Data for Brain Reference Architecture of NY24CanonicalCorticalMicrocircuitsDecisionMaking
Canonical cortical microcircuits reference architecture for decision making
DOI:
https://doi.org/10.51094/jxiv.1048Keywords:
Brain Reference Architecture, Canonical Cortical Microcircuits, Reinforcement learningAbstract
Canonical cortical microcircuits (CCMs) is the six-layer structure preserved throughout the mammalian neocortex and is thought as a fundamental computational unit. This dataset reverse-engineers CCMs and presents a computational model to achieve decision-making. The data consist of the anatomical connectivity of CCMs and the functions hierarchically achieved from each uniform circuit. First, information on the anatomical connections of CCMs was collected from seven review papers. Next, reinforcement learning was determined as the algorithm for decision-making, which CCMs can implement. Finally, we describe how top-level functions are achieved from excitatory neural populations and circuit motif based on inhibitory neural populations, assigning output semantics to each excitatory neural population. The data are described in a brain reference architecture format and stored in the BRA data repository. This dataset provides experimentally testable hypotheses about neural activity patterns in cortical layers.
Conflicts of Interest Disclosure
Yoshimasa Tawatsuji and Hiroshi Yamakawa are BRAES managers but did not participate in the editorial process or decisions related to this manuscript.Downloads *Displays the aggregated results up to the previous day.
References
Audette, N. J., Urban-Ciecko, J., Matsushita, M., & Barth, A. L. (2017). Pom thalamocortical input drives layer-specific microcircuits in somatosensory cortex. Cerebral Cortex , 28 (4), 1312–1328. DOI: 10.1093/cercor/bhx044
Bastos, A. M., Usrey, W. M., Adams, R. A., Mangun, G. R., Fries, P., & Friston, K. J. (2012). Canonical microcircuits for predictive coding. Neuron, 76 (4), 695–711.
Billeh, Y. N., Cai, B., Gratiy, S. L., Dai, K., Iyer, R., Gouwens, N. W., . . . Arkhipov, A. (2020). Systematic integration of structural and functional data into multi-scale models of mouse primary visual cortex. Neuron, 106 (3), 388–403.e18. DOI: 10.1016/j.neuron.2020.01.040
Braganza, O., & Beck, H. (2018). The circuit motif as a conceptual tool for multilevel neuroscience. Trends in Neurosciences, 41 (3), 128–136. DOI: 10.1016/j.tins.2018.01.002
Constantinople, C. M., & Bruno, R. M. (2013). Deep cortical layers are activated directly by thalamus. Science, 340 (6140), 1591–1594. DOI: 10.1126/science.1236425
Doya, K. (2021). Canonical cortical circuits and the duality of bayesian inference and optimal control. Current Opinion in Behavioral Sciences, 41 , 160–167. DOI: 10.1016/j.cobeha.2021.07.003
Dura-Bernal, S., Neymotin, S. A., Suter, B. A., Dacre, J., Moreira, J. V., Urdapilleta, E., . . . Lytton, W. W. (2023). Multiscale model of primary motor cortex circuits predicts in vivo cell-type-specific, behavioral state-dependent dynamics. Cell Reports, 42 (6), 112574. DOI: 10.1016/j.celrep.2023.112574
Felleman, D. J., & Van Essen, D. C. (1991). Distributed hierarchical processing in the primate cerebral cortex. Cerebral Cortex , 1 (1), 1-47. DOI: 10.1093/cercor/1.1.1-a
Friston, K. J., Parr, T., & de Vries, B. (2017). The graphical brain: Belief propagation and active inference. Network Neuroscience, 1 (4), 381–414. DOI: 10.1162/netna00018
