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Table 3 The PC-LogicNet performance is evaluated for different values of c = α + β, i.e. c = 500, 750, 1000 and 1250. The PC-LogicNet is applied to reconstruct the directed network and logic functions among the regulatory genes in the E. coli, by using 10 gene expression samples and 100 repeats of the whole simulation study. Reported values for the TP, FP, TN, FN are the total of the corresponding values over 100 repeats of the whole simulation study

From: LogicNet: probabilistic continuous logics in reconstructing gene regulatory networks

  Graph TP FP TN FN TPR FPR PPV ACC MCC F-measure
c = 500 Undirected a 716 165 2835 784 0.48 0.06 0.81 0.79 0.50 0.60
Directed b 616 592 6908 884 0.41 0.08 0.51 0.84 0.36 0.45
Directed logical c 614 592 885 0.41 0.51 0.45
c = 750 Undirected 720 155 2845 780 0.48 0.05 0.82 0.79 0.51 0.61
Directed 620 590 6910 880 0.41 0.08 0.51 0.84 0.37 0.46
Directed logical 605 590 899 0.40 0.51 0.45
c = 1000 Undirected 724 157 2843 776 0.48 0.05 0.82 0.79 0.51 0.61
Directed 624 588 6912 876 0.42 0.08 0.51 0.84 0.37 0.46
Directed logical 625 588 868 0.42 0.52 0.46
c = 1250 Undirected 758 147 2853 742 0.51 0.05 0.84 0.80 0.54 0.63
Directed 658 571 6929 842 0.44 0.08 0.54 0.84 0.39 0.48
Directed logical 632 571 845 0.43 0.53 0.47
  1. a The edge direction is not taken into account in calculating the performance
  2. b The edge direction is taken into account in calculating the performance
  3. c The integrative performance of the LogicNet in reconstructing both the edge direction and logic function among regulatory genes is evaluated