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Drug similarity has been studied to support downstream clinical tasks such as inferring novel properties of drugs (e.g. side effects, indications, interactions) from known properties. The growing availability of new types of drug features…

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…

Recent advancements in the area of deep learning have shown the effectiveness of very large neural networks in several applications. However, as these deep neural networks continue to grow in size, it becomes more and more difficult to…

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…

The prediction modeling of drug-target interactions is crucial to drug discovery and design, which has seen rapid advancements owing to deep learning technologies. Recently developed methods, such as those based on graph neural networks…

Drug-drug interactions (DDIs) are a leading cause of preventable adverse events, often complicating treatment and increasing healthcare costs. At the same time, knowing which drugs do not interact is equally important, as such knowledge…

Dense subgraph extraction is a fundamental problem in graph analysis and data mining, aimed at identifying cohesive and densely connected substructures within a given graph. It plays a crucial role in various domains, including social…

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…

The discovery of drug-target interactions (DTIs) is a pivotal process in pharmaceutical development. Computational approaches are a promising and efficient alternative to tedious and costly wet-lab experiments for predicting novel DTIs from…

As a fundamental topic in graph mining, Densest Subgraph Discovery (DSD) has found a wide spectrum of real applications. Several DSD algorithms, including exact and approximation algorithms, have been proposed in the literature. However,…

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…

Illuminating the interconnections between drugs and genes is an important topic in drug development and precision medicine. Currently, computational predictions of drug-gene interactions mainly focus on the binding interactions without…

Drug discovery remains a slow and expensive process that involves many steps, from detecting the target structure to obtaining approval from the Food and Drug Administration (FDA), and is often riddled with safety concerns. Accurate…

In silico prediction of drug-target interactions (DTI) is significant for drug discovery because it can largely reduce timelines and costs in the drug development process. Specifically, deep learning-based DTI approaches have been shown…

Accurately predicting drug-drug interactions (DDIs) is crucial for pharmaceutical research and clinical safety. Recent deep learning models often suffer from high computational costs and limited generalization across datasets. In this…

Adverse drug-drug interactions (DDIs) remain a leading cause of morbidity and mortality. Identifying potential DDIs during the drug design process is critical for patients and society. Although several computational models have been…

Predicting and discovering drug-drug interactions (DDIs) is an important problem and has been studied extensively both from medical and machine learning point of view. Almost all of the machine learning approaches have focused on text data…

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…

Drug-target interaction (DTI) prediction has become a foundational task in drug repositioning, polypharmacology, drug discovery, as well as drug resistance and side-effect prediction. DTI identification using machine learning is gaining…

Detecting probable Drug Target Interaction (DTI) is a critical task in drug discovery. Conventional DTI studies are expensive, labor-intensive, and take a lot of time, hence there are significant reasons to construct useful computational…