Table 6 Classification performance on DPI benchmark with ratio 1:10. Reported are the mean (std) over the 5 best models scored on the test folds. Values in bold indicate the highest metric for each feature type

Random

LR

0.129 ± 0.003

0.597 ± 0.001

0.602 ± 0.010

MLP

0.139 ± 0.006

0.635 ± 0.014

0.594 ± 0.004

RF

0.192 ± 0.004

0.720 ± 0.005

0.889 ± 0.001

Structural

LR

0.153 ± 0.003

0.690 ± 0.010

0.617 ± 0.010

MLP

0.244 ± 0.006

0.771 ± 0.003

0.665 ± 0.010

RF

0.398 ± 0.021

0.871 ± 0.008

0.885 ± 0.016

ComplEx

LR

0.170 ± 0.002

0.706 ± 0.004

0.639 ± 0.004

MLP

0.339 ± 0.006

0.838 ± 0.004

0.755 ± 0.003

RF

0.352 ± 0.014

0.849 ± 0.003

0.892 ± 0.008

RotatE

LR

0.180 ± 0.002

0.722 ± 0.005

0.643 ± 0.003

MLP

0.453 ± 0.008

0.886 ± 0.002

0.794 ± 0.006

RF

0.404 ± 0.005

0.885 ± 0.006

0.905 ± 0.006

TransE

LR

0.170 ± 0.003

0.691 ± 0.021

0.650 ± 0.017

MLP

0.350 ± 0.009

0.846 ± 0.005

0.750 ± 0.003

RF

0.380 ± 0.012

0.868 ± 0.010

0.894 ± 0.015

BioBLP-D

LR

0.177 ± 0.003

0.723 ± 0.003

0.641 ± 0.002

MLP

0.447 ± 0.008

0.885 ± 0.003

0.792 ± 0.002

RF

0.397 ± 0.003

0.883 ± 0.004

0.907 ± 0.004

BioBLP-M

LR

0.166 ± 0.002

0.713 ± 0.002

0.634 ± 0.003

MLP

0.401 ± 0.007

0.865 ± 0.002

0.764 ± 0.002

RF

0.415 ± 0.003

0.881 ± 0.004

0.895 ± 0.006

BioBLP-P

LR

0.170 ± 0.006

0.683 ± 0.005

0.636 ± 0.005

MLP

0.343 ± 0.008

0.820 ± 0.005

0.744 ± 0.015

RF

0.317 ± 0.006

0.832 ± 0.004

0.899 ± 0.002