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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…

Predicting drug-gene associations is crucial for drug development and disease treatment. While graph neural networks (GNN) have shown effectiveness in this task, they face challenges with data sparsity and efficient contrastive learning…

We propose an end-to-end model to predict drug-drug interactions (DDIs) by employing graph-augmented convolutional networks. And this is implemented by combining graph CNN with an attentive pooling network to extract structural relations…

Complex or co-existing diseases are commonly treated using drug combinations, which can lead to higher risk of adverse side effects. The detection of polypharmacy side effects is usually done in Phase IV clinical trials, but there are still…

The discovery of drug-target interactions (DTIs) plays a crucial role in pharmaceutical development. The deep learning model achieves more accurate results in DTI prediction due to its ability to extract robust and expressive features from…

Drug Side-Effects (DSEs) have a high impact on public health, care system costs, and drug discovery processes. Predicting the probability of side-effects, before their occurrence, is fundamental to reduce this impact, in particular on drug…

Drug synergy arises when the combined impact of two drugs exceeds the sum of their individual effects. While single-drug effects on cell lines are well-documented, the scarcity of data on drug synergy, considering the vast array of…

Gaining more comprehensive knowledge about drug-drug interactions (DDIs) is one of the most important tasks in drug development and medical practice. Recently graph neural networks have achieved great success in this task by modeling drugs…

Predicting drug side-effects before they occur is a key task in keeping the number of drug-related hospitalizations low and to improve drug discovery processes. Automatic predictors of side-effects generally are not able to process the…

Motivation: Exploring drug-protein interactions (DPIs) work as a pivotal step in drug discovery. The fast expansion of available biological data enables computational methods effectively assist in experimental methods. Among them, deep…

Background: Drug-drug interactions (DDIs) refer to processes triggered by the administration of two or more drugs leading to side effects beyond those observed when drugs are administered by themselves. Due to the massive number of possible…

Accurate prediction of drug-target interaction (DTI) is essential for in silico drug design. For the purpose, we propose a novel approach for predicting DTI using a GNN that directly incorporates the 3D structure of a protein-ligand…

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…

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…

Subgraph-based methods have proven to be effective and interpretable in predicting drug-drug interactions (DDIs), which are essential for medical practice and drug development. Subgraph selection and encoding are critical stages in these…

Drug combinations offer therapeutic benefits but also carry the risk of adverse drug-drug interactions (DDIs), especially under complex molecular structures. Accurate DDI event prediction requires capturing fine-grained inter-drug…

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…

Recent studies suggest that drug-drug interaction (DDI) prediction via computational approaches has significant importance for understanding the functions and co-prescriptions of multiple drugs. However, the existing silico DDI prediction…

Adverse drug-drug interactions~(DDIs) can compromise the effectiveness of concurrent drug administration, posing a significant challenge in healthcare. As the development of new drugs continues, the potential for unknown adverse effects…

Drug-drug interaction(DDI) prediction is an important task in the medical health machine learning community. This study presents a new method, multi-view graph contrastive representation learning for drug-drug interaction prediction,…