A novel two-way rebalancing strategy for identifying carbonylation sites

• Published in: BMC bioinformatics 2023-11, Vol.24 (1), p.1-429, Article 429
• Main Authors: Chen, Linjun, Jing, Xiao-Yuan, Hao, Yaru, Liu, Wei, Zhu, Xiaoke, Han, Wei
• Format: Article
• Language: English
• Subjects: Aging; Amino acids; Analysis; Attention technique; Carbonylation; Carbonyls; Deep learning; Disease; Evaluation; Feasibility; Generative adversarial networks; Health aspects; Identifying protein carbonylation sites; Imports; Laws, regulations, etc; Multiple sclerosis; Post-translation; Post-translational modification; Predictions; Protein carbonylation; Proteins; Rebalance; Resampling; Simulation; Support vector machines
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-023-05551-2

As an irreversible post-translational modification, protein carbonylation is closely related to many diseases and aging. Protein carbonylation prediction for related patients is significant, which can help clinicians make appropriate therapeutic schemes. Because carbonylation sites can be used to indicate change or loss of protein function, integrating these protein carbonylation site data has been a promising method in prediction. Based on these protein carbonylation site data, some protein carbonylation prediction methods have been proposed. However, most data is highly class imbalanced, and the number of un-carbonylation sites greatly exceeds that of carbonylation sites. Unfortunately, existing methods have not addressed this issue adequately. In this work, we propose a novel two-way rebalancing strategy based on the attention technique and generative adversarial network (Carsite_AGan) for identifying protein carbonylation sites. Specifically, Carsite_AGan proposes a novel undersampling method based on attention technology that allows sites with high importance value to be selected from un-carbonylation sites. The attention technique can obtain the value of each sample's importance. In the meanwhile, Carsite_AGan designs a generative adversarial network-based oversampling method to generate high-feasibility carbonylation sites. The generative adversarial network can generate high-feasibility samples through its generator and discriminator. Finally, we use a classifier like a nonlinear support vector machine to identify protein carbonylation sites. Experimental results demonstrate that our approach significantly outperforms other resampling methods. Using our approach to resampling carbonylation data can significantly improve the effect of identifying protein carbonylation sites.