Optimal one-bit perturbation in Boolean networks based on cascading aggregation

PAN Jin-feng; MENG Min

doi:10.1631/FITEE.1900411

Your Location：

Home >

Browse articles >

Optimal one-bit perturbation in Boolean networks based on cascading aggregation

Special Issue on Complex Systems and Networks with Their Applications | Updated：2022-05-19

- Optimal one-bit perturbation in Boolean networks based on cascading aggregation
- 基于级联聚合算法下的布尔网络最优单点摄动
- Frontiers of Information Technology & Electronic Engineering Vol. 21, Issue 2, Pages: 294-303(2020)
- Affiliations：
  
  School of Mathematics and Information Sciences, Weifang University, Weifang 261061, China
  School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore
- Author bio：
  
  Jin-feng PAN, E-mail: panjinfeng1989@163.com
  [ "Min MENG, E-mail: mengminmath@gmail.com" ]
- Funds：
- DOI：10.1631/FITEE.1900411
  CLC： O223
- Received：17 August 2019，
  
  Revised：2019-11-15，
  
  Published：2020-02
- Accepted：
Scan QR Code
PAN Jin-feng, MENG Min. Optimal one-bit perturbation in Boolean networks based on cascading aggregation[J]. Frontiers of Information Technology & Electronic Engineering, 2020, 21(2): 294-303.
DOI：

PAN Jin-feng, MENG Min. Optimal one-bit perturbation in Boolean networks based on cascading aggregation[J]. Frontiers of Information Technology & Electronic Engineering, 2020, 21(2): 294-303. DOI： 10.1631/FITEE.1900411.

摘要

研究级联聚合算法分割下的大型布尔网络最优单点摄动问题；最大化期望吸引子吸引域，同时最小化非期望吸引子吸引域。首先，通过级联聚合算法给出一个在单点摄动下保持期望吸引子不变的充要条件。其次，提出一个判定是否出现新吸引子的算法。然后，提出另一算法给出单点摄动下吸引子吸引域的大小变化。最后，将本文理论应用于寻找T细胞受体网络的最优单点摄动问题。

Abstract

We investigate the problem of finding optimal one-bit perturbation that maximizes the size of the basin of attractions (BOAs) of desired attractors and minimizes the size of the BOAs of undesired attractors for large-scale Boolean networks by cascading aggregation. First

via the aggregation

a necessary and sufficient condition is given to ensure the invariance of desired attractors after one-bit perturbation. Second

an algorithm is proposed to identify whether the one-bit perturbation will cause the emergence of new attractors or not. Next

the change of the size of BOAs after one-bit perturbation is provided in an algorithm. Finally

the efficiency of the proposed method is verified by a T-cell receptor network.

关键词

Keywords

references

C Campbell , , , R Albert . . Stabilization of perturbed Boolean network attractors through compensatory interactions . . BMC Syst Biol , , 2014 . . 8 53 DOI: 10.1186/1752-0509-8-53 http://doi.org/10.1186/1752-0509-8-53 . .

DZ Cheng , , , HS Qi , , , ZQ Li . . Analysis and Control of Boolean Networks: a Semi-tensor Product Approach . . Springer, London, UK. , , 2011 . . DOI: 10.1007/978-0-85729-097-7 http://doi.org/10.1007/978-0-85729-097-7 . .

XY Ding , , , HT Li , , , QQ Yang , , , 等 . . Stochastic stability and stabilization of $$n$$ -person random evolutionary Boolean games . . Appl Math Comput , , 2017 . . 306 1 - - 12 . . DOI: 10.1016/j.amc.2017.02.020 http://doi.org/10.1016/j.amc.2017.02.020 . .

HB Fan , , , JE Feng , , , M Meng , , , 等 . . General decomposition of fuzzy relations: semi-tensor product approach . . Fuzzy Sets Syst , , 2020 . . 384 75 - - 90 . . DOI: 10.1016/j.fss.2018.12.012 http://doi.org/10.1016/j.fss.2018.12.012 . .

MX Hu , , , LZ Shen , , , XZ Zan , , , 等 . . An efficient algorithm to identify the optimal one-bit perturbation based on the basin-of-state size of Boolean networks . . Sci Rep , , 2016 . . 6 26247 DOI: 10.1038/srep26247 http://doi.org/10.1038/srep26247 . .

SA Kauffman . . Metabolic stability and epigenesis in randomly constructed genetic nets . . J Theor Biol , , 1969 . . 22 ( ( 3 ): ): 437 - - 467 . . DOI: 10.1016/0022-5193(69)90015-0 http://doi.org/10.1016/0022-5193(69)90015-0 . .

S Klamt , , , J Saez-Rodriguez , , , JA Lindquist , , , 等 . . A methodology for the structural and functional analysis of signaling and regulatory networks . . BMC Bioinform , , 2006 . . 7 56 DOI: 10.1186/1471-2105-7-56 http://doi.org/10.1186/1471-2105-7-56 . .

