Inference of threshold network models of the tryptophan operon in Escherichia coli

Gonzalo A. Ruz

doi:10.1109/CIBCB56990.2023.10264894

Inference of threshold network models of the tryptophan operon in Escherichia coli

Gonzalo A. Ruz

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

2 Scopus citations

Abstract

A recent Boolean model of the tryptophan operon in Escherichia coli has been introduced, which exhibits a desired set of fixed points modeling the operon state being on or off. Nevertheless, when updated synchronously, the model also reveals spurious limit cycles with a larger basin of attraction than the desired fixed points. This paper presents the search via evolutionary computation for threshold network models that exhibit the desired fixed points without any limit cycles. The proposed framework was applied using differential evolution and particle swarm optimization, the latter being the most efficient and effective method based on the results obtained by the simulations. Particle swarm optimization found two correct threshold networks, one of which has only weight values -1,0,1, making the model more interpretable.

Original language	English
Title of host publication	CIBCB 2023 - 20th IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology
Publisher	Institute of Electrical and Electronics Engineers Inc.
ISBN (Electronic)	9798350310177
DOIs	https://doi.org/10.1109/CIBCB56990.2023.10264894
State	Published - 2023
Externally published	Yes
Event	20th IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2023 - Eindhoven, Netherlands Duration: 29 Aug 2023 → 31 Aug 2023

Publication series

Name	CIBCB 2023 - 20th IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology

Conference

Conference	20th IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2023
Country/Territory	Netherlands
City	Eindhoven
Period	29/08/23 → 31/08/23

Keywords

Boolean network
Differential evolution
Evolutionary Computation
Particle swarm optimization
Threshold network
Tryptophan operon

Access to Document

10.1109/CIBCB56990.2023.10264894

Cite this

Ruz, G. A. (2023). Inference of threshold network models of the tryptophan operon in Escherichia coli. In CIBCB 2023 - 20th IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2023 - 20th IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/CIBCB56990.2023.10264894

Ruz, Gonzalo A. / Inference of threshold network models of the tryptophan operon in Escherichia coli. CIBCB 2023 - 20th IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology. Institute of Electrical and Electronics Engineers Inc., 2023. (CIBCB 2023 - 20th IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology).

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title = "Inference of threshold network models of the tryptophan operon in Escherichia coli",

abstract = "A recent Boolean model of the tryptophan operon in Escherichia coli has been introduced, which exhibits a desired set of fixed points modeling the operon state being on or off. Nevertheless, when updated synchronously, the model also reveals spurious limit cycles with a larger basin of attraction than the desired fixed points. This paper presents the search via evolutionary computation for threshold network models that exhibit the desired fixed points without any limit cycles. The proposed framework was applied using differential evolution and particle swarm optimization, the latter being the most efficient and effective method based on the results obtained by the simulations. Particle swarm optimization found two correct threshold networks, one of which has only weight values -1,0,1, making the model more interpretable.",

keywords = "Boolean network, Differential evolution, Evolutionary Computation, Particle swarm optimization, Threshold network, Tryptophan operon",

author = "Ruz, {Gonzalo A.}",

note = "Publisher Copyright: {\textcopyright} 2023 IEEE.; 20th IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2023 ; Conference date: 29-08-2023 Through 31-08-2023",

year = "2023",

doi = "10.1109/CIBCB56990.2023.10264894",

language = "English",

series = "CIBCB 2023 - 20th IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology",

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

booktitle = "CIBCB 2023 - 20th IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology",

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Ruz, GA 2023, Inference of threshold network models of the tryptophan operon in Escherichia coli. in CIBCB 2023 - 20th IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology. CIBCB 2023 - 20th IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, Institute of Electrical and Electronics Engineers Inc., 20th IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2023, Eindhoven, Netherlands, 29/08/23. https://doi.org/10.1109/CIBCB56990.2023.10264894

Inference of threshold network models of the tryptophan operon in Escherichia coli. / Ruz, Gonzalo A.
CIBCB 2023 - 20th IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology. Institute of Electrical and Electronics Engineers Inc., 2023. (CIBCB 2023 - 20th IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology).

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

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Ruz GA. Inference of threshold network models of the tryptophan operon in Escherichia coli. In CIBCB 2023 - 20th IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology. Institute of Electrical and Electronics Engineers Inc. 2023. (CIBCB 2023 - 20th IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology). doi: 10.1109/CIBCB56990.2023.10264894

Inference of threshold network models of the tryptophan operon in Escherichia coli

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Keywords

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