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A Framework for Implementing Metaheuristic Algorithms Using Intercellular Communication
Indexado
WoS WOS:000653076200001
Scopus SCOPUS_ID:85107074861
DOI 10.3389/FBIOE.2021.660148
Año 2021
Tipo artículo de investigación

Citas Totales

Autores Afiliación Chile

Instituciones Chile

% Participación
Internacional

Autores
Afiliación Extranjera

Instituciones
Extranjeras


Abstract



Metaheuristics (MH) are Artificial Intelligence procedures that frequently rely on evolution. MH approximate difficult problem solutions, but are computationally costly as they explore large solution spaces. This work pursues to lay the foundations of general mappings for implementing MH using Synthetic Biology constructs in cell colonies. Two advantages of this approach are: harnessing large scale parallelism capability of cell colonies and, using existing cell processes to implement basic dynamics defined in computational versions. We propose a framework that maps MH elements to synthetic circuits in growing cell colonies to replicate MH behavior in cell colonies. Cell-cell communication mechanisms such as quorum sensing (QS), bacterial conjugation, and environmental signals map to evolution operators in MH techniques to adapt to growing colonies. As a proof-of-concept, we implemented the workflow associated to the framework: automated MH simulation generators for the gro simulator and two classes of algorithms (Simple Genetic Algorithms and Simulated Annealing) encoded as synthetic circuits. Implementation tests show that synthetic counterparts mimicking MH are automatically produced, but also that cell colony parallelism speeds up the execution in terms of generations. Furthermore, we show an example of how our framework is extended by implementing a different computational model: The Cellular Automaton.

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Disciplinas de Investigación



WOS
Biotechnology & Applied Microbiology
Multidisciplinary Sciences
Engineering, Biomedical
Scopus
Sin Disciplinas
SciELO
Sin Disciplinas

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Publicaciones WoS (Ediciones: ISSHP, ISTP, AHCI, SSCI, SCI), Scopus, SciELO Chile.

Colaboración Institucional



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Autores - Afiliación



Ord. Autor Género Institución - País
1 Ortiz, Yerko - Universidad Diego Portales - Chile
2 Carrion, Javier Hombre Universidad Diego Portales - Chile
3 Lahoz-Beltra, Rafael Hombre UNIV COMPLUTENSE MADRID - España
Universidad Complutense de Madrid - España
4 GUTIERREZ-PESCARMONA, MARTIN EDUARDO Hombre Universidad Diego Portales - Chile

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Financiamiento



Fuente
Luciano Ahumada
Marco Clavero

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Agradecimientos



Agradecimiento
The authors thank Nicolás Hidalgo for his support and help in making this paper possible. The authors also thank Luciano Ahumada, Marco Clavero, Sebastián Antón and Pablo Ramos for their comments and valuable discussions, Guillermo Iglesias for helping in automating and running the SA gro simulations, José Undurraga for the new gro version (gro 63) and Luis Muñoz for collaborating, Aaron Adler and Fusun Yaman for their valuable insight in the initial stages of this work at the AI for Synthetic Biology Workshop, 2018. The authors are also grateful for all feedback received at IWBDA 2019 for developing this work. This work is dedicated to the memory of Mr. Gastón Luis Ortiz Soto.

Muestra la fuente de financiamiento declarada en la publicación.