Related papers: Graph-augmented Convolutional Networks on Drug-Dru…

Protein-protein interactions (PPIs) play key roles in a broad range of biological processes. Numerous strategies have been proposed for predicting PPIs, and among them, graph-based methods have demonstrated promising outcomes owing to the…

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…

Drug-drug interactions (DDI) can cause severe adverse drug reactions and pose a major challenge to medication therapy. Recently, informatics-based approaches are emerging for DDI studies. In this paper, we aim to identify key…

Computer-Aided Drug Discovery research has proven to be a promising direction in drug discovery. In recent years, Deep Learning approaches have been applied to problems in the domain such as Drug-Target Interaction Prediction and have shown…

Graphs are general and powerful data representations which can model complex real-world phenomena, ranging from chemical compounds to social networks; however, effective feature extraction from graphs is not a trivial task, and much work…

Drug-drug interactions (DDIs) remain a major source of preventable harm, and many clinically important mechanisms are still unknown. Existing models either rely on pharmacologic knowledge graphs (KGs), which fail on unseen drugs, or on…

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…

In this work, we aim to predict the future motion of vehicles in a traffic scene by explicitly modeling their pairwise interactions. Specifically, we propose a graph neural network that jointly predicts the discrete interaction modes and…

Graph Neural Networks (GNNs) have gained traction in the complex domain of drug discovery because of their ability to process graph-structured data such as drug molecule models. This approach has resulted in a myriad of methods and models…

Drug synergy, characterized by the amplified combined effect of multiple drugs, is critically important for optimizing therapeutic outcomes. Limited data on drug synergy, arising from the vast number of possible drug combinations and…

Accurate identification of drug-target interactions (DTI) remains a central challenge in computational pharmacology, where sequence-based methods offer scalability. This work introduces a sequence-based drug-target interaction framework…

Drug discovery requires a tremendous amount of time and cost. Computational drug-target interaction prediction, a significant part of this process, can reduce these requirements by narrowing the search space for wet lab experiments. In this…

Latent representations of drugs and their targets produced by contemporary graph autoencoder models have proved useful in predicting many types of node-pair interactions on large networks, including drug-drug, drug-target, and target-target…

The paper utilizes the graph embeddings generated for entities of a large biomedical database to perform link prediction to capture various new relationships among different entities. A novel node similarity measure is proposed that…

Protein-ligand interactions (PLIs) are fundamental to biochemical research and their identification is crucial for estimating biophysical and biochemical properties for rational therapeutic design. Currently, experimental characterization…

Drug-target interaction (DTI) prediction is a challenging, albeit essential task in drug repurposing. Learning on graph models have drawn special attention as they can significantly reduce drug repurposing costs and time commitment.…

Prediction of new drug-target interactions is extremely important as it can lead the researchers to find new uses for old drugs and to realize the therapeutic profiles or side effects thereof. However, experimental prediction of drug-target…

For translational impact, both accurate drug response prediction and biological plausibility of predictive features are needed. We present drGT, a heterogeneous graph deep learning model over drugs, genes, and cell lines that couples…

Drug-drug interactions pose a significant challenge in clinical pharmacology, with severe class imbalance among interaction types limiting the effectiveness of predictive models. Common interactions dominate datasets, while rare but…

Interaction between pharmacological agents can trigger unexpected adverse events. Capturing richer and more comprehensive information about drug-drug interactions (DDI) is one of the key tasks in public health and drug development.…