Graph Neural Networks (GNNs) have become the dominant paradigm for machine learning on relational data, yet they remain susceptible to overfitting and noise in graph structures. While data augmentation has proven effective for regularization across domains, existing graph methods operate at coarse levels, such as perturbing entire structures or mixing node features. These approaches are context-agnostic and do not target the core computational process of GNNs: message passing. We introduce MessageShift, a novel fine-grained data augmentation paradigm that operates directly on the messages, the atomic units of information, as they flow through the GNN. The core idea is to apply a contextual perturbation to each message by shifting it towards or away from the center of its local neighborhood. This provides a rich regularization effect, capable of both smoothing noisy messages and sharpening distinctive ones. Extensive experiments on a wide range of benchmark datasets demonstrate that MessageShift consistently outperforms strong baselines across multiple GNN backbones.

The ''pre-train, prompt'' paradigm, designed to bridge the gap between pre-training tasks and downstream objectives, has been extended from the NLP domain to the graph domain and has achieved remarkable progress. Current mainstream graph prompt-tuning methods modify input or output features using learnable prompt vectors. However, existing approaches are confined to single-granularity (e.g., node-level or subgraph-level) during prompt generation, overlooking the inherently multi-scale structural information in graph data, which limits the diversity of prompt semantics. To address this issue, we pioneer the integration of multi-scale information into graph prompt and propose a Multi-Scale Graph Chain-of-Thought (MSGCOT) prompting framework. Specifically, we design a lightweight, low-rank coarsening network to efficiently capture multi-scale structural features as hierarchical basis vectors for prompt generation. Subsequently, mimicking human cognition from coarse-to-fine granularity, we dynamically integrate multi-scale information at each reasoning step, forming a progressive coarse-to-fine prompt chain. Extensive experiments on eight benchmark datasets demonstrate that MSGCOT outperforms the state-of-the-art single-granularity graph prompt-tuning method, particularly in few-shot scenarios, showcasing superior performance. The code is available at: https://github.com/zhengziyu77/MSGCOT.

Masked Graph Auto-Encoder, a powerful graph self-supervised training paradigm, has recently shown superior performance in graph representation learning. Existing works typically rely on node contextual information to recover the masked information. However, they fail to generalize well to heterophilic graphs where connected nodes may be not similar, because they focus only on capturing the neighborhood information and ignoring the discrepancy information between different nodes, resulting in indistinguishable node representations. In this paper, to address this issue, we propose a Discrepancy-Aware Graph Mask Auto-Encoder (DGMAE). It obtains more distinguishable node representations by reconstructing the discrepancy information of neighboring nodes during the masking process. We conduct extensive experiments on 17 widely-used benchmark datasets. The results show that our DGMAE can effectively preserve the discrepancies of nodes in low-dimensional space. Moreover, DGMAE significantly outperforms state-of-the-art graph self-supervised learning methods on three graph analytic including tasks node classification, node clustering, and graph classification, demonstrating its remarkable superiority. The code of DGMAE is available at https://github.com/zhengziyu77/DGMAE.

Real-world networks usually have a property of node heterophily, that is, the connected nodes usually have different features or different labels. This heterophily issue has been extensively studied in homogeneous graphs but remains under-explored in heterogeneous graphs, where there are multiple types of nodes and edges. Capturing node heterophily in heterogeneous graphs is very challenging since both node/edge heterogeneity and node heterophily should be carefully taken into consideration. Existing methods typically convert heterogeneous graphs into homogeneous ones to learn node heterophily, which will inevitably lose the potential heterophily conveyed by heterogeneous relations. To bridge this gap, we propose Relation-Aware Separation of Homophily and Heterophily (RASH), a novel contrastive learning framework that explicitly models high-order semantics of heterogeneous interactions and adaptively separates homophilic and heterophilic patterns. Particularly, RASH introduces dual heterogeneous hypergraphs to encode multi-relational bipartite subgraphs and dynamically constructs homophilic graphs and heterophilic graphs based on relation importance. A multi-relation contrastive loss is designed to align heterogeneous and homophilic/heterophilic views by maximizing mutual information. In this way, RASH simultaneously resolves the challenges of heterogeneity and heterophily in heterogeneous graphs. Extensive experiments on benchmark datasets demonstrate the effectiveness of RASH across various downstream tasks. The code is available at: https://github.com/zhengziyu77/RASH.

Heterogeneous hypergraph is a kind of structural data that contains multiple types of nodes and multiple types of hyperedges. Each hyperedge type corresponds to a specific multi-ary relation (called hyper-relation) among subsets of nodes, which goes beyond traditional pair-wise relations in simple graphs. Existing representation learning methods for heterogeneous hypergraphs typically learn embeddings for nodes and hyperedges based on graph neural networks. Although achieving promising performance, they are still limited in capturing more complex structural features and richer semantics conveyed by the composition of various hyper-relations. To fill this research gap, in this work, we propose the concept of hyper-meta-path for heterogeneous hypergraphs, which is defined as the composition of a sequence of hyper-relations. Besides, we design an attention-based heterogeneous hypergraph neural network (HHNN) to automatically learn the importance of hyper-meta-paths. By exploiting useful ones, HHNN is able to capture more complex structural features to boost the model's performance, as well as leverage their conveyed semantics to improve the model's interpretability. Extensive experiments show that HHNN can achieve significantly better performance than state-of-the-art baselines, and the discovered hyper-meta-paths bring good interpretability for the model predictions. To facilitate the reproducibility of this work, we provide our dataset as well as anonymized source code at: https://github.com/zhengziyu77/HHNN.

The detection of therapeutic peptides is a topic of immense interest in the biomedical field. Conventional biochemical experiment-based detection techniques are tedious and time-consuming. Computational biology has become a useful tool for improving the detection efficiency of therapeutic peptides. Most computational methods do not consider the deviation caused by noise. To improve the generalization performance of therapeutic peptide prediction methods, this work presents a sequence homology score-based deep fuzzy echo-state network with maximizing mixture correntropy (SHS-DFESN-MMC) model. Our method is compared with the existing methods on eight types of therapeutic peptide datasets. The model parameters are determined by 10 fold cross-validation on their training sets and verified by independent test sets. Across the 8 datasets, the average area under the receiver operating characteristic curve (AUC) values of SHS-DFESN-MMC are the highest on both the training (0.926) and independent sets (0.923).