Application of Deep Learning in Microbiome

Authors

Qiang Zhu^{1, 4}, Ban Huo^{2, 4}, Han Sun^{3, 4}, Bojing Li^{2, 4}, Xingpeng Jiang^{2, 4, *,}

¹School of Mathematics and Computer Science, Wuhan Textile University, Wuhan, Hubei, China

²Hubei Provincial Key Laboratory of Artificial Intelligence and Smart Learning, Central China Normal University, Wuhan, Hubei, China

³School of Mathematics and Statistics, Central China Normal University, Wuhan, Hubei, China

⁴School of Computer, Central China Normal University, Wuhan, Hubei, China

^*Corresponding author. Email: xpjiang@mail.ccnu.edu.cn

DOI

10.2991/jaims.d.201028.001How to use a DOI?

Keywords

Microbiome; Deep learning; Phylogeny

Abstract

With the rapid development of high-throughput sequencing technology, massive microbial data has been accumulated. The understanding of the microbial data could help us to find the relationships between microbes and diseases. However, due to the high dimensionality, sparseness, and complexity of the data, traditional machine learning methods have insufficient learning and representational ability. Meanwhile, the rise of deep learning enables us to deal with these complex problems effectively. In this survey, we introduce the application of machine learning in microbial data analysis and focus on microbial classification and feature selection tasks. In particular, we discuss the current application and challenges of deep learning in microbial studies. Based on these discussions, we recommend that before using deep learning to conduct microbiome-wide association studies, it is essential to consider prior knowledge such as phylogeny, which would improve the accuracy and interpretability of the model.

Copyright

© 2020 The Authors. Published by Atlantis Press B.V.

Open Access

This is an open access article distributed under the CC BY-NC 4.0 license (http://creativecommons.org/licenses/by-nc/4.0/).

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TY  - JOUR
AU  - Qiang Zhu
AU  - Ban Huo
AU  - Han Sun
AU  - Bojing Li
AU  - Xingpeng Jiang
PY  - 2020
DA  - 2020/11/04
TI  - Application of Deep Learning in Microbiome
JO  - Journal of Artificial Intelligence for Medical Sciences
SP  - 23
EP  - 29
VL  - 1
IS  - 1-2
SN  - 2666-1470
UR  - https://doi.org/10.2991/jaims.d.201028.001
DO  - 10.2991/jaims.d.201028.001
ID  - Zhu2020
ER  -