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Metabolites 2018, 8(1), 4; https://doi.org/10.3390/metabo8010004

Machine Learning Methods for Analysis of Metabolic Data and Metabolic Pathway Modeling

Digital Technologies Research Center, National Research Council of Canada, 1200 Montreal Road, Ottawa, ON K1A 0R6, Canada
Received: 13 December 2017 / Revised: 8 January 2018 / Accepted: 9 January 2018 / Published: 11 January 2018
(This article belongs to the Special Issue Metabolomics Modelling)
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Abstract

Machine learning uses experimental data to optimize clustering or classification of samples or features, or to develop, augment or verify models that can be used to predict behavior or properties of systems. It is expected that machine learning will help provide actionable knowledge from a variety of big data including metabolomics data, as well as results of metabolism models. A variety of machine learning methods has been applied in bioinformatics and metabolism analyses including self-organizing maps, support vector machines, the kernel machine, Bayesian networks or fuzzy logic. To a lesser extent, machine learning has also been utilized to take advantage of the increasing availability of genomics and metabolomics data for the optimization of metabolic network models and their analysis. In this context, machine learning has aided the development of metabolic networks, the calculation of parameters for stoichiometric and kinetic models, as well as the analysis of major features in the model for the optimal application of bioreactors. Examples of this very interesting, albeit highly complex, application of machine learning for metabolism modeling will be the primary focus of this review presenting several different types of applications for model optimization, parameter determination or system analysis using models, as well as the utilization of several different types of machine learning technologies. View Full-Text
Keywords: system biology; metabolomics; metabolism modeling; machine learning; genomics system biology; metabolomics; metabolism modeling; machine learning; genomics
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Cuperlovic-Culf, M. Machine Learning Methods for Analysis of Metabolic Data and Metabolic Pathway Modeling. Metabolites 2018, 8, 4.

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