Switching state space model for simultaneously estimating state transitions and nonstationary firing rates

We propose an algorithm for simultaneously estimating state transitions among neural states, the number of neural states, and nonstationary firing rates using a switching state space model (SSSM). This model enables us to detect state transitions based not only on the discontinuous changes of mean firing rates but also on discontinuous changes in temporal profiles of firing rates, e.g., temporal correlation. We derive a variational Bayes algorithm for a non-Gaussian SSSM whose non-Gaussian property is caused by binary spike events. Synthetic data analysis reveals the high performance of our algorithm in estimating state transitions, the number of neural states, and nonstationary firing rates compared to previous methods. We also analyze neural data recorded from the medial temporal area. The statistically detected neural states probably coincide with transient and sustained states, which have been detected heuristically. Estimated parameters suggest that our algorithm detects the state transition based on discontinuous change in the temporal correlation of firing rates, which transitions previous methods cannot detect. This result suggests the advantage of our algorithm in real-data analysis.