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BERT4Bitter: A bidirectional encoder representations from transformers (BERT)-based model for improving the prediction of bitter peptides

Charoenkwan, P | Nantasenamat, C | Hasan, MM | Manavalan, B  | Shoombuatong, W
Bioinformatics (Oxford, England), 37(17). : 2556-2562, 2021
Journal Title
Bioinformatics (Oxford, England)
Motivation: The identification of bitter peptides through experimental approaches is an expensive and timeconsuming endeavor. Due to the huge number of newly available peptide sequences in the post-genomic era, the development of automated computational models for the identification of novel bitter peptides is highly desirable. Results: In this work, we present BERT4Bitter, a bidirectional encoder representation from transformers (BERT)- based model for predicting bitter peptides directly from their amino acid sequence without using any structural information. To the best of our knowledge, this is the first time a BERT-based model has been employed to identify bitter peptides. Compared to widely used machine learning models, BERT4Bitter achieved the best performance with an accuracy of 0.861 and 0.922 for cross-validation and independent tests, respectively. Furthermore, extensive empirical benchmarking experiments on the independent dataset demonstrated that BERT4Bitter clearly outperformed the existing method with improvements of 8.0% accuracy and 16.0% Matthews coefficient correlation, highlighting the effectiveness and robustness of BERT4Bitter. We believe that the BERT4Bitter method proposed herein will be a useful tool for rapidly screening and identifying novel bitter peptides for drug development and nutritional research.
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Journal Papers > School of Medicine / Graduate School of Medicine > Physiology
Ajou Authors
Balachandran, Manavalan
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