George, D., & Hawkins, J. (2009). Towards a mathematical theory of cortical micro-circuits. PLoS Computational Biology, 5 (10), e1000532. DOI: 10.1371/journal.pcbi.1000532
Harris, J. A., Mihalas, S., Hirokawa, K. E., Whitesell, J. D., Choi, H., Bernard, A., . . . Zeng, H. (2019). Hierarchical organization of cortical and thalamic connectivity. Nature, 575 (7781), 195–202. DOI: 10.1038/s41586-019-1716-z
Harris, K. D., & Mrsic-Flogel, T. D. (2013). Cortical connectivity and sensory coding. Nature, 503 (7474), 51–58. DOI: 10.1038/nature12654
Kermani Nejad, K., Anastasiades, P., Hert¨ag, L., & Costa, R. P. (2024). Self-supervised predictive learning accounts for cortical layer-specificity. DOI: 10.1101/2024.04.24.590916
Larkum, M. (2013). A cellular mechanism for cortical associations: an organizing principle for the cerebral cortex. Trends in Neurosciences, 36 (3), 141–151. DOI: 10.1016/j.tins.2012.11.006
Levine, S. (2018). Reinforcement learning and control as probabilistic inference: Tutorial and review. arXiv. DOI: 10.48550/ARXIV.1805.00909
Maruoka, H., Kubota, K., Kurokawa, R., Tsuruno, S., & Hosoya, T. (2011). Periodic organization of a major subtype of pyramidal neurons in neocortical layer v. The Journal of Neuroscience, 31 (50), 18522–18542. DOI: 10.1523/jneurosci.3117-11.2011
Miyashita, Y. (2024). Cortical layer-dependent signaling in cognition: Three computational modes of the canonical circuit. Annual Review of Neuroscience, 47 (1), 211–234. DOI: 10.1146/annurev-neuro- 081623-091311
Mountcastle, V. (1997). The columnar organization of the neocortex. Brain, 120 (4), 701–722. DOI: 10.1093/brain/120.4.701
Rao, R. P. (2024). A sensory–motor theory of the neocortex. Nature Neuroscience, 27 (7), 1221–1235.
Shepherd, G. M. G., & Yamawaki, N. (2021). Untangling the cortico-thalamo-cortical loop: cellular pieces of a knotty circuit puzzle. Nature Reviews Neuroscience, 22 (7), 389–406. DOI: 10.1038/s41583- 021-00459-3
Shipp, S. (2007). Structure and function of the cerebral cortex. Current Biology, 17 (12), R443–R449.
Thomson, A. M. (2007). Functional maps of neocortical local circuitry. Frontiers in Neuroscience, 1 (1), 19–42. DOI: 10.3389/neuro.01.1.1.002.2007
Todorov, E. (2008). General duality between optimal control and estimation. In 2008 47th ieee conference on decision and control (p. 4286-4292). DOI: 10.1109/CDC.2008.4739438
Tremblay, R., Lee, S., & Rudy, B. (2016). Gabaergic interneurons in the neocortex: From cellular properties to circuits. Neuron, 91 (2), 260–292. DOI: 10.1016/j.neuron.2016.06.033
Vitrac, C., & Benoit-Marand, M. (2017). Monoaminergic modulation of motor cortex function. Frontiers in Neural Circuits, 11 . DOI: 10.3389/fncir.2017.00072
Wang, X.-J., & Yang, G. R. (2018). A disinhibitory circuit motif and flexible information routing in the brain. Current Opinion in Neurobiology, 49 , 75–83. DOI: 10.1016/j.conb.2018.01.002
Weiler, N., Wood, L., Yu, J., Solla, S. A., & Shepherd, G. M. G. (2008). Top-down laminar organization of the excitatory network in motor cortex. Nature Neuroscience, 11 (3), 360–366. DOI: 10.1038/nn2049
Yamakawa, H. (2021). The whole brain architecture approach: Accelerating the development of artificial general intelligence by referring to the brain. Neural Networks, 144 , 478–495. DOI: 10.1016/j.neunet.2021.09.004
Downloads
Posted
Submitted: 2025-01-18 12:27:56 UTC
Published: 2025-01-24 01:06:30 UTC
License
Copyright (c) 2025
Naohiro Yamauchi
Yoshimasa Tawatsuji
Yudai Suzuki
Kenji Doya
Hiroshi Yamakawa

This work is licensed under a Creative Commons Attribution 4.0 International License.