HT Li , , , XY Ding . . A control Lyapunov function approach to feedback stabilization of logical control networks . . SIAM J Contr Optim , , 2019 . . 57 ( ( 2 ): ): 810 - - 831 . . DOI: 10.1137/18M1170443 http://doi.org/10.1137/18M1170443 . .

HT Li , , , YZ Wang , , , ZB Liu . . Function perturbation impact on the topological structure of Boolean networks . . Proc 10$^{\textrm{th}}$ World Congress on Intelligent Control and Automation , , 2012 . . p.1241 - - 1246 . . DOI: 10.1109/WCICA.2012.6358071 http://doi.org/10.1109/WCICA.2012.6358071 . .

HT Li , , , XJ Xu , , , XY Ding . . Finite-time stability analysis of stochastic switched Boolean networks with impulsive effect . . Appl Math Comput , , 2019 . . 347 557 - - 565 . . DOI: 10.1016/j.amc.2018.11.018 http://doi.org/10.1016/j.amc.2018.11.018 . .

JY Liu , , , Y Liu , , , YQ Guo , , , 等 . . Sampled-data state-feedback stabilization of probabilistic Boolean control networks: a control Lyapunov function approach . . IEEE Trans Cybern, in press , , 2019 . . DOI: 10.1109/TCYB.2019.2932914 http://doi.org/10.1109/TCYB.2019.2932914 . .

M Liu . . Analysis and Synthesis of Boolean Networks . . Licentiate Thesis, KTH School of Information and Communication Technology, Sweden. , , 2015 . . .

Y Liu , , , BW Li , , , JQ Lu , , , 等 . . Pinning control for the disturbance decoupling problem of Boolean networks . . IEEE Trans Autom Contr , , 2017 . . 62 ( ( 12 ): ): 6595 - - 6601 . . DOI: 10.1109/TAC.2017.2715181 http://doi.org/10.1109/TAC.2017.2715181 . .

YS Liu , , , YT Zheng , , , HT Li , , , 等 . . Control design for output tracking of delayed Boolean control networks . . J Comput Appl Math , , 2018 . . 327 188 - - 195 . . DOI: 10.1016/j.cam.2017.06.016 http://doi.org/10.1016/j.cam.2017.06.016 . .

JQ Lu , , , J Zhong , , , C Huang , , , 等 . . On pinning controllability of Boolean control networks . . IEEE Trans Autom Contr , , 2016 . . 61 ( ( 6 ): ): 1658 - - 1663 . . DOI: 10.1109/TAC.2015.2478123 http://doi.org/10.1109/TAC.2015.2478123 . .

JQ Lu , , , HT Li , , , Y Liu , , , 等 . . Survey on semi-tensor product method with its applications in logical networks and other finite-valued systems . . IET Contr Theory Appl , , 2017 . . 11 ( ( 13 ): ): 2040 - - 2047 . . DOI: 10.1049/iet-cta.2016.1659 http://doi.org/10.1049/iet-cta.2016.1659 . .

JQ Lu , , , ML Li , , , Y Liu , , , 等 . . Nonsingularity of Grain-like cascade FSRs via semi-tensor product . . Sci China Inform Sci , , 2018a . . 61 010204 DOI: 10.1007/s11432-017-9269-6 http://doi.org/10.1007/s11432-017-9269-6 . .

JQ Lu , , , LJ Sun , , , Y Liu , , , 等 . . Stabilization of Boolean control networks under aperiodic sampled-data control . . SIAM J Contr Optim , , 2018b . . 56 ( ( 6 ): ): 4385 - - 4404 . . DOI: 10.1137/18M1169308 http://doi.org/10.1137/18M1169308 . .

JQ Lu , , , ML Li , , , TW Huang , , , 等 . . The transformation between the Galois NLFSRs and the Fibonacci NLFSRs via semi-tensor product of matrices . . Automatica , , 2018c . . 96 393 - - 397 . . DOI: 10.1016/j.automatica.2018.07.011 http://doi.org/10.1016/j.automatica.2018.07.011 . .

M Ostrowski , , , L Paulevé , , , T Schaub , , , 等 . . Boolean network identification from perturbation time series data combining dynamics abstraction and logic programming . . Biosystems , , 2016 . . 149 139 - - 153 . . DOI: 10.1016/j.biosystems.2016.07.009 http://doi.org/10.1016/j.biosystems.2016.07.009 . .

I Shmulevich , , , ER Dougherty , , , W Zhang . . From Boolean to probabilistic Boolean networks as models of genetic regulatory networks . . Proc IEEE , , 2002a . . 90 ( ( 11 ): ): 1778 - - 1792 . . DOI: 10.1109/JPROC.2002.804686 http://doi.org/10.1109/JPROC.2002.804686 . .

