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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…

Drug-target interaction is fundamental in understanding how drugs affect biological systems, and accurately predicting drug-target affinity (DTA) is vital for drug discovery. Recently, deep learning methods have emerged as a significant…

Accurately predicting the binding affinity between drugs and proteins is an essential step for computational drug discovery. Since graph neural networks (GNNs) have demonstrated remarkable success in various graph-related tasks, GNNs have…

Drug recommendation is an essential task in machine learning-based clinical decision support systems. However, the risk of drug-drug interactions (DDI) between co-prescribed medications remains a significant challenge. Previous studies have…

Background: In silico drug-target interaction (DTI) prediction plays an integral role in drug repositioning: the discovery of new uses for existing drugs. One popular method of drug repositioning is network-based DTI prediction, which uses…

Brain connectivity alternations associated with brain disorders have been widely reported in resting-state functional imaging (rs-fMRI) and diffusion tensor imaging (DTI). While many dual-modal fusion methods based on graph neural networks…

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…

MiRNAs, due to their role in gene regulation, have paved a new pathway for pharmacology, focusing on drug development that targets miRNAs. However, traditional wet lab experiments are limited by efficiency and cost constraints, making it…

Graph neural networks (GNNs) have been used extensively for addressing problems in drug design and discovery. Both ligand and target molecules are represented as graphs with node and edge features encoding information about atomic elements…

Graph neural networks (GNNs) have shown great ability in modeling graphs, however, their performance would significantly degrade when there are noisy edges connecting nodes from different classes. To alleviate negative effect of noisy edges…

Graphs are useful for representing various realworld objects. However, graph neural networks (GNNs) tend to suffer from over-smoothing, where the representations of nodes of different classes become similar as the number of layers…

Accurate drug response prediction (DRP) is a crucial yet challenging task in precision medicine. This paper presents a novel Attention-Guided Multi-omics Integration (AGMI) approach for DRP, which first constructs a Multi-edge Graph (MeG)…

Graph representation learning is to learn universal node representations that preserve both node attributes and structural information. The derived node representations can be used to serve various downstream tasks, such as node…

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,…

Predicting unknown drug-drug interactions (DDIs) is crucial for improving medication safety. Previous efforts in DDI prediction have typically focused on binary classification or predicting DDI categories, with the absence of explanatory…

Graph Convolutional Networks (GCN) is a pioneering model for graph-based semi-supervised learning. However, GCN does not perform well on sparsely-labeled graphs. Its two-layer version cannot effectively propagate the label information to…

Graph embedding learning that aims to automatically learn low-dimensional node representations, has drawn increasing attention in recent years. To date, most recent graph embedding methods are evaluated on social and information networks…

Drug-target interaction (DTI) prediction is crucial for identifying new therapeutics and detecting mechanisms of action. While structure-based methods accurately model physical interactions between a drug and its protein target, cell-based…

Drug combination therapy is a powerful solution for the treatment of complex disease such as cancers due to its capability of therapeutic efficacy and reducing side effects. Nevertheless, it is very difficult to screen all drug combinations…

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…