Granger Causal Inference from Spiking Observations via Latent Variable Modeling

Extracting directional connectivity in a neuronal ensemble from spiking observations is a key challenge in understanding the circuit mechanisms of brain function. Existing methods proceed in two stages, by first estimating the latent processes that govern spiking, followed by characterizing connectivity using said estimates. As such, the extracted networks in the second stage are highly sensitive to the accuracy of the estimates in the first stage. In this work, we introduce a framework to directly extract Granger causal links from spiking observations, without requiring intermediate time-domain estimation, by explicitly modeling the endogenous and exogenous latent processes that underlie spiking activity. Our proposed method integrates several techniques such as point processes, state-space modeling and Polya-Gamma augmentation. We demonstrate the utility of our proposed approach using simulated data and application to real data from the rat brain during sleep.