Integrating Traditional Machine Learning and Deep Learning for Precision Screening of Anticancer Peptides: A Novel Approach for Efficient Drug Discovery

The rapid and effective identification of anticancer peptides (ACPs) by computer technology provides a new perspective for cancer treatment. In the identification process of ACPs, accurate sequence encoding and effective classification models are crucial for predicting their biological activity. Traditional machine learning methods have been widely applied in sequence analysis, but deep learning provides a new approach to capture sequence complexity. In this study, a two-stage ACPs classification model was innovatively proposed. Three novel coding strategies were explored; two mainstream Natural Language Processing (NLP) models and 11 machine learning models were fused to identify ACPs, which significantly improved the prediction accuracy of ACPs. We analyzed the correlation between peptide chain amino acids and evaluated the relevant performance of the model by the ROC curve and t-SNE dimensionality reduction technique. The results indicated that the deep learning and machine learning fusion models of M3E-base and KNeighborsDist models, especially when considering the semantic information on amino acid sequences, achieved the highest average accuracy (AvgAcc) of 0.939, with an AUC value as high as 0.97. Then, in vitro cell experiments were used to verify that the two ACPs predicted by the model had antitumor efficacy. This study provides a convenient and effective method for screening ACPs. With further optimization and testing, these strategies have the potential to play an important role in drug discovery and design.