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From Biological to Numerical Experiments in Systemic Neuroscience: A Simulation Platform

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Advances in Neurotechnology, Electronics and Informatics

Part of the book series: Biosystems & Biorobotics ((BIOSYSROB,volume 12))

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Abstract

Studying and modeling the brain as a whole is a real challenge. For such systemic models (in contrast to models of one brain area or aspect), there is a real need for new tools designed to perform complex numerical experiments, beyond usual tools distributed in the computer science and neuroscience communities. Here, we describe an effective solution, freely available on line and already in use, to validate such models of the brain functions. We explain why this is the best choice, as a complement to robotic setup, and what are the general requirements for such a benchmarking platform. In this experimental setup, the brainy-bot implementing the model to study is embedded in a simplified but realistic controlled environment. From visual, tactile and olfactory input, to body, arm and eye motor command, in addition to vital interoceptive cues, complex survival behaviors can be experimented. We also discuss here algorithmic high-level cognitive modules, making the job of building biologically plausible bots easier. The key point is to possibly alternate the use of symbolic representation and of complementary and usual neural coding. As a consequence, algorithmic principles have to be considered at higher abstract level, beyond a given data representation, which is an interesting challenge.

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Notes

  1. 1.

    Such a structure is of common use in computer science: It corresponds to, e.g., a XML logical-structure, or the Json syntax underlying data model.

  2. 2.

    The following scalar values are used: bool for an either true or false Boolean value, percent for a proportion value between 0 and 1, degree for an angle in degree, index stands for a non-negative integer index, count stands for a non-negative integer count value, color stands for a RGB color value, real stands for a unbounded decimal value.

  3. 3.

    Sets are unordered lists without repetition, Sequences are sequential lists, and t-uples map strings, or names, to their corresponding value.

  4. 4.

    Definition available on https://en.wikipedia.org .

References

  1. Taouali, W., Viéville, T., Rougier, N.P., Alexandre, F.: No clock to rule them all. J. Physiol. Paris 105, 83–90 (2011)

    Article  Google Scholar 

  2. Uithol, S., van Rooij, I., Bekkering, H., Haselager, P.: Hierarchies in action and motor control. J. Cogn. Neurosci. 24, 1077–1086 (2012)

    Article  Google Scholar 

  3. Hyvärinen, A.: Natural image statistics a probabilistic approach to early computational vision. Hardcover (2009)

    Google Scholar 

  4. Teftef, E., Escobar, M.J., Astudillo, A., Carvajal, C., Cessac, B., Palacios, A., Viéville, T., Alexandre, F.: Modeling non-standard retinal in/out function using computer vision variational methods. Rapport de recherche RR-8217, INRIA (2013)

    Google Scholar 

  5. Friston, K.: A free energy principle for biological systems. Entropy 14, 2100–2121 (2012)

    Article  MathSciNet  MATH  Google Scholar 

  6. Viéville, T., Crahay, S.: Using an hebbian learning rule for multi-class SVM classifiers. J. Comput. Neurosci. (2004)

    Google Scholar 

  7. Viéville, T., Vadot, C.: An improved biologically plausible trajectory generator. Technical Report 4539-2, INRIA (2006)

    Google Scholar 

  8. Connolly, C.I., Grupen, R.A.: The applications of harmonic functions to robotic. J. Robot. Syst. 10, 931–946 (1993)

    Article  MATH  Google Scholar 

  9. Todorov, E.: Optimality principles in sensorimotor control. Nat. Neurosci. 7 (2004)

    Google Scholar 

  10. Cofer, D., Cymbalyuk, G., Reid, J., Zhu, Y., Heitler, W.J., Edwards, D.H.: AnimatLab: a 3D graphics environment for neuromechanical simulations. J. Neurosci. Methods 187, 280–288 (2010)

    Article  Google Scholar 

  11. Brette, R., Rudolph, M., Carnevale, T., Hines, M., Beeman, D., Bower, J.M., Diesmann, M., Morrison, A., Goodman, P.H., Harris, F.C., Zirpe, M., Natschläger, T., Pecevski, D., Ermentrout, B., Djurfeldt, M., Lansner, A., Rochel, O., Vieville, T., Muller, E., Davison, A.P., El Boustani, S., Destexhe, A.: Simulation of networks of spiking neurons: a review of tools and strategies. J. Comput. Neurosci. 23, 349–398 (2007)

    Article  MathSciNet  Google Scholar 

  12. Davison, A.P., Brüderle, D., Eppler, J., Kremkow, J., Muller, E., Pecevski, D., Perrinet, L., Yger, P.: PyNN: A Common interface for neuronal network simulators. Frontiers Neuroinform. 2 (2008)

    Google Scholar 

  13. Chemla, S., Chavane, F., Vieville, T., Kornprobst, P.: Biophysical cortical column model for optical signal analysis. BMC Neurosci. 8, P140 (2007)

    Article  Google Scholar 

  14. Herry, C., Ciocchi, S., Senn, V., Demmou, L., Muller, C., Luthi, A.: Switching on and off fear by distinct neuronal circuits. Nature 454, 600–606 (2008)

    Article  Google Scholar 

  15. LeDoux, J.: The amygdala. Curr. Biol. 17, R868–R874 (2007)

    Article  Google Scholar 

  16. Eichenbaum, H., Sauvage, M., Fortin, N., Komorowski, R., Lipton, P.: Towards a functional organization of episodic memory in the medial temporal lobe. Neurosci. Biobehav. Rev. 36, 1597–1608 (2012)

    Article  Google Scholar 

  17. Rolls, E.T.: A computational theory of episodic memory formation in the hippocampus. Behav. Brain Res. 215, 180–196 (2010)

    Article  Google Scholar 

  18. Gorojosky, R., Alexandre, F.: Models of Hippocampus for pavlovian learning. Rapport de recherche RR-8377, INRIA (2013)

    Google Scholar 

  19. Beati, T., Carrere, M., Alexandre, F.: Which reinforcing signals in autonomous systems? In: Third International Symposium on Biology of Decision Making, Paris, France (2013)

    Google Scholar 

  20. Carrere, M., Alexandre, F.: Émergence de catégories par interaction entre systèmes d’apprentissage. In: Preux, P., Tommasi, M. (eds.) Conférence Francophone sur l’Apprentissage Automatique (CAP). Lille, France (2013)

    Google Scholar 

  21. Denoyelle, N., Pouget, F., Viéville, T., Alexandre, F.: VirtualEnaction: A platform for systemic neuroscience simulation. In: International Congress on Neurotechnology, Electronics and Informatics, Rome, Italy (2014)

    Google Scholar 

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Acknowledgments

Huge thanks to Nicolas Rougier for precious advice.

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Correspondence to Thierry Viéville .

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Denoyelle, N., Carrere, M., Pouget, F., Viéville, T., Alexandre, F. (2016). From Biological to Numerical Experiments in Systemic Neuroscience: A Simulation Platform. In: Londral, A., Encarnação, P. (eds) Advances in Neurotechnology, Electronics and Informatics. Biosystems & Biorobotics, vol 12. Springer, Cham. https://doi.org/10.1007/978-3-319-26242-0_1

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  • DOI: https://doi.org/10.1007/978-3-319-26242-0_1

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