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A guided multiverse study of neuroimaging analyses

Author

Listed:
  • Jessica Dafflon

    (King’s College London)

  • Pedro F. Da Costa

    (King’s College London
    Birkbeck College)

  • František Váša

    (King’s College London)

  • Ricardo Pio Monti

    (University College London)

  • Danilo Bzdok

    (McGill University
    Mila - Quebec Artificial Intelligence Institute)

  • Peter J. Hellyer

    (King’s College London)

  • Federico Turkheimer

    (King’s College London)

  • Jonathan Smallwood

    (Queen’s University)

  • Emily Jones

    (Birkbeck College)

  • Robert Leech

    (King’s College London)

Abstract

For most neuroimaging questions the range of possible analytic choices makes it unclear how to evaluate conclusions from any single analytic method. One possible way to address this issue is to evaluate all possible analyses using a multiverse approach, however, this can be computationally challenging and sequential analyses on the same data can compromise predictive power. Here, we establish how active learning on a low-dimensional space capturing the inter-relationships between pipelines can efficiently approximate the full spectrum of analyses. This approach balances the benefits of a multiverse analysis without incurring the cost on computational and predictive power. We illustrate this approach with two functional MRI datasets (predicting brain age and autism diagnosis) demonstrating how a multiverse of analyses can be efficiently navigated and mapped out using active learning. Furthermore, our presented approach not only identifies the subset of analysis techniques that are best able to predict age or classify individuals with autism spectrum disorder and healthy controls, but it also allows the relationships between analyses to be quantified.

Suggested Citation

  • Jessica Dafflon & Pedro F. Da Costa & František Váša & Ricardo Pio Monti & Danilo Bzdok & Peter J. Hellyer & Federico Turkheimer & Jonathan Smallwood & Emily Jones & Robert Leech, 2022. "A guided multiverse study of neuroimaging analyses," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-31347-8
    DOI: 10.1038/s41467-022-31347-8
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    References listed on IDEAS

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    1. Mikail Rubinov, 2016. "Constraints and spandrels of interareal connectomes," Nature Communications, Nature, vol. 7(1), pages 1-11, December.
    2. Matthew F. Glasser & Timothy S. Coalson & Emma C. Robinson & Carl D. Hacker & John Harwell & Essa Yacoub & Kamil Ugurbil & Jesper Andersson & Christian F. Beckmann & Mark Jenkinson & Stephen M. Smith , 2016. "A multi-modal parcellation of human cerebral cortex," Nature, Nature, vol. 536(7615), pages 171-178, August.
    3. Romy Lorenz & Ines R. Violante & Ricardo Pio Monti & Giovanni Montana & Adam Hampshire & Robert Leech, 2018. "Dissociating frontoparietal brain networks with neuroadaptive Bayesian optimization," Nature Communications, Nature, vol. 9(1), pages 1-14, December.
    4. Ricardo Pio Monti & Alex Gibberd & Sandipan Roy & Matthew Nunes & Romy Lorenz & Robert Leech & Takeshi Ogawa & Motoaki Kawanabe & Aapo Hyvärinen, 2020. "Interpretable brain age prediction using linear latent variable models of functional connectivity," PLOS ONE, Public Library of Science, vol. 15(6), pages 1-25, June.
    5. Marc-Andre Schulz & B. T. Thomas Yeo & Joshua T. Vogelstein & Janaina Mourao-Miranada & Jakob N. Kather & Konrad Kording & Blake Richards & Danilo Bzdok, 2020. "Different scaling of linear models and deep learning in UKBiobank brain images versus machine-learning datasets," Nature Communications, Nature, vol. 11(1), pages 1-15, December.
    6. Rotem Botvinik-Nezer & Felix Holzmeister & Colin F. Camerer & Anna Dreber & Juergen Huber & Magnus Johannesson & Michael Kirchler & Roni Iwanir & Jeanette A. Mumford & R. Alison Adcock & Paolo Avesani, 2020. "Variability in the analysis of a single neuroimaging dataset by many teams," Nature, Nature, vol. 582(7810), pages 84-88, June.
    7. J. Kruskal, 1964. "Nonmetric multidimensional scaling: A numerical method," Psychometrika, Springer;The Psychometric Society, vol. 29(2), pages 115-129, June.
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