Automated Large-Scale Control of Gene Regulatory Networks

Date

2010-04-01

Author

Tan, Mehmet
Alhajj, Reda
Polat, Faruk

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Controlling gene regulatory networks (GRNs) is an important and hard problem. As it is the case in all control problems, the curse of dimensionality is the main issue in real applications. It is possible that hundreds of genes may regulate one biological activity in an organism; this implies a huge state space, even in the case of Boolean models. This is also evident in the literature that shows that only models of small portions of the genome could be used in control applications. In this paper, we empower our framework for controlling GRNs by eliminating the need for expert knowledge to specify some crucial threshold that is necessary for producing effective results. Our framework is characterized by applying the factored Markov decision problem ( FMDP) method to the control problem of GRNs. The FMDP is a suitable framework for large state spaces as it represents the probability distribution of state transitions using compact models so that more space and time efficient algorithms could be devised for solving control problems. We successfully mapped the GRN control problem to an FMDP and propose a model reduction algorithm that helps find approximate solutions for large networks by using existing FMDP solvers. The test results reported in this paper demonstrate the efficiency and effectiveness of the proposed approach.

Subject Keywords

Control and Systems Engineering, Human-Computer Interaction, Electrical and Electronic Engineering, Software, Information Systems, General Medicine, Computer Science Applications

URI

https://hdl.handle.net/11511/34946

Journal

IEEE TRANSACTIONS ON SYSTEMS MAN AND CYBERNETICS PART B-CYBERNETICS

DOI

https://doi.org/10.1109/tsmcb.2009.2014736

Collections

Department of Computer Engineering, Article

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Citation Formats

M. Tan, R. Alhajj, and F. Polat, “Automated Large-Scale Control of Gene Regulatory Networks,” IEEE TRANSACTIONS ON SYSTEMS MAN AND CYBERNETICS PART B-CYBERNETICS, pp. 286–297, 2010, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/34946.