A comprehensive review and evaluation of graph neural networks for non-coding RNA and complex disease associations

Author:

Hu Xiaowen1,Liu Dayun1,Zhang Jiaxuan2,Fan Yanhao1,Ouyang Tianxiang1,Luo Yue1,Zhang Yuanpeng3,Deng Lei1

Affiliation:

1. School of Computer Science and Engineering, Central South University ,410075 Changsha, China

2. Department of Electrical and Computer Engineering, University of California , San Diego,92093 CA, USA

3. school of software, Xinjiang University , 830046 Urumqi , China

Abstract

Abstract Non-coding RNAs (ncRNAs) play a critical role in the occurrence and development of numerous human diseases. Consequently, studying the associations between ncRNAs and diseases has garnered significant attention from researchers in recent years. Various computational methods have been proposed to explore ncRNA–disease relationships, with Graph Neural Network (GNN) emerging as a state-of-the-art approach for ncRNA–disease association prediction. In this survey, we present a comprehensive review of GNN-based models for ncRNA–disease associations. Firstly, we provide a detailed introduction to ncRNAs and GNNs. Next, we delve into the motivations behind adopting GNNs for predicting ncRNA–disease associations, focusing on data structure, high-order connectivity in graphs and sparse supervision signals. Subsequently, we analyze the challenges associated with using GNNs in predicting ncRNA–disease associations, covering graph construction, feature propagation and aggregation, and model optimization. We then present a detailed summary and performance evaluation of existing GNN-based models in the context of ncRNA–disease associations. Lastly, we explore potential future research directions in this rapidly evolving field. This survey serves as a valuable resource for researchers interested in leveraging GNNs to uncover the complex relationships between ncRNAs and diseases.

Funder

National Natural Science Foundation of China

Publisher

Oxford University Press (OUP)

Subject

Molecular Biology,Information Systems

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