I Shmulevich , , , ER Dougherty , , , W Zhang . . Control of stationary behavior in probabilistic Boolean networks by means of structural intervention . . J Biol Syst , , 2002b . . 10 ( ( 4 ): ): 431 - - 445 . . DOI: 10.1142/S0218339002000706 http://doi.org/10.1142/S0218339002000706 . .

I Shmulevich , , , ER Dougherty , , , W Zhang . . Gene perturbation and intervention in probabilistic Boolean networks . . Bioinformatics , , 2002c . . 18 ( ( 10 ): ): 1319 - - 1331 . . DOI: 10.1093/bioinformatics/18.10.1319 http://doi.org/10.1093/bioinformatics/18.10.1319 . .

B Wang , , , JE Feng . . On detectability of probabilistic Boolean networks . . Inform Sci , , 2019 . . 483 383 - - 395 . . DOI: 10.1016/j.ins.2019.01.055 http://doi.org/10.1016/j.ins.2019.01.055 . .

B Wang , , , JE Feng , , , M Meng . . Model matching of switched asynchronous sequential machines via matrix approach . . Int J Contr , , 2019 . . 92 ( ( 10 ): ): 2430 - - 2440 . . DOI: 10.1080/00207179.2018.1441552 http://doi.org/10.1080/00207179.2018.1441552 . .

YF Xiao , , , ER Dougherty . . The impact of function perturbations in Boolean networks . . Bioinformatics , , 2007 . . 23 ( ( 10 ): ): 1265 - - 1273 . . DOI: 10.1093/bioinformatics/btm093 http://doi.org/10.1093/bioinformatics/btm093 . .

XJ Xu , , , HT Li , , , YL Li , , , 等 . . Output tracking control of Boolean control networks with impulsive effects . . Math Methods Appl Sci , , 2018 . . 41 ( ( 4 ): ): 1554 - - 1564 . . DOI: 10.1002/mma.4685 http://doi.org/10.1002/mma.4685 . .

YY Yu , , , JE Feng , , , JF Pan , , , 等 . . Block decoupling of Boolean control networks . . IEEE Trans Autom Contr , , 2019a . . 64 ( ( 8 ): ): 3129 - - 3140 . . DOI: 10.1109/TAC.2018.2880411 http://doi.org/10.1109/TAC.2018.2880411 . .

YY Yu , , , B Wang , , , JE Feng . . Input observability of Boolean control networks . . Neurocomputing , , 2019b . . 333 22 - - 28 . . DOI: 10.1016/j.neucom.2018.12.014 http://doi.org/10.1016/j.neucom.2018.12.014 . .

LQ Zhang , , , JE Feng , , , XH Feng , , , 等 . . Further results on disturbance decoupling of mix-valued logical networks . . IEEE Trans Autom Contr , , 2014 . . 59 ( ( 6 ): ): 1630 - - 1634 . . DOI: 10.1109/TAC.2013.2292733 http://doi.org/10.1109/TAC.2013.2292733 . .

Y Zhao , , , J Kim , , , M Filippone . . Aggregation algorithm towards large-scale Boolean network analysis . . IEEE Trans Autom Contr , , 2013 . . 58 ( ( 8 ): ): 1976 - - 1985 . . DOI: 10.1109/TAC.2013.2251819 http://doi.org/10.1109/TAC.2013.2251819 . .

Y Zhao , , , BK Ghosh , , , DZ Cheng . . Control of large-scale Boolean networks via network aggregation . . IEEE Trans Neur Netw Learn Syst , , 2016 . . 27 ( ( 7 ): ): 1527 - - 1536 . . DOI: 10.1109/TNNLS.2015.2442593 http://doi.org/10.1109/TNNLS.2015.2442593 . .

J Zhong , , , BW Li , , , Y Liu , , , 等 . . Output feedback stabilizer design of Boolean networks based on network structure . . Front Inform Technol Electron Eng , , 2020 . . 21 ( ( 2 ): ): 247 - - 259 . . DOI: 10.1631/FITEE.1900229 http://doi.org/10.1631/FITEE.1900229 . .

QX Zhu , , , Y Liu , , , JQ Lu , , , 等 . . On the optimal control of Boolean control networks . . SIAM J Contr Optim , , 2018 . . 56 ( ( 2 ): ): 1321 - - 1341 . . DOI: 10.1137/16M1070281 http://doi.org/10.1137/16M1070281 . .

Views

Downloads

CSCD

Alert me when the article has been cited

Submit

Tools

Publicity Resources

No data

Related Author

No data

Related Institution

No data

Chat

Address：Zhejiang University Press, 148 Tianmushan Road, Hangzhou, China Postal code：310028
Tel：+86-571-88273162 Email：fitee@zju.edu.cn
It is recommended to read the content of this site in Chrome&IE9+. Please switch to extreme mode in browser 360.
Cookies We use cookies to help provide and enhance our service and tailor content. By continuing, you agree to the use of cookies.

⁰