Deep in the Bowel: Highly Interpretable Neural Encoder-Decoder Networks Predict Gut Metabolites from Gut Microbiome.

BMC Genomics
Vuong LeSvetha Venkatesh

Abstract

Technological advances in next-generation sequencing (NGS) and chromatographic assays [e.g., liquid chromatography mass spectrometry (LC-MS)] have made it possible to identify thousands of microbe and metabolite species, and to measure their relative abundance. In this paper, we propose a sparse neural encoder-decoder network to predict metabolite abundances from microbe abundances. Using paired data from a cohort of inflammatory bowel disease (IBD) patients, we show that our neural encoder-decoder model outperforms linear univariate and multivariate methods in terms of accuracy, sparsity, and stability. Importantly, we show that our neural encoder-decoder model is not simply a black box designed to maximize predictive accuracy. Rather, the network's hidden layer (i.e., the latent space, comprised only of sparsely weighted microbe counts) actually captures key microbe-metabolite relationships that are themselves clinically meaningful. Although this hidden layer is learned without any knowledge of the patient's diagnosis, we show that the learned latent features are structured in a way that predicts IBD and treatment status with high accuracy. By imposing a non-negative weights constraint, the network becomes a directed graph wh...Continue Reading

References

Nov 22, 2005·Journal of Lipid Research·Jason M RidlonPhillip B Hylemon
Feb 3, 2007·Journal of Proteome Research·Julian R MarchesiYulan Wang
Jul 27, 2007·Nature·R J Xavier, D K Podolsky
Aug 22, 2012·Nature Reviews. Gastroenterology & Hepatology·Chaysavanh ManichanhFrancisco Guarner
Sep 28, 2012·Genome Biology·Xochitl C MorganCurtis Huttenhower
Feb 21, 2014·F1000Research·Scott A Chamberlain, Eduard Szöcs
Feb 25, 2014·Gastroenterology·Aleksandar D KosticDirk Gevers
Dec 23, 2014·IEEE Transactions on Neural Networks and Learning Systems·Jan Chorowski, Jacek M Zurada
Jan 18, 2015·Current Treatment Options in Gastroenterology·Jonathan J Hansen, R Balfour Sartor
Aug 11, 2015·Nature Genetics·Eric R GamazonHae Kyung Im
Sep 18, 2015·GigaScience·Peter E Larsen, Yang Dai
Feb 14, 2016·Bioinformatics·Yifei ChenXiaohui Xie
Mar 13, 2016·Briefings in Bioinformatics·Chen MengAedín C Culhane
Feb 14, 2017·Nature Microbiology·Jonas HalfvarsonJanet K Jansson
Dec 7, 2017·Nature Communications·Claire DuvalletEric J Alm
Oct 27, 2016·F1000Research·Thomas QuinnStephen Glatt
Apr 3, 2018·Bioinformatics·Thomas P QuinnTamsyn M Crowley
Apr 6, 2018·Journal of the Royal Society, Interface·Travers ChingCasey S Greene
May 29, 2018·Analytica Chimica Acta·Agnieszka SmolinskaFrederik-Jan van Schooten
Dec 12, 2018·Nature Microbiology·Eric A FranzosaRamnik J Xavier
Dec 18, 2018·Analytical Biochemistry·Yijun YouTianlu Chen
Feb 6, 2019·Therapeutic Advances in Gastroenterology·Jonathan P SegalJulian R Marchesi
Mar 1, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Kathrin Laura Kohnen-Johannsen, Oliver Kayser
May 31, 2019·Nature·Jason Lloyd-PriceCurtis Huttenhower

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Citations

Dec 9, 2020·Bioinformatics·Beatriz García-JiménezMark D Wilkinson
Jan 6, 2021·Nature Methods·Thomas P Quinn, Ionas Erb
May 18, 2021·PLoS Computational Biology·Derek ReimanYang Dai
Oct 30, 2020·Bioinformatics·Thin NguyenSvetha Venkatesh

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Software Mentioned

LASSO
net
randomForest R package
Sparsity
Integrated Taxonomic Information System ( ITIS )
cmultRepl
zCompositions
vegan R package
R package taxize
exprso R package

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