Hu et al.
[123]
|
\(\checkmark\)
|
\(\checkmark\)
| | |
\(\checkmark\)
| |
CNN
|
KEGG and DrugBank
|
CV, ROC and Comp(Acc, Sen, F1, and AUC)
|
R-TIs
|
Han et al.
[99]
|
\(\checkmark\)
| |
\(\checkmark\)
|
\(\checkmark\)
|
\(\checkmark\)
| |
TM, GCN, and MF
|
OMIM
|
CV and Comp(MAP, AUC, and NDCG)
|
D-GAs
|
Zeng et al.
[106]
|
\(\checkmark\)
| |
\(\checkmark\)
| |
\(\checkmark\)
| |
MM-AE and V-AE
|
DrugBank, repoDB, and ClinicalTrials.gov
|
CV, AUC, AUC-PR, and Comp(Rec-TK)
|
R-DIs
|
Yang et al.
[127]
|
\(\checkmark\)
| |
\(\checkmark\)
| | |
\(\checkmark\)
|
ARM and LP
|
PharmGKB, SIDER, and MedHelp
[128]
|
CV, AUC, AUC-PR, and Comp(Send, Spc, and F1)
|
R-DIs
|
Ozsoy et al.
[119]
|
\(\checkmark\)
|
\(\checkmark\)
|
\(\checkmark\)
| |
\(\checkmark\)
| |
SM, PDo, and CF
|
PubChem, UniProt, SIDER, and TIRs
[35]
|
CV and Comp(Prec, Rec, F1, Spc, and AUC)
|
R-DIs
|
Segler et al.
[124]
| |
\(\checkmark\)
| | |
\(\checkmark\)
| |
RNN
|
SMILES
|
EOR
|
R-DIs
|
Altae-Tran et al.
[122]
| |
\(\checkmark\)
|
\(\checkmark\)
| |
\(\checkmark\)
| |
CCN and LSTM
|
SIDER and Tox21
[129]
|
Acc and AUC
|
R-DIs
|
Papanikolaou et al.
[105]
| |
\(\checkmark\)
| |
\(\checkmark\)
| | |
NER
|
DrugBank
|
—
|
R-RAs
|
Brown et al.
[104]
| |
\(\checkmark\)
| |
\(\checkmark\)
|
\(\checkmark\)
| |
SM and Clust
|
MEDLINE and DrugBank
|
CSs
|
R-DIs
|
Nugent et al.
[59]
| | |
\(\checkmark\)
|
\(\checkmark\)
| | |
SCM
|
Twitter
|
Comp(Acc)
|
R-DIs
|
Aliper et al.
[121]
|
\(\checkmark\)
| | | |
\(\checkmark\)
| |
DNN
|
LINCS
|
CV, F1, NNCM, Spr, and Comp(Acc)
|
R-RAs
|
Lim et al.
[118]
|
\(\checkmark\)
|
\(\checkmark\)
| | |
\(\checkmark\)
| |
SM and CF
|
ZINC
[130]
|
CV and Comp(Acc,and Rec)
|
R-TIs
|
Sridhar et al.
[60]
|
\(\checkmark\)
|
\(\checkmark\)
|
\(\checkmark\)
| |
\(\checkmark\)
| |
SM and PSL
|
DrugBank
|
Comp(AUC, AUC-PR, F1) and CSs
|
R-RIs
|
Zheng et al.
[39]
| |
\(\checkmark\)
| |
\(\checkmark\)
|
\(\checkmark\)
| |
SM
|
BindingDB
[131]
|
CV, Acc, Spc, Sen, AUC, Prec, F1, Comp(AUC, Sen, and Spc), and CSs
|
R-TIs
|
Rastegar-Mojarad et al.
[103]
|
\(\checkmark\)
| | |
\(\checkmark\)
| |
\(\checkmark\)
|
TM and SM
|
SemMedDB
[132], UMLS
[133], CTD
[134], and Medline
|
Comp(CoS)
|
R-DIs
|
Rakshit et al.
[126]
|
\(\checkmark\)
| | |
\(\checkmark\)
| |
\(\checkmark\)
|
TM and Genotator
[135], PolySearch
[95], Pescador
[136], and DrugBank
|
Comp(Acc)
|
R-TIs
| |
Huang et al.
