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VBA: A Probabilistic Treatment of Nonlinear Models for Neurobiological and Behavioural Data

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  • Jean Daunizeau
  • Vincent Adam
  • Lionel Rigoux

Abstract

This work is in line with an on-going effort tending toward a computational (quantitative and refutable) understanding of human neuro-cognitive processes. Many sophisticated models for behavioural and neurobiological data have flourished during the past decade. Most of these models are partly unspecified (i.e. they have unknown parameters) and nonlinear. This makes them difficult to peer with a formal statistical data analysis framework. In turn, this compromises the reproducibility of model-based empirical studies. This work exposes a software toolbox that provides generic, efficient and robust probabilistic solutions to the three problems of model-based analysis of empirical data: (i) data simulation, (ii) parameter estimation/model selection, and (iii) experimental design optimization.

Suggested Citation

  • Jean Daunizeau & Vincent Adam & Lionel Rigoux, 2014. "VBA: A Probabilistic Treatment of Nonlinear Models for Neurobiological and Behavioural Data," PLOS Computational Biology, Public Library of Science, vol. 10(1), pages 1-16, January.
  • Handle: RePEc:plo:pcbi00:1003441
    DOI: 10.1371/journal.pcbi.1003441
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    References listed on IDEAS

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    1. Jean Daunizeau & Kerstin Preuschoff & Karl Friston & Klaas Stephan, 2011. "Optimizing Experimental Design for Comparing Models of Brain Function," PLOS Computational Biology, Public Library of Science, vol. 7(11), pages 1-18, November.
    2. Will D Penny & Klaas E Stephan & Jean Daunizeau & Maria J Rosa & Karl J Friston & Thomas M Schofield & Alex P Leff, 2010. "Comparing Families of Dynamic Causal Models," PLOS Computational Biology, Public Library of Science, vol. 6(3), pages 1-14, March.
    3. Jean Daunizeau & Hanneke E M den Ouden & Matthias Pessiglione & Stefan J Kiebel & Klaas E Stephan & Karl J Friston, 2010. "Observing the Observer (I): Meta-Bayesian Models of Learning and Decision-Making," PLOS ONE, Public Library of Science, vol. 5(12), pages 1-10, December.
    4. repec:dau:papers:123456789/1908 is not listed on IDEAS
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    Cited by:

