Network or regression-based methods for disease discrimination: a comparison study

BACKGROUND: In stark contrast to network-centric view for complex disease, regression-based methods are preferred in disease prediction, especially for epidemiologists and clinical professionals. It remains a controversy whether the network-based methods have advantageous performance than regression-based methods, and to what extent do they outperform. METHODS: Simulations under different scenarios (the input variables are independent or in network relationship) as well as an application were conducted to assess the prediction performance of four typical methods including Bayesian network, neural network, logistic regression and regression splines. RESULTS: The simulation results reveal that Bayesian network showed a better performance when the variables were in a network relationship or in a chain structure. For the special wheel network structure, logistic regression had a considerable performance compared to others. Further application on GWAS of leprosy show Bayesian network still outperforms other methods. CONCLUSION: Although regression-based methods are still popular and widely used, network-based approaches should be paid more attention, since they capture the complex relationship between variables. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12874-016-0207-2) contains supplementary material, which is available to authorized users.