[27]
|
\(\checkmark\)
| | | |
\(\checkmark\)
|
\(\checkmark\)
|
SM and BGL
|
CMap
|
CV, AUC, Comp(AUC), and CSs
|
R-TIs
|
Zhu et al.
[108]
|
\(\checkmark\)
|
\(\checkmark\)
| |
\(\checkmark\)
| | |
SM and WOL
|
PharmGKB
|
CSs
|
R-DIs
|
Tari et al.
[102]
|
\(\checkmark\)
|
\(\checkmark\)
| |
\(\checkmark\)
| | |
TM and LFRs
|
Medline, GO, UniProt, NCBI, CancerQuest
[137], and DrugBank
|
Comp(Rec) and CSs
|
R-DIs
|
Okada et al.
[23]
|
\(\checkmark\)
|
\(\checkmark\)
| |
\(\checkmark\)
| | |
GWAS
|
GWASs
|
P and CSs
|
R-DIs
|
Yang et al.
[117]
|
\(\checkmark\)
|
\(\checkmark\)
| | |
\(\checkmark\)
| |
CI-PMF
|
DrugBank, BioCarta
[138], and CTD
[134]
|
Comp(AUC and Prec) and CSs
|
R-DIs
|
Zhang et al.
[116]
|
\(\checkmark\)
|
\(\checkmark\)
|
\(\checkmark\)
| |
\(\checkmark\)
| |
SM and BCD
|
DrugBank, NDF-RT
[139], and HPRD
[140]
|
CV, Comp(AUC), and CSs
|
R-DIs
|
Bisgin et al.
[58]
| | |
\(\checkmark\)
| |
\(\checkmark\)
|
\(\checkmark\)
|
SM and LDA
|
SIDER
|
Acc and CSs
|
R-TIs
|
Tan et al.
[38]
|
\(\checkmark\)
|
\(\checkmark\)
| | | |
\(\checkmark\)
|
SM and Clust
|
PubChem and DrugBank
|
Comp(Acc)
|
R-TIs
|
Ye et al.
[57]
| | |
\(\checkmark\)
| | |
\(\checkmark\)
|
SM
|
SIDER
|
CV, Acc, and CSs
|
R-TIs
|
Menden et al.
[114]
|
\(\checkmark\)
|
\(\checkmark\)
| | |
\(\checkmark\)
| |
FF-PNN and RF
|
CCL
[18]
|
CV, Acc, \(R_{p}\), \(R^{2}\), RMSE, and CSs
|
R-TIs
|
Napolitano et al.
[115]
|
\(\checkmark\)
|
\(\checkmark\)
| | |
\(\checkmark\)
| |
SVM and CF
|
CMap, NCBI, DrugBank, and ATC
[141]
|
CV, Acc, Comp(AUC)
|
R-DIs
|
Wang et al.
[37]
|
\(\checkmark\)
|
\(\checkmark\)
|
\(\checkmark\)
| |
\(\checkmark\)
|
\(\checkmark\)
|
SM, KF, and SVM
|
PubChem, KEGG, BRENDA
[142], SuperTarget
[143], DrugBank, and SIDER
|
CV, Comp(AUC, Acc, Sens, Spc, Prec, and F1), $ CSs
|
R-DIs
|
Gottlieb et al.
[56]
|
\(\checkmark\)
|
\(\checkmark\)
|
\(\checkmark\)
|
\(\checkmark\)
|
\(\checkmark\)
| |
SM
|
DrugBank, Drugs.com, and SIDER
|
CV, Acc, AUC, and CSs
|
R-TIs
|
Wu et al.
[125]
|
\(\checkmark\)
|
\(\checkmark\)
|
\(\checkmark\)
| |
\(\checkmark\)
|
\(\checkmark\)
|
SM and Clust
|
KEGG
|
CV, Comp(Acc), and CSs
|
R-DIs
|
Chen et al.
