JIDT: An information-theoretic toolkit for studying the dynamics of complex systems

Complex systems are increasingly being viewed as distributed information processing systems, particularly in the domains of computational neuroscience, bioinformatics and Artificial Life. This trend has resulted in a strong uptake in the use of (Shannon) information-theoretic measures to analyse the dynamics of complex systems in these fields. We introduce the Java Information Dynamics Toolkit (JIDT): a Google code project which provides a standalone, (GNU GPL v3 licensed) open-source code implementation for empirical estimation of information-theoretic measures from time-series data. While the toolkit provides classic information-theoretic measures (e.g. entropy, mutual information, conditional mutual information), it ultimately focusses on implementing higher-level measures for information dynamics. That is, JIDT focusses on quantifying information storage, transfer and modification, and the dynamics of these operations in space and time. For this purpose, it includes implementations of the transfer entropy and active information storage, their multivariate extensions and local or pointwise variants. JIDT provides implementations for both discrete and continuous-valued data for each measure, including various types of estimator for continuous data (e.g. Gaussian, box-kernel and Kraskov-Stoegbauer-Grassberger) which can be swapped at run-time due to Java's object-oriented polymorphism. Furthermore, while written in Java, the toolkit can be used directly in MATLAB, GNU Octave, Python and other environments. We present the principles behind the code design, and provide several examples to guide users.Comment: 37 pages, 4 figure

Optimal Rates for Regularized Conditional Mean Embedding Learning

We address the consistency of a kernel ridge regression estimate of the conditional mean embedding (CME), which is an embedding of the conditional distribution of $Y$ given $X$ into a target reproducing kernel Hilbert space $\mathcal{H}_Y$. The CME allows us to take conditional expectations of target RKHS functions, and has been employed in nonparametric causal and Bayesian inference. We address the misspecified setting, where the target CME is in the space of Hilbert-Schmidt operators acting from an input interpolation space between $\mathcal{H}_X$ and $L_2$, to $\mathcal{H}_Y$. This space of operators is shown to be isomorphic to a newly defined vector-valued interpolation space. Using this isomorphism, we derive a novel and adaptive statistical learning rate for the empirical CME estimator under the misspecified setting. Our analysis reveals that our rates match the optimal $O(\log n / n)$ rates without assuming $\mathcal{H}_Y$ to be finite dimensional. We further establish a lower bound on the learning rate, which shows that the obtained upper bound is optimal

Nonparametric approximation of conditional expectation operators

Given the joint distribution of two random variables $X,Y$ on some second countable locally compact Hausdorff space, we investigate the statistical approximation of the $L^2$-operator defined by $[Pf](x) := \mathbb{E}[ f(Y) \mid X = x ]$ under minimal assumptions. By modifying its domain, we prove that $P$ can be arbitrarily well approximated in operator norm by Hilbert--Schmidt operators acting on a reproducing kernel Hilbert space. This fact allows to estimate $P$ uniformly by finite-rank operators over a dense subspace even when $P$ is not compact. In terms of modes of convergence, we thereby obtain the superiority of kernel-based techniques over classically used parametric projection approaches such as Galerkin methods. This also provides a novel perspective on which limiting object the nonparametric estimate of $P$ converges to. As an application, we show that these results are particularly important for a large family of spectral analysis techniques for Markov transition operators. Our investigation also gives a new asymptotic perspective on the so-called kernel conditional mean embedding, which is the theoretical foundation of a wide variety of techniques in kernel-based nonparametric inference