Gene regulatory networks with binary weights

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Abstract

An evolutionary computation framework to learn binary threshold networks is presented. Inspired by the recent trend of binary neural networks, where weights and activation thresholds are represented using 1 and -1 such that they can be stored in 1-bit instead of full precision, we explore this approach for gene regulatory network modeling. We test our method by inferring binary threshold networks of two regulatory network models: Quorum sensing systems in bacterium Paraburkholderia phytofirmans PsJN and the fission yeast cell-cycle. We considered differential evolution and particle swarm optimization for the simulations. Results for weights having only 1 and -1 values, and different activation thresholds are presented. Full binary threshold networks were found with minimum error (2 bits), whereas when the binary restriction is relaxed for the activation thresholds, networks with 0 bit error were found.

Original languageEnglish
Article number104902
JournalBioSystems
Volume227-228
DOIs
StatePublished - May 2023
Externally publishedYes

Keywords

  • Binary threshold networks
  • Differential evolution
  • Gene regulatory networks
  • Particle swarm optimization

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