Recent Advances in Intervention in Markovian Regulatory Networks

Babak      Faryabi; Golnaz      Vahedi; Aniruddha      Datta; Jean-Francois      Chamberland; Edward   R.   Dougherty

doi:10.2174/138920209789208246

Abstract

Markovian regulatory networks constitute a class of discrete state-space models used to study gene regulatory dynamics and discover methods that beneficially alter those dynamics. Thereby, this class of models provides a framework to discover effective drug targets and design potent therapeutic strategies. The salient translational goal is to design therapeutic strategies that desirably modify network dynamics via external signals that vary the expressions of a control gene. The objective of an intervention strategy is to reduce the likelihood of the pathological cellular function related to a disease. The task of finding an effective intervention strategy can be formulated as a sequential decision making problem for a pre-defined cost of intervention and a cost-per-stage function that discriminates the gene-activity profiles. An effective intervention strategy prescribes the actions associated with an external signal that result in the minimum expected cost. This strategy in turn can be used as a treatment that reduces the long-run likelihood of gene expressions favorable to the disease. In this tutorial, we briefly summarize the first method proposed to design such therapeutic interventions, and then move on to some of the recent refinements that have been proposed. Each of these recent intervention methods is motivated by practical or analytical considerations. The presentation of the key ideas is facilitated with the help of two case studies.

Keywords: Regulatory networks, markovian decision processes, translational genomics, systems biology

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