High Fidelity Modeling of Pulse Dynamics using Logic Networks

Cole A. Lyman; Matthew M. Morris; Spencer Richman; Hongbao Cao; Antony Scerri; Chris Cheadle; Gordon Broderick

doi:10.1109/BIBM52615.2021.9669437

High Fidelity Modeling of Pulse Dynamics using Logic Networks

Cole A. Lyman, Matthew M. Morris, Spencer Richman, Hongbao Cao, Antony Scerri, Chris Cheadle, Gordon Broderick

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

2 Scopus citations

Abstract

Pulsatile dynamics are a key regulatory behavior in many biological systems, but perform poorly using conventional logic network methods. This work addresses the relatively poor performance of logic network models when applied to pulse dynamic scenarios by implementing a novel update scheme. Models from this novel update scheme and a traditional update scheme are compared using canonical examples, i.e. the van der Pol oscillator and the Hypothalamic-Pituitary-Gonadal (HPG) axis. By incorporating this new update scheme, the authors show a 35% (11%) reduction of global minimum error in the van der Pol model (HPG axis) when compared with traditional methods.

Original language	English
Title of host publication	Proceedings - 2021 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021
Editors	Yufei Huang, Lukasz Kurgan, Feng Luo, Xiaohua Tony Hu, Yidong Chen, Edward Dougherty, Andrzej Kloczkowski, Yaohang Li
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	197-204
Number of pages	8
ISBN (Electronic)	9781665401265
DOIs	https://doi.org/10.1109/BIBM52615.2021.9669437
State	Published - 2021
Externally published	Yes
Event	2021 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021 - Virtual, Online, United States Duration: Dec 9 2021 → Dec 12 2021

Publication series

Name	Proceedings - 2021 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021

Conference

Conference	2021 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021
Country/Territory	United States
City	Virtual, Online
Period	12/9/21 → 12/12/21

Keywords

HPG axis
logic model
update scheme

Access to Document

10.1109/BIBM52615.2021.9669437

Cite this

Lyman, C. A., Morris, M. M., Richman, S., Cao, H., Scerri, A., Cheadle, C., & Broderick, G. (2021). High Fidelity Modeling of Pulse Dynamics using Logic Networks. In Y. Huang, L. Kurgan, F. Luo, X. T. Hu, Y. Chen, E. Dougherty, A. Kloczkowski, & Y. Li (Eds.), Proceedings - 2021 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021 (pp. 197-204). (Proceedings - 2021 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM52615.2021.9669437

Lyman, Cole A. ; Morris, Matthew M. ; Richman, Spencer et al. / High Fidelity Modeling of Pulse Dynamics using Logic Networks. Proceedings - 2021 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021. editor / Yufei Huang ; Lukasz Kurgan ; Feng Luo ; Xiaohua Tony Hu ; Yidong Chen ; Edward Dougherty ; Andrzej Kloczkowski ; Yaohang Li. Institute of Electrical and Electronics Engineers Inc., 2021. pp. 197-204 (Proceedings - 2021 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021).

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title = "High Fidelity Modeling of Pulse Dynamics using Logic Networks",

abstract = "Pulsatile dynamics are a key regulatory behavior in many biological systems, but perform poorly using conventional logic network methods. This work addresses the relatively poor performance of logic network models when applied to pulse dynamic scenarios by implementing a novel update scheme. Models from this novel update scheme and a traditional update scheme are compared using canonical examples, i.e. the van der Pol oscillator and the Hypothalamic-Pituitary-Gonadal (HPG) axis. By incorporating this new update scheme, the authors show a 35% (11%) reduction of global minimum error in the van der Pol model (HPG axis) when compared with traditional methods.",

keywords = "HPG axis, logic model, update scheme",

author = "Lyman, {Cole A.} and Morris, {Matthew M.} and Spencer Richman and Hongbao Cao and Antony Scerri and Chris Cheadle and Gordon Broderick",

note = "Publisher Copyright: {\textcopyright} 2021 IEEE.; 2021 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021 ; Conference date: 09-12-2021 Through 12-12-2021",

year = "2021",

doi = "10.1109/BIBM52615.2021.9669437",

language = "Ingl{\'e}s",

series = "Proceedings - 2021 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021",

publisher = "Institute of Electrical and Electronics Engineers Inc.",

pages = "197--204",

editor = "Yufei Huang and Lukasz Kurgan and Feng Luo and Hu, {Xiaohua Tony} and Yidong Chen and Edward Dougherty and Andrzej Kloczkowski and Yaohang Li",

booktitle = "Proceedings - 2021 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021",

