Challenges in translational machine learning.
Journal
Human genetics
ISSN: 1432-1203
Titre abrégé: Hum Genet
Pays: Germany
ID NLM: 7613873
Informations de publication
Date de publication:
Sep 2022
Sep 2022
Historique:
received:
09
05
2021
accepted:
08
02
2022
pubmed:
6
3
2022
medline:
11
8
2022
entrez:
5
3
2022
Statut:
ppublish
Résumé
Machine learning (ML) algorithms are increasingly being used to help implement clinical decision support systems. In this new field, we define as "translational machine learning", joint efforts and strong communication between data scientists and clinicians help to span the gap between ML and its adoption in the clinic. These collaborations also improve interpretability and trust in translational ML methods and ultimately aim to result in generalizable and reproducible models. To help clinicians and bioinformaticians refine their translational ML pipelines, we review the steps from model building to the use of ML in the clinic. We discuss experimental setup, computational analysis, interpretability and reproducibility, and emphasize the challenges involved. We highly advise collaboration and data sharing between consortia and institutes to build multi-centric cohorts that facilitate ML methodologies that generalize across centers. In the end, we hope that this review provides a way to streamline translational ML and helps to tackle the challenges that come with it.
Identifiants
pubmed: 35246744
doi: 10.1007/s00439-022-02439-8
pii: 10.1007/s00439-022-02439-8
pmc: PMC8896412
doi:
Types de publication
Journal Article
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
1451-1466Subventions
Organisme : Fonds Wetenschappelijk Onderzoek
ID : FWOTBM20190001
Organisme : Vlaamse Overheid
ID : Onderzoeksprogramma Artificiële Intelligentie (AI) Vlaanderen
Organisme : Vlaams Instituut voor Biotechnologie
ID : VR 2016 2312 Doc.1521/4
Commentaires et corrections
Type : CommentIn
Informations de copyright
© 2022. The Author(s).
Références
Nat Methods. 2021 Oct;18(10):1122-1127
pubmed: 34316068
Nature. 2017 Jun 28;546(7660):686
pubmed: 28658222
Nature. 2013 Oct 17;502(7471):317-20
pubmed: 24132288
Transl Oncol. 2021 Jan;14(1):100907
pubmed: 33217646
FEBS J. 2009 Feb;276(4):923-42
pubmed: 19215298
Bioinformatics. 2016 Aug 15;32(16):2473-80
pubmed: 27153628
NPJ Digit Med. 2020 Sep 11;3:118
pubmed: 32984550
IEEE Trans Pattern Anal Mach Intell. 1979 Feb;1(2):224-7
pubmed: 21868852
Nat Commun. 2021 Mar 25;12(1):1882
pubmed: 33767197
Nat Methods. 2021 Oct;18(10):1128-1131
pubmed: 34433960
J Med Internet Res. 2020 Jul 20;22(7):e18477
pubmed: 32706670
Nucleic Acids Res. 2021 Apr 19;49(7):e42
pubmed: 33524142
Front Genet. 2018 Jul 12;9:242
pubmed: 30050560
Nat Commun. 2017 Apr 06;8:14825
