Table 5.

Results of DREAM 2 Challenge #3 Data Compared to Other Approaches

Challenge	Best submitted	Our method	No self-regulations
DIRECTED-SIGNED-EXCITATORY	AUC = 0.79	AUC = 0.61	AUC = 0.79
	AUCPR = 0.72	AUCPR = 0.25	AUCPR = 0.54
DIRECTED-SIGNED-INHIBITORY	AUC = 0.63	AUC = 0.96	AUC = 0.96
	AUCPR = 0.14	AUCPR = 0.45	AUCPR = 0.45
DIRECTED-UNSIGNED	AUC = 0.73	AUC = 0.56	AUC = 0.79
	AUCPR = 0.55	AUCPR = 0.30	AUCPR = 0.57

Results of the DREAM 2 challenge #3 data of our method (second column) compared to submitted best results from [53] (first column). The third column gives the AUC values for our method when self-regulations are omitted. Our method clearly outperforms all submitted methods in the DIRECTED-SIGNED-INHIBITORY challenge; furthermore, when neglecting self-regulations, we also beat the best submitted method in the DIRECTED-UNSIGNED challenge.