Table 3.

Stability tests of α, n, π _i and the relative weights of the structural penalties

Default setting n=25,π i=0.5i	n=50,π i=0.5i	n=75,π i=0.5i	π i=0.25i, n=50	π i=3i, n=50
0.41	0.41	0.41	0.41	0.42
Default setting α=10−5	α=10−2	α=10−3	α=10−4	α=10−6
0.41	0.37	0.40	0.41	0.42
Default setting g4=2.0	g4=0.0	g4=1.0	g4=5.0	g4=10.0
0.41	0.39	0.41	0.41	0.41
Default setting r=25.0	r=0.0	r=1.0	r=15.0	g=35.0
0.41	0.36	0.38	0.41	0.41
Default setting a=25.0	a=0.0	a=50.0	a=75.0	a=100.0
0.41	0.40	0.41	0.41	0.41

The average AUPR score on a subset of 15 GENIE3 predictions is shown and compared to the score using default settings. Parameters not listed were set to default values. (g4 = graphlet, r = regulatory, a = anti-dominating)