pubmed: 28382969
Cytometry A. 2021 Aug;99(8):814-824
pubmed: 33942494
Bioinformatics. 2020 Aug 15;36(16):4415-4422
pubmed: 32415966
Biochim Biophys Acta. 2014 May;1844(5):899-908
pubmed: 24412545
Front Genet. 2019 Mar 27;10:256
pubmed: 30972106
PLoS One. 2021 Feb 19;16(2):e0247491
pubmed: 33606850
N Engl J Med. 2019 Oct 24;381(17):1684-1686
pubmed: 31644852
Genome Biol. 2020 May 6;21(1):106
pubmed: 32375897
Comput Struct Biotechnol J. 2021 May 24;19:3255-3268
pubmed: 34141144
Nat Med. 2016 Jul;22(7):792-9
pubmed: 27322744
BMJ Open. 2021 Jul 9;11(7):e048008
pubmed: 34244270
Nat Med. 2018 Nov;24(11):1716-1720
pubmed: 30349085
Nat Med. 2003 Apr;9(4):416-23
pubmed: 12640447
NPJ Digit Med. 2020 Oct 30;3:142
pubmed: 33145438
J Am Med Inform Assoc. 2020 Dec 9;27(12):2016-2019
pubmed: 32951036
J Immunol Methods. 2019 Dec;475:112631
pubmed: 31306640
Anal Chem. 2009 Aug 15;81(16):6813-22
pubmed: 19601617
Neuroimage. 2018 Oct 15;180(Pt A):68-77
pubmed: 28655633
AJR Am J Roentgenol. 2019 Jan;212(1):38-43
pubmed: 30332290
Nat Med. 2020 Sep;26(9):1351-1363
pubmed: 32908284
Nat Biotechnol. 2019 May;37(5):547-554
pubmed: 30936559
Nat Rev Genet. 2015 Mar;16(3):133-45
pubmed: 25628217
Comput Struct Biotechnol J. 2020 Mar 31;18:874-886
pubmed: 32322369
Cell. 2019 Oct 31;179(4):829-845.e20
pubmed: 31675496
Circ Cardiovasc Qual Outcomes. 2019 Jul;12(7):e005122
pubmed: 31284738
Ann Intern Med. 2019 Jan 1;170(1):W1-W33
pubmed: 30596876
Genome Biol. 2019 Dec 23;20(1):297
pubmed: 31870419
BMC Bioinformatics. 2003 Oct 13;4:48
pubmed: 14552657
Cytometry A. 2022 Apr;101(4):325-338
pubmed: 34549881
Cytometry A. 2016 Dec;89(12):1084-1096
pubmed: 27992111
Exp Dermatol. 2016 Oct;25(10):767-74
pubmed: 27193975
Commun Biol. 2021 Feb 10;4(1):183
pubmed: 33568741
Sci Robot. 2019 Dec 18;4(37):
pubmed: 33137719
F1000Res. 2017 May 26;6:748
pubmed: 28663787
Nat Commun. 2020 Jun 18;11(1):3092
pubmed: 32555183
Mayo Clin Proc. 2019 May;94(5):783-792
pubmed: 31054606
JAMA. 2020 Sep 22;324(12):1212-1213
pubmed: 32960230
Cell Syst. 2021 Feb 17;12(2):176-194.e6
pubmed: 33338399
Nat Commun. 2019 Jul 23;10(1):3069
pubmed: 31337762
Int J Comput Assist Radiol Surg. 2019 Mar;14(3):451-461
pubmed: 30542975
J Am Heart Assoc. 2021 May 4;10(9):e019905
pubmed: 33899504
Cell. 2019 Mar 7;176(6):1265-1281.e24
pubmed: 30827681
Commun Biol. 2019 May 14;2:183
pubmed: 31098416
Ann Intern Med. 2015 Jan 6;162(1):W1-73
pubmed: 25560730
BMJ. 2020 Apr 7;369:m1328
pubmed: 32265220
Nat Commun. 2020 Jan 9;11(1):166
pubmed: 31919373
PLoS Med. 2018 Nov 6;15(11):e1002683
pubmed: 30399157
Orphanet J Rare Dis. 2020 Jun 9;15(1):145
pubmed: 32517778
PLoS One. 2019 Nov 7;14(11):e0224365
pubmed: 31697686
Nat Rev Genet. 2019 Jul;20(7):389-403
pubmed: 30971806
