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Bridging the Gap between Mechanistic Biological Models and Machine Learning Surrogates

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Submitted:

28 September 2022

Posted:

29 September 2022

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Abstract
Mechanistic models have been used for centuries to describe complex interconnected processes, including biological ones. As the scope of these models has widened, so have their computational demands. This complexity can limit their suitability when running many simulations or when real-time results are required. Surrogate machine learning models can be used to approximate the behaviour of complex mechanistic models, and once built, their computational demands are several orders of magnitude lower. This paper provides an overview of the relevant literature, both from an applicability and a theoretical perspective. For the latter, the paper focuses on the design and training of the underlying machine learning models. Application-wise, we show how machine learning surrogates have been used to approximate different mechanistic models. We present a perspective on how these approaches can be applied to models representing biological processes with potential industrial applications (e.g., metabolism and whole-cell modelling) and show why surrogate machine learning models may hold the key to making the simulation of complex biological models possible using a typical desktop computer.
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Subject: Computer Science and Mathematics  -   Artificial Intelligence and Machine Learning
Copyright: This open access article is published under a Creative Commons CC BY 4.0 license, which permit the free download, distribution, and reuse, provided that the author and preprint are cited in any reuse.
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