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Motivation: Drug repurposing is a viable solution for reducing the time and cost associated with drug development. However, thus far, the proposed drug repurposing approaches still need to meet expectations. Therefore, it is crucial to…

In recent decades, traditional drug research and development have been facing challenges such as high cost, long timelines, and high risks. To address these issues, many computational approaches have been suggested for predicting the…

Machine learning, particularly graph learning, is gaining increasing recognition for its transformative impact across various fields. One such promising application is in the realm of molecule design and discovery, notably within the…

Accurate and explainable health event predictions are becoming crucial for healthcare providers to develop care plans for patients. The availability of electronic health records (EHR) has enabled machine learning advances in providing these…

Knowledge Graphs have been one of the fundamental methods for integrating heterogeneous data sources. Integrating heterogeneous data sources is crucial, especially in the biomedical domain, where central data-driven tasks such as drug…

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,…

Accumulated clinical studies show that microbes living in humans interact closely with human hosts, and get involved in modulating drug efficacy and drug toxicity. Microbes have become novel targets for the development of antibacterial…

The drug development pipeline for a new compound can last 10-20 years and cost over 10 billion. Drug repurposing offers a more time- and cost-effective alternative. Computational approaches based on biomedical knowledge graph…

There is abundant interest in assessing the joint effects of multiple exposures on human health. This is often referred to as the mixtures problem in environmental epidemiology and toxicology. Classically, studies have examined the adverse…

Clinicians prescribe antibiotics by looking at the patient's health record with an experienced eye. However, the therapy might be rendered futile if the patient has drug resistance. Determining drug resistance requires time-consuming…

Image-based characterization and disease understanding involve integrative analysis of morphological, spatial, and topological information across biological scales. The development of graph convolutional networks (GCNs) has created the…

We introduced a methodology to efficiently exploit natural-language expressed biomedical knowledge for repurposing existing drugs towards diseases for which they were not initially intended. Leveraging on developments in Computational…

Psychiatric disorders have been traditionally conceptualized as latent conditions producing observable symptoms, but recent studies suggest that psychopathology may emerge from symptoms interactions. Psychometric networking model these…

Predicting the interaction between a compound and a target is crucial for rapid drug repurposing. Deep learning has been successfully applied in drug-target affinity (DTA) problem. However, previous deep learning-based methods ignore…

Recently, the cycle-consistent generative adversarial networks (CycleGAN) has been widely used for synthesis of multi-domain medical images. The domain-specific nonlinear deformations captured by CycleGAN make the synthesized images…

Sampling is an established technique to scale graph neural networks to large graphs. Current approaches however assume the graphs to be homogeneous in terms of relations and ignore relation types, critically important in biomedical graphs.…

Estimating the impact of continuous treatment variables (e.g., dosage amount) on binary outcomes presents significant challenges in modeling and estimation because many existing approaches make strong assumptions that do not hold for…

Graph convolutional network (GCN) is generalization of convolutional neural network (CNN) to work with arbitrarily structured graphs. A binary adjacency matrix is commonly used in training a GCN. Recently, the attention mechanism allows the…

Drug-drug interactions (DDIs) remain a major source of preventable harm, and many clinically important mechanisms are still unknown. Existing models either rely on pharmacologic knowledge graphs (KGs), which fail on unseen drugs, or on…

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…