Related papers: Graph Distance Neural Networks for Predicting Mult…

Graph are a ubiquitous data representation, as they represent a flexible and compact representation. For instance, the 3D structure of RNA can be efficiently represented as $\textit{2.5D graphs}$, graphs whose nodes are nucleotides and…

Graph similarity search is among the most important graph-based applications, e.g. finding the chemical compounds that are most similar to a query compound. Graph similarity computation, such as Graph Edit Distance (GED) and Maximum Common…

Molecular interaction prediction plays a crucial role in forecasting unknown interactions between molecules, such as drug-target interaction (DTI) and drug-drug interaction (DDI), which are essential in the field of drug discovery and…

Efficient and effective drug-target binding affinity (DTBA) prediction is a challenging task due to the limited computational resources in practical applications and is a crucial basis for drug screening. Inspired by the good representation…

Developing and discovering new drugs is a complex and resource-intensive endeavor that often involves substantial costs, time investment, and safety concerns. A key aspect of drug discovery involves identifying novel drug-target (DT)…

We explore the feasibility of combining Graph Neural Network-based policy architectures with Deep Reinforcement Learning as an approach to problems in systems. This fits particularly well with operations on networks, which naturally take…

The recent introduction of Graph Neural Networks (GNNs) and their growing popularity in the past few years has enabled the application of deep learning algorithms to non-Euclidean, graph-structured data. GNNs have achieved state-of-the-art…

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…

Graph Neural Network (GNN) based recommender systems have been attracting more and more attention in recent years due to their excellent performance in accuracy. Representing user-item interactions as a bipartite graph, a GNN model…

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…

Graph classification is an important area in both modern research and industry. Multiple applications, especially in chemistry and novel drug discovery, encourage rapid development of machine learning models in this area. To keep up with…

Graph neural networks (GNNs) are important tools for transductive learning tasks, such as node classification in graphs, due to their expressive power in capturing complex interdependency between nodes. To enable graph neural network…

Predicting the effect of amino acid mutations on enzyme thermodynamic stability (DDG) is fundamental to protein engineering and drug design. While recent deep learning approaches have shown promise, they often process sequence and structure…

Medication Recommendation (MR) is a promising research topic which booms diverse applications in the healthcare and clinical domains. However, existing methods mainly rely on sequential modeling and static graphs for representation…

Driven by the outstanding performance of neural networks in the structured Euclidean domain, recent years have seen a surge of interest in developing neural networks for graphs and data supported on graphs. The graph is leveraged at each…

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…

Explainable Graph Neural Networks (GNNs) have been developed and applied to drug-protein binding prediction to identify the key chemical structures in a drug that have active interactions with the target proteins. However, the key…

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…

Sampling is an established technique to scale graph neural networks to large graphs. Current approaches however assume the graphs to be homogeneous in terms of relations and ignore relation types, critically important in biomedical graphs.…

Recently, implicit graph neural networks (GNNs) have been proposed to capture long-range dependencies in underlying graphs. In this paper, we introduce and justify two weaknesses of implicit GNNs: the constrained expressiveness due to their…