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The tremendous boost in the next generation sequencing and in the omics technologies makes it possible to characterize human gut microbiome (the collective genomes of the microbial community that reside in our gastrointestinal tract). While…

Predicting the patient's clinical outcome from the historical electronic medical records (EMR) is a fundamental research problem in medical informatics. Most deep learning-based solutions for EMR analysis concentrate on learning the…

With recent advancements in non-invasive techniques for measuring brain activity, such as magnetic resonance imaging (MRI), the study of structural and functional brain networks through graph signal processing (GSP) has gained notable…

Large-scale perturbations in the microbiome constitution are strongly correlated, whether as a driver or a consequence, with the health and functioning of human physiology. However, understanding the difference in the microbiome profiles of…

There has been huge interest in studying human brain connectomes inferred from different imaging modalities and exploring their relationship with human traits, such as cognition. Brain connectomes are usually represented as networks, with…

Knowledge Graph (KG) alignment aims at finding equivalent entities and relations (i.e., mappings) between two KGs. The existing approaches utilize either reasoning-based or semantic embedding-based techniques, but few studies explore their…

Addressing the incompleteness problem in knowledge graph remains a significant challenge. Current knowledge graph completion methods have their limitations. For example, ComDensE is prone to overfitting and suffers from the degradation with…

In clinical treatment, identifying potential adverse reactions of drugs can help assist doctors in making medication decisions. In response to the problems in previous studies that features are high-dimensional and sparse, independent…

A significant portion of the data today, e.g, social networks, web connections, etc., can be modeled by graphs. A proper analysis of graphs with Machine Learning (ML) algorithms has the potential to yield far-reaching insights into many…

Increasing evidence has shown that gene-gene interactions have important effects on biological processes of human diseases. Due to the high dimensionality of genetic measurements, existing interaction analysis methods usually suffer from a…

Heterogeneity is a fundamental characteristic of cancer. To accommodate heterogeneity, subgroup identification has been extensively studied and broadly categorized into unsupervised and supervised analysis. Compared to unsupervised…

One component of precision medicine is to construct prediction models with their predictive ability as high as possible, e.g. to enable individual risk prediction. In genetic epidemiology, complex diseases have a polygenic basis and a…

Link prediction is a popular research topic in network analysis. In the last few years, new techniques based on graph embedding have emerged as a powerful alternative to heuristics. In this article, we study the problem of systematic biases…

Clinical trials play important roles in drug development but often suffer from expensive, inaccurate and insufficient patient recruitment. The availability of massive electronic health records (EHR) data and trial eligibility criteria (EC)…

Understanding how distributed brain regions coordinate to produce behavior requires models that are both predictive and interpretable. We introduce Behavior-Adaptive Connectivity Estimation (BACE), an end-to-end framework that learns…

Predicting whether a chemical structure shares a desired biological effect can have a significant impact for in-silico compound screening in early drug discovery. In this study, we developed a deep learning model where compound structures…

Drug repurposing is more relevant than ever due to drug development's rising costs and the need to respond to emerging diseases quickly. Knowledge graph embedding enables drug repurposing using heterogeneous data sources combined with…

Interpretability is crucial to enhance trust in machine learning models for medical diagnostics. However, most state-of-the-art image classifiers based on neural networks are not interpretable. As a result, clinicians often resort to known…

In the last decades, people have been consuming and combining more drugs than before, increasing the number of Drug-Drug Interactions (DDIs). To predict unknown DDIs, recently, studies started incorporating Knowledge Graphs (KGs) since they…

Motivation: Biological data and knowledge bases increasingly rely on Semantic Web technologies and the use of knowledge graphs for data integration, retrieval and federated queries. In the past years, feature learning methods that are…