On approximate stochastic control in genetic regulatory networks

IET Systems Biology
Babak FaryabiEdward R Dougherty

Abstract

The control of probabilistic Boolean networks as a model of genetic regulatory networks is formulated as an optimal stochastic control problem and has been solved using dynamic programming; however, the proposed methods fail when the number of genes in the network goes beyond a small number. There are two dimensionality problems. First, the complexity of optimal stochastic control exponentially increases with the number of genes. Second, the complexity of estimating the probability distributions specifying the model increases exponentially with the number of genes. We propose an approximate stochastic control method based on reinforcement learning that mitigates the curses of dimensionality and provides polynomial time complexity. Using a simulator, the proposed method eliminates the complexity of estimating the probability distributions and, because the method is a model-free method, it eliminates the impediment of model estimation. The method can be applied on networks for which dynamic programming cannot be used owing to computational limitations. Experimental results demonstrate that the performance of the method is close to optimal stochastic control.

References

Sep 7, 1987·Journal of Theoretical Biology·S Kauffman, S Levin
Mar 1, 1969·Journal of Theoretical Biology·S A Kauffman
Jun 28, 2002·Cancer Cell·Ashani T WeeraratnaJeffrey M Trent
Oct 12, 2002·Bioinformatics·Ilya ShmulevichWei Zhang
Nov 9, 2004·Bioinformatics·Ranadip PalEdward R Dougherty
Sep 10, 2005·Bioinformatics·Ranadip PalEdward R Dougherty
Oct 31, 2006·Journal of Theoretical Biology·Tatsuya AkutsuMichael K Ng

❮ Previous
Next ❯

Citations

Apr 28, 2010·Bioinformatics·Noushin GhaffariEdward R Dougherty
May 1, 2013·Bioinformatics·Mohammadmahdi R Yousefi, Edward R Dougherty
Sep 17, 2008·EURASIP Journal on Bioinformatics & Systems Biology·Morihiro HayashidaWai-Ki Ching
Jun 3, 2008·EURASIP Journal on Bioinformatics & Systems Biology·Babak FaryabiEdward R Dougherty
May 1, 2009·EURASIP Journal on Bioinformatics & Systems Biology·Babak FaryabiEdward R Dougherty
Jun 17, 2009·BMC Systems Biology·Xiaoning QianEdward R Dougherty
Jul 31, 2009·IET Systems Biology·S Z DenicR Palanivelu
Mar 18, 2010·IET Systems Biology·Q LiuT Zhou
Oct 8, 2008·IEEE Transactions on Bio-medical Engineering·Golnaz VahediEdward R Dougherty
Mar 11, 2009·IEEE Transactions on Bio-medical Engineering·Golnaz VahediEdward R Dougherty
Aug 3, 2016·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Utku SirinReda Alhajj
Apr 30, 2017·Scientific Reports·Yuhu WuWei Wang
Aug 24, 2020·Artificial Intelligence in Medicine·Cyntia Eico Hayama NishidaAnna Helena Reali Costa

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.