Dataset Information

MGATRx: Discovering Drug Repositioning Candidates Using Multi-View Graph Attention.

ABSTRACT: In-silico drug repositioning or predicting new indications for approved or late-stage clinical trial drugs is a resourceful and time-efficient strategy in drug discovery. However, inferring novel candidate drugs for a disease is challenging, given the heterogeneity and sparseness of the underlying biological entities and their relationships (e.g., disease/drug annotations). By integrating drug-centric and disease-centric annotations as multi-views, we propose a multi-view graph attention network for indication discovery (MGATRx). Unlike most current similarity-based methods, we employ graph attention network on the heterogeneous drug and disease data to learn the representation of nodes and identify associations. MGATRx outperformed four other state-of-art methods used for computational drug repositioning. Further, several of our predicted novel indications are either currently investigated or are supported by literature evidence, demonstrating the overall translational utility of MGATRx.

SUBMITTER: Yella JK

PROVIDER: S-EPMC10038065 | biostudies-literature | 2022 Sep-Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

MGATRx: Discovering Drug Repositioning Candidates Using Multi-View Graph Attention.

Yella Jaswanth K JK Jegga Anil G AG

IEEE/ACM transactions on computational biology and bioinformatics 20220901 5

In-silico drug repositioning or predicting new indications for approved or late-stage clinical trial drugs is a resourceful and time-efficient strategy in drug discovery. However, inferring novel candidate drugs for a disease is challenging, given the heterogeneity and sparseness of the underlying biological entities and their relationships (e.g., disease/drug annotations). By integrating drug-centric and disease-centric annotations as multi-views, we propose a multi-view graph attention network ...[more]

PMID: 34014830

Similar Datasets

Project description:Since side-effects of drugs are one of the primary reasons for their failure in clinical trials, predicting their side-effects can help reduce drug development costs. We proposed a method based on heterogeneous graph transformer and capsule networks for side-effect-drug-association prediction (TCSD). The method encodes and integrates attributes from multiple types of neighbor nodes, connection semantics, and multi-view pairwise information. In each drug-side-effect heterogeneous graph, a target node has two types of neighbor nodes, the drug nodes and the side-effect ones. We proposed a new heterogeneous graph transformer-based context representation learning module. The module is able to encode specific topology and the contextual relations among multiple kinds of nodes. There are similarity and association connections between the target node and its various types of neighbor nodes, and these connections imply semantic diversity. Therefore, we designed a new strategy to measure the importance of a neighboring node to the target node and incorporate different semantics of the connections between the target node and its multi-type neighbors. Furthermore, we designed attentions at the neighbor node type level and at the graph level, respectively, to obtain enhanced informative neighbor node features and multi-graph features. Finally, a pairwise multi-view feature learning module based on capsule networks was built to learn the pairwise attributes from the heterogeneous graphs. Our prediction model was evaluated using a public dataset, and the cross-validation results showed it achieved superior performance to several state-of-the-art methods. Ablation experiments undertaken demonstrated the effectiveness of heterogeneous graph transformer-based context encoding, the position enhanced pairwise attribute learning, and the neighborhood node category-level attention. Case studies on five drugs further showed TCSD's ability in retrieving potential drug-related side-effect candidates, and TCSD inferred the candidate side-effects for 708 drugs.

Dataset Information

MGATRx: Discovering Drug Repositioning Candidates Using Multi-View Graph Attention.

Publications

MGATRx: Discovering Drug Repositioning Candidates Using Multi-View Graph Attention.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets