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Extending Transfer Entropy Improves Identification of Effective Connectivity in a Spiking Cortical Network Model

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  • Shinya Ito
  • Michael E Hansen
  • Randy Heiland
  • Andrew Lumsdaine
  • Alan M Litke
  • John M Beggs

Abstract

Transfer entropy (TE) is an information-theoretic measure which has received recent attention in neuroscience for its potential to identify effective connectivity between neurons. Calculating TE for large ensembles of spiking neurons is computationally intensive, and has caused most investigators to probe neural interactions at only a single time delay and at a message length of only a single time bin. This is problematic, as synaptic delays between cortical neurons, for example, range from one to tens of milliseconds. In addition, neurons produce bursts of spikes spanning multiple time bins. To address these issues, here we introduce a free software package that allows TE to be measured at multiple delays and message lengths. To assess performance, we applied these extensions of TE to a spiking cortical network model (Izhikevich, 2006) with known connectivity and a range of synaptic delays. For comparison, we also investigated single-delay TE, at a message length of one bin (D1TE), and cross-correlation (CC) methods. We found that D1TE could identify 36% of true connections when evaluated at a false positive rate of 1%. For extended versions of TE, this dramatically improved to 73% of true connections. In addition, the connections correctly identified by extended versions of TE accounted for 85% of the total synaptic weight in the network. Cross correlation methods generally performed more poorly than extended TE, but were useful when data length was short. A computational performance analysis demonstrated that the algorithm for extended TE, when used on currently available desktop computers, could extract effective connectivity from 1 hr recordings containing 200 neurons in ∼5 min. We conclude that extending TE to multiple delays and message lengths improves its ability to assess effective connectivity between spiking neurons. These extensions to TE soon could become practical tools for experimentalists who record hundreds of spiking neurons.

Suggested Citation

  • Shinya Ito & Michael E Hansen & Randy Heiland & Andrew Lumsdaine & Alan M Litke & John M Beggs, 2011. "Extending Transfer Entropy Improves Identification of Effective Connectivity in a Spiking Cortical Network Model," PLOS ONE, Public Library of Science, vol. 6(11), pages 1-13, November.
  • Handle: RePEc:plo:pone00:0027431
    DOI: 10.1371/journal.pone.0027431
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    Cited by:

    1. Zhai, Lu-Sheng & Zong, Yan-Bo & Wang, Hong-Mei & Yan, Cong & Gao, Zhong-Ke & Jin, Ning-De, 2017. "Characterization of flow pattern transitions for horizontal liquid–liquid pipe flows by using multi-scale distribution entropy in coupled 3D phase space," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 469(C), pages 136-147.
    2. Yifan Gu & Yang Qi & Pulin Gong, 2019. "Rich-club connectivity, diverse population coupling, and dynamical activity patterns emerging from local cortical circuits," PLOS Computational Biology, Public Library of Science, vol. 15(4), pages 1-34, April.
    3. Shinya Ito & Fang-Chin Yeh & Emma Hiolski & Przemyslaw Rydygier & Deborah E Gunning & Pawel Hottowy & Nicholas Timme & Alan M Litke & John M Beggs, 2014. "Large-Scale, High-Resolution Multielectrode-Array Recording Depicts Functional Network Differences of Cortical and Hippocampal Cultures," PLOS ONE, Public Library of Science, vol. 9(8), pages 1-16, August.
    4. Nicholas Timme & Shinya Ito & Maxym Myroshnychenko & Fang-Chin Yeh & Emma Hiolski & Pawel Hottowy & John M Beggs, 2014. "Multiplex Networks of Cortical and Hippocampal Neurons Revealed at Different Timescales," PLOS ONE, Public Library of Science, vol. 9(12), pages 1-43, December.

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