Multi-Layer and Recursive Neural Networks for Metagenomic Classification

IEEE Transactions on Nanobioscience
Gregory DitzlerGail Rosen

Abstract

Recent advances in machine learning, specifically in deep learning with neural networks, has made a profound impact on fields such as natural language processing, image classification, and language modeling; however, feasibility and potential benefits of the approaches to metagenomic data analysis has been largely under-explored. Deep learning exploits many layers of learning nonlinear feature representations, typically in an unsupervised fashion, and recent results have shown outstanding generalization performance on previously unseen data. Furthermore, some deep learning methods can also represent the structure in a data set. Consequently, deep learning and neural networks may prove to be an appropriate approach for metagenomic data. To determine whether such approaches are indeed appropriate for metagenomics, we experiment with two deep learning methods: i) a deep belief network, and ii) a recursive neural network, the latter of which provides a tree representing the structure of the data. We compare these approaches to the standard multi-layer perceptron, which has been well-established in the machine learning community as a powerful prediction algorithm, though its presence is largely missing in metagenomics literature. We...Continue Reading

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Citations

Mar 24, 2016·Molecular Pharmaceutics·Polina MamoshinaAlex Zhavoronkov
Dec 19, 2017·BioMed Research International·Shao-Wu ZhangTeng Zhang
Mar 15, 2018·BMC Bioinformatics·Diego FioravantiCesare Furlanello
Jul 10, 2019·European Journal of Nuclear Medicine and Molecular Imaging·Marius E MayerhoeferHeiko Schöder
Jul 12, 2019·Frontiers in Genetics·Yi-Hui Zhou, Paul Gallins
Apr 6, 2018·Journal of the Royal Society, Interface·Travers ChingCasey S Greene
May 5, 2020·Briefings in Bioinformatics·Shuting JinXiangrong Liu
Apr 12, 2019·Frontiers in Genetics·Binhua TangAsif Khateeb
Jun 30, 2018·Journal of Medical Systems·Kun LanNilanjan Dey
Jan 26, 2020·Artificial Intelligence in Medicine·Ivan LorencinZlatan Car
Apr 22, 2021·Journal of Gastroenterology and Hepatology·Yufeng LinJoseph J Y Sung
Jun 22, 2021·Briefings in Bioinformatics·Xingjian ChenKa-Chun Wong
Aug 3, 2021·Frontiers in Big Data·Hamid Reza Hassanzadeh, May D Wang
Sep 23, 2021·PLoS Computational Biology·Zhengqiao ZhaoGail L Rosen
Nov 16, 2021·Emerging Topics in Life Sciences·Kristen D CurryTodd J Treangen

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