Interpretable and accurate prediction models for metagenomics data.

GigaScience
Edi PriftiJean-Daniel Zucker

Abstract

Microbiome biomarker discovery for patient diagnosis, prognosis, and risk evaluation is attracting broad interest. Selected groups of microbial features provide signatures that characterize host disease states such as cancer or cardio-metabolic diseases. Yet, the current predictive models stemming from machine learning still behave as black boxes and seldom generalize well. Their interpretation is challenging for physicians and biologists, which makes them difficult to trust and use routinely in the physician-patient decision-making process. Novel methods that provide interpretability and biological insight are needed. Here, we introduce "predomics", an original machine learning approach inspired by microbial ecosystem interactions that is tailored for metagenomics data. It discovers accurate predictive signatures and provides unprecedented interpretability. The decision provided by the predictive model is based on a simple, yet powerful score computed by adding, subtracting, or dividing cumulative abundance of microbiome measurements. Tested on >100 datasets, we demonstrate that predomics models are simple and highly interpretable. Even with such simplicity, they are at least as accurate as state-of-the-art methods. The family...Continue Reading

References

May 4, 2004·Hepatology : Official Journal of the American Association for the Study of Liver Diseases·Qing LiuStephen M Riordan
Jul 22, 2005·Proceedings of the National Academy of Sciences of the United States of America·Ruth E LeyJeffrey I Gordon
May 17, 2006·Anaerobe·Kim HolmstrømPaul A Lawson
Jul 13, 2007·International Journal of Systematic and Evolutionary Microbiology·Céline RobertAnnick Bernalier-Donadille
Dec 17, 2009·The Biochemical Journal·Andrew D HansonValérie de Crécy-Lagard
May 1, 2010·Microbiology·Maria S Poptsova, J Peter Gogarten
Dec 14, 2011·Nature Communications·Shiri FreilichEytan Ruppin
Mar 1, 2012·Nutrition in Clinical Practice : Official Publication of the American Society for Parenteral and Enteral Nutrition·Rosa Krajmalnik-BrownJohn K DiBaise
May 11, 2012·Gut Microbes·Charles O Elson, Yingzi Cong
Jul 17, 2012·Nature Reviews. Microbiology·Karoline Faust, Jeroen Raes
Aug 30, 2013·Nature·Emmanuelle Le ChatelierOluf Pedersen
Aug 30, 2013·Nature·Aurélie CotillardStanislav Dusko Ehrlich
Jan 1, 2014·Journal of Hepatology·Jasmohan S BajajPatrick M Gillevet
Apr 1, 2014·FEBS Letters·Calum J WalshPaul D Cotter
Jul 7, 2014·Nature Biotechnology·Junhua LiUNKNOWN MetaHIT Consortium
Nov 14, 2014·Current Opinion in Gastroenterology·Andrew B ShreinerVincent B Young
Nov 30, 2014·Molecular Systems Biology·Georg ZellerPeer Bork
Jun 23, 2015·The Journal of Clinical Investigation·Ting-Chin David ShenGary D Wu
Aug 21, 2015·Hepatology : Official Journal of the American Association for the Study of Liver Diseases·Benjamin Y Winer, Alexander Ploss
Jun 10, 2016·Biomarkers in Cancer·Harry B Burke
Sep 30, 2016·The New England Journal of Medicine·Ziad Obermeyer, Ezekiel J Emanuel
Jan 21, 2017·BMC Bioinformatics·Séverine AffeldtJean-Daniel Zucker
Feb 2, 2017·MSystems·James T MortonRob Knight
Feb 10, 2017·Cell Host & Microbe·Elizabeth R HughesSebastian E Winter
May 27, 2017·Journal of the American College of Cardiology·Chayakrit KrittanawongTakeshi Kitai
Nov 1, 2017·Nature Methods·Edoardo PasolliLevi Waldron
Feb 24, 2018·The British Journal of General Practice : the Journal of the Royal College of General Practitioners·Varun H BuchMahiben Maruthappu
May 15, 2018·Developmental Medicine and Child Neurology·Robert J Reynolds, Steven M Day
Jun 15, 2018·Gut·Judith Aron-WisnewskyKarine Clément
Jul 24, 2018·MSystems·J Rivera-PintoM L Calle
Apr 6, 2019·Journal of Advanced Nursing·Roger Watson
Jul 12, 2019·Frontiers in Genetics·Yi-Hui Zhou, Paul Gallins
Mar 10, 2020·GigaScience·Edi PriftiJean-Daniel Zucker

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Citations

Mar 10, 2020·GigaScience·Edi PriftiJean-Daniel Zucker
Jul 11, 2020·Nature Reviews. Gastroenterology & Hepatology·Giovanni CammarotaGiampaolo Tortora
Dec 18, 2020·Journal of Pharmaceutical and Biomedical Analysis·Carolin A Kolmeder, Willem M de Vos
Feb 27, 2021·Scientific Reports·Anna Paola CarrieriEdward O Pyzer-Knapp
Apr 22, 2021·Journal of Gastroenterology and Hepatology·Henley Cheung, Jun Yu
Apr 22, 2021·Journal of Gastroenterology and Hepatology·Tao ZengZhangran Chen
Sep 10, 2021·Bioinformatics·Elliott Gordon-RodriguezJohn P Cunningham

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Methods Mentioned

BETA
chips
MDA

Key Resources (RRID) Mentioned

SCR_017415

Software Mentioned

ScaleNet
Predomics
ENET
ExperimentHub
reshape2
randomForest
doRNG
kernlab
gridExtra
plyr

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