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.

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.

The premise for the great advancement of molecular machine learning is dependent on a considerable amount of labeled data. In many real-world scenarios, the labeled molecules are limited in quantity or laborious to derive. Recent pseudo-labeling methods are usually designed based on a single domain knowledge, thereby failing to understand the comprehensive molecular configurations and limiting their adaptability to generalize across diverse biochemical context. To this end, we introduce an innovative paradigm for dealing with the molecule pseudo-labeling, named as Molecular Data Programming (MDP). In particular, we adopt systematic supervision sources via crafting multiple graph labeling functions, which covers various molecular structural knowledge of graph kernels, molecular fingerprints, and topological features. Each of them creates an uncertain and biased labels for the unlabeled molecules. To address the decision conflicts among the diverse pseudo-labels, we design a label synchronizer to differentiably model confidences and correlations between the labeling functions, which yields probabilistic molecular labels to adapt for specific applications. These probabilistic molecular labels are used to train a molecular classifier for improving its generalization capability. On eight bench-mark datasets, we empirically demonstrate the effectiveness of MDP on the weakly supervised molecule classification tasks, achieving an average improvement of 9.5%. The code is in: https://github.com/xinjuan1/MDP/.

Graph neural networks (GNNs) have emerged as a successful method on graph structured data. Limited by expensive labeled data, contrastive learning has been adopted to the graph domain. In most existing node-level graph contrastive learning methods, when applying contrastive learning to a certain unlabeled node (the center node), its corresponding “similar” node (positive sample) is usually generated by data augmentation. Other nodes in the graph are served as the “dissimilar” nodes (negative samples), which leads to two major problems. First, the computational cost can be prohibitively expensive, especially when the graph is large. Second, utilizing some nodes which share the same label with the center node as the negative samples will damage the learning process. Hence, to address these issues, we explore the feasibility of only sampling a part of nodes for graph contrastive learning process. And unlike the previous self-supervised contrastive methods, we use joint training to exploit supervised signals as much as possible in contrastive learning. Hence, we propose a Negative Samples Selecting Strategy to utilize the classification prediction to guide the selection of the negative samples for sampled nodes. Then, we further incorporate this strategy for performing contrastive learning on graphs and propose a framework named Graph Contrastive Learning with Negative Samples Selecting Strategy (GCNSS). We demonstrate that GCNSS can be trained much faster with much less computation memory than graph contrastive learning baselines, and GCNSS can effectively boost the performance of existing GNN models on semi-supervised node classification tasks across many different datasets. The code is in: https://github.com/MR9812/GCNSS.