Table 2.

Target prediction performance on the LINCS phase II data

Cell lines	Number of compounds	Top 100 accuracy (SSGCN)	Top 30 accuracy (SSGCN)	Top 100 accuracy (CMap)	Top 30 accuracy (CMap)
PC3	249	0.53	0.30	0.29	0.12
A549	41	0.66	0.51	0.31	0.20
MCF7	240	0.53	0.30	0.24	0.10
A375	245	0.51	0.31	0.30	0.15
HA1E	238	0.56	0.34	0.27	0.13
HCC515	39	0.65	0.46	0.15	0.05

The bold means the best model