Application of network link prediction in drug discovery

Abbas, Khushnood; Abbasi, Alireza; Dong, Shi; Niu, Ling; Yu, Laihang; Chen, Bolun; Cai, Shi-Min; Hasan, Qambar

doi:10.1186/s12859-021-04082-y

BMC Bioinformatics

Table 2 Model performance according to the three evaluation metrics: AUROC, AUPR, and F1-score

From: Application of network link prediction in drug discovery

Datasets	DGA			DDA			DTI			Matador			DDI
Models	AUROC	AUPR	F1	AUROC	AUPR	F1	AUROC	AUPR	F1	AUROC	AUPR	F1	AUROC	AUPR	F1
CN	0.5733	0.7803	0.5	0.5733	0.7803	0.5	0.5733	0.7803	0.5	0.5733	0.7803	0.5	0.5733	0.7803	0.5
Salton	0.5732	0.7776	0.5	0.5732	0.7776	0.5	0.5732	0.7776	0.5	0.5732	0.7776	0.5	0.5732	0.7776	0.5
Jaccard	0.5732	0.7765	0.5	0.5732	0.7765	0.5	0.5732	0.7765	0.5	0.5732	0.7765	0.5	0.5732	0.7765	0.5
Sorensen	0.5732	0.7765	0.5	0.5732	0.7765	0.5	0.5732	0.7765	0.5	0.5732	0.7765	0.5	0.5732	0.7765	0.5
HPI	0.5733	0.7265	0.5	0.5733	0.7265	0.5	0.5733	0.7265	0.5	0.5733	0.7265	0.5	0.5733	0.7265	0.5
HDI	0.5732	0.7765	0.5	0.5732	0.7765	0.5	0.5732	0.7765	0.5	0.5732	0.7765	0.5	0.5732	0.7765	0.5
LHN	0.5732	0.7773	0.5	0.5732	0.7773	0.5	0.5732	0.7773	0.5	0.5732	0.7773	0.5	0.5732	0.7773	0.5
AA	0.5733	0.7807	0.5	0.5733	0.7807	0.5	0.5733	0.7807	0.5	0.5733	0.7807	0.5	0.5733	0.7807	0.5
RA	0.5733	0.7805	0.5	0.5733	0.7805	0.5	0.5733	0.7805	0.5	0.5733	0.7805	0.5	0.5733	0.7805	0.5
PA	0.451	0.5183	0.5	0.451	0.5183	0.5	0.451	0.5183	0.5	0.451	0.5183	0.5	0.451	0.5183	0.5
LNBCN	0.5733	0.7811	0.5	0.5733	0.7811	0.5	0.5733	0.7811	0.5	0.5733	0.7811	0.5	0.5733	0.7811	0.5
LNBAA	0.5733	0.7809	0.5	0.5733	0.7809	0.5	0.5733	0.7809	0.5	0.5733	0.7809	0.5	0.5733	0.7809	0.5
LNBRA	0.5733	0.7808	0.5	0.5733	0.7808	0.5	0.5733	0.7808	0.5	0.5733	0.7808	0.5	0.5733	0.7808	0.5
LocalP	0.6133	0.8004	0.5	0.6133	0.8004	0.5	0.6133	0.8004	0.5	0.6133	0.8004	0.5	0.6133	0.8004	0.5
Katz .01	0.596	0.728	0.5	0.596	0.728	0.5	0.596	0.728	0.5	0.596	0.728	0.5	0.596	0.728	0.5
\(\sim .001\)	0.596	0.728	0.5	0.596	0.728	0.5	0.596	0.728	0.5	0.596	0.728	0.5	0.596	0.728	0.5
LHN2 .9	0.596	0.728	0.5	0.596	0.728	0.5	0.596	0.728	0.5	0.596	0.728	0.5	0.596	0.728	0.5
\(\sim .95\)	0.6488	0.7606	0.7492	0.6488	0.7606	0.7492	0.6488	0.7606	0.7492	0.6488	0.7606	0.7492	0.6488	0.7606	0.7492
