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1. Unsupervised Discovery of Dynamic Neural Circuits

   Colin Graber, Ryan Loh (January 2019, 33rd Conference on Neural Information Processing Systems)

   What can we learn about the functional organization of cortical microcircuits from large-scale recordings of neural activity? To obtain an explicit and interpretable model of time-dependent functional connections between neurons and to establish the dynamics of the cortical information flow, we develop ‘dynamic neural relational inference’ (dNRI). We study both synthetic and real-world neural spiking data and demonstrate that the developed method is able to uncover the dynamic relations between neurons more reliably than existing baselines. 

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2. Input correlations impede suppression of chaos and learning in balanced firing-rate networks

   https://doi.org/10.1371/journal.pcbi.1010590  

   Engelken, Rainer; Ingrosso, Alessandro; Khajeh, Ramin; Goedeke, Sven; Abbott, L. F. (December 2022, PLOS Computational Biology)

   Aljadeff, Johnatan (Ed.)

   Neural circuits exhibit complex activity patterns, both spontaneously and evoked by external stimuli. Information encoding and learning in neural circuits depend on how well time-varying stimuli can control spontaneous network activity. We show that in firing-rate networks in the balanced state, external control of recurrent dynamics, i.e., the suppression of internally-generated chaotic variability, strongly depends on correlations in the input. A distinctive feature of balanced networks is that, because common external input is dynamically canceled by recurrent feedback, it is far more difficult to suppress chaos with common input into each neuron than through independent input. To study this phenomenon, we develop a non-stationary dynamic mean-field theory for driven networks. The theory explains how the activity statistics and the largest Lyapunov exponent depend on the frequency and amplitude of the input, recurrent coupling strength, and network size, for both common and independent input. We further show that uncorrelated inputs facilitate learning in balanced networks. 

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3. Bayesian Inference for Spatial Count Data that May be Over-Dispersed or Under-Dispersed with Application to the 2016 US Presidential Election

   https://doi.org/10.6339/21-JDS1032  

   Yang, Hou-Cheng; Bradley, Jonathan R. (July 2022, Journal of Data Science)

   We propose a method of spatial prediction using count data that can be reasonably modeled assuming the Conway-Maxwell Poisson distribution (COM-Poisson). The COM-Poisson model is a two parameter generalization of the Poisson distribution that allows for the flexibility needed to model count data that are either over or under-dispersed. The computationally limiting factor of the COM-Poisson distribution is that the likelihood function contains multiple intractable normalizing constants and is not always feasible when using Markov Chain Monte Carlo (MCMC) techniques. Thus, we develop a prior distribution of the parameters associated with the COM-Poisson that avoids the intractable normalizing constant. Also, allowing for spatial random effects induces additional variability that makes it unclear if a spatially correlated Conway-Maxwell Poisson random variable is over or under-dispersed. We propose a computationally efficient hierarchical Bayesian model that addresses these issues. In particular, in our model, the parameters associated with the COM-Poisson do not include spatial random effects (leading to additional variability that changes the dispersion properties of the data), and are then spatially smoothed in subsequent levels of the Bayesian hierarchical model. Furthermore, the spatially smoothed parameters have a simple regression interpretation that facilitates computation. We demonstrate the applicability of our approach using simulated examples, and a motivating application using 2016 US presidential election voting data in the state of Florida obtained from the Florida Division of Elections. 

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4. Bayesian Clustering of Neural Spiking Activity Using a Mixture of Dynamic Poisson Factor Analyzers

   Wei, G; Stevenson, IH; Wang X (January 2022, Advances in neural information processing systems)

   Modern neural recording techniques allow neuroscientists to observe the spiking activity of many neurons simultaneously. Although previous work has illustrated how activity within and between known populations of neurons can be summarized by low-dimensional latent vectors, in many cases what determines a unique population may be unclear. Neurons differ in their anatomical location, but also, in their cell types and response properties. Moreover, multiple distinct populations may not be well described by a single low-dimensional, linear representation.To tackle these challenges, we develop a clustering method based on a mixture of dynamic Poisson factor analyzers (DPFA) model, with the number of clusters treated as an unknown parameter. To do the analysis of DPFA model, we propose a novel Markov chain Monte Carlo (MCMC) algorithm to efficiently sample its posterior distribution. Validating our proposed MCMC algorithm with simulations, we find that it can accurately recover the true clustering and latent states and is insensitive to the initial cluster assignments. We then apply the proposed mixture of DPFA model to multi-region experimental recordings, where we find that the proposed method can identify novel, reliable clusters of neurons based on their activity, and may, thus, be a useful tool for neural data analysis. 

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5. Time‐Varying Spatial Propagation of Brain Networks in fMRI Data

   https://doi.org/10.1002/hbm.70131  

   Bostami, Biozid; Lewis, Noah; Agcaoglu, Oktay; Turner, Jessica_A; van_Erp, Theo; Ford, Judith_M; Fouladivanda, Mahshid; Calhoun, Vince; Iraji, Armin (January 2025, Human Brain Mapping)

   ABSTRACT Spontaneous neural activity coherently relays information across the brain. Several efforts have been made to understand how spontaneous neural activity evolves at the macro‐scale level as measured by resting‐state functional magnetic resonance imaging (rsfMRI). Previous studies observe the global patterns and flow of information in rsfMRI using methods such as sliding window or temporal lags. However, to our knowledge, no studies have examined spatial propagation patterns evolving with time across multiple overlapping 4D networks. Here, we propose a novel approach to study how dynamic states of the brain networks spatially propagate and evaluate whether these propagating states contain information relevant to mental illness. We implement a lagged windowed correlation approach to capture voxel‐wise network‐specific spatial propagation patterns in dynamic states. Results show systematic spatial state changes over time, which we confirmed are replicable across multiple scan sessions using human connectome project data. We observe networks varying in propagation speed; for example, the default mode network (DMN) propagates slowly and remains positively correlated with blood oxygenation level‐dependent (BOLD) signal for 6–8 s, whereas the visual network propagates much quicker. We also show that summaries of network‐specific propagative patterns are linked to schizophrenia. More specifically, we find significant group differences in multiple dynamic parameters between patients with schizophrenia and controls within four large‐scale networks: default mode, temporal lobe, subcortical, and visual network. Individuals with schizophrenia spend more time in certain propagating states. In summary, this study introduces a promising general approach to exploring the spatial propagation in dynamic states of brain networks and their associated complexity and reveals novel insights into the neurobiology of schizophrenia. 

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