A Feature Selection Method for Prediction Essential Protein

作者：Zhong, Jiancheng; Wang, Jianxin^*; Peng, Wei; Zhang, Zhen; Li, Min

来源：Tsinghua Science and Technology, 2015, 20(5): 491-499.

DOI：10.1109/TST.2015.7297748

• essential protein
• feature selection
• Protein-Protein Interaction (PPI)
• machine learning
• centrality algorithm

Essential proteins are vital to the survival of a cell. There are various features related to the essentiality of proteins, such as biological and topological features. Many computational methods have been developed to identify essential proteins by using these features. However, it is still a big challenge to design an effective method that is able to select suitable features and integrate them to predict essential proteins. In this work, we first collect 26 features, and use SVM-RFE to select some of them to create a feature space for predicting essential proteins, and then remove the features that share the biological meaning with other features in the feature space according to their Pearson Correlation Coefficients (PCC). The experiments are carried out on S. cerevisiae data. Six features are determined as the best subset of features. To assess the prediction performance of our method, we further compare it with some machine learning methods, such as SVM, Naive Bayes, Bayes Network, and NBTree when inputting the different number of features. The results show that those methods using the 6 features outperform that using other features, which confirms the effectiveness of our feature selection method for essential protein prediction.

• 出版日期2015-10
• 单位湖南师范大学; 昆明理工大学; 中南大学