An efficient top-down search algorithm for learning Boolean networks of gene expression

Boolean networks provide a simple and intuitive model for gene regulatory networks, but a critical defect is the time required to learn the networks. In recent years, efficient network search algorithms have been developed for a noise-free case and for a limited function class. In general, the conventional algorithm has the high time complexity of O(2^{2k mn k+1}) where m is the number of measurements, n is the number of nodes (genes), and k is the number of input parents. Here, we suggest a simple and new approach to Boolean networks, and provide a randomized network search algorithm with average time complexity O ^{(mn k+1}/ (log m)^(k−1)). We show the efficiency of our algorithm via computational experiments, and present optimal parameters. Additionally, we provide tests for yeast expression data. Editor: David Page