Provided is a method for diagnosing a disease risk based on a complex biomarker network. More particularly, provided is a method for predicting or diagnosing a disease risk by constructing a complex disease relation network from biomarkers extracted from a liquid biological specimen and automatically extracting a disease marker from the complex disease relation network. It was confirmed that the method for predicting or diagnosing a disease risk using the biomarkers extracted from the liquid biological specimen developed according to the present invention applies an improved network analysis and learning method as compared to conventional methods, and thus enables disease-related diagnosis which shows high sensitivity and specificity even when only a few biomarkers are applied, which indicates that the method of the present invention shows superior extraction performance, compared to the methods using conventional variational dropout-based biomarker extraction.