A Framework for Effective Application of Machine Learning to Microbiome-Based Classification Problems.
16S rRNA gene
colon cancer
machine learning
microbial ecology
microbiome
Journal
mBio
ISSN: 2150-7511
Titre abrégé: mBio
Pays: United States
ID NLM: 101519231
Informations de publication
Date de publication:
09 06 2020
09 06 2020
Historique:
entrez:
11
6
2020
pubmed:
11
6
2020
medline:
10
4
2021
Statut:
epublish
Résumé
Machine learning (ML) modeling of the human microbiome has the potential to identify microbial biomarkers and aid in the diagnosis of many diseases such as inflammatory bowel disease, diabetes, and colorectal cancer. Progress has been made toward developing ML models that predict health outcomes using bacterial abundances, but inconsistent adoption of training and evaluation methods call the validity of these models into question. Furthermore, there appears to be a preference by many researchers to favor increased model complexity over interpretability. To overcome these challenges, we trained seven models that used fecal 16S rRNA sequence data to predict the presence of colonic screen relevant neoplasias (SRNs) (
Identifiants
pubmed: 32518182
pii: mBio.00434-20
doi: 10.1128/mBio.00434-20
pmc: PMC7373189
pii:
doi:
Substances chimiques
RNA, Ribosomal, 16S
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : NCI NIH HHS
ID : R01 CA215574
Pays : United States
Organisme : NIDDK NIH HHS
ID : P30 DK034933
Pays : United States
Informations de copyright
Copyright © 2020 Topçuoğlu et al.
Références
Conf Proc IEEE Eng Med Biol Soc. 2017 Jul;2017:4269-4272
pubmed: 29060840
Microbiome. 2018 Apr 11;6(1):70
pubmed: 29642940
Appl Environ Microbiol. 2009 Dec;75(23):7537-41
pubmed: 19801464
mBio. 2019 Jul 2;10(4):
pubmed: 31266879
Microbiome. 2016 Nov 14;4(1):59
pubmed: 27842559
Genome Med. 2016 Apr 06;8(1):37
pubmed: 27056827
Cancer Prev Res (Phila). 2014 Nov;7(11):1112-21
pubmed: 25104642
Gigascience. 2019 May 1;8(5):
pubmed: 31042284
Cancer Epidemiol Biomarkers Prev. 2017 Jan;26(1):85-94
pubmed: 27672054
PeerJ. 2016 Oct 18;4:e2584
pubmed: 27781170
Genome Biol. 2011 Jun 24;12(6):R60
pubmed: 21702898
mSphere. 2017 Mar 8;2(2):
pubmed: 28289728
Cell Host Microbe. 2011 Oct 20;10(4):292-6
pubmed: 22018228
Sci Rep. 2017 May 25;7(1):2427
pubmed: 28546534
Oncotarget. 2017 Feb 7;8(6):9546-9556
pubmed: 28061434
Genes (Basel). 2018 Oct 02;9(10):
pubmed: 30279327
BMJ Open Gastroenterol. 2019 May 27;6(1):e000297
pubmed: 31275588
FEBS Lett. 2014 Nov 17;588(22):4223-33
pubmed: 25307765
Nat Med. 2019 Apr;25(4):679-689
pubmed: 30936547
Nat Med. 2019 Apr;25(4):667-678
pubmed: 30936548
FEMS Microbiol Rev. 2011 Mar;35(2):343-59
pubmed: 21039646
Gut. 2017 Aug;66(8):1441-1448
pubmed: 27797940
Nature. 2014 Sep 4;513(7516):59-64
pubmed: 25079328
Gut. 2018 Sep;67(9):1743-1745
pubmed: 29055911
Nature. 2016 Dec 22;540(7634):544-551
pubmed: 27906159
mBio. 2016 Aug 23;7(4):
pubmed: 27555308
PLoS Comput Biol. 2016 Jul 11;12(7):e1004977
pubmed: 27400279
Mayo Clin Proc. 2016 Jan;91(1):61-70
pubmed: 26520415
Microbiome. 2013 Apr 05;1(1):11
pubmed: 24456583
BMC Bioinformatics. 2007 Jan 25;8:25
pubmed: 17254353
Gut. 2018 Aug;67(8):1454-1463
pubmed: 28988196
Mol Syst Biol. 2014 Nov 28;10:766
pubmed: 25432777
Nat Med. 2019 Sep;25(9):1337-1340
pubmed: 31427808
Bioinformatics. 2010 May 15;26(10):1340-7
pubmed: 20385727
mBio. 2018 Jun 5;9(3):
pubmed: 29871916
Genome Med. 2016 Apr 28;8(1):49
pubmed: 27121964