PAUSE: principled feature attribution for unsupervised gene expression analysis.
Deep learning
Explainable AI
Feature attribution
Gene expression
Transcriptomics
Unsupervised learning
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
19 04 2023
19 04 2023
Historique:
received:
30
04
2022
accepted:
17
03
2023
medline:
21
4
2023
pubmed:
20
4
2023
entrez:
19
04
2023
Statut:
epublish
Résumé
As interest in using unsupervised deep learning models to analyze gene expression data has grown, an increasing number of methods have been developed to make these models more interpretable. These methods can be separated into two groups: post hoc analyses of black box models through feature attribution methods and approaches to build inherently interpretable models through biologically-constrained architectures. We argue that these approaches are not mutually exclusive, but can in fact be usefully combined. We propose PAUSE ( https://github.com/suinleelab/PAUSE ), an unsupervised pathway attribution method that identifies major sources of transcriptomic variation when combined with biologically-constrained neural network models.
Identifiants
pubmed: 37076856
doi: 10.1186/s13059-023-02901-4
pii: 10.1186/s13059-023-02901-4
pmc: PMC10114348
doi:
Types de publication
Journal Article
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
81Subventions
Organisme : NIGMS NIH HHS
ID : R35 GM128638
Pays : United States
Organisme : NIA NIH HHS
ID : P30 AG013280
Pays : United States
Organisme : NIA NIH HHS
ID : R01 AG061132
Pays : United States
Informations de copyright
© 2023. The Author(s).
Références
Infect Immun. 2015 Jul;83(7):2926-34
pubmed: 25964470
BMC Bioinformatics. 2018 Dec 17;19(1):510
pubmed: 30558539
Neuromolecular Med. 2004;5(2):147-62
pubmed: 15075441
Nucleic Acids Res. 2008 Jan;36(Database issue):D13-21
pubmed: 18045790
Autophagy. 2007 Nov-Dec;3(6):569-80
pubmed: 17675890
Nat Cell Biol. 2023 Feb;25(2):337-350
pubmed: 36732632
Nat Rev Immunol. 2015 Apr;15(4):203-16
pubmed: 25720354
EBioMedicine. 2015 Apr 1;2(4):294-305
pubmed: 26086035
Bioinformatics. 2005 Aug 15;21(16):3439-40
pubmed: 16082012
PLoS Genet. 2021 Aug 19;17(8):e1009754
pubmed: 34411094
Nat Protoc. 2009;4(8):1184-91
pubmed: 19617889
Cell. 2015 May 21;161(5):1202-1214
pubmed: 26000488
Nat Mach Intell. 2020 Jan;2(1):56-67
pubmed: 32607472
Nat Biotechnol. 2022 Jan;40(1):121-130
pubmed: 34462589
Nature. 2021 Oct;598(7880):348-352
pubmed: 34552244
Nat Methods. 2017 Mar;14(3):297-301
pubmed: 28099430
Genome Biol. 2020 May 11;21(1):109
pubmed: 32393369
Bioinformatics. 2020 Dec 30;36(Suppl_2):i573-i582
pubmed: 33381842
Genome Biol. 2021 Oct 29;22(1):301
pubmed: 34715899
Curr Alzheimer Res. 2012 Jul;9(6):718-23
pubmed: 22471861
Proc Natl Acad Sci U S A. 2009 Nov 24;106(47):20057-62
pubmed: 19897719
Science. 2019 Aug 23;365(6455):786-793
pubmed: 31395745
Mol Neurodegener. 2020 May 29;15(1):30
pubmed: 32471464
PLoS One. 2017 Feb 22;12(2):e0172477
pubmed: 28225806
Geroscience. 2019 Dec;41(6):961-973
pubmed: 31728898
Neurogenetics. 1997 May;1(1):13-9
pubmed: 10735269
Immunol Rev. 2009 Mar;228(1):288-311
pubmed: 19290935
Bioinformatics. 2020 Jun 1;36(11):3418-3421
pubmed: 32176273
Nat Methods. 2018 Dec;15(12):1053-1058
pubmed: 30504886
Curr Med Chem. 2009;16(10):1266-77
pubmed: 19355884
Front Immunol. 2018 Sep 25;9:2144
pubmed: 30319613
J Vis Exp. 2009 May 12;(27):
pubmed: 19488025
Cancer Chemother Rep. 1966 Mar;50(3):163-70
pubmed: 5910392
Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50
pubmed: 16199517
Genetics. 1974 May;77(1):71-94
pubmed: 4366476
Gigascience. 2020 Nov 3;9(11):
pubmed: 33140829
Mol Neurodegener. 2012 Nov 21;7:57
pubmed: 23171715
Nat Biotechnol. 2008 Mar;26(3):303-4
pubmed: 18327243
Nat Commun. 2020 Aug 27;11(1):4296
pubmed: 32855387
Nat Rev Immunol. 2005 May;5(5):375-86
pubmed: 15864272
J Alzheimers Dis. 2016 Apr 8;52(3):1081-8
pubmed: 27079706
Nat Rev Neurol. 2021 Mar;17(3):157-172
pubmed: 33318676
Nat Biotechnol. 2018 Jan;36(1):89-94
pubmed: 29227470
Nucleic Acids Res. 2016 Jul 8;44(W1):W90-7
pubmed: 27141961
Aging Cell. 2008 Jun;7(3):394-404
pubmed: 18331616
Bioinformatics. 2019 Oct 1;35(19):3743-3751
pubmed: 30850846
Nat Methods. 2019 Nov;16(11):1139-1145
pubmed: 31591579
Nucleic Acids Res. 2018 Jan 4;46(D1):D649-D655
pubmed: 29145629
mSystems. 2016 Jan 19;1(1):
pubmed: 27822512
Nucleic Acids Res. 2017 Jan 4;45(D1):D362-D368
pubmed: 27924014
Nature. 2017 Nov 16;551(7680):333-339
pubmed: 29144463
Sci Data. 2018 Aug 07;5:180142
pubmed: 30084846
Cell Syst. 2017 Jul 26;5(1):63-71.e6
pubmed: 28711280
Nat Commun. 2017 Jan 16;8:14049
pubmed: 28091601
Chem Cent J. 2015 Nov 26;9:65
pubmed: 26617668
J Mol Biol. 1990 Oct 5;215(3):403-10
pubmed: 2231712
Nat Commun. 2021 Sep 28;12(1):5684
pubmed: 34584103