Subcellular Protein Patterns Classification Using Extreme Gradient Boosting with Deep Transfer Learning as Feature Extractor

Proteins are essential structural and functional components of human cells. Understanding and identifying proteins can provide valuable insights into their structure, function and role in human body. Subcellular proteins provide the expression that characterizes the many proteins and their conditions across cell types. This work proposed a classification model for subcellular protein patterns using XGBoost with transfer learning of CNN as the feature extractor. In the model training process, we used ResNet50, VGG16, Xception, and MobileNet as the pre-trained models based on the transfer learning technique to extract different features. The proposed model was used to classify subcellular proteins into 28 patterns. The XGBoost with ResNet50, VGG16, MobileNet, and Xception model achieved an accuracy level of 92.20% 92.77%, 91.63%, and 91.44%, respectively. The XGBoost with ResNet50, VGG16, MobileNet, and Xception model obtained an F1 score of 0.9179, 0.9233, 0.9131, and 0.9152, respectively. Considering the F1 score, All XGBoost with transfer learning of CNN models gave a high score. Therefore, all evaluation parameters clearly demonstrate the high performance of the subcellular protein pattern classification model.