Date of Original Version
Journal of Bioinformatics and Computational Biology, 7(2) pp. 323 – 338, 2009
Abstract or Description
We present an exact algorithm, based on techniques from the field of Model Checking, for finding control policies for Boolean Networks (BN) with control nodes. Given a BN, a set of starting states, I, a set of goal states, F, and a target time, t, our algorithm automatically finds a sequence of control signals that deterministically drives the BN from I to F at, or before time t, or else guarantees that no such policy exists. Despite recent hardness-results for finding control policies for BNs, we show that, in practice, our algorithm runs in seconds to minutes on over 13,400 BNs of varying sizes and topologies, including a BN model of embryogenesis in Drosophila melanogaster with 15,360 Boolean variables. We then extend our method to automatically identify a set of Boolean transfer functions that reproduce the qualitative behavior of gene regulatory networks. Specifically, we automatically learn a BN model of D. melanogaster embryogenesis in 5.3 seconds, from a space containing 6.9 × 1010 possible models.