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.

``How is information decoded in the brain?'' is one of the most difficult and important questions in neuroscience. Whether neural correlation is important or not in decoding neural activities is of special interest. We have developed a general framework for investigating how far the decoding process in the brain can be simplified. First, we hierarchically construct simplified probabilistic models of neural responses that ignore more than $K$th-order correlations by using a maximum entropy principle. Then, we compute how much information is lost when information is decoded using the simplified models, i.e., ``mismatched decoders''. We introduce an information theoretically correct quantity for evaluating the information obtained by mismatched decoders. We applied our proposed framework to spike data for vertebrate retina. We used 100-ms natural movies as stimuli and computed the information contained in neural activities about these movies. We found that the information loss is negligibly small in population activities of ganglion cells even if all orders of correlation are ignored in decoding. We also found that if we assume stationarity for long durations in the information analysis of dynamically changing stimuli like natural movies, pseudo correlations seem to carry a large portion of the information.

Neural activity is non-stationary and varies across time. Hidden Markov Models (HMMs) have been used to track the state transition among quasi-stationary discrete neural states. Within this context, independent Poisson models have been used for the output distribution of HMMs; hence, the model is incapable of tracking the change in correlation without modulating the firing rate. To achieve this, we applied a multivariate Poisson distribution with correlation terms for the output distribution of HMMs. We formulated a Variational Bayes (VB) inference for the model. The VB could automatically determine the appropriate number of hidden states and correlation types while avoiding the overlearning problem. We developed an efficient algorithm for computing posteriors using the recursive relationship of a multivariate Poisson distribution. We demonstrated the performance of our method on synthetic data and a real spike train recorded from a songbird.

Neural activity is non-stationary and varies across time.

We considered a gamma distribution of interspike intervals as a statistical modelfor neuronal spike generation. The model parameters consist of a time-dependent firing rate and a shape parameter that characterizes spiking irregularities of individual neurons. Because the environment changes with time, observed data are generated from the time-dependent firing rate, which is an unknown function. A statistical model with an unknown function is called a semiparametric model, which is one of the unsolved problem in statistics and is generally very difficult to solve. We used a novel method of estimating functions in information geometry to estimate the shape parameter without estimating the unknown function. We analytically obtained an optimal estimating function for the shape parameter independent of the functional form of the firing rate. This estimation is efficient without Fisher information loss and better than maximum likelihood estimation.

We considered a gamma distribution of interspike intervals as a statistical model for neuronal spike generation. The model parameters consist of a time-dependent firing rate and a shape parameter that characterizes spiking irregularities of individual neurons. Because the environment changes with time, observed data are generated from the time-dependent firing rate, which is an unknown function. A statistical model with an unknown function is called a semiparametric model, which is one of the unsolved problem in statistics and is generally very difficult to solve. We used a novel method of estimating functions in information geometry to estimate the shape parameter without estimating the unknown function. We analytically obtained an optimal estimating function for the shape parameter independent of the functional form of the firing rate. This estimation is efficient without Fisher information loss and better than maximum likelihood estimation.

Repeated spike patterns have often been taken as evidence for the synfire chain, a phenomenon that a stable spike synchrony propagates through a feedforward network. Inter-spike intervals which represent a repeated spike pattern are influenced by the propagation speed of a spike packet. However, the relation between the propagation speed and network structure is not well understood. While it is apparent that the propagation speed depends on the excitatory synapse strength, it might also be related to spike patterns. We analyze a feedforward network with Mexican-Hattype connectivity (FMH) using the Fokker-Planck equation. We show that both a uniform and a localized spike packet are stable in the FMH in a certain parameter region. We also demonstrate that the propagation speed depends on the distinct firing patterns in the same network.

Repeated spike patterns have often been taken as evidence for the synfire chain, a phenomenon that a stable spike synchrony propagates through a feedforward network. Inter-spike intervals which represent a repeated spike pattern are influenced by the propagation speed of a spike packet. However, the relation between the propagation speed and network structure isnot well understood. While it is apparent that the propagation speed depends on the excitatory synapse strength, it might also be related to spike patterns. We analyze a feedforward network with Mexican-Hattype connectivity(FMH) using the Fokker-Planck equation. We show that both a uniform and a localized spike packet are stable in the FMH in a certain parameter region. We also demonstrate that the propagation speed depends on the distinct firing patterns in the same network.

This paper proposes neural mechanisms of transcranial magnetic stimulation (TMS). TMS can stimulate the brain non-invasively through a brief magnetic pulse delivered by a coil placed on the scalp, interfering with specific cortical functions with a high temporal resolution. Due to these advantages, TMS has been a popular experimental tool in various neuroscience fields. However, the neural mechanisms underlying TMSinduced interference are still unknown; a theoretical basis for TMS has not been developed. This paper provides computational evidence that inhibitory interactions in a neural population, not an isolated single neuron, play a critical role in yielding the neural interference induced by TMS.

This paper proposes neural mechanisms of transcranial magnetic stimulation (TMS).TMS can stimulate the brain non-invasively through a brief magnetic pulse delivered by a coil placed on the scalp, interfering with specific cortical functions with a high temporal resolution. Due to these advantages, TMS has been a popular experimental tool in various neuroscience fields. However, the neural mechanisms underlying TMSinduced interferenceare still unknown; a theoretical basis for TMS has not been developed. This paper provides computational evidence that inhibitory interactionsin a neural population, not an isolated single neuron, play a critical role in yielding the neural interference induced by TMS.