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International initiatives such as METABRIC (Molecular Taxonomy of Breast Cancer International Consortium) have collected several multigenomic and clinical data sets to identify the undergoing molecular processes taking place throughout the…
Graph neural networks (GNNs) based on message passing between neighboring nodes are known to be insufficient for capturing long-range interactions in graphs. In this project we study hierarchical message passing models that leverage a…
Graph heterophily, where connected nodes have different labels, has attracted significant interest recently. Most existing works adopt a simplified approach - using low-pass filters for homophilic graphs and high-pass filters for…
Graph Neural Networks (GNNs) have received much attention in the graph deep learning domain. However, recent research empirically and theoretically shows that deep GNNs suffer from over-fitting and over-smoothing problems. The usual…
Graph representation of structured data can facilitate the extraction of stereoscopic features, and it has demonstrated excellent ability when working with deep learning systems, the so-called Graph Neural Networks (GNNs). Choosing a…
Individual cancer cells carry a bewildering number of distinct genomic alterations i.e., copy number variations and mutations, making it a challenge to uncover genomic-driven mechanisms governing tumorigenesis. Here we performed…
With the rapid development of the World Wide Web (WWW), heterogeneous graphs (HG) have explosive growth. Recently, heterogeneous graph neural network (HGNN) has shown great potential in learning on HG. Current studies of HGNN mainly focus…
Heterogeneous graph neural networks (HGNNs) have attracted increasing research interest in recent three years. Most existing HGNNs fall into two classes. One class is meta-path-based HGNNs which either require domain knowledge to handcraft…
Early detection of cancer plays a key role in improving survival rates, but identifying reliable biomarkers from RNA-seq data is still a major challenge. The data are high-dimensional, and conventional statistical methods often fail to…
We propose AGS-GNN, a novel attribute-guided sampling algorithm for Graph Neural Networks (GNNs) that exploits node features and connectivity structure of a graph while simultaneously adapting for both homophily and heterophily in graphs.…
Graph Neural Networks (GNNs) have gained traction in the complex domain of drug discovery because of their ability to process graph-structured data such as drug molecule models. This approach has resulted in a myriad of methods and models…
Graph neural networks (GNNs) are powerful graph-based deep-learning models that have gained significant attention and demonstrated remarkable performance in various domains, including natural language processing, drug discovery, and…
Various Graph Neural Networks (GNNs) have been successful in analyzing data in non-Euclidean spaces, however, they have limitations such as oversmoothing, i.e., information becomes excessively averaged as the number of hidden layers…
Distinguishing the automorphic equivalence of nodes in a graph plays an essential role in many scientific domains, e.g., computational biologist and social network analysis. However, existing graph neural networks (GNNs) fail to capture…
In this paper, we propose a novel framework to automatically utilize task-dependent semantic information which is encoded in heterogeneous information networks (HINs). Specifically, we search for a meta graph, which can capture more complex…
Network data can be conveniently modeled as a graph signal, where data values are assigned to the nodes of a graph describing the underlying network topology. Successful learning from network data requires methods that effectively exploit…
Graphs play an important role in many applications. Recently, Graph Neural Networks (GNNs) have achieved promising results in graph analysis tasks. Some state-of-the-art GNN models have been proposed, e.g., Graph Convolutional Networks…
Graph Neural Networks (GNNs) have achieved unprecedented success in identifying categorical labels of graphs. However, most existing graph classification problems with GNNs follow the protocol of balanced data splitting, which misaligns…
Graph Neural Networks (GNNs) have emerged as a prominent research topic in the field of machine learning. Existing GNN models are commonly categorized into two types: spectral GNNs, which are designed based on polynomial graph filters, and…
Graph neural networks (GNNs) have been successfully applied in many structured data domains, with applications ranging from molecular property prediction to the analysis of social networks. Motivated by the broad applicability of GNNs, we…