RESEARCH Open Access Predicting protein complex in protein interaction network- a supervised learning based method

Background: Protein complexes are important for understanding principles of cellular organization and function. High-throughput experimental techniques have produced a large amount of protein interactions, making it possible to predict protein complexes from protein-protein interaction networks. However, most of current methods are unsupervised learning based methods which can’t utilize the information of the large amount of available known complexes. Methods: We present a supervised learning-based method for predicting protein complexes in protein- protein interaction networks. The method extracts rich features from both the unweighted and weighted networks to train a Regression model, which is then used for the cliques filtering, growth, and candidate complex filtering. The model utilizes additional “uncertainty ” samples and, therefore, is more discriminative when used in the complex detection algorithm. In addition, our method uses the maximal cliques found by the Cliques algorithm as the initial cliques, which has been proven to be more effective than the method of expanding from the seeding proteins used in other methods. Results: The experimental results on several PIN datasets show that in most cases the performance of our method are superior to comparable state-of-the-art protein complex detection techniques