Computational capabilities of a multicellular reservoir computing system.
The capacity of cells to process information is currently used to design cell-based tools for ecological, industrial, and biomedical applications such as detecting dangerous chemicals or for bioremediation. In most applications, individual cells are used as the information processing unit. However,...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2023-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0282122 |
| _version_ | 1797837905467539456 |
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| author | Vladimir Nikolić Moriah Echlin Boris Aguilar Ilya Shmulevich |
| author_facet | Vladimir Nikolić Moriah Echlin Boris Aguilar Ilya Shmulevich |
| author_sort | Vladimir Nikolić |
| collection | DOAJ |
| description | The capacity of cells to process information is currently used to design cell-based tools for ecological, industrial, and biomedical applications such as detecting dangerous chemicals or for bioremediation. In most applications, individual cells are used as the information processing unit. However, single cell engineering is limited by the necessary molecular complexity and the accompanying metabolic burden of synthetic circuits. To overcome these limitations, synthetic biologists have begun engineering multicellular systems that combine cells with designed subfunctions. To further advance information processing in synthetic multicellular systems, we introduce the application of reservoir computing. Reservoir computers (RCs) approximate a temporal signal processing task via a fixed-rule dynamic network (the reservoir) with a regression-based readout. Importantly, RCs eliminate the need of network rewiring, as different tasks can be approximated with the same reservoir. Previous work has already demonstrated the capacity of single cells, as well as populations of neurons, to act as reservoirs. In this work, we extend reservoir computing in multicellular populations with the widespread mechanism of diffusion-based cell-to-cell signaling. As a proof-of-concept, we simulated a reservoir made of a 3D community of cells communicating via diffusible molecules and used it to approximate a range of binary signal processing tasks, focusing on two benchmark functions-computing median and parity functions from binary input signals. We demonstrate that a diffusion-based multicellular reservoir is a feasible synthetic framework for performing complex temporal computing tasks that provides a computational advantage over single cell reservoirs. We also identified a number of biological properties that can affect the computational performance of these processing systems. |
| first_indexed | 2024-04-09T15:32:13Z |
| format | Article |
| id | doaj.art-5b9c6966ed1740d0a8c1d02f46a20cc9 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-09T15:32:13Z |
| publishDate | 2023-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-5b9c6966ed1740d0a8c1d02f46a20cc92023-04-28T05:31:49ZengPublic Library of Science (PLoS)PLoS ONE1932-62032023-01-01184e028212210.1371/journal.pone.0282122Computational capabilities of a multicellular reservoir computing system.Vladimir NikolićMoriah EchlinBoris AguilarIlya ShmulevichThe capacity of cells to process information is currently used to design cell-based tools for ecological, industrial, and biomedical applications such as detecting dangerous chemicals or for bioremediation. In most applications, individual cells are used as the information processing unit. However, single cell engineering is limited by the necessary molecular complexity and the accompanying metabolic burden of synthetic circuits. To overcome these limitations, synthetic biologists have begun engineering multicellular systems that combine cells with designed subfunctions. To further advance information processing in synthetic multicellular systems, we introduce the application of reservoir computing. Reservoir computers (RCs) approximate a temporal signal processing task via a fixed-rule dynamic network (the reservoir) with a regression-based readout. Importantly, RCs eliminate the need of network rewiring, as different tasks can be approximated with the same reservoir. Previous work has already demonstrated the capacity of single cells, as well as populations of neurons, to act as reservoirs. In this work, we extend reservoir computing in multicellular populations with the widespread mechanism of diffusion-based cell-to-cell signaling. As a proof-of-concept, we simulated a reservoir made of a 3D community of cells communicating via diffusible molecules and used it to approximate a range of binary signal processing tasks, focusing on two benchmark functions-computing median and parity functions from binary input signals. We demonstrate that a diffusion-based multicellular reservoir is a feasible synthetic framework for performing complex temporal computing tasks that provides a computational advantage over single cell reservoirs. We also identified a number of biological properties that can affect the computational performance of these processing systems.https://doi.org/10.1371/journal.pone.0282122 |
| spellingShingle | Vladimir Nikolić Moriah Echlin Boris Aguilar Ilya Shmulevich Computational capabilities of a multicellular reservoir computing system. PLoS ONE |
| title | Computational capabilities of a multicellular reservoir computing system. |
| title_full | Computational capabilities of a multicellular reservoir computing system. |
| title_fullStr | Computational capabilities of a multicellular reservoir computing system. |
| title_full_unstemmed | Computational capabilities of a multicellular reservoir computing system. |
| title_short | Computational capabilities of a multicellular reservoir computing system. |
| title_sort | computational capabilities of a multicellular reservoir computing system |
| url | https://doi.org/10.1371/journal.pone.0282122 |
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