Figure 1.
Venn diagram of confusion matrix incorporating network inferability.
denotes the set of all possible (directed) edges among nodes in the network. FN = false negative. FP = false positive. TP = true positive. TN = true negative.
= non-inferable edges.
Figure 2.
Inferability of network motifs from single-gene KO/KD experiments.
The new assessment procedure omits edges that are not inferable from single-gene KO/KD experiments, from the scoring of submissions. Compared to the assessment in the DREAM 4 challenge, FPs and FNs associated with cycles, cascades and FFLs are considered in the new assessment.
Figure 3.
Comparison of the team rankings between the new and the original assessment.
The two assessment procedures are applied to the 10-gene subchallenge (left) and the 100-gene subchallenge (right) of the DREAM 4 In Silico Network Challenge.
Table 1.
Network Sizes in the DREAM 4 In Silico Network Challenge.
Table 2.
Spearman's rank correlation, two-sided.
Figure 4.
Fractions of FPs (left) and FNs (right) that are non-inferable from single-gene KO/KD experiments.
Error bars show standard deviation over five 100-gene networks.
Table 3.
Common FNs among 100-gene network predictions.