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Molecular systems biology
Aug, 2024;20 (8): 848-858.

Molecular causality in the advent of foundation models.

Sebastian Lobentanzer, Pablo Rodriguez-Mier, Stefan Bauer, Julio Saez-Rodriguez
Author Information
  1. Sebastian Lobentanzer: Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany. sebastian.lobentanzer@gmail.com. ORCID
  2. Pablo Rodriguez-Mier: Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany. ORCID
  3. Stefan Bauer: Helmholtz AI and TU Munich, Munich, Germany. ORCID
  4. Julio Saez-Rodriguez: Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany. pub.saez@uni-heidelberg.de. ORCID
PMID: 38890548 DOI: 10.1038/s44320-024-00041-w

Abstract

Correlation is not causation: this simple and uncontroversial statement has far-reaching implications. Defining and applying causality in biomedical research has posed significant challenges to the scientific community. In this perspective, we attempt to connect the partly disparate fields of systems biology, causal reasoning, and machine learning to inform future approaches in the field of systems biology and molecular medicine.

Keywords

Causality Foundation Models Inductive Bias Latent Spaces Systems Biology

References

  1. Found Comut Math. 2022 Aug 1;:1-35 [PMID: 35935470]
  2. Proc Natl Acad Sci U S A. 2023 Dec 26;120(52):e2319169120 [PMID: 38117857]
  3. Cell. 2016 Dec 15;167(7):1853-1866.e17 [PMID: 27984732]
  4. PLoS One. 2011;6(11):e27755 [PMID: 22132135]
  5. Psychol Rev. 2004 Jan;111(1):3-32 [PMID: 14756583]
  6. Nat Methods. 2024 Feb 26;: [PMID: 38409223]
  7. Int J Mol Sci. 2019 Mar 25;20(6): [PMID: 30934534]
  8. Nature. 2023 Jun;618(7965):616-624 [PMID: 37258680]
  9. Nat Methods. 2021 Oct;18(10):1169-1180 [PMID: 34608321]
  10. Nat Methods. 2021 Oct;18(10):1196-1203 [PMID: 34608324]
  11. Nat Commun. 2023 Aug 3;14(1):4669 [PMID: 37537192]
  12. Nat Commun. 2022 Apr 1;13(1):1728 [PMID: 35365602]
  13. Nat Rev Genet. 2015 Mar;16(3):146-58 [PMID: 25645874]
  14. Nature. 2023 Jul;619(7971):686-689 [PMID: 37491395]
  15. Nature. 2010 Oct 28;467(7319):1061-73 [PMID: 20981092]
  16. Nat Biotechnol. 2020 Mar;38(3):365-373 [PMID: 31819260]
  17. N Engl J Med. 2011 Jun 30;364(26):2507-16 [PMID: 21639808]
  18. Neural Comput. 1997 Nov 15;9(8):1735-80 [PMID: 9377276]
  19. Nat Commun. 2021 Sep 15;12(1):5471 [PMID: 34526509]
  20. Nat Biotechnol. 2024 Jun;42(6):927-935 [PMID: 37592036]
  21. Genome Biol. 2020 Aug 3;21(1):190 [PMID: 32746932]
  22. Nat Methods. 2016 Apr;13(4):310-8 [PMID: 26901648]
  23. Nat Methods. 2018 Dec;15(12):1053-1058 [PMID: 30504886]
  24. Science. 2011 Mar 11;331(6022):1279-85 [PMID: 21393536]
  25. Nat Biotechnol. 2023 Aug;41(8):1056-1059 [PMID: 37337100]
  26. Nat Biotechnol. 2024 Mar;42(3):371-373 [PMID: 38273064]
  27. Nat Rev Genet. 2014 Feb;15(2):107-20 [PMID: 24430943]
  28. Cell Syst. 2021 Feb 17;12(2):128-140.e4 [PMID: 33373583]
  29. Nat Cell Biol. 2023 Feb;25(2):337-350 [PMID: 36732632]
  30. Nat Commun. 2018 Jan 18;9(1):284 [PMID: 29348443]
  31. Nat Rev Drug Discov. 2012 Nov;11(11):873-86 [PMID: 23060265]
  32. PLoS Comput Biol. 2023 Aug 17;19(8):e1011288 [PMID: 37590228]
  33. Sci Signal. 2019 Jan 22;12(565): [PMID: 30670635]
  34. NPJ Syst Biol Appl. 2023 Oct 10;9(1):50 [PMID: 37816807]
  35. Diagnostics (Basel). 2022 Jun 26;12(7): [PMID: 35885463]
  36. Int J Mol Sci. 2017 Apr 02;18(4): [PMID: 28368335]
  37. Nat Rev Genet. 2016 Jul 15;17(8):470-86 [PMID: 27418159]
  38. Mol Syst Biol. 2022 Jul;18(7):e11036 [PMID: 35880747]
  39. Nat Commun. 2022 Jun 2;13(1):3069 [PMID: 35654811]

Grants

  1. 951773/EC | Horizon 2020 Framework Programme (H2020)
  2. 965193/EC | Horizon 2020 Framework Programme (H2020)

MeSH Term

Systems Biology
Humans
Machine Learning
Causality
Biomedical Research
Models, Biological
Journal Article Review
Article has an altmetric score of 48

Word Cloud

Created with Highcharts 10.0.0causalitysystemsbiologyCorrelationcausation:simpleuncontroversialstatementfar-reachingimplicationsDefiningapplyingbiomedicalresearchposedsignificantchallengesscientificcommunityperspectiveattemptconnectpartlydisparatefieldscausalreasoningmachinelearninginformfutureapproachesfieldmolecularmedicineMolecularadventfoundationmodelsCausalityFoundationModelsInductiveBiasLatentSpacesSystemsBiology

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