Reservoir Computing Using DNA Oscillators

Xingyi Liu, Keshab K. Parhi

Research output: Contribution to journalArticlepeer-review

4 Scopus citations


This paper presents novel implementations for reservoir computing (RC) using DNA oscillators. An RC system consists of two parts: reservoir and readout layer. The reservoir projects input signals into a high-dimensional feature space which is formed by the state of the reservoir. The internal connectivity structure of the reservoir remains unchanged throughout computation. After training, the readout layer maps the projected features into the desired output. It has been shown in prior work that coupled deoxyribozyme oscillators can be used as the reservoir. In this paper, we utilize the n-phase molecular oscillator (n ≥ 3) presented in our prior work. The readout layer implements a matrix-vector multiplication using molecular reactions based on molecular analog multiplication. All molecular reactions are mapped to DNA strand displacement (DSD) reactions. We also introduce a novel encoding method that can significantly reduce the reaction time. The feasibility of the proposed RC systems based on the DNA oscillator is demonstrated for the handwritten digit recognition task and a second-order nonlinear prediction task.

Original languageEnglish (US)
Pages (from-to)780-787
Number of pages8
JournalACS Synthetic Biology
Issue number2
StatePublished - Feb 18 2022

Bibliographical note

Funding Information:
This research was supported in part by the Army Research Office by grant number W911NF-21-1-0265.

Publisher Copyright:
© 2022 American Chemical Society


  • DNA oscillator
  • DNA readout layer
  • DNA reservoir computing
  • digit classification
  • encoding from time domain to space domain
  • time-series prediction
  • Neural Networks, Computer
  • DNA

PubMed: MeSH publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Journal Article


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