EntropyHub: An open-source toolkit for entropic time series analysis.

Matthew W Flood, Bernd Grimm
Author Information
  1. Matthew W Flood: Human Motion, Orthopaedics, Sports Medicine and Digital Methods (HOSD), Luxembourg Institute of Health (LIH), Eich, Luxembourg. ORCID
  2. Bernd Grimm: Human Motion, Orthopaedics, Sports Medicine and Digital Methods (HOSD), Luxembourg Institute of Health (LIH), Eich, Luxembourg.

Abstract

An increasing number of studies across many research fields from biomedical engineering to finance are employing measures of entropy to quantify the regularity, variability or randomness of time series and image data. Entropy, as it relates to information theory and dynamical systems theory, can be estimated in many ways, with newly developed methods being continuously introduced in the scientific literature. Despite the growing interest in entropic time series and image analysis, there is a shortage of validated, open-source software tools that enable researchers to apply these methods. To date, packages for performing entropy analysis are often run using graphical user interfaces, lack the necessary supporting documentation, or do not include functions for more advanced entropy methods, such as cross-entropy, multiscale cross-entropy or bidimensional entropy. In light of this, this paper introduces EntropyHub, an open-source toolkit for performing entropic time series analysis in MATLAB, Python and Julia. EntropyHub (version 0.1) provides an extensive range of more than forty functions for estimating cross-, multiscale, multiscale cross-, and bidimensional entropy, each including a number of keyword arguments that allows the user to specify multiple parameters in the entropy calculation. Instructions for installation, descriptions of function syntax, and examples of use are fully detailed in the supporting documentation, available on the EntropyHub website- www.EntropyHub.xyz. Compatible with Windows, Mac and Linux operating systems, EntropyHub is hosted on GitHub, as well as the native package repository for MATLAB, Python and Julia, respectively. The goal of EntropyHub is to integrate the many established entropy methods into one complete resource, providing tools that make advanced entropic time series analysis straightforward and reproducible.

