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Pangenome variation graphs (PVGs) allow for the representation of genetic diversity in a more nuanced way than traditional reference-based approaches. Here we focus on how PVGs are a powerful tool for studying genetic variation in viruses,…
Mapping complex input data into suitable lower dimensional manifolds is a common procedure in machine learning. This step is beneficial mainly for two reasons: (1) it reduces the data dimensionality and (2) it provides a new data…
The inducibility of a graph $H$ measures the maximum number of induced copies of $H$ a large graph $G$ can have. Generalizing this notion, we study how many induced subgraphs of fixed order $k$ and size $\ell$ a large graph $G$ on $n$…
Recently a variety of methods have been developed to encode graphs into low-dimensional vectors that can be easily exploited by machine learning algorithms. The majority of these methods start by embedding the graph nodes into a…
Graph neural networks have pushed state-of-the-arts in graph classifications recently. Typically, these methods are studied within the context of supervised end-to-end training, which necessities copious task-specific labels. However, in…
Graph-level anomaly detection aims to identify anomalous graphs or subgraphs within graph datasets, playing a vital role in various fields such as fraud detection, review classification, and biochemistry. While Graph Neural Networks (GNNs)…
Graph-based Anomaly Detection (GAD) is becoming prevalent due to the powerful representation abilities of graphs as well as recent advances in graph mining techniques. These GAD tools, however, expose a new attacking surface, ironically due…
DNA sequencing is the process of determining the exact order of the nucleotide bases of an individual's genome in order to catalogue sequence variation and understand its biological implications. Whole-genome sequencing techniques produce…
Graph Neural Networks (GNNs) are widely used for graph representation learning in many application domains. The expressiveness of vanilla GNNs is upper-bounded by 1-dimensional Weisfeiler-Leman (1-WL) test as they operate on rooted subtrees…
A labelled, undirected graph is a graph whose edges have assigned labels, from a specific set. Given a labelled, undirected graph, the well-known minimum labelling spanning tree problem is aimed at finding the spanning tree of the graph…
We present novel graph kernels for graphs with node and edge labels that have ordered neighborhoods, i.e. when neighbor nodes follow an order. Graphs with ordered neighborhoods are a natural data representation for evolving graphs where…
Graph Neural Networks (GNNs) are widely applied for graph anomaly detection. As one of the key components for GNN design is to select a tailored spectral filter, we take the first step towards analyzing anomalies via the lens of the graph…
Omics data, such as transcriptomics, proteomics, and metabolomics, provide critical insights into disease mechanisms and clinical outcomes. However, their high dimensionality, small sample sizes, and intricate biological networks pose major…
Recently, techniques for applying convolutional neural networks to graph-structured data have emerged. Graph convolutional neural networks (GCNNs) have been used to address node and graph classification and matrix completion. Although the…
A properly edge-colored graph is a graph with a coloring of its edges such that no vertex is incident to two or more edges of the same color. A subgraph is called rainbow if all its edges have different colors. The problem of finding…
The identification of cancer genes is a critical yet challenging problem in cancer genomics research. Existing computational methods, including deep graph neural networks, fail to exploit the multilayered gene-gene interactions or provide…
In this paper, we introduce a generalization of graphlets to heterogeneous networks called typed graphlets. Informally, typed graphlets are small typed induced subgraphs. Typed graphlets generalize graphlets to rich heterogeneous networks…
Unsupervised graph anomaly detection (GAD) has received increasing attention in recent years, which aims to identify data anomalous patterns utilizing only unlabeled node information from graph-structured data. However, prevailing…
The graph structure is a commonly used data storage mode, and it turns out that the low-dimensional embedded representation of nodes in the graph is extremely useful in various typical tasks, such as node classification, link prediction ,…
Graph data, with its structurally variable nature, represents complex real-world phenomena like chemical compounds, protein structures, and social networks. Traditional Graph Neural Networks (GNNs) primarily utilize the message-passing…