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Journal Articles PLoS Computational Biology Year : 2019

Estimating information in time-varying signals

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Abstract

Across diverse biological systems-ranging from neural networks to intracellular signaling and genetic regulatory networks-the information about changes in the environment is frequently encoded in the full temporal dynamics of the network nodes. A pressing data-analysis challenge has thus been to efficiently estimate the amount of information that these dynamics convey from experimental data. Here we develop and evaluate decoding-based estimation methods to lower bound the mutual information about a finite set of inputs, encoded in single-cell high-dimensional time series data. For biological reaction networks governed by the chemical Master equation, we derive model-based information approximations and analytical upper bounds, against which we benchmark our proposed model-free decoding estimators. In contrast to the frequently-used k-nearest-neighbor estimator, decoding-based estimators robustly extract a large fraction of the available information from high-dimensional trajectories with a realistic number of data samples. We apply these estimators to previously published data on Erk and Ca 2+ signaling in mammalian cells and to yeast stress-response, and find that substantial amount of information about environmental state can be encoded by non-trivial response statistics even in stationary signals. We argue that these single-cell, decoding-based information estimates, rather than the commonly-used tests for significant differences between selected population response statistics, provide a proper and unbiased measure for the performance of biological signaling networks.
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Dates and versions

hal-02304413 , version 1 (03-10-2019)

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Sarah Anhala Cepeda-Humerez, Jakob Ruess, Gašper Tkačik. Estimating information in time-varying signals. PLoS Computational Biology, 2019, 15 (9:e1007290), pp.1--33. ⟨10.1371/journal.pcbi.1007290⟩. ⟨hal-02304413⟩
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