BERT-Promoter: An improved sequence-based predictor of DNA promoter using BERT pre-trained model and SHAP feature selection

Author:

Le Nguyen Quoc Khanh,Ho Quang-Thai,Nguyen Van-Nui,Chang Jung-Su

Funder

Ministry of Science and Technology, Taiwan

Publisher

Elsevier BV

Subject

Computational Mathematics,Organic Chemistry,Biochemistry,Structural Biology

Reference30 articles.

1. Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment;Bajic;Genome Biol.,2006

2. Charoenkwan, P., et al., BERT4Bitter: a bidirectional encoder representations from transformers (BERT)-based model for improving the prediction of bitter peptides. Bioinformatics, 2021.

3. iLearn: an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data;Chen;Brief. Bioinform.,2020

4. Computational identification of promoters and first exons in the human genome;Davuluri;Nat. Genet.,2001

5. Devlin, J., et al. BERT: pre-training of deep bidirectional transformers for language understanding. In: Proceedings of the 2019 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, 1 (Long and Short Papers). 2019.

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