DELAY uncovers causal, cyclic, and context-specific gene-regulatory relationships. A) The network's performance when inferring putative transcription factor-target gene pairs across two- and three-gene motifs in the validation set suggests that DELAY can distinguish between different types of hierarchical and cyclic gene regulation. Upon exclusion of one or more neighbor genes C from the input features of the validation examples, the network's performance declines significantly if C is a shared or sequential regulator of A and B, but not if C is a shared target. B) GO-term enrichment indicates that DELAY performs best on zinc-finger proteins (PHD-type, GATA-type, C2H2-type, NHR-type, and C5HC2-type), bHLH factors (Myc-type), and other chromatin remodelers (SNF2-related, chromodomain, bromodomain, HDA domain, and helicase). Markers and error bars in A) show the average values and full range of performance across five model replicates. The statistical significance in A) was assessed with a one-sided Wilcoxon signed-rank test (*P ≤ 0.05) and in B) with a Fisher's exact test (P_adjusted ≤ 0.05).