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bioRxiv · 10.1101/2021.04.27.441365

Prediction of RNA-protein interactions using a nucleotide language model

Yamada, K.·Hamada, M.
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Abstract

MotivationThe accumulation of sequencing data has enabled researchers to predict the interactions between RNA sequences and RNA-binding proteins (RBPs) using novel machine learning techniques. However, existing models are often difficult to interpret and require additional information to sequences. Bidirectional encoder representations from Transformer (BERT) is a language-based deep learning model that is highly interpretable. Therefore, a model based on BERT architecture can potentially overcome such limitations. ResultsHere, we propose BERT-RBP as a model to predict RNA-RBP interactions by adapting the BERT architecture pre-trained on a human reference genome. Our model outperformed state-of-the-art prediction models using the eCLIP-seq data of 154 RBPs. The detailed analysis further revealed that BERT-RBP could recognize both the transcript region type and RNA secondary structure only from sequence information. Overall, the results provide insights into the fine-tuning mechanism of BERT in biological contexts and provide evidence of the applicability of the model to other RNA-related problems. AvailabilityPython source codes are freely available at https://github.com/kkyamada/bert-rbp. Contactmhamada@waseda.jp

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Yamada, K., Hamada, M.. 2021-04-28. Prediction of RNA-protein interactions using a nucleotide language model. https://doi.org/10.1101/2021.04.27.441365

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