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Predicting genetic perturbations enables the identification of potentially crucial genes prior to wet-lab experiments, significantly improving overall experimental efficiency. Since genes are the foundation of cellular life, building gene…

Network biology has been successfully used to help reveal complex mechanisms of disease, especially cancer. On the other hand, network biology requires in-depth knowledge to construct disease-specific networks, but our current knowledge is…

-Background. Network neuroscience examines the brain as a complex system represented by a network (or connectome), providing deeper insights into the brain morphology and function, allowing the identification of atypical brain connectivity…

Biomedical information graphs are crucial for interaction discovering of biomedical information in modern age, such as identification of multifarious molecular interactions and drug discovery, which attracts increasing interests in…

Infrared and visible image fusion has gradually proved to be a vital fork in the field of multi-modality imaging technologies. In recent developments, researchers not only focus on the quality of fused images but also evaluate their…

Understanding disease-gene associations is essential for unravelling disease mechanisms and advancing diagnostics and therapeutics. Traditional approaches based on manual curation and literature review are labour-intensive and not scalable,…

Understanding disease similarity is critical for advancing diagnostics, drug discovery, and personalized treatment strategies. We present PhenoGnet, a novel graph-based contrastive learning framework designed to predict disease similarity…

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…

Graph neural networks (GNNs) face significant challenges with class imbalance, leading to biased inference results. To address this issue in heterogeneous graphs, we propose a novel framework that combines Graph Neural Network (GNN) and…

This paper explores the applications and challenges of graph neural networks (GNNs) in processing complex graph data brought about by the rapid development of the Internet. Given the heterogeneity and redundancy problems that graph data…

Machine learning methods can detect complex relationships between variables, but usually do not exploit domain knowledge. This is a limitation because in many scientific disciplines, such as systems biology, domain knowledge is available in…

In this thesis we present the novel semi-supervised network-based algorithm P-Net, which is able to rank and classify patients with respect to a specific phenotype or clinical outcome under study. The peculiar and innovative characteristic…

Discovering distinct features and their relations from data can help us uncover valuable knowledge crucial for various tasks, e.g., classification. In neuroimaging, these features could help to understand, classify, and possibly prevent…

Small subgraphs (graphlets) are important features to describe fundamental units of a large network. The calculation of the subgraph frequency distributions has a wide application in multiple domains including biology and engineering.…

Graphs can be used to effectively represent complex data structures. Learning these irregular data in graphs is challenging and still suffers from shallow learning. Applying deep learning on graphs has recently showed good performance in…

Heterogeneous graph representation learning aims to learn low-dimensional vector representations of different types of entities and relations to empower downstream tasks. Existing methods either capture semantic relationships but indirectly…

Graphs are fundamental data structures which concisely capture the relational structure in many important real-world domains, such as knowledge graphs, physical and social interactions, language, and chemistry. Here we introduce a powerful…

Graph Neural Networks (GNNs) have led to state-of-the-art performance on a variety of machine learning tasks such as recommendation, node classification and link prediction. Graph neural network models generate node embeddings by merging…

In this work, we propose a new deep learning model for Genomic Prediction (GP), which involves correlating genotypic data with phenotypic. The genotypes are typically fed as a sequence of characters to the 1D-Convolution Neural Network…

Graph learning (GL) can dynamically capture the distribution structure (graph structure) of data based on graph convolutional networks (GCN), and the learning quality of the graph structure directly influences GCN for semi-supervised…