\(\sim .99\)	0.6486	0.76	0.7481	0.6486	0.76	0.7481	0.6486	0.76	0.7481	0.6486	0.76	0.7481	0.6486	0.76	0.7481
ACT	0.8134	0.7868	0.7272	0.8134	0.7868	0.7272	0.8134	0.7868	0.7272	0.8134	0.7868	0.7272	0.8134	0.7868	0.7272
CosPlus	0.6975	0.7409	0.7192	0.6975	0.7409	0.7192	0.6975	0.7409	0.7192	0.6975	0.7409	0.7192	0.6975	0.7409	0.7192
RWR .85	0.5988	0.7321	0.5	0.5988	0.7321	0.5	0.5988	0.7321	0.5	0.5988	0.7321	0.5	0.5988	0.7321	0.5
\(\sim .95\)	0.5994	0.7331	0.5	0.5994	0.7331	0.5	0.5994	0.7331	0.5	0.5994	0.7331	0.5	0.5994	0.7331	0.5
SimR	0.7019	0.8202	0.5	0.7019	0.8202	0.5	0.7019	0.8202	0.5	0.7019	0.8202	0.5	0.7019	0.8202	0.5
LRW 3	0.6607	0.8054	0.4462	0.6607	0.8054	0.4462	0.6607	0.8054	0.4462	0.6607	0.8054	0.4462	0.6607	0.8054	0.4462
\(\sim 4\)	0.7033	0.8255	0.4462	0.7033	0.8255	0.4462	0.7033	0.8255	0.4462	0.7033	0.8255	0.4462	0.7033	0.8255	0.4462
\(\sim 5\)	0.7376	0.8443	0.7335	0.7376	0.8443	0.7335	0.7376	0.8443	0.7335	0.7376	0.8443	0.7335	0.7376	0.8443	0.7335
SRW 3	0.6606	0.8042	0.4462	0.6606	0.8042	0.4462	0.6606	0.8042	0.4462	0.6606	0.8042	0.4462	0.6606	0.8042	0.4462
\(\sim 4\)	0.7034	0.8261	0.4462	0.7034	0.8261	0.4462	0.7034	0.8261	0.4462	0.7034	0.8261	0.4462	0.7034	0.8261	0.4462
\(\sim 5\)	0.7376	0.8432	0.7334	0.7376	0.8432	0.7334	0.7376	0.8432	0.7334	0.7376	0.8432	0.7334	0.7376	0.8432	0.7334
MFI	0.5978	0.7302	0.5	0.5978	0.7302	0.5	0.5978	0.7302	0.5	0.5978	0.7302	0.5	0.5978	0.7302	0.5
TSCN	0.5906	0.7196	0.5	0.5906	0.7196	0.5	0.5906	0.7196	0.5	0.5906	0.7196	0.5	0.5906	0.7196	0.5
Prone	0.7389	0.6995	0.647	0.7864	0.6803	0.7269	0.8373	0.8129	0.7158	0.9486	0.9346	0.9063	0.9405	0.9108	0.8854
NetMF	0.7548	0.7262	0.692	0.4916	0.5078	0.5156	0.8879	0.8826	0.8182	0.955	0.941	0.9238	0.854	0.8435	0.8025
Node2vec	0.5898	0.5621	0.5153	0.5819	0.5175	0.5646	0.6973	0.6457	0.5543	0.9157	0.8864	0.8526	0.8065	0.7876	0.7357
Deepwalk	0.5871	0.5592	0.5098	0.5805	0.516	0.5657	0.698	0.6463	0.5548	0.9151	0.8863	0.8491	0.8057	0.7869	0.7336
Hope	0.6304	0.5313	0.5542	0.6086	0.5542	0.6075	0.7318	0.6172	0.6128	0.8304	0.7457	0.7841	0.8894	0.866	0.8076
NetSMF	0.5721	0.5282	0.5153	0.3822	0.3994	0.4111	0.7191	0.6449	0.5987	0.7923	0.7191	0.7431	0.7095	0.6736	0.6733
Grarep	0.0724	0.277	0	0.2765	0.3671	0.318	0.3796	0.3252	0.1624	0.2992	0.3522	0.2538	0.6739	0.6286	0.6435

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