Kengo Sato is an assistant professor at the department of Biosciences and Informatics at Keio University, Japan. He received his Ph.D. in Computer Science from Keio University, Japan, in 2003. His research interests include bioinformatics, machine learning and life sciences. He develops innovative algorithms for sequence analysis and RNA informatics.
PhD in Computer Science, 2003
MEng in Computer Science, 1997
BSc in Mathematics, 1995
Accurate predictions of RNA secondary structures can help uncover the roles of functional non-coding RNAs. Although machine learning-based models have achieved high performance in terms of prediction accuracy, overfitting is a common risk for such highly parameterized models. Here we show that overfitting can be minimized when RNA folding scores learnt using a deep neural network are integrated together with Turner’s nearest-neighbor free energy parameters. Training the model with thermodynamic regularization ensures that folding scores and the calculated free energy are as close as possible. In computational experiments designed for newly discovered non-coding RNAs, our algorithm (MXfold2) achieves the most robust and accurate predictions of RNA secondary structures without sacrificing computational efficiency compared to several other algorithms. The results suggest that integrating thermodynamic information could help improve the robustness of deep learning-based predictions of RNA secondary structure.