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HyperIT

Hyperscanning Analyses using Information-Theoretic Measures!

Documentation Status Unit Testing

The HyperIT Class is a framework that calculates Mutual Information (MI), Transfer Entropy (TE), and Integrated Information Decomposition ($\Phi\text{ID}$) for both hyperscanning and intra-brain analyses.

Handling continuous time-series data (epoched or otherwise), HyperIT computes these information-theoretic measures at different spatial scales of organisation (micro, meso, and macro) — compatible with EEG, MEG, fMRI, and fNIRS data. Offers parameter customisation and estimator selection (Histogram/Binning, KSG, Box Kernel, Gaussian, and Symbolic) via JIDT. Most estimators are equipped with statistical significance testing based on permutation/bootstrapping approaches, too. Visualisations of MI/TE matrices are also provided.

In all, HyperIT is designed to allow researchers to analyse various complex systems at different scales of organisation deploying information-theoretic measures, particularly focusing on neural time-series data in the context of hyperscanning.

Read the JOSS pre-print here: "HyperIT: A Python toolbox for an information-theoretic social neuroscience"

Usage

HyperIT uses a Class/OOP framework, allowing multiple instances of HyperIT objects (instantiated with different data). MI, TE, and $\Phi\text{ID}$ atoms can be computed by calling the following functions:

from hyperit import HyperIT
from phyid.utils import PhiID_atoms_abbr

# Only needs to be called once
HyperIT.setup_JVM()

# Gather your data here ...

# Create instance
it = HyperIT(data1, data2, channel_names, verbose)

# ROIs can be specified and then reset back to default
it.roi(roi_list)
it.reset_roi()

# Calculate Mutual Information and Transfer Entropy
mi = it.compute_mi(estimator='kernel',
                   include_intra=True,
                   epoch_average=False
                   calc_sigstats=True,
                   vis=True,
                   plot_epochs=[1,6], # use -1 to plot all epochs
                   kwargs) # Pass estimator-specific parameters here

te = it.compute_te(estimator='gaussian',
                   include_intra=False,
                   epoch_average=True
                   calc_sigstats=True,
                   vis=True,
                   kwargs) 

# Calculate Integrated Information Decomposition
atoms = it.compute_atoms(tau=5, redundancy='MMI', include_intra=True, epoch_average=True)
print({key: value for key, value in zip(PhiID_atoms_abbr, atoms)})

For specific estimator types and general functionality, see Documentation and Tutorial.

Installation

To install HyperIT, simply use pip:

pip install git+https://github.com/EdoardoChidichimo/HyperIT.git

Dependencies

numpy
scipy
matplotlib
jpype1
phyid

See:

https://jpype.readthedocs.io/en/latest/

https://github.com/Imperial-MIND-lab/integrated-info-decomp/tree/main

Acknowledgements

For MI and TE calculations, HyperIT depends on JIDT by Lizier and colleagues, accessible here, and published here:

  • Lizier, J. T. (2014). "JIDT: An information-theoretic toolkit for studying the dynamics of complex systems", Frontiers in Robotics and AI 1(11). doi:10.3389/frobt.2014.00011 (pre-print: arXiv:1408.3270)

For $\Phi\text{ID}$ atom calculations, HyperIT depends on phyid from Imperial Mind Lab, with thanks to Pedro Mediano and Eric Ceballos Dominguez for providing the code and guidance.

  • Mediano, P. A. M., Rosas, F. E., Luppi, A. I., Carhart-Harris, R. L., Bor, D., Seth, A. K., & Barrett, A. B. (2021). Towards an extended taxonomy of information dynamics via Integrated Information Decomposition. https://doi.org/10.48550/ARXIV.2109.13186
  • Luppi, A. I., Mediano, P. A. M., Rosas, F. E., Holland, N., Fryer, T. D., O’Brien, J. T., Rowe, J. B., Menon, D. K., Bor, D., & Stamatakis, E. A. (2022). A synergistic core for human brain evolution and cognition. Nature Neuroscience, 25(6), 771–782. https://doi.org/10.1038/s41593-022-01070-0