TABLE 1.

Summary of typical applications.

Classification	Biological problems	Publications	Task of graph neural networks
			Node level	Edge level	Graph level
Disease association prediction	RNA–disease association prediction	Wang L. et al., 2020	√
		Li C. et al., 2019; Zhang J. et al., 2019; Ding et al., 2020; Li J. et al., 2020; Wu et al., 2020; Zheng et al., 2020		√
	Inter-cell interaction prediction	Wang et al., 2021		√
	scRNA-Seq clustering	Zeng et al., 2020	√
	Impute the dropout events in scRNA-Seq data	Jiahua et al., 2020		√
	Simulate cell differentiation	Bica et al., 2020			√
	Disease state prediction	Ravindra et al., 2020	√
	Disease genetic prioritization	Rao et al., 2018		√
		Li Y. et al., 2019		√
	Disease–gene association prediction	Singh and Lio, 2019		√	√
		Wang et al., 2019a		√
		Han et al., 2019			√
	Cancer genetic judgment	Iglehart and Silver, 2009	√
	Synthetic lethality prediction	Cai et al., 2020		√
	Breast cancer metastasis prediction	Chereda et al., 2021			√
	Breast cancer subtype classification	Rhee et al., 2018		√
	Disease protein judgment	Eyuboglu and Freeman, 2004	√
	Discussion on the relationship between drug and disease	Bajaj et al., 2017		√
	RNA classification	Rossi et al., 2019			√
	Predict the binding site of RNA protein	Uhl et al., 2019			√
		Yan et al., 2020			√
	RNA interaction prediction	Huang et al., 2019			√
	Targeted gene prediction of lncRNA	Zhao et al., 2020			√
	Biomedical data classification	Wang T. et al., 2020			√
Drug development and discovery	Protein structure prediction	Zamora-Resendiz and Crivelli, 2019	√
	Protein design	Ingraham et al., 2019; Strokach et al., 2020			√
	Protein function prediction	Gligorijevic et al., 2019			√
		Fout et al., 2017		√
	Protein functional sites prediction	Toomer, 2020	√
	Interface prediction between protein pairs	Yao et al., 2020			√
	Protein–protein interaction network denoising	Liu X. et al., 2020		√
	Prediction of the influence of protein mutation on binding	Cao and Shen, 2020	√
	Protein docking model evaluation	Johansson-Åkhe et al., 2020			√
	Assessment of docked peptide conformations	Feng et al., 2018			√
	Drug–target interaction prediction	Gao et al., 2018; Miyazaki et al., 2020; Nguyen et al., 2021		√
		Neil et al., 2018; Torng and Altman, 2019; Jiang et al., 2020; Zhong et al., 2020; Zhao et al., 2021			√
	Molecular structure coding	Duvenaud et al., 2015; Kearnes et al., 2016			√
	Drug properties prediction	Liu et al., 2019			√
	Esp surface detection of ligands	Rathi et al., 2019	√
	Compound–protein interaction prediction	Li S. et al., 2020		√
		Tsubaki et al., 2018			√
	Compound stability prediction	Li et al., 2019b			√
	De novo molecule design	Dai et al., 2018; Li et al., 2018a,b; You et al., 2018; Khemchandani et al., 2020			√
	Prediction of the association between miRNA and drug resistance	Huang et al., 2020		√
	Prediction of the effect of drugs on cancer cell growth	Liu Q. et al., 2020; Singha et al., 2020			√
	Prediction of drug-induced liver damage	Hwang et al., 2020			√
	Side effects prediction between drugs	Zitnik et al., 2018		√
	Drug similarity prediction	Ma et al., 2018		√
	Drug combination design	Long et al., 2020		√
	Drug recommendation	Mao et al., 2019		√
	Alkaloid classification	Eguchi et al., 2019			√
	Product prediction of organic reactions	Coley et al., 2019			√
	Chemical network prediction	Li Q. et al., 2018		√
Medical image processing	Image segmentation	Gopinath et al., 2019; Wang et al., 2019b; Tian et al., 2020a,b	√
	Image classification	Shi et al., 2019; Zhou et al., 2019; Adnan et al., 2020	√
	abnormal detection	Wu et al., 2019	√
	Image visualization	Levy et al., 2020; Sureka et al., 2020			√
	Image enhancement	Hu et al., 2020	√
	Image registration	Hansen et al., 2019	√
	Image retrieval	Zhai et al., 2019	√
	Surgical image analysis	Zhang et al., 2018	√
	Disease prediction	Parisot et al., 2017; Kazi et al., 2018, 2019a,b, 2019c; Anirudh and Thiagarajan, 2019; Yang et al., 2019; Arya et al., 2020; Stankevičiūtė et al., 2020		√
	Brain connection research	Ktena et al., 2017, 2018; Li X. et al., 2019a; Mirakhorli and Mirakhorli, 2019; Grigis et al., 2020; Zhang and Pierre, 2020; Zhang et al., 2021		√
		Li et al., 2020		√	√