Benchmark evaluation: NFkappaB-HMGIY
| Track | Sn | Sp | PPV | PC | ASP | F | Acc | CC | sSn | sSn | sPPV | sPC | sASP | sF |
| Baseline | 0.629 | 0.926 | 0.133 | 0.125 | 0.381 | 0.218 | 0.921 | 0.264 | 0.686 | 0.686 | 0.75 | 0.597 | 0.718 | 0.715 |
| Conserved0 | 0.64 | 0.919 | 0.124 | 0.12 | 0.382 | 0.207 | 0.914 | 0.255 | 0.686 | 0.686 | 0.75 | 0.621 | 0.718 | 0.715 |
| Conserved10 | 0.875 | 0.917 | 0.156 | 0.153 | 0.516 | 0.265 | 0.916 | 0.349 | 0.843 | 0.843 | 0.983 | 0.834 | 0.913 | 0.908 |
| Conserved30 | 0.892 | 0.92 | 0.164 | 0.16 | 0.528 | 0.276 | 0.919 | 0.362 | 0.857 | 0.857 | 1 | 0.857 | 0.929 | 0.923 |
| Conserved60 | 0.753 | 0.92 | 0.141 | 0.135 | 0.447 | 0.238 | 0.917 | 0.303 | 0.686 | 0.686 | 0.8 | 0.589 | 0.743 | 0.738 |
| Interacting10 | 0.824 | 0.926 | 0.163 | 0.157 | 0.493 | 0.271 | 0.924 | 0.345 | 0.819 | 0.819 | 0.933 | 0.786 | 0.876 | 0.872 |
| Interacting20 | 0.437 | 0.912 | 0.081 | 0.075 | 0.259 | 0.136 | 0.904 | 0.156 | 0.514 | 0.514 | 0.6 | 0.411 | 0.557 | 0.554 |
| C10_I10 | 0.882 | 0.921 | 0.163 | 0.16 | 0.523 | 0.276 | 0.92 | 0.36 | 0.843 | 0.843 | 0.983 | 0.834 | 0.913 | 0.908 |
| C30_I10 | 0.882 | 0.921 | 0.163 | 0.16 | 0.523 | 0.276 | 0.92 | 0.36 | 0.843 | 0.843 | 0.983 | 0.834 | 0.913 | 0.908 |
| C60_I10 | 0.774 | 0.918 | 0.143 | 0.137 | 0.458 | 0.241 | 0.916 | 0.309 | 0.714 | 0.714 | 0.833 | 0.625 | 0.774 | 0.769 |
| C10_I20 | 0.892 | 0.921 | 0.166 | 0.163 | 0.529 | 0.28 | 0.921 | 0.365 | 0.857 | 0.857 | 1 | 0.857 | 0.929 | 0.923 |
| C30_I20 | 0.892 | 0.921 | 0.166 | 0.163 | 0.529 | 0.28 | 0.921 | 0.365 | 0.857 | 0.857 | 1 | 0.857 | 0.929 | 0.923 |
| C60_I20 | 0.774 | 0.918 | 0.143 | 0.137 | 0.458 | 0.241 | 0.916 | 0.309 | 0.714 | 0.714 | 0.833 | 0.625 | 0.774 | 0.769 |