Protein–peptide interactions play a crucial role in various cellular processes and are implicated in abnormal cellular behaviors leading to diseases such as cancer. Therefore, understanding these interactions is vital for both functional genomics and drug discovery efforts. Despite a significant increase in the availability of protein–peptide complexes, experimental methods for studying these interactions remain laborious, time-consuming, and expensive. Computational methods offer a complementary approach but often fall short in terms of prediction accuracy. To address these challenges, we introduce PepCNN, a deep learning-based prediction model that incorporates structural and sequence-based information from primary protein sequences. By utilizing a combination of half-sphere exposure, position specific scoring matrices from multiple-sequence alignment tool, and embedding from a pre-trained protein language model, PepCNN outperforms state-of-the-art methods in terms of specificity, precision, and AUC. The PepCNN software and datasets are publicly available at
This content will become publicly available on August 20, 2025
Discrimination-aware classification methods remedy socioeconomic disparities exacerbated by machine learning systems. In this paper, we propose a novel data pre-processing technique that assigns weights to training instances in order to reduce discrimination without changing any of the inputs or labels. While the existing reweighing approach only looks into sensitive attributes, we refine the weights by utilizing both sensitive and insensitive ones. We formulate our weight assignment as a linear programming problem. The weights can be directly used in any classification model into which they are incorporated. We demonstrate three advantages of our approach on synthetic and benchmark datasets. First, discrimination reduction comes at a small cost in accuracy. Second, our method is more scalable than most other pre-processing methods. Third, the trade-off between fairness and accuracy can be explicitly monitored by model users. Code is available at
- PAR ID:
- 10535313
- Publisher / Repository:
- PLOS
- Date Published:
- Journal Name:
- PLOS ONE
- Volume:
- 19
- Issue:
- 8
- ISSN:
- 1932-6203
- Page Range / eLocation ID:
- e0308661
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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