Entropy 2008, 10, 71-99; DOI: 10.3390/entropy-e10020071 OPEN ACCESS entropy ISSN 1099-4300 Article www.mdpi.org/entropy Estimating the Entropy of Binary Time Series: Methodology, Some Theory and a Simulation Study Yun Gao 1, Ioannis Kontoyiannis 2;? and Elie Bienenstock 3 1 Knight Equity Markets, L.P., Jersey City, NJ 07310, USA 2 Department of Informatics, Athens University of Economics and Business, Athens 10434, Greece 3 Division of Applied Mathematics and Department of Neuroscience, Brown University, Providence, RI 02912, USA E-Mails:
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[email protected] ? Author to whom correspondence should be addressed. Received: 6 March 2008; in revised form: 9 June 2008 / Accepted: 17 June 2008 / Published: 17 June 2008 Abstract: Partly motivated by entropy-estimation problems in neuroscience, we present a detailed and extensive comparison between some of the most popular and effective entropy estimation methods used in practice: The plug-in method, four different estimators based on the Lempel-Ziv (LZ) family of data compression algorithms, an estimator based on the Context-Tree Weighting (CTW) method, and the renewal entropy estimator. METHODOLOGY: Three new entropy estimators are introduced; two new LZ-based estimators, and the “renewal entropy estimator,” which is tailored to data generated by a binary renewal process. For two of the four LZ-based estimators, a bootstrap procedure is described for evaluating their standard error, and a practical rule of thumb is heuristically derived for selecting the values of their parameters in practice. THEORY: We prove that, unlike their earlier versions, the two new LZ-based estimators are universally consistent, that is, they converge to the entropy rate for every finite-valued, stationary and ergodic process.