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Register a new userIDTxl: The Information Dynamics Toolkit xl: a Python package for the efficient analysis of multivariate information dynamics in networks
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Added by
Patricia Wollstadt
Publication date
2018
fields
Informatics Engineering
and research's language is
English
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The Information Dynamics Toolkit xl (IDTxl) is a comprehensive software package for efficient inference of networks and their node dynamics from multivariate time series data using information theory. IDTxl provides functionality to estimate the following measures: 1) For network inference: multivariate transfer entropy (TE)/Granger causality (GC), multivariate mutual information (MI), bivariate TE/GC, bivariate MI 2) For analysis of node dynamics: active information storage (AIS), partial information decomposition (PID) IDTxl implements estimators for discrete and continuous data with parallel computing engines for both GPU and CPU platforms. Written for Python3.4.3+.
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The information that two random variables $Y$, $Z$ contain about a third random variable $X$ can have aspects of shared information (contained in both $Y$ and $Z$), of complementary information (only available from $(Y,Z)$ together) and of unique information (contained exclusively in either $Y$ or $Z$). Here, we study measures $widetilde{SI}$ of shared, $widetilde{UI}$ unique and $widetilde{CI}$ complementary information introduced by Bertschinger et al., which are motivated from a decision theoretic perspective. We find that in most cases the intuitive rule that more variables contain more information applies, with the exception that $widetilde{SI}$ and $widetilde{CI}$ information are not monotone in the target variable $X$. Additionally, we show that it is not possible to extend the bivariate information decomposition into $widetilde{SI}$, $widetilde{UI}$ and $widetilde{CI}$ to a non-negative decomposition on the partial information lattice of Williams and Beer. Nevertheless, the quantities $widetilde{UI}$, $widetilde{SI}$ and $widetilde{CI}$ have a well-defined interpretation, even in the multivariate setting.
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 Javas 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.
The authors have recently defined the Renyi information dimension rate $d({X_t})$ of a stationary stochastic process ${X_t,,tinmathbb{Z}}$ as the entropy rate of the uniformly-quantized process divided by minus the logarithm of the quantizer step size $1/m$ in the limit as $mtoinfty$ (B. Geiger and T. Koch, On the information dimension rate of stochastic processes, in Proc. IEEE Int. Symp. Inf. Theory (ISIT), Aachen, Germany, June 2017). For Gaussian processes with a given spectral distribution function $F_X$, they showed that the information dimension rate equals the Lebesgue measure of the set of harmonics where the derivative of $F_X$ is positive. This paper extends this result to multivariate Gaussian processes with a given matrix-valued spectral distribution function $F_{mathbf{X}}$. It is demonstrated that the information dimension rate equals the average rank of the derivative of $F_{mathbf{X}}$. As a side result, it is shown that the scale and translation invariance of information dimension carries over from random variables to stochastic processes.
The entropy of a pair of random variables is commonly depicted using a Venn diagram. This representation is potentially misleading, however, since the multivariate mutual information can be negative. This paper presents new measures of multivariate information content that can be accurately depicted using Venn diagrams for any number of random variables. These measures complement the existing measures of multivariate mutual information and are constructed by considering the algebraic structure of information sharing. It is shown that the distinct ways in which a set of marginal observers can share their information with a non-observing third party corresponds to the elements of a free distributive lattice. The redundancy lattice from partial information decomposition is then subsequently and independently derived by combining the algebraic structures of joint and shared information content.
This article introduces a model-agnostic approach to study statistical synergy, a form of emergence in which patterns at large scales are not traceable from lower scales. Our framework leverages various multivariate extensions of Shannons mutual information, and introduces the O-information as a metric capable of characterising synergy- and redundancy-dominated systems. We develop key analytical properties of the O-information, and study how it relates to other metrics of high-order interactions from the statistical mechanics and neuroscience literature. Finally, as a proof of concept, we use the proposed framework to explore the relevance of statistical synergy in Baroque music scores.
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