Data-driven Boolean network inference using a genetic algorithm with marker-based encoding

Xiang Liu, Ning Shi, Yan Wang, Zhicheng Ji, Shan He

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The inference of Boolean networks is crucial for analyzing the topology and dynamics of gene regulatory networks. Many data-driven approaches using evolutionary algorithms have been proposed based on time-series data. However, the ability to infer both network topology and dynamics is restricted by their inflexible encoding schemes. To address this problem, we propose a novel Boolean network inference algorithm for inferring both network topology and dynamics simultaneously. The main idea is that, we use a marker-based genetic algorithm to encode both regulatory nodes and logical operators in a chromosome. By using the markers and introducing more logical operators, the proposed algorithm can infer more diverse candidate Boolean functions. The proposed algorithm is applied to five networks, including two artificial Boolean networks and three real-world gene regulatory networks. Compared with other algorithms, the experimental results demonstrate that our proposed algorithm infers more accurate topology and dynamics.
Original languageEnglish
Number of pages12
JournalIEEE - ACM Transactions on Computational Biology and Bioinformatics
Publication statusAccepted/In press - 26 Jan 2021


  • Boolean network inference
  • Data driven
  • Evolutionary algorithm
  • Gene regulatory network
  • Marker-based encoding

ASJC Scopus subject areas

  • Biotechnology
  • Genetics
  • Applied Mathematics


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