Pengyu Liu1, Jiangning Song2, Chun-Yu Lin3,4, Tatsuya Akutsu5. 1. Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, 611-0011, Japan. 2. Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia. 3. Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan. 4. Center for Intelligent Drug Systems and Smart Bio-devices, National Chiao Tung University, Hsinchu, 300, Taiwan. 5. Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, 611-0011, Japan. takutsu@kuicr.kyoto-u.ac.jp.
Abstract
BACKGROUND: Human dicer is an enzyme that cleaves pre-miRNAs into miRNAs. Several models have been developed to predict human dicer cleavage sites, including PHDCleav and LBSizeCleav. Given an input sequence, these models can predict whether the sequence contains a cleavage site. However, these models only consider each sequence independently and lack interpretability. Therefore, it is necessary to develop an accurate and explainable predictor, which employs relations between different sequences, to enhance the understanding of the mechanism by which human dicer cleaves pre-miRNA. RESULTS: In this study, we develop an accurate and explainable predictor for human dicer cleavage site - ReCGBM. We design relational features and class features as inputs to a lightGBM model. Computational experiments show that ReCGBM achieves the best performance compared to the existing methods. Further, we find that features in close proximity to the center of pre-miRNA are more important and make a significant contribution to the performance improvement of the developed method. CONCLUSIONS: The results of this study show that ReCGBM is an interpretable and accurate predictor. Besides, the analyses of feature importance show that it might be of particular interest to consider more informative features close to the center of the pre-miRNA in future predictors.
BACKGROUND:Humandicer is an enzyme that cleaves pre-miRNAs into miRNAs. Several models have been developed to predict humandicer cleavage sites, including PHDCleav and LBSizeCleav. Given an input sequence, these models can predict whether the sequence contains a cleavage site. However, these models only consider each sequence independently and lack interpretability. Therefore, it is necessary to develop an accurate and explainable predictor, which employs relations between different sequences, to enhance the understanding of the mechanism by which humandicer cleaves pre-miRNA. RESULTS: In this study, we develop an accurate and explainable predictor for humandicer cleavage site - ReCGBM. We design relational features and class features as inputs to a lightGBM model. Computational experiments show that ReCGBM achieves the best performance compared to the existing methods. Further, we find that features in close proximity to the center of pre-miRNA are more important and make a significant contribution to the performance improvement of the developed method. CONCLUSIONS: The results of this study show that ReCGBM is an interpretable and accurate predictor. Besides, the analyses of feature importance show that it might be of particular interest to consider more informative features close to the center of the pre-miRNA in future predictors.
Authors: Huiling He; Krystian Jazdzewski; Wei Li; Sandya Liyanarachchi; Rebecca Nagy; Stefano Volinia; George A Calin; Chang-Gong Liu; Kaarle Franssila; Saul Suster; Richard T Kloos; Carlo M Croce; Albert de la Chapelle Journal: Proc Natl Acad Sci U S A Date: 2005-12-19 Impact factor: 11.205