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Antimicrobial peptides (AMPs) are promising therapeutic approaches against drug-resistant pathogens. Recently, deep generative models are used to discover new AMPs. However, previous studies mainly focus on peptide sequence attributes and…

Existing studies show that node representations generated by graph neural networks (GNNs) are vulnerable to adversarial attacks, such as unnoticeable perturbations of adjacent matrix and node features. Thus, it is requisite to learn robust…

Graph alignment, the problem of identifying corresponding nodes across multiple graphs, is fundamental to numerous applications. Most existing unsupervised methods embed node features into latent representations to enable cross-graph…

Graph Neural Networks (GNNs) are characterized by their capacity of processing graph-structured data. However, due to the sparsity of labels under semi-supervised learning, they have been found to exhibit biased performance on specific…

Whilst spectral Graph Neural Networks (GNNs) are theoretically well-founded in the spectral domain, their practical reliance on polynomial approximation implies a profound linkage to the spatial domain. As previous studies rarely examine…

Unsupervised graph anomaly detection aims at identifying rare patterns that deviate from the majority in a graph without the aid of labels, which is important for a variety of real-world applications. Recent advances have utilized Graph…

Recent research has shown that alignment between the structure of graph data and the geometry of an embedding space is crucial for learning high-quality representations of the data. The uniform geometry of Euclidean and hyperbolic spaces…

Repetitive DNA (repeats) poses significant challenges for accurate and efficient genome assembly and sequence alignment. This is particularly true for metagenomic data, where genome dynamics such as horizontal gene transfer, gene…

The problem of class imbalance refers to an uneven distribution of quantity among classes in a dataset, where some classes are significantly underrepresented compared to others. Class imbalance is also prevalent in graph-structured data.…

Graph embedding is an important approach for graph analysis tasks such as node classification and link prediction. The goal of graph embedding is to find a low dimensional representation of graph nodes that preserves the graph information.…

Graph classification has gained significant attention due to its applications in chemistry, social networks, and bioinformatics. While Graph Neural Networks (GNNs) effectively capture local structural patterns, they often overlook global…

Graph Neural Networks (GNNs) have achieved significant success in addressing node classification tasks. However, the effectiveness of traditional GNNs degrades on heterophilic graphs, where connected nodes often belong to different labels…

Graph anomaly detection (GAD) is a challenging binary classification problem due to its different structural distribution between anomalies and normal nodes -- abnormal nodes are a minority, therefore holding high heterophily and low…

Semi-supervised node classification is a foundational task in graph machine learning, yet state-of-the-art Graph Neural Networks (GNNs) are hindered by significant computational overhead and reliance on strong homophily assumptions.…

Graph machine learning (GML) has made great progress in node classification, link prediction, graph classification and so on. However, graphs in reality are often structurally imbalanced, that is, only a few hub nodes have a denser local…

Attributed graph embedding, which learns vector representations from graph topology and node features, is a challenging task for graph analysis. Recently, methods based on graph convolutional networks (GCNs) have made great progress on this…

The crux of graph classification lies in the effective representation learning for the entire graph. Typical graph neural networks focus on modeling the local dependencies when aggregating features of neighboring nodes, and obtain the…

In this study, we focus on the graph representation learning (a.k.a. network embedding) in attributed graphs. Different from existing embedding methods that treat the incorporation of graph structure and semantic as the simple combination…

Heterogeneous graph neural networks (HGNNs) have significantly propelled the information retrieval (IR) field. Still, the effectiveness of HGNNs heavily relies on high-quality labels, which are often expensive to acquire. This challenge has…

Graph serves as a powerful tool for modeling data that has an underlying structure in non-Euclidean space, by encoding relations as edges and entities as nodes. Despite developments in learning from graph-structured data over the years, one…