Ziyu Zheng

Ziyu Zheng, Yaming Yang, Ziyu Guan et al.

Multi-domain graph pre-training is a crucial step in constructing foundational graph models with cross-domain generalization capabilities. However, existing methods predominantly rely on jointly training all source domain graphs, resulting in high computational costs. Furthermore, it remains unclear whether all source domain graph data contribute equally to effective transfer. This paper empirically reveals significant data redundancy in multi-domain graph pre-training. Based on this finding, we propose the Multi-domain Graph Pre-training Framework, MDGMIX, which combines boundary-aware subgraph mixing with hierarchical discrimination. By selecting boundary nodes to construct challenging mixed-domain subgraphs, MDGMIX employs coarse-grained domain discrimination and fine-grained domain decomposition losses to decouple shared patterns from domain-specific patterns. During adaptation, MDGMIX employs a lightweight prompt weighting mechanism to transfer source domain knowledge. Extensive experiments demonstrate that MDGMIX consistently outperforms strong baselines in few-shot classification tasks while exhibiting superior time and memory efficiency. The code is available at: https://github.com/zhengziyu77/MDGMIX.

Ziyu Zheng, Yaming Yang, Zhe Wang et al.

While Graph Foundation Models (GFMs) have achieved remarkable success in homogeneous graphs, extending them to multi-domain heterogeneous graphs (MDHGs) remains a formidable challenge due to cross-type feature shifts and intra-domain relation gaps. Existing global feature alignment methods (PCA or SVD) enforce a shared feature space blindly, which distorts type-specific semantics and disrupts original topologies, inevitably leading to "Type Collapse" and "Relation Confusion". To address these fundamental limitations, we propose Decoupled relation Subspace Alignment (DRSA), a novel, plug-and-play relation-driven alignment framework. DRSA fundamentally shifts the paradigm by decoupling feature semantics from relation structures. Specifically, it introduces a dual-relation subspace projection mechanism to coordinate cross-type interactions within a shared low-rank relation subspace explicitly. Furthermore, a feature-structure decoupled representation is designed to decompose aligned features into a semantic projection component and a structural residual term, adaptively absorbing intra-domain variations. Optimized via a stable alternating minimization strategy based on Block Coordinate Descent, DRSA constructs a well-calibrated, structure-aware latent space. Extensive experiments on multiple real-world benchmark datasets demonstrate that DRSA can be seamlessly integrated as a universal preprocessing module, significantly and consistently enhancing the cross-domain and few-shot knowledge transfer capabilities of state-of-the-art GFMs. The code is available at: https://github.com/zhengziyu77/DSRA.

Ziyu Zheng, Yaming Yang, Ziyu Guan et al.

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.

Ziyu Zheng, Yaming Yang, Ziyu Guan et al.

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.

Ziyu Zheng, Yaming Yang, Ziyu Guan et al.

The "pre-train, prompt" paradigm has successfully evolved in representation learning. While current prompt-tuning methods often introduce learnable prompts, they predominantly treat prompts as isolated, independent components across different network layers. This overlooks the complex and synergistic higher-order interactions that exist between prompts at various hierarchical depths, consequently limiting the expressive power and semantic richness of the prompted model. To address this fundamental gap, we propose a novel framework that explicitly models the Higher-order Interactions of Multi-layer Prompt. Our approach conceptualizes prompts from different layers not as separate entities, but as a cohesive system where their inter-relationships are critical. We design an innovative interaction module that captures these sophisticated, non-linear correlations among multi-layer prompts, effectively modeling their cooperative effects. This allows the model to dynamically aggregate and refine prompt information across the network's depth, leading to a more integrated and powerful prompting strategy. Extensive experiments on eight benchmark datasets demonstrate that our method, by leveraging these higher-order interactions, consistently surpasses state-of-the-art prompt-tuning baselines. The performance advantage is particularly pronounced in few-shot scenarios, validating that capturing the intricate interplay between multi-layer prompts is key to unlocking more robust and generalizable representation learning.

Yuqing Qian, Ziyu Zheng, Prayag Tiwari et al.

Drug-side effect prediction has become an essential area of research in the field of pharmacology. As the use of medications continues to rise, so does the importance of understanding and mitigating the potential risks associated with them. At present, researchers have turned to data-driven methods to predict drug-side effects. Drug-side effect prediction is a link prediction problem, and the related data can be described from various perspectives. To process these kinds of data, a multi-view method, called Multiple Kronecker RLS fusion-based link propagation (MKronRLSF-LP), is proposed. MKronRLSF-LP extends the Kron-RLS by finding the consensus partitions and multiple graph Laplacian constraints in the multi-view setting. Both of these multi-view settings contribute to a higher quality result. Extensive experiments have been conducted on drug-side effect datasets, and our empirical results provide evidence that our approach is effective and robust.