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bioRxiv · 10.1101/2020.02.06.937979

A framework for implementing metaheuristic algorithms using intercellular communication

Gutierrez, M. E.·Ortiz, Y. M.·Carrion, J.
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Abstract

Metaheuristic procedures (MH) have been a trend driving Artificial Intelligence (AI) researchers for the past 50 years. A variety of tools and applications (not only in Computer Science) stem from these techniques. Also, MH frequently rely on evolution, a trademark process involved in cell colony growth. Generally, MH are used to approximate the solution to difficult problems but require a large amount of computational resources. Cell colonies harboring synthetic distributed circuits using intercell communication offer a direction for tackling this problem, as they process information in a massively parallel fashion. In this work, we propose a framework that maps MH elements to synthetic circuits in growing cell colonies. The framework relies on cell-cell communication mechanisms such as quorum sensing (QS) and bacterial conjugation. As a proof-of-concept, we also implemented the workflow associated to the framework, and tested the execution of two specific MH (Genetic Algorithms and Simulated Annealing) encoded as synthetic circuits on the gro simulator. Furthermore, we show an example of how our framework can be extended by implementing another kind of computational model: The Cellular Automaton. This work seeks to lay the foundations of mappings for implementing AI algorithms in a general manner using Synthetic Biology constructs in cell colonies.

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Gutierrez, M. E., Ortiz, Y. M., Carrion, J.. 2020-02-07. A framework for implementing metaheuristic algorithms using intercellular communication. https://doi.org/10.1101/2020.02.06.937979

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