Computational Complexity of Minimal Trap Spaces in Boolean Networks

Abstract: A Boolean network (BN) is a discrete dynamical system defined by a Boolean function that maps to the domain itself. A trap space of a BN is a generalization of a fixed point, which is defined as the sub-hypercubes closed by the function of the BN. A trap space is minimal if it does not contain any smaller trap space. Minimal trap spaces have applications for the analysis of attractors of BNs with various update modes. This paper establishes the computational complexity results of three decision problems related to minimal trap spaces: the decision of the trap space property of a sub-hypercube, the decision of its minimality, and the decision of the membership of a given configuration to a minimal trap space. Under several cases on Boolean function representations, we investigate the computational complexity of each problem. In the general case, we demonstrate that the trap space property is coNP-complete, and the minimality and the membership properties are $\Pi_2^{\text P}$-complete. The complexities drop by one level in the polynomial hierarchy whenever the local functions of the BN are either unate, or are represented using truth-tables, binary decision diagrams, or double DNFs (Petri net encoding): the trap space property can be decided in a polynomial time, whereas deciding the minimality and the membership are coNP- complete. When the BN is given as its functional graph, all these problems are in P.