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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…

Over the years several studies have demonstrated the ability to identify potential drug-drug interactions via data mining from the literature (MEDLINE), electronic health records, public databases (Drugbank), etc. While each one of these…

Protein (receptor)--ligand interaction prediction is a critical component in computer-aided drug design, significantly influencing molecular docking and virtual screening processes. Despite the development of numerous scoring functions in…

Adverse drug interactions are largely preventable causes of medical accidents, which frequently result in physician and emergency room encounters. The detection of drug interactions in a lab, prior to a drug's use in medical practice, is…

Graph Machine Learning (GML) is receiving growing interest within the pharmaceutical and biotechnology industries for its ability to model biomolecular structures, the functional relationships between them, and integrate multi-omic datasets…

Characterizing interactions between drugs is important to avoid potentially harmful combinations, to reduce off-target effects of treatments and to fight antibiotic resistant pathogens, among others. Here we present a network inference…

Predicting drug-drug interactions (DDI) is the problem of predicting side effects (unwanted outcomes) of a pair of drugs using drug information and known side effects of many pairs. This problem can be formulated as predicting labels (i.e.…

Complementary and alternative medicine are commonly used concomitantly with conventional medications leading to adverse drug reactions and even fatality in some cases. Furthermore, the vast possibility of herb-drug interactions prevents…

Predicting interspecies interactions is a key challenge in microbial ecology, as these interactions are critical to determining the structure and activity of microbial communities. In this work, we used data on monoculture growth…

Accurate prediction of drug-drug interactions (DDI) is crucial for medication safety and effective drug development. However, existing methods often struggle to capture structural information across different scales, from local functional…

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…

Multi-scale biomedical knowledge networks are expanding with emerging experimental technologies that generates multi-scale biomedical big data. Link prediction is increasingly used especially in bipartite biomedical networks to identify…

Drug synergy is profoundly influenced by cellular context, as variations in protein interaction landscapes and pathway activities across cell types reshape how drugs act in combination. Most existing models overlook this heterogeneity,…

In silico drug-target interaction (DTI) prediction is an important and challenging problem in biomedical research with a huge potential benefit to the pharmaceutical industry and patients. Most existing methods for DTI prediction including…

Adverse drug interactions are a critical concern in pharmacovigilance, as both clinical trials and spontaneous reporting systems often lack the breadth to detect complex drug interactions. This study introduces a computational framework for…

When patients need to take medicine, particularly taking more than one kind of drug simultaneously, they should be alarmed that there possibly exists drug-drug interaction. Interaction between drugs may have a negative impact on patients or…

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…

Multi-Label Image Classification (MLIC) aims to predict a set of labels that present in an image. The key to deal with such problem is to mine the associations between image contents and labels, and further obtain the correct assignments…

The identification of drug-target binding affinity (DTA) has attracted increasing attention in the drug discovery process due to the more specific interpretation than binary interaction prediction. Recently, numerous deep learning-based…

The intrinsic complexity of human biology presents ongoing challenges to scientific understanding. Researchers collaborate across disciplines to expand our knowledge of the biological interactions that define human life. AI methodologies…