifically, PGR-MOOD hinges on three innovations: i) An effective metric to comprehensively quantify the matching degree of input and reconstructed molecules according to their discrete edges and continuous node features; ii) A creative graph generator to construct a list of prototypical graphs that are in line with ID distribution but away from OOD one; iii) An efficient and scalable OOD detector to compare the similarity between test samples and pre-constructed prototypical graphs and omit the generative process on every new molecule. Extensive experiments on ten benchmark datasets and six baselines are conducted to demonstrate our superiority: PGR-MOOD achieves more than 8% of average improvement in terms of detection AUC and AUPR accompanied by the reduced cost of testing time and memory consumption. The anonymous code is in: https://github.com/se7esx/PGR-MOOD.

Training graph neural networks (GNNs) with good generalizability on large-scale graphs is a challenging problem. Existing methods mainly divide the input graph into multiple subgraphs and train them in different batches to improve training scalability. However, the local batches obtained by such a strategy could contain topological bias compared with the complete graph structure. It has been studied that the topological bias results in more significant gaps between training and testing performances, or worse generalization robustness. A straightforward solution is to utilize contrastive learning, and train node embeddings to be robust and invariant among the augmented imperfect graphs. However, most of the existing work are inefficient by contrasting extensive node pairs at the large-scale graph. With random data augmentation, they may deteriorate the embedding process by transforming well-sampled batches into meaningless graph structures.

BACKGROUND: RNA secondary structure is very important for deciphering cell's activity and disease occurrence. The first method which was used by the academics to predict this structure is biological experiment, But this method is too expensive, causing the promotion to be affected. Then, computing methods emerged, which has good efficiency and low cost. However, the accuracy of computing methods are not satisfactory. Many machine learning methods have also been applied to this area, but the accuracy has not improved significantly. Deep learning has matured and achieves great success in many areas such as computer vision and natural language processing. It uses neural network which is a kind of structure that has good functionality and versatility, but its effect is highly correlated with the quantity and quality of the data. At present, there is no model with high accuracy, low data dependence and high convenience in predicting RNA secondary structure. RESULTS: This paper designs a neural network called LTPConstraint to predict RNA secondary structure. The network is based on many network structure such as Bidirectional LSTM, Transformer and generator. It also uses transfer learning to train modelso that the data dependence can be reduced. CONCLUSIONS: LTPConstraint has achieved high accuracy in RNA secondary structure prediction. Compared with the previous methods, the accuracy improves obviously both in predicting the structure with pseudoknot and the structure without pseudoknot. At the same time, LTPConstraint is easy to operate and can achieve result very quickly.