    1. Marie Devaine & Guillaume Hollard & Jean Daunizeau, 2014. "The Social Bayesian Brain: Does Mentalizing Make a Difference When We Learn?," PLOS Computational Biology, Public Library of Science, vol. 10(12), pages 1-14, December.
    2. Chih-Chung Ting & Nahuel Salem-Garcia & Stefano Palminteri & Jan B. Engelmann & Maël Lebreton, 2023. "Neural and computational underpinnings of biased confidence in human reinforcement learning," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    3. Antoine Collomb-Clerc & Maëlle C. M. Gueguen & Lorella Minotti & Philippe Kahane & Vincent Navarro & Fabrice Bartolomei & Romain Carron & Jean Regis & Stephan Chabardès & Stefano Palminteri & Julien B, 2023. "Human thalamic low-frequency oscillations correlate with expected value and outcomes during reinforcement learning," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    4. Giovanni Leone & Charlotte Postel & Alison Mary & Florence Fraisse & Thomas Vallée & Fausto Viader & Vincent Sayette & Denis Peschanski & Jaques Dayan & Francis Eustache & Pierre Gagnepain, 2022. "Altered predictive control during memory suppression in PTSD," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    5. Chen Hu & Philippe Domenech & Mathias Pessiglione, 2020. "Order matters: How covert value updating during sequential option sampling shapes economic preference," PLOS Computational Biology, Public Library of Science, vol. 16(8), pages 1-23, August.
    6. Flavia Mancini & Suyi Zhang & Ben Seymour, 2022. "Computational and neural mechanisms of statistical pain learning," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    7. Nura Sidarus & Stefano Palminteri & Valérian Chambon, 2019. "Cost-benefit trade-offs in decision-making and learning," PLOS Computational Biology, Public Library of Science, vol. 15(9), pages 1-28, September.
    8. Stefano Palminteri & Germain Lefebvre & Emma J Kilford & Sarah-Jayne Blakemore, 2017. "Confirmation bias in human reinforcement learning: Evidence from counterfactual feedback processing," PLOS Computational Biology, Public Library of Science, vol. 13(8), pages 1-22, August.
    9. Marie Devaine & Jean Daunizeau, 2017. "Learning about and from others' prudence, impatience or laziness: The computational bases of attitude alignment," PLOS Computational Biology, Public Library of Science, vol. 13(3), pages 1-28, March.
    10. Lefebvre, Germain & Nioche, Aurélien & Bourgeois-Gironde, Sacha & Palminteri, Stefano, 2018. "An Empirical Investigation of the Emergence of Money: Contrasting Temporal Difference and Opportunity Cost Reinforcement Learning," MPRA Paper 85586, University Library of Munich, Germany.
    11. Joaquina Couto & Leendert van Maanen & Maël Lebreton, 2020. "Investigating the origin and consequences of endogenous default options in repeated economic choices," PLOS ONE, Public Library of Science, vol. 15(8), pages 1-19, August.
    12. Luigi Acerbi & Kalpana Dokka & Dora E Angelaki & Wei Ji Ma, 2018. "Bayesian comparison of explicit and implicit causal inference strategies in multisensory heading perception," PLOS Computational Biology, Public Library of Science, vol. 14(7), pages 1-38, July.
    13. Wojciech Białaszek & Przemysław Marcowski & Paweł Ostaszewski, 2017. "Physical and cognitive effort discounting across different reward magnitudes: Tests of discounting models," PLOS ONE, Public Library of Science, vol. 12(7), pages 1-25, July.
    14. Laurel S Morris & Agnes Norbury & Derek A Smith & Neil A Harrison & Valerie Voon & James W Murrough, 2020. "Dissociating self-generated volition from externally-generated motivation," PLOS ONE, Public Library of Science, vol. 15(5), pages 1-13, May.
    15. Alizée Lopez-Persem & Lionel Rigoux & Sacha Bourgeois-Gironde & Jean Daunizeau & Mathias Pessiglione, 2017. "Choose, rate or squeeze: Comparison of economic value functions elicited by different behavioral tasks," PLOS Computational Biology, Public Library of Science, vol. 13(11), pages 1-18, November.
    16. Maël Lebreton & Karin Bacily & Stefano Palminteri & Jan B Engelmann, 2019. "Contextual influence on confidence judgments in human reinforcement learning," PLOS Computational Biology, Public Library of Science, vol. 15(4), pages 1-27, April.
    17. Zixuan Tang & Chen Qu & Yang Hu & Julien Benistant & Frederic Moisan & Edmund Derrington & Jean-Claude Dreher, 2023. "Strengths of social ties modulate brain computations for third-party punishment," Post-Print hal-04325737, HAL.
    18. He A Xu & Alireza Modirshanechi & Marco P Lehmann & Wulfram Gerstner & Michael H Herzog, 2021. "Novelty is not surprise: Human exploratory and adaptive behavior in sequential decision-making," PLOS Computational Biology, Public Library of Science, vol. 17(6), pages 1-32, June.
    19. Fabien Vinckier & Lionel Rigoux & Irma T Kurniawan & Chen Hu & Sacha Bourgeois-Gironde & Jean Daunizeau & Mathias Pessiglione, 2019. "Sour grapes and sweet victories: How actions shape preferences," PLOS Computational Biology, Public Library of Science, vol. 15(1), pages 1-24, January.
    20. Jeroen P. H. Verharen & Johannes W. Jong & Yichen Zhu & Stephan Lammel, 2023. "A computational analysis of mouse behavior in the sucrose preference test," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    21. Stefano Palminteri & Emma J Kilford & Giorgio Coricelli & Sarah-Jayne Blakemore, 2016. "The Computational Development of Reinforcement Learning during Adolescence," PLOS Computational Biology, Public Library of Science, vol. 12(6), pages 1-25, June.

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