Sci Rep. 2018 Feb 21;8(1):3395
pubmed: 29467373
PLoS Med. 2014 Oct 14;11(10):e1001744
pubmed: 25314315
Nat Med. 2002 Jan;8(1):68-74
pubmed: 11786909
Nat Methods. 2021 Oct;18(10):1132-1135
pubmed: 34462593
Bioinformatics. 2011 Nov 1;27(21):3017-23
pubmed: 21893520
Nature. 2021 Mar;591(7851):639-644
pubmed: 33461210
F1000Res. 2016 Aug 31;5:2122
pubmed: 27909575
Curr Protoc Cytom. 2013 Jan;Chapter 1:1.27.1-1.27.13
pubmed: 23292705
Radiology. 2021 Jan;298(1):38-46
pubmed: 33078996
J Neurosci Methods. 2013 Oct 30;220(1):85-91
pubmed: 24012917
BMC Med Imaging. 2021 Feb 15;21(1):27
pubmed: 33588786
Sci Rep. 2019 Jun 20;9(1):8914
pubmed: 31222035
Am J Clin Pathol. 1997 Oct;108(4):378-82
pubmed: 9322589
Curr Protoc Cytom. 2017 Jan 5;79:1.3.1-1.3.27
pubmed: 28055116
Cytometry A. 2015 Jul;87(7):636-45
pubmed: 25573116
Med Phys. 2020 Jan;47(1):1-4
pubmed: 31663612
BMJ. 2019 Mar 12;364:l886
pubmed: 30862612
Am Fam Physician. 2020 Mar 1;101(5):307-308
pubmed: 32109029
JACC Cardiovasc Interv. 2008 Jun;1(3):211-7
pubmed: 19463302
Psychiatry Res. 2009 Jul 15;173(1):8-14
pubmed: 19443186
JAMA Intern Med. 2018 Nov 1;178(11):1544-1547
pubmed: 30128552
Nat Genet. 2020 Nov;52(11):1158-1168
pubmed: 33106633
BMC Med Res Methodol. 2019 Jul 24;19(1):162
pubmed: 31340753
Sci Rep. 2019 Mar 26;9(1):5233
pubmed: 30914743
J Math Psychol. 2000 Mar;44(1):108-132
pubmed: 10733860
Comput Struct Biotechnol J. 2020 Mar 05;18:509-517
pubmed: 32206210
NPJ Digit Med. 2021 Apr 7;4(1):65
pubmed: 33828217
F1000Res. 2018 Jul 26;7:1141
pubmed: 30271584
Genome Biol. 2018 Dec 19;19(1):224
pubmed: 30567574
Nat Med. 2020 Sep;26(9):1364-1374
pubmed: 32908283
Stat Med. 2009 Nov 20;28(26):3294-315
pubmed: 19750510
Cytometry A. 2021 Oct;99(10):1007-1021
pubmed: 33606354
Science. 1965 Nov 12;150(3698):910-1
pubmed: 5891056
Nat Med. 2019 Jan;25(1):44-56
pubmed: 30617339
Front Med. 2020 Apr;14(2):185-192
pubmed: 32170560
Nat Med. 2020 Sep;26(9):1320-1324
pubmed: 32908275
BMC Med Inform Decis Mak. 2012 Feb 15;12:8
pubmed: 22336388
Nat Med. 2019 Jan;25(1):24-29
pubmed: 30617335
Invest Ophthalmol Vis Sci. 2016 Oct 01;57(13):5200-5206
pubmed: 27701631
Science. 2019 Oct 25;366(6464):447-453
pubmed: 31649194
BMC Bioinformatics. 2021 Mar 22;22(1):137
pubmed: 33752595
Nat Methods. 2015 Nov;12(11):1033-8
pubmed: 26389570
Nat Med. 2021 Apr;27(4):582-584
pubmed: 33820998
J Am Med Inform Assoc. 2021 Mar 18;28(4):890-894
pubmed: 33340404
Mol Syst Biol. 2019 Jun 19;15(6):e8746
pubmed: 31217225
Evol Comput. 2012 Summer;20(2):249-75
pubmed: 22339368
Acad Med. 2010 Mar;85(3):470-5
pubmed: 20182120
Sci Rep. 2019 Dec 30;9(1):20353
pubmed: 31889137
Bioinformatics. 2007 Oct 1;23(19):2507-17
pubmed: 17720704
Nat Methods. 2009 May;6(5):377-82
pubmed: 19349980