[107]
|
\(\checkmark\)
| |
\(\checkmark\)
| |
\(\checkmark\)
|
\(\checkmark\)
|
SM and LP
|
Chem2Bio2RDF
[144], DrugBank, and Matador
[143]
|
Acc, AUC, Copm(Acc and AUC), and CSs
|
R-TIs
|
Li and Lu
[96]
|
\(\checkmark\)
| | |
\(\checkmark\)
| |
\(\checkmark\)
|
TM
|
ClinicalTrials.gov and PharmGKB
|
Acc, Comp(Acc), and CSs
|
PGx
|
Li and Lu
[35]
|
\(\checkmark\)
|
\(\checkmark\)
|
\(\checkmark\)
|
\(\checkmark\)
| |
\(\checkmark\)
|
SM and BGL
|
DrugBank, NDF-RT
[139], HPRD
[140], and ClinicalTrials.gov
|
CV (Sen, Spc, and AUC), Comp(Spc, Sen, and AUC), and CSs
|
R-TIs
|
Hoehndorf et al.
[55]
|
\(\checkmark\)
| |
\(\checkmark\)
| |
\(\checkmark\)
| |
SM
|
PhenomeNET
[145] and PharmGKB
|
AUC and CSs
|
R-TIs
|
Gottlieb et al.
[113]
|
\(\checkmark\)
|
\(\checkmark\)
|
\(\checkmark\)
| |
\(\checkmark\)
| |
SM and LR
|
DrugBank, SMILES, Matador
[143], DCDB
[146], KEGG, DailyMed
[147], SIDER, GO, UniPort, and ClinicalTrials.gov
|
CV, Acc, P, AUC, and Comp(Acc and AUC)
|
R-DIs
|
Sirota et al.
[14]
|
\(\checkmark\)
| | | |
\(\checkmark\)
| |
Clust and SM
|
GEO and CMap
|
CSs
|
R-DIs
|
Hu and Agarwal
[13]
|
\(\checkmark\)
| | | | |
\(\checkmark\)
|
SM
|
GEO, CMap, and DrugBank
|
Acc, Comp(Rec and Sens), and CSs
|
R-DIs
|
Li et al.
[101]
|
\(\checkmark\)
|
\(\checkmark\)
| |
\(\checkmark\)
|
\(\checkmark\)
| |
TM, SM and CMap
|
OPHID
[148], PubMed
|
CV, Comp(Sen, Spc, PPV, F1, and Acc), and CSs
|
R-DIs
|
Bleakley et al.
[32]
|
\(\checkmark\)
|
\(\checkmark\)
| | |
\(\checkmark\)
|
\(\checkmark\)
|
SM, BGL, and SVM
|
KEGG, BRENDA
[142], SuperTarget
[143], and DrugBank
|
CV, Comp(AYC and AUC-PR), and CSs
|
R-TIs
|
Kinnings et al.
[31]
|
\(\checkmark\)
|
\(\checkmark\)
| | | |
\(\checkmark\)
|
SM
|
MDDR
[149]
|
Comp(Acc) and CSs
|
R-TIs
|
Keiser et al.
[9]
| |
\(\checkmark\)
| | |
\(\checkmark\)
|
\(\checkmark\)
|
SM and BGL
|
KEGG, BRENDA
[142], SuperTarget
[143], and DrugBank
|
CV, Comp(AUC, Sens, Spc, and PPV), and CSs
|
R-TIs
|
Yamanishi et al.
[30]
|
\(\checkmark\)
|
\(\checkmark\)
| | |
\(\checkmark\)
|
\(\checkmark\)
|
SM and BGL
|
KEGG, BRENDA
[142], SuperTarget
[143], and DrugBank
|
CV, Comp(AUC, Sens, Spc, and PPV), and CSs
|
R-TIs
|
Cheng et al.
[95]
|
\(\checkmark\)
| | |
\(\checkmark\)
| |
\(\checkmark\)
|
TM
|
PubMed, UniPort, HGMD
[150], DrugBank, HMDB
[151]
|
Comp(F1) and CSs
|
BER
|
Campillos et al.
[53]
|
\(\checkmark\)
|
\(\checkmark\)
|
\(\checkmark\)
| |
\(\checkmark\)
| |
SM
|
Matador
[143], DrugBank, PDSP Ki
[152], and STRING
[153]
|
Comp(Spc and Sen) and CSs
|
R-DIs
|
Lamb et al.
[12]
|
\(\checkmark\)
| | | |
\(\checkmark\)
| |
Clust and CMap
|
CHC
|
CSs
|
R-DIs
|