Table 3

Results with the networks of size 100 nodes from the DREAM4 benchmark
Network + reconstruction method TP TN FP FN AUROC AUPR
Network 1 (176 edges)
-perturbation graph 114 9467 257 62 0.8851 0.5138
-perturbation graph + CUTTER-U 107 9532 192 69 0.8848 0.5082
-perturbation graph + TRANSWESD 108 9547 177 68 0.8854 0.5366
-perturbation graph + CUTTER-W 109 9582 142 67 0.8857 0.5475
Network 2 (249 edges)
-perturbation graph 106 9389 262 143 0.7877 0.3577
-perturbation graph + CUTTER-U 98 9411 240 151 0.7871 0.3455
-perturbation graph + TRANSWESD 92 9473 178 157 0.7874 0.3636
-perturbation graph + CUTTER-W 85 9516 135 164 0.7874 0.3604
Network 3 (195 edges)
-perturbation graph 93 9446 259 102 0.8490 0.3353
-perturbation graph + CUTTER-U 91 9451 254 104 0.8488 0.3313
-perturbation graph + TRANSWESD 90 9543 162 105 0.8495 0.3574
-perturbation graph + CUTTER-W 89 9563 142 106 0.8496 0.3673
Network 4 (211 edges)
-perturbation graph 112 9403 286 99 0.8474 0.3932
-perturbation graph + CUTTER-U 111 9418 271 100 0.8474 0.3938
-perturbation graph + TRANSWESD 101 9510 179 110 0.8478 0.4214
-perturbation graph + CUTTER-W 96 9538 151 115 0.8477 0.4201
Network 5 (193 edges)
-perturbation graph 66 9230 477 127 0.7667 0.1580
-perturbation graph + CUTTER-U 66 9230 477 127 0.7667 0.1580
-perturbation graph + TRANSWESD 56 9409 298 137 0.7665 0.1653
-perturbation graph + CUTTER-W 52 9495 212 141 0.7666 0.1661

TP = true positives, TN = true negatives, FP = false positives, FN = false negatives. AUROC = area under the receiver-operator characteristics curve and AUPR = area under the precision-recall curve are computed by the DREAM 4 evaluation scripts.

Bošnački et al.

Bošnački et al. BMC Bioinformatics 2012 13:281   doi:10.1186/1471-2105-13-281

Open Data