Chapter

DNA Computing and Molecular Programming

Volume 8141 of the series Lecture Notes in Computer Science pp 76-89

DNA Reservoir Computing: A Novel Molecular Computing Approach

  • Alireza GoudarziAffiliated withDepartment of Computer Science, University of New Mexico
  • , Matthew R. LakinAffiliated withDepartment of Computer Science, University of New Mexico
  • , Darko StefanovicAffiliated withDepartment of Computer Science, University of New MexicoCenter for Biomedical Engineering, University of New Mexico

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Abstract

We propose a novel molecular computing approach based on reservoir computing. In reservoir computing, a dynamical core, called a reservoir, is perturbed with an external input signal while a readout layer maps the reservoir dynamics to a target output. Computation takes place as a transformation from the input space to a high-dimensional spatiotemporal feature space created by the transient dynamics of the reservoir. The readout layer then combines these features to produce the target output. We show that coupled deoxyribozyme oscillators can act as the reservoir. We show that despite using only three coupled oscillators, a molecular reservoir computer could achieve 90% accuracy on a benchmark temporal problem.