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Lyman, CA, Morris, MM, Richman, S, Cao, H, Scerri, A , Cheadle, C & Broderick, G 2021, High Fidelity Modeling of Pulse Dynamics using Logic Networks. in Y Huang, L Kurgan, F Luo, XT Hu, Y Chen, E Dougherty, A Kloczkowski & Y Li (eds), Proceedings - 2021 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021. Proceedings - 2021 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021, Institute of Electrical and Electronics Engineers Inc., pp. 197-204, 2021 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021, Virtual, Online, United States, 12/9/21. https://doi.org/10.1109/BIBM52615.2021.9669437

High Fidelity Modeling of Pulse Dynamics using Logic Networks. / Lyman, Cole A.; Morris, Matthew M.; Richman, Spencer et al.
Proceedings - 2021 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021. ed. / Yufei Huang; Lukasz Kurgan; Feng Luo; Xiaohua Tony Hu; Yidong Chen; Edward Dougherty; Andrzej Kloczkowski; Yaohang Li. Institute of Electrical and Electronics Engineers Inc., 2021. p. 197-204 (Proceedings - 2021 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - High Fidelity Modeling of Pulse Dynamics using Logic Networks

AU - Lyman, Cole A.

AU - Morris, Matthew M.

AU - Richman, Spencer

AU - Cao, Hongbao

AU - Scerri, Antony

AU - Cheadle, Chris

AU - Broderick, Gordon

PY - 2021

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N2 - Pulsatile dynamics are a key regulatory behavior in many biological systems, but perform poorly using conventional logic network methods. This work addresses the relatively poor performance of logic network models when applied to pulse dynamic scenarios by implementing a novel update scheme. Models from this novel update scheme and a traditional update scheme are compared using canonical examples, i.e. the van der Pol oscillator and the Hypothalamic-Pituitary-Gonadal (HPG) axis. By incorporating this new update scheme, the authors show a 35% (11%) reduction of global minimum error in the van der Pol model (HPG axis) when compared with traditional methods.

AB - Pulsatile dynamics are a key regulatory behavior in many biological systems, but perform poorly using conventional logic network methods. This work addresses the relatively poor performance of logic network models when applied to pulse dynamic scenarios by implementing a novel update scheme. Models from this novel update scheme and a traditional update scheme are compared using canonical examples, i.e. the van der Pol oscillator and the Hypothalamic-Pituitary-Gonadal (HPG) axis. By incorporating this new update scheme, the authors show a 35% (11%) reduction of global minimum error in the van der Pol model (HPG axis) when compared with traditional methods.

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M3 - Contribución a la conferencia

AN - SCOPUS:85125204115

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SP - 197

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BT - Proceedings - 2021 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021

A2 - Huang, Yufei

A2 - Kurgan, Lukasz

A2 - Luo, Feng

A2 - Hu, Xiaohua Tony

A2 - Chen, Yidong

A2 - Dougherty, Edward

A2 - Kloczkowski, Andrzej

A2 - Li, Yaohang

PB - Institute of Electrical and Electronics Engineers Inc.

T2 - 2021 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021

Y2 - 9 December 2021 through 12 December 2021

ER -

Lyman CA, Morris MM, Richman S, Cao H, Scerri A , Cheadle C et al. High Fidelity Modeling of Pulse Dynamics using Logic Networks. In Huang Y, Kurgan L, Luo F, Hu XT, Chen Y, Dougherty E, Kloczkowski A, Li Y, editors, Proceedings - 2021 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021. Institute of Electrical and Electronics Engineers Inc. 2021. p. 197-204. (Proceedings - 2021 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021). doi: 10.1109/BIBM52615.2021.9669437

High Fidelity Modeling of Pulse Dynamics using Logic Networks

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