Application of Markov chain Monte Carlo and machine learning for identifying active modules in biological graphs

In biology, information about interactions between the proteins or genes under study can be represented as a biological graph. A connected subgraph, whose vertices perform a common biological function, is called an active module. The Markov Chain Monte Carlo (MCMC) algorithm is an effective method for identifying active modules in biological graphs. In the context of protein-protein interactions, accurately identifying the active module allows for determining which protein function disruption leads to certain changes (e.g., diseases) in a biological system (cell/organism). This study demonstrates that applying MCMC in combination with models (that take graph topology into account) provides higher accuracy in identifying the active module. This study independently utilizes a protein-protein interaction graph (InWebIM) and the GeneMANIA functional association network for training the model and comparing it with the known MCMC-based method. To search for the active module, a combination of MCMC and a machine learning method, gradient boosting (xgboost), was employed. The combined use of the MCMC-based method and gradient boosting improves the accuracy of active module identification compared to the MCMC-based method alone on simulated data. Improving the accuracy of active module identification is crucial for studying the biological mechanisms of diseases and discovering individual proteins functionally associated with the development of diseases.