Background: Proteomics endeavors to study the structures, functions and interactions of proteins. Information of the protein-protein interactions (PPIs) helps to improve our knowledge of the functions and the 3D structures of proteins. Thus determining the PPIs is essential for the study of the proteomics. Keywords: Ensemble learning algorithm, Escherichia coli, machine learning, Protein-Protein Interactions (PPI), random forest (RF), support vector machine (SVM).