Table A3.

Relationship-based DL methods for DTI prediction.

Reference	Models	Relationship Data Type	Datasets	Algorithm Type	Evaluation Metrics	Year
Xie et al. [71]	MLP	LINCS signature	DrugBank; CTD; DGIdb; STITCH	Regression	Accuracy; F-score; TPR	2018
Lee and Kim [63]	MLP; node2vec	LINCS signature; PPI (Protein-protein interaction); Pathway	LINCS; ChEMBL; TTD; MATADOR; KEGG; IUPHAR; PharmGKB; KiDB	Classification	AUC; Precision	2019
Gao et al. [119]	CNN; LSTM	LINCS signature; GO term	BindingDB	Regression	Accuracy; AUC; AUPR	2018
Shao and Zhang [147]	CNN; GCN	LINCS signature	LINCS; DrugBank	Classification	Accuracy; AUC	2020
Thafar et al. [67]	node2vec	Drug similarity (structure, side effects); Target similarity (sequence, GO); PPI	Yamanishi; KEGG; BRENDA; SuperTarget; DrugBank; BioGRID; SIDER	Classification	AUPR; AUC	2020
Zong et al. [13]	DeepWalk [130]	Drug-target association; Drug-disease association; Disease-target association	DrugBank; Human diseasome [211]	Classification	AUC	2017
Mongia and Majumdar [212]	Multi-graph deep matrix factorization	Drug similarity (structure); Target similarity (sequence)	Yamanishi; KEGG; BRENDA; SuperTarget; DrugBank	Classification	AUPR; AUC	2020
Wang et al. [59]	AE	Drug similarity (structure, side effects); Target similarity (sequence, GO); PPI	Yamanishi; KEGG; BRENDA; SuperTarget; DrugBank; SIDER	Classification	AUPR; AUC	2020
Zhao et al. [68]	CNN; AE	Drug similarity (structure); Target similarity (sequence); PPI	DrugBank; STRING	Classification	Accuracy; AUPR; AUC	2020
Peng et al. [97]	CNN; AE	Drug-target association; Drug-disease association; Disease-target association; Drug similarity (structure, side effects); Target similarity (sequence, GO); PPI	DrugBank; Human Protein Reference Database [2009]; CTD; SIDER;	Classification	AUPR; AUC	2020
Zhong et al. [213]	GCN	LINCS signature; PPI	ChEMBL; LINCS; STRING	Classification	Accuracy; F-score; AUPR; Precision; Recall; AUC	2020