Overview of Modeling

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Network Enumeration

We use three nodes as a minimal framework: one node that receives input( A in Figure 2 ), a second node that transmits output( C in Figure 2 ), and a third node that can play diverse regulatory roles( B in Figure 2 ). There are 9 direct links among the three nodes and there are altogether 39=19683 three-node topologies. With 3,645 topologies that have no direct or indirect links from the input to the output occluded, there remain a total of 16,038 possible three-node topologies that contain at least one direct or indirect causal link from the input node to the output node. For each topology, we sampled 10,000 sets of network parameters with the method of latin hypercube sampling (LHS, Figure 3). In all, we have analyzed a total of 16,038*10,000 different circuits. This search resulted in an exhaustive circuit function map used to extract core topological motifs essential for IOA.
Figure 2 Three-node network with all of its possible directed links(Ref. 7) There are altogether 9 possible links and the input here is Hg(Ⅱ), and the concentration of C is taken as output.
Figure 3 Latin Hypercube Sampling When sampling a function of N variables, the range of each variable is divided into M equally probable intervals, M sample points are then placed to satisfy the Latin Hypercube requirements. Then each sample is theonly one in each axis-aligned hyperplane containing it.