Predictive coding and active sensing

Choi, Pasupathy, Shea-Brown (2018) Neural Computation

Predictive coding has been proposed as a method to create efficient neural codes. It postulates that the brain learns and represents information about the world through hierarchical interactions across cortical areas and layers. Active sensing, on the other hand, is a strategy used by animals to optimally sample relevant sensory information to effectively update the internal representation. Our goal is to understand the neural correlates of predictive coding and active sensing. To achieve this, we incorporate biologically-realistic connectivity and neural dynamics to study predictive coding and active sensing models of cortical and other neural circuitries.

Related publications (selected):

2024, A. H. Balwani*, S. Cho, H. Choi*, “Exploring the architectural biases of the canonical cortical microcircuit”, bioRxiv preprint: doi.org/10.1101/2024.05.23.595629

2024, A. Sharafeldin*, N. Imam*, H. Choi*, “Active sensing with predictive coding and uncertainty minimization”, Patterns 5: 100983

2023, D.G. Wyrick, N. Cain, R.S. Larsen, J. Lecoq, M. Valley, R. Ahmed, J. Bowlus, G. Boyer, S. Caldejon, L. Casal, M. Chvilicek, M. DePartee, P.A.Groblewski, C. Huang, K. Johnson, I. Kato, J. Larkin, E. Lee, E, Liang, J. Luviano, K. Mace, C. Nayan, T. Nguyen, M. Reding, S. Seid, J. Sevigny, M. Stoecklin, A. Williford, H. Choi*+, M. Garrett*+, L. Mazzucato*+, “Differential encoding of temporal context and expectation under representational drift across hierarchically connected areasbioRxiv preprint: doi.org/10.1101/2023.06.02.543483

2018, H. Choi*, A. Pasupathy, E. Shea-Brown, “Predictive coding in area V4: dynamical shape discrimination under partial occlusion”, Neural Computation 30(5):1209–1257

2017, A.M. Fyall+, Y. El-Shamayleh+, H. Choi, E. Shea-Brown, A. Pasupathy, “Dynamic representation of partially occluded objects in primate prefrontal and visual cortex”, eLife 6:e25784

Related presentations (selected):

2023, A. Balwani, S. Cho, H. Choi, “Exploring the architectural biases of the canonical cortical microcircuit” Cosyne, Montreal, Canada. Watch Aish’s talk here!

Topology and computations of anatomical and functional neural networks

Harris, Mihalas, Hirokawa, Whitesell, Choi et al
(2019) Nature

The exquisite ability of the brain to perform adaptable, efficient, and robust computation in changing environment is attributed to complex connectivity structure of underlying networks. At multiple scales ranging from microscopic cell-to-cell connectivity to a large-scale network of brain regions, biological neural networks are characterized by topological complexities observed in both anatomical connectomes as well as in functional connectivity constructed from correlated neural activities. We use data-driven modeling to probe the precise connections between network complexity and computation, in close collaboration with experimental neuroscientists.

Related publications (selected):

2024, D. Tang*, J. Zylberberg*+, X. Jia*+, H. Choi*+, “Stimulus type shapes the topology of cellular functional networks in mouse visual cortex”, Nature Communications 15: 5753

2024, C. Li, S. H. Kim, C. Rodgers, H. Choi, A. Wu*, “One-hot generalized linear model for switching brain state discovery”, The 12th International Conference on Learning Representations (ICLR): 1-22

2023, U.B. Sikandar*, H. Choi, J. Putney, H. Yang, S. Ferrari, S. Sponberg, “Predicting visually modulated precisely-timed spikes across a coordinated and comprehensive motor program”, International Joint Conference on Neural Networks (IJCNN) :1–8

2020, J.H. Siegle+, X. Jia+, S. Durand, S. Gale, C. Bennett, N. Graddis, G. Heller, T. Ramirez, H. Choi, J.A. Luviano, …, S.R. Olsen, C. Koch, “Survey of spiking in the mouse visual system reveals functional hierarchy”,  Nature 592:86–92

2019, J.A. Harris+, S. Mihalas+, K.E. Hirokawa, J.D. Whitesell, H. Choi, …, C. Koch, H. Zeng, “Hierarchical organization of cortical and thalamic connectivity”, Nature 575:195-202

Neural dynamics of single cells, populations, and networks

Choi, Mihalas (2019)
PLOS Computational Biology

Neurons communicate diverse information of sensory stimuli, decision signals, and motor commands, using their rich dynamics at both single cell and population levels. Their operating modes characterized by different spiking patterns are determined by various biophysiological factors including intrinsic properties of individual neurons such as ion channels and synaptic variables as well as network properties defining population composition and connectivity among heterogeneous neurons. In addition, sensory stimuli, behavioral states, and relevant tasks to perform shape neural dynamics at both the local and global scales. We investigate how changes in these variables instigate and shape transitions between different phases of dynamics in single neurons represented by spiking as well as in neural populations described by excitatory-inhibitory balanced dynamics and synchronizability.

Related publications (selected):

2023, J. Del Rosario, S. Coletta+, S. H. Kim+, Z. Mobille, K. Peelman, B. Williams, A. J. Otsuki, A. Del Castillo Valerio, K. Worden, L. T. Blanpain, L. Lovell, H. Choi, B. Haider*, “Lateral inhibition in V1 controls neural and perceptual contrast sensitivity“, bioRxiv preprint: doi.org/10.1101/2023.11.10.566605

2019, H. Choi*, S. Mihalas, “Synchronization dependent on spatial structures of a mesoscopic whole-brain network”, PLOS Computational Biology 15(4): e1006978

2014, H. Choi, L. Zhang, M.S. Cembrowski, C.F. Sabottke, A.L. Markowitz, D.A. Butts, W.L. Kath, J.H. Singer*, and H. Riecke*, “Intrinsic bursting of AII amacrine cells underlies oscillations in rd1 mouse retina”, Journal of Neurophysiology 112: 1491-1504