Comparison and benchmark of deep learning methods for non-coding RNA classification

• Published in: PLoS computational biology 2024-09, Vol.20 (9), p.e1012446
• Main Authors: Creux, Constance, Zehraoui, Farida, Radvanyi, François, Tahi, Fariza
• Format: Article
• Language: English
• Subjects: Benchmarks; Bioinformatics; Biology and life sciences; Computer and Information Sciences; Computer Science; Engineering and Technology; Identification and classification; Machine learning; Methods; Physical Sciences; Research and Analysis Methods; RNA; RNA sequencing
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1012446

The involvement of non-coding RNAs in biological processes and diseases has made the exploration of their functions crucial. Most non-coding RNAs have yet to be studied, creating the need for methods that can rapidly classify large sets of non-coding RNAs into functional groups, or classes. In recent years, the success of deep learning in various domains led to its application to non-coding RNA classification. Multiple novel architectures have been developed, but these advancements are not covered by current literature reviews. We present an exhaustive comparison of the different methods proposed in the state-of-the-art and describe their associated datasets. Moreover, the literature lacks objective benchmarks. We perform experiments to fairly evaluate the performance of various tools for non-coding RNA classification on popular datasets. The robustness of methods to non-functional sequences and sequence boundary noise is explored. We also measure computation time and CO2 emissions. With regard to these results, we assess the relevance of the different architectural choices and provide recommendations to consider in future methods.