References

  1. Biomed Tech (Berl). 2006 Oct;51(4):272-5 [PMID: 17061956]
  2. Entropy (Basel). 2021 Mar 08;23(3): [PMID: 33800469]
  3. Ann Biomed Eng. 2013 Feb;41(2):349-65 [PMID: 23064819]
  4. IEEE Trans Biomed Eng. 2017 Nov.;64(11):2711-2718 [PMID: 28182552]
  5. Annu Int Conf IEEE Eng Med Biol Soc. 2019 Jul;2019:733-736 [PMID: 31946001]
  6. Entropy (Basel). 2021 Feb 11;23(2): [PMID: 33670121]
  7. Comput Methods Programs Biomed. 2020 Dec;197:105718 [PMID: 32866762]
  8. Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Feb;87(2):022911 [PMID: 23496595]
  9. IEEE Trans Affect Comput. 2020 Apr-Jun;11(2):200-213 [PMID: 32489521]
  10. Chaos. 2009 Mar;19(1):013123 [PMID: 19334987]
  11. Entropy (Basel). 2019 Jul 15;21(7): [PMID: 33267408]
  12. Phys Rev E. 2017 Jun;95(6-1):062114 [PMID: 28709192]
  13. Science. 2013 May 17;340(6134):814-5 [PMID: 23687031]
  14. Complexity. 2019;2019: [PMID: 31341377]
  15. Brain Cogn. 2018 Jun;123:126-135 [PMID: 29562207]
  16. Phys Rev Lett. 2002 Apr 29;88(17):174102 [PMID: 12005759]
  17. Phys Rev Lett. 2004 Feb 27;92(8):089803; author reply 089804 [PMID: 14995828]
  18. Comput Methods Programs Biomed. 2005 Dec;80(3):187-94 [PMID: 16219385]
  19. Entropy (Basel). 2018 Feb 22;20(2): [PMID: 33265229]
  20. Biol Cybern. 1999 Aug;81(2):119-29 [PMID: 10481240]
  21. Entropy (Basel). 2019 Apr 10;21(4): [PMID: 33267099]
  22. Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Feb;85(2 Pt 1):021906 [PMID: 22463243]
  23. Electroencephalogr Clin Neurophysiol. 1991 Sep;79(3):204-10 [PMID: 1714811]
  24. Nature. 2020 Sep;585(7825):357-362 [PMID: 32939066]
  25. Am J Physiol Heart Circ Physiol. 2000 Jun;278(6):H2039-49 [PMID: 10843903]
  26. Biomed Eng Online. 2017 Sep 21;16(1):112 [PMID: 28934961]
  27. Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Feb;71(2 Pt 1):021906 [PMID: 15783351]
  28. IEEE Trans Biomed Eng. 2001 Dec;48(12):1424-33 [PMID: 11759923]
  29. J Neural Eng. 2013 Jun;10(3):036023 [PMID: 23676901]
  30. Nat Methods. 2020 Mar;17(3):261-272 [PMID: 32015543]
  31. Sensors (Basel). 2019 Nov 27;19(23): [PMID: 31783659]
  32. Physiol Meas. 2015 Feb;36(2):303-14 [PMID: 25585603]
  33. Entropy (Basel). 2018 Mar 20;20(3): [PMID: 33265301]
  34. J Neurophysiol. 2019 Sep 1;122(3):1147-1162 [PMID: 31365308]
  35. Proc Natl Acad Sci U S A. 1991 Mar 15;88(6):2297-301 [PMID: 11607165]
  36. Cogn Neurodyn. 2011 Sep;5(3):277-84 [PMID: 22942916]
  37. Clin Neurophysiol. 2005 Aug;116(8):1826-34 [PMID: 15979403]
  38. Physiol Meas. 2019 Nov 04;40(10):105006 [PMID: 31574498]
  39. IEEE Trans Biomed Eng. 2009 Sep;56(9):2202-13 [PMID: 19457745]
  40. Med Biol Eng Comput. 2015 Jan;53(1):77-87 [PMID: 25351477]
  41. Gigascience. 2016 Jul 11;5(1):30 [PMID: 27401684]
  42. Bull Math Biol. 1991;53(5):665-78 [PMID: 1933033]
  43. Entropy (Basel). 2019 Dec 29;22(1): [PMID: 33285820]
  44. Math Biosci Eng. 2019 Jul 26;16(6):6842-6857 [PMID: 31698591]
  45. Comput Biol Med. 2018 Dec 1;103:148-160 [PMID: 30368171]
  46. Entropy (Basel). 2019 Apr 16;21(4): [PMID: 33267118]
  47. Clin Neurophysiol. 2019 Feb;130(2):259-269 [PMID: 30583273]
  48. Comput Methods Programs Biomed. 2016 May;128:40-51 [PMID: 27040830]
  49. Biomed Eng Online. 2019 Mar 20;18(1):30 [PMID: 30894180]
  50. Comput Math Methods Med. 2013;2013:231762 [PMID: 24174987]
  51. Cardiovasc Eng Technol. 2015 Dec;6(4):557-76 [PMID: 26577486]
  52. Phys Rev Lett. 2002 Aug 5;89(6):068102 [PMID: 12190613]
  53. Comput Biol Med. 2018 Apr 1;95:13-23 [PMID: 29433037]
  54. Comput Biol Med. 2019 Jun;109:280-289 [PMID: 31100581]
  55. Am J Physiol Regul Integr Comp Physiol. 2008 Aug;295(2):R550-7 [PMID: 18495836]
  56. IEEE Eng Med Biol Mag. 2001 May-Jun;20(3):70-5 [PMID: 11446213]
  57. IEEE Trans Neural Syst Rehabil Eng. 2007 Jun;15(2):266-72 [PMID: 17601197]

MeSH Term

Access to Information
Algorithms
Entropy
Humans
Time Factors

Word Cloud

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