Rich parameterization improves RNA structure prediction

Research output: Contribution to journalArticlepeer-review


Current approaches to RNA structure prediction range from physics-based methods, which rely on thousands of experimentally measured thermodynamic parameters, to machine-learning (ML) techniques. While the methods for parameter estimation are successfully shifting toward ML-based approaches, the model parameterizations so far remained fairly constant. We study the potential contribution of increasing the amount of information utilized by RNA folding prediction models to the improvement of their prediction quality. This is achieved by proposing novel models, which refine previous ones by examining more types of structural elements, and larger sequential contexts for these elements. Our proposed fine-grained models are made practical thanks to the availability of large training sets, advances in machine-learning, and recent accelerations to RNA folding algorithms. We show that the application of more detailed models indeed improves prediction quality, while the corresponding running time of the folding algorithm remains fast. An additional important outcome of this experiment is a new RNA folding prediction model (coupled with a freely available implementation), which results in a significantly higher prediction quality than that of previous models. This final model has about 70,000 free parameters, several orders of magnitude more than previous models. Being trained and tested over the same comprehensive data sets, our model achieves a score of 84% according to the F 1-measure over correctly-predicted base-pairs (i.e., 16% error rate), compared to the previously best reported score of 70% (i.e., 30% error rate). That is, the new model yields an error reduction of about 50%. Trained models and source code are available at∼negevcb/contextfold.

Original languageAmerican English
Pages (from-to)1525-1542
Number of pages18
JournalJournal of Computational Biology
Issue number11
StatePublished - 1 Nov 2011


  • RNA secondary structure prediction
  • machine learning

All Science Journal Classification (ASJC) codes

  • Modelling and Simulation
  • Molecular Biology
  • Genetics
  • Computational Mathematics
  • Computational Theory and Mathematics


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