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Biomedical Knowledge Graphs (BKGs) integrate diverse datasets to elucidate complex relationships within the biomedical field. Effective link prediction on these graphs can uncover valuable connections, such as potential novel drug-disease…

Most existing methods for predicting drug-drug interactions (DDI) predominantly concentrate on capturing the explicit relationships among drugs, overlooking the valuable implicit correlations present between drug pairs (DPs), which leads to…

Background: Discovering potential drug-drug interactions (DDIs) is a long-standing challenge in clinical treatments and drug developments. Recently, deep learning techniques have been developed for DDI prediction. However, they generally…

Interference between pharmacological substances can cause serious medical injuries. Correctly predicting so-called drug-drug interactions (DDI) does not only reduce these cases but can also result in a reduction of drug development cost.…

Relation prediction for knowledge graphs aims at predicting missing relationships between entities. Despite the importance of inductive relation prediction, most previous works are limited to a transductive setting and cannot process…

The development of deep neural networks has improved representation learning in various domains, including textual, graph structural, and relational triple representations. This development opened the door to new relation extraction beyond…

Knowledge graphs and structural causal models have each proven valuable for organizing biomedical knowledge and estimating causal effects, but remain largely disconnected: knowledge graphs encode qualitative relationships focusing on facts…

Understanding how small molecules perturb gene expression is essential for uncovering drug mechanisms, predicting off-target effects, and identifying repurposing opportunities. While prior deep learning frameworks have integrated multimodal…

Drug-drug interaction (DDI) prediction is central to drug discovery and clinical development, particularly in the context of increasingly prevalent polypharmacy. Although existing computational methods achieve strong performance on standard…

Relation-aware graph structure embedding is promising for predicting multi-relational drug-drug interactions (DDIs). Typically, most existing methods begin by constructing a multi-relational DDI graph and then learning relation-aware graph…

Drug combination therapy is a well-established strategy for disease treatment with better effectiveness and less safety degradation. However, identifying novel drug combinations through wet-lab experiments is resource intensive due to the…

Drug-drug interactions (DDIs) represent a critical challenge in pharmacology, often leading to adverse drug reactions with significant implications for patient safety and healthcare outcomes. While graph-based methods have achieved strong…

In recent years, artificial intelligence has played an important role on accelerating the whole process of drug discovery. Various of molecular representation schemes of different modals (e.g. textual sequence or graph) are developed. By…

Drug-drug interactions (DDIs) are a major concern in clinical practice, as they can lead to reduced therapeutic efficacy or severe adverse effects. Traditional computational approaches often struggle to capture the complex relationships…

Accurately predicting drug-target interactions (DTIs) is pivotal for advancing drug discovery and target validation techniques. While machine learning approaches including those that are based on Graph Neural Networks (GNN) have achieved…

Examining Drug-Drug Interactions (DDIs) is a pivotal element in the process of drug development. DDIs occur when one drug's properties are affected by the inclusion of other drugs. Detecting favorable DDIs has the potential to pave the way…

Recent advances and achievements of artificial intelligence (AI) as well as deep and graph learning models have established their usefulness in biomedical applications, especially in drug-drug interactions (DDIs). DDIs refer to a change in…

We introduce Bi-GNN for modeling biological link prediction tasks such as drug-drug interaction (DDI) and protein-protein interaction (PPI). Taking drug-drug interaction as an example, existing methods using machine learning either only…

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…

Predicating macroscopic influences of drugs on human body, like efficacy and toxicity, is a central problem of small-molecule based drug discovery. Molecules can be represented as an undirected graph, and we can utilize graph convolution…