This disclosure discloses a method and system for predicting disease quantification parameters for an anatomical structure. The method includes extracting a centerline structure based on a medical image. The method further includes predicting the disease quantification parameter for each sampling point on the extracted centerline structure by using a GNN, with each node corresponds to a sampling point on the extracted centerline structure and each edge corresponds to a spatial constraint relationship between the sampling points. For each node, a local feature is extracted based on the image patch for the corresponding sampling point by using a local feature encoder, and a global feature is extracted by using a global feature encoder based on a set of image patches for a set of sampling points, which include the corresponding sampling point and have a spatial constraint relationship defined by the centerline structure. Then, an embed feature is obtained based on both the local feature and the global feature and input into to the node. The method is able to integrate local and global consideration factors of the sampling points into the GNN to improve the prediction accuracy.