Modeling the temporal network dynamics of neuronal cultures

Neurons form complex networks that evolve over multiple time scales. In order to thoroughly characterize these networks, time dependencies must be explicitly modeled. Here, we present a statistical model that captures both the underlying structural and temporal dynamics of neuronal networks. Our model combines the class of Stochastic Block Models for community formation with Gaussian processes to model changes in the community structure as a smooth function of time. We validate our model on synthetic data and demonstrate its utility on three different studies using in vitro cultures of dissociated neurons.

[1]  K. Kulp,et al.  Evaluation of in vitro neuronal platforms as surrogates for in vivo whole brain systems , 2018, Scientific Reports.

[2]  Scott T. Grafton,et al.  Dynamic reconfiguration of human brain networks during learning , 2010, Proceedings of the National Academy of Sciences.

[3]  Daniele Durante,et al.  Bayesian Logistic Gaussian Process Models for Dynamic Networks , 2014, AISTATS.

[4]  Jonas Richiardi,et al.  Graph analysis of functional brain networks: practical issues in translational neuroscience , 2014, Philosophical Transactions of the Royal Society B: Biological Sciences.

[5]  Andrew F M Johnstone,et al.  Burst and principal components analyses of MEA data for 16 chemicals describe at least three effects classes. , 2014, Neurotoxicology.

[6]  O. Sporns,et al.  Complex brain networks: graph theoretical analysis of structural and functional systems , 2009, Nature Reviews Neuroscience.

[7]  M. P. van den Heuvel,et al.  The Ontogeny of the Human Connectome , 2013, The Neuroscientist : a review journal bringing neurobiology, neurology and psychiatry.

[8]  John M. Beggs,et al.  Large-Scale, High-Resolution Multielectrode-Array Recording Depicts Functional Network Differences of Cortical and Hippocampal Cultures , 2014, PloS one.

[9]  M. Greicius,et al.  Default-mode network activity distinguishes Alzheimer's disease from healthy aging: Evidence from functional MRI , 2004, Proc. Natl. Acad. Sci. USA.

[10]  Andrew Morton,et al.  Quantitative differences in developmental profiles of spontaneous activity in cortical and hippocampal cultures , 2014, Neural Development.

[11]  Kathryn B. Laskey,et al.  Stochastic blockmodels: First steps , 1983 .

[12]  Sergey Yekhanin,et al.  Towards 3-query locally decodable codes of subexponential length , 2008, JACM.

[13]  Sujit K Sikdar,et al.  Small‐world network topology of hippocampal neuronal network is lost, in an in vitro glutamate injury model of epilepsy , 2007, The European journal of neuroscience.

[14]  Slawomir J. Nasuto,et al.  Emergence of a Small-World Functional Network in Cultured Neurons , 2012, PLoS Comput. Biol..

[15]  Nir Ailon,et al.  Aggregating inconsistent information: Ranking and clustering , 2008 .

[16]  Bryon A. Mueller,et al.  Altered resting state complexity in schizophrenia , 2012, NeuroImage.

[17]  Andrew F M Johnstone,et al.  Microelectrode arrays: a physiologically based neurotoxicity testing platform for the 21st century. , 2010, Neurotoxicology.

[18]  Le Song,et al.  Dynamic mixed membership blockmodel for evolving networks , 2009, ICML '09.

[19]  Maxym Myroshnychenko,et al.  Multiplex networks of cortical and hippocampal neurons revealed at different timescales , 2014, BMC Neuroscience.

[20]  Vincent Miele,et al.  Statistical clustering of temporal networks through a dynamic stochastic block model , 2015, 1506.07464.

[21]  O. Sporns,et al.  Rich-Club Organization of the Human Connectome , 2011, The Journal of Neuroscience.

[22]  Yihong Gong,et al.  Detecting communities and their evolutions in dynamic social networks—a Bayesian approach , 2011, Machine Learning.

[23]  K. Kulp,et al.  Tissue-specific extracellular matrix accelerates the formation of neural networks and communities in a neuron-glia co-culture on a multi-electrode array , 2019, Scientific Reports.

[24]  John Salvatier,et al.  Probabilistic programming in Python using PyMC3 , 2016, PeerJ Comput. Sci..

[25]  E. Bullmore,et al.  Emergence of Rich-Club Topology and Coordinated Dynamics in Development of Hippocampal Functional Networks In Vitro , 2015, The Journal of Neuroscience.

[26]  J Martinerie,et al.  Complex modular structure of large-scale brain networks. , 2009, Chaos.