DOI: 10.1093/bioinformatics/btad457 ISSN: 1367-4811

LegNet: a best-in-class deep learning model for short DNA regulatory regions

Dmitry Penzar, Daria Nogina, Elizaveta Noskova, Arsenii Zinkevich, Georgy Meshcheryakov, Andrey Lando, Abdul Muntakim Rafi, Carl de Boer, Ivan V Kulakovskiy
  • Computational Mathematics
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Molecular Biology
  • Biochemistry
  • Statistics and Probability



The increasing volume of data from high-throughput experiments including parallel reporter assays facilitates the development of complex deep-learning approaches for modeling DNA regulatory grammar.


Here, we introduce LegNet, an EfficientNetV2-inspired convolutional network for modeling short gene regulatory regions. By approaching the sequence-to-expression regression problem as a soft classification task, LegNet secured first place for the team in the DREAM 2022 challenge of predicting gene expression from gigantic parallel reporter assays. Using published data, here, we demonstrate that LegNet outperforms existing models and accurately predicts gene expression per se as well as the effects of single-nucleotide variants. Furthermore, we show how LegNet can be used in a diffusion network manner for the rational design of promoter sequences yielding the desired expression level.

Availability and implementation The GitHub repository includes Jupyter Notebook tutorials and Python scripts under the MIT license to reproduce the results presented in the study.

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