Estimation of mutual information between (multidimensional) real-valued variables is used in analysis of complex systems, biological systems, and recently also quantum systems. This estimation is a hard problem, and universally good estimators provably do not exist. Kraskov et al. (PRE, 2004) introduced a successful mutual information estimation approach based on the statistics of distances between neighboring data points, which empirically works for a wide class of underlying probability distributions. Here we improve this estimator by (i) expanding its range of applicability, and by providing (ii) a self-consistent way of verifying the absence of bias, (iii) a method for estimation of its variance, and (iv) a criterion for choosing the values of the free parameter of the estimator. We demonstrate the performance of our estimator on synthetic data sets, as well as on neurophysiological and systems biology data sets.
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