In this dissertation we present rule-based machine learning methods for solving problems with high-dimensional or complex datasets. We are applying decision tree methods on blood-based biomarkers and neuropsychological tests to predict Alzheimer’s disease in its early stages. We are also using tree-based methods to identify disparity in dementia related biomarkers among three female ethnic groups. In another part of this research, we tried to use rule-based methods to identify homogeneous subgroups of subjects who share the same risk patterns out of a heterogeneous population. Finally, we applied