hmp 1.0.0b2

Package for fitting Hidden Multivariate pattern model to time-series

HMP

HMP is an open-source Python package to analyze neural time-series (e.g. EEG) to estimate Hidden Multivariate Patterns. HMP is described in Weindel, van Maanen & Borst (2024, paper ) and is a generalized and simplified version of the HsMM-MVPA method developed by Anderson, Zhang, Borst, & Walsh (2016).

As a summary of the method, an HMP model parses the reaction time into a number of successive events determined based on patterns in a neural time-serie (e.g. EEG, MEG). Hence any reaction time (or any other relevant behavioral duration) can then be described by a number of cognitive events and the duration between them estimated using HMP. The important aspect of HMP is that it is a whole-brain analysis (or whole scalp analysis) that estimates the peak of trial-recurrent multivariate events on a single-trial basis. These by-trial estimates allow you then to further dig into any aspect you are interested in a signal:

• Describing an experiment or a clinical sample in terms of events detected in the EEG signal
• Describing experimental effects based on the time onset of a particular event
• Estimating the effect of trial-wise manipulations on the identified event presence and time occurrence (e.g. the by-trial variation of stimulus strength or the effect of time-on-task)
• Time-lock EEG signal to the onset of a given event and perform classical ERPs or time-frequency analysis based on the onset of a new event
• And many more (e.g. evidence accumulation models, classification based on the number of events in the signal,...)

Documentation

The documentation for the latest version is available on readthedocs: https://hmp.readthedocs.io/en/latest/welcome.html

To get started

To get started with the code you can run the different tutorials in docs/source/notebooks after having installed HMP (see documentation)

• General aspects on HMP (tutorial 1)
• The different estimation methods (tutorial 2)
• Applying HMP to real data (tutorial 3)
• Load your own EEG data

Citation:

To cite the HMP method you can use the following paper:

Weindel, G., van Maanen, L., & Borst, J. P. (2024). Trial-by-trial detection of cognitive events in neural time-series. Imaging Neuroscience, 2, 1-28.