Dataset Information

Systems biology approaches integrated with artificial intelligence for optimized food-focused metabolic engineering.

ABSTRACT: Metabolic engineering aims to maximize the production of bio-economically important substances (compounds, enzymes, or other proteins) through the optimization of the genetics, cellular processes and growth conditions of microorganisms. This requires detailed understanding of underlying metabolic pathways involved in the production of the targeted substances, and how the cellular processes or growth conditions are regulated by the engineering. To achieve this goal, a large system of experimental techniques, compound libraries, computational methods and data resources, including the multi-omics data, are used. The recent advent of multi-omics systems biology approaches significantly impacted the field by opening new avenues to perform dynamic and large-scale analyses that deepen our knowledge on the manipulations. However, with the enormous transcriptomics, proteomics and metabolomics available, it is a daunting task to integrate the data for a more holistic understanding. Novel data mining and analytics approaches, including Artificial Intelligence (AI), can provide breakthroughs where traditional low-throughput experiment-alone methods cannot easily achieve. Here, we review the latest attempts of combining systems biology and AI in metabolic engineering research, and highlight how this alliance can help overcome the current challenges facing industrial biotechnology, especially for food-related substances and compounds using microorganisms.

SUBMITTER: Helmy M

PROVIDER: S-EPMC7546651 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

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Systems biology approaches integrated with artificial intelligence for optimized metabolic engineering.

Helmy Mohamed M Smith Derek D Selvarajoo Kumar K

Metabolic engineering communications 20201009

Metabolic engineering aims to maximize the production of bio-economically important substances (compounds, enzymes, or other proteins) through the optimization of the genetics, cellular processes and growth conditions of microorganisms. This requires detailed understanding of underlying metabolic pathways involved in the production of the targeted substances, and how the cellular processes or growth conditions are regulated by the engineering. To achieve this goal, a large system of experimental ...[more]

PMID: 33072513

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Project description:Artificial intelligence and machine learning techniques have proved fertile methods for attacking difficult problems in medicine and public health. These techniques have garnered strong interest for the analysis of the large, multi-domain open science datasets that are increasingly available in health research. Discovery science in large datasets is challenging given the unconstrained nature of the learning environment where there may be a large number of potential predictors and appropriate ranges for model hyperparameters are unknown. As well, it is likely that explainability is at a premium in order to engage in future hypothesis generation or analysis. Here, we present a novel method that addresses these challenges by exploiting evolutionary algorithms to optimize machine learning discovery science while exploring a large solution space and minimizing bias. We demonstrate that our approach, called integrated evolutionary learning (IEL), provides an automated, adaptive method for jointly learning features and hyperparameters while furnishing explainable models where the original features used to make predictions may be obtained even with artificial neural networks. In IEL the machine learning algorithm of choice is nested inside an evolutionary algorithm which selects features and hyperparameters over generations on the basis of an information function to converge on an optimal solution. We apply IEL to three gold standard machine learning algorithms in challenging, heterogenous biobehavioral data: deep learning with artificial neural networks, decision tree-based techniques and baseline linear models. Using our novel IEL approach, artificial neural networks achieved ≥ 95% accuracy, sensitivity and specificity and 45-73% R 2 in classification and substantial gains over default settings. IEL may be applied to a wide range of less- or unconstrained discovery science problems where the practitioner wishes to jointly learn features and hyperparameters in an adaptive, principled manner within the same algorithmic process. This approach offers significant flexibility, enlarges the solution space and mitigates bias that may arise from manual or semi-manual hyperparameter tuning and feature selection and presents the opportunity to select the inner machine learning algorithm based on the results of optimized learning for the problem at hand.

Dataset Information

Systems biology approaches integrated with artificial intelligence for optimized food-focused metabolic engineering.

Publications

Systems biology approaches integrated with artificial intelligence for optimized metabolic engineering.

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