A sticky Poisson Hidden Markov Model for solving the problem of over-segmentation and rapid state switching in cortical datasets

The application of hidden Markov models (HMMs) to neural data has uncovered hidden states and signatures of neural dynamics that are relevant for sensory and cognitive processes. However, training an HMM on cortical data requires a careful handling of model selection, since models with more numerous hidden states generally have a higher likelihood on new (unseen) data. A potentially related problem is the occurrence of very rapid state switching after decoding the data with an HMM. The first problem can lead to overfitting and over-segmentation of the data. The second problem is due to intermediate-to-low self-transition probabilities and is at odds with many reports that hidden states in cortex tend to last from hundred of milliseconds to seconds. Here, we show that we can alleviate both problems by regularizing a Poisson-HMM during training so as to enforce large self-transition probabilities. We call this algorithm the ‘sticky Poisson-HMM’ (sPHMM). The sPHMM successfully eliminates rapid state switching, outperforming an alternative strategy based on an HMM with a large prior on the self-transition probabilities. When used together with the Bayesian Information Criterion for model selection, the sPHMM also captures the ground truth in surrogate datasets built to resemble the statistical properties of the experimental data.