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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…

Accurate drug-target interaction (DTI) prediction is essential for computational drug discovery, yet existing models often rely on single-modality predefined molecular descriptors or sequence-based embeddings with limited…

Drug-drug interaction (DDI) prediction is a critical task in computational biomedicine, as adverse interactions between co-administered drugs can cause severe side effects and clinical risks. A key challenge is unseen-drug generalization,…

Repurposing existing drugs to treat new diseases is a cost-effective alternative to de novo drug development, but there are millions of potential drug-disease combinations to be considered with only a small fraction being viable. In silico…

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…

The discovery of novel drug target (DT) interactions is an important step in the drug development process. The majority of computer techniques for predicting DT interactions have focused on binary classification, with the goal of…

Off-the-shelf biomedical embeddings obtained from the recently released various pre-trained language models (such as BERT, XLNET) have demonstrated state-of-the-art results (in terms of accuracy) for the various natural language…

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…

Entity interaction prediction is essential in many important applications such as chemistry, biology, material science, and medical science. The problem becomes quite challenging when each entity is represented by a complex structure,…

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…

The identification of novel drug-target (DT) interactions is a substantial part of the drug discovery process. Most of the computational methods that have been proposed to predict DT interactions have focused on binary classification, where…

It is a common practice in modern medicine to prescribe multiple medications simultaneously to treat diseases. However, these medications could have adverse reactions between them, known as Drug-Drug Interactions (DDI), which have the…

Preventable adverse drug reactions as a result of medical errors present a growing concern in modern medicine. As drug-drug interactions (DDIs) may cause adverse reactions, being able to extracting DDIs from drug labels into…

Drug-target interaction (DTI) prediction, which aims at predicting whether a drug will be bounded to a target, have received wide attention recently, with the goal to automate and accelerate the costly process of drug design. Most of the…

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…

Predicting interactions between structured entities lies at the core of numerous tasks such as drug regimen and new material design. In recent years, graph neural networks have become attractive. They represent structured entities as graphs…

Drug-drug interactions (DDIs) are a major concern in polypharmacy. Public databases often provide only qualitative descriptions without pharmacokinetic context. We present an interactive web tool that integrates 191,541 descriptive DDI…

To mitigate the potential adverse health effects of simultaneous multi-drug use, including unexpected side effects and interactions, accurately identifying and predicting drug-drug interactions (DDIs) is considered a crucial task in the…

Understanding the interaction between different drugs (drug-drug interaction or DDI) is critical for ensuring patient safety and optimizing therapeutic outcomes. Existing DDI datasets primarily focus on textual information, overlooking…

With the advancements in Artificial intelligence (AI) and the accumulation of healthrelated big data, it has become increasingly feasible and commonplace to leverage machine learning technologies to analyze clinical and omics metadata to…