Generating Boolean networks with a prescribed attractor structure

Bioinformatics
Ranadip PalEdward R Dougherty

Abstract

Dynamical modeling of gene regulation via network models constitutes a key problem for genomics. The long-run characteristics of a dynamical system are critical and their determination is a primary aspect of system analysis. In the other direction, system synthesis involves constructing a network possessing a given set of properties. This constitutes the inverse problem. Generally, the inverse problem is ill-posed, meaning there will be many networks, or perhaps none, possessing the desired properties. Relative to long-run behavior, we may wish to construct networks possessing a desirable steady-state distribution. This paper addresses the long-run inverse problem pertaining to Boolean networks (BNs). The long-run behavior of a BN is characterized by its attractors. The rest of the state transition diagram is partitioned into level sets, the j-th level set being composed of all states that transition to one of the attractor states in exactly j transitions. We present two algorithms for the attractor inverse problem. The attractors are specified, and the sizes of the predictor sets and the number of levels are constrained. Algorithm complexity and performance are analyzed. The algorithmic solutions have immediate application. Un...Continue Reading

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