Given recent experimental results suggesting that neural circuits may evolve through multiple firing states, we develop a framework for estimating state-dependent neural response properties from spike-train data. We modify the traditional hidden Markov model (HMM) framework to incorporate stimulus-driven, non-Poisson point process observations. For maximal flexibility, we allow external, time-varying stimuli and the neurons' own spike histories to drive both the spiking behavior in each state

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... d the transitioning behavior between states. We employ an appropriately modified expectation-maximization algorithm to estimate the model parameters. The expectation step is solved by the standard forward-backward algorithm for HMMs. The maximization step reduces to a set of separable concave optimization problems if the model is restricted slightly. We first test our algorithm on simulated data and are able both to fully recover the parameters used to generate the data and to accurately recapitulate the sequence of hidden states. We then apply our algorithm to a recently published data set in which the observed neuronal ensembles displayed multi-state behavior and show that inclusion of spike-history information significantly improves the fit of the model. Additionally, we show that a simple reformulation of the state-space of the underlying Markov chain allows us to implement a hybrid half-multistate/half-histogram model which may be more appropriate for capturing the complexity of certain data sets than either a simple HMM or a simple peri-stimulus time histogram (PSTH) model alone.