Unsupervised, data-driven methods are commonly used in neuroscience to automatically decompose data into interpretable patterns. These patterns differ from one another depending on the assumptions of the models. How these assumptions affect specific data decompositions in practice, however, is often unclear, which hinders model applicability and interpretability. For instance, the hidden Markov model (HMM) automatically detects characteristic, recurring activity patterns (so-called states) from time series data. States are defined by a certain probability distribution, whose state-specific parameters are estimated from the data. But what specific features, from all of those that the data contain, do the states capture? That depends on the choice of probability distribution and on other model hyperparameters. Using both synthetic and real data, we aim at better characterising the behaviour of two HMM types that can be applied to electrophysiological data. Specifically, we study which differences in data features (such as frequency, amplitude or signal-to-noise ratio) are more salient to the models and therefore more likely to drive the state decomposition. Overall, we aim at providing guidance for an appropriate use of this type of analysis on one or two-channel neural electrophysiological data, and an informed interpretation of its results given the characteristics of the data and the purpose of the analysis.
