Graph neural networks and their current applications in bioinformatics

XM Zhang, L Liang, L Liu, MJ Tang - Frontiers in genetics, 2021 - frontiersin.org
Graph neural networks (GNNs), as a branch of deep learning in non-Euclidean space,
perform particularly well in various tasks that process graph structure data. With the rapid …

Graph signal processing, graph neural network and graph learning on biological data: a systematic review

R Li, X Yuan, M Radfar, P Marendy, W Ni… - IEEE Reviews in …, 2021 - ieeexplore.ieee.org
Graph networks can model data observed across different levels of biological systems that
span from population graphs (with patients as network nodes) to molecular graphs that …

Tail-gnn: Tail-node graph neural networks

Z Liu, TK Nguyen, Y Fang - Proceedings of the 27th ACM SIGKDD …, 2021 - dl.acm.org
The prevalence of graph structures in real-world scenarios enables important tasks such as
node classification and link prediction. Graphs in many domains follow a long-tailed …

Pre-training graph neural networks for link prediction in biomedical networks

Y Long, M Wu, Y Liu, Y Fang, CK Kwoh, J Chen… - …, 2022 - academic.oup.com
Motivation Graphs or networks are widely utilized to model the interactions between different
entities (eg proteins, drugs, etc.) for biomedical applications. Predicting potential …

[HTML][HTML] Network learning for biomarker discovery

Y Ding, M Fu, P Luo, FX Wu - International Journal of Network Dynamics …, 2023 - sciltp.com
Everything is connected and thus networks are instrumental in not only modeling complex
systems with many components, but also accommodating knowledge about their …

KG4SL: knowledge graph neural network for synthetic lethality prediction in human cancers

S Wang, F Xu, Y Li, J Wang, K Zhang, Y Liu… - …, 2021 - academic.oup.com
Motivation Synthetic lethality (SL) is a promising gold mine for the discovery of anti-cancer
drug targets. Wet-lab screening of SL pairs is afflicted with high cost, batch-effect, and off …

Recent advances in network-based methods for disease gene prediction

SK Ata, M Wu, Y Fang, L Ou-Yang… - Briefings in …, 2021 - academic.oup.com
Disease–gene association through genome-wide association study (GWAS) is an arduous
task for researchers. Investigating single nucleotide polymorphisms that correlate with …

SynLethDB 2.0: a web-based knowledge graph database on synthetic lethality for novel anticancer drug discovery

J Wang, M Wu, X Huang, L Wang, S Zhang, H Liu… - Database, 2022 - academic.oup.com
Two genes are synthetic lethal if mutations in both genes result in impaired cell viability,
while mutation of either gene does not affect the cell survival. The potential usage of …

Ensembling graph attention networks for human microbe–drug association prediction

Y Long, M Wu, Y Liu, CK Kwoh, J Luo, X Li - Bioinformatics, 2020 - academic.oup.com
Motivation Human microbes get closely involved in an extensive variety of complex human
diseases and become new drug targets. In silico methods for identifying potential microbe …

Predicting human microbe–disease associations via graph attention networks with inductive matrix completion

Y Long, J Luo, Y Zhang, Y **a - Briefings in bioinformatics, 2021 - academic.oup.com
Motivation human microbes play a critical role in an extensive range of complex human
diseases and become a new target in precision medicine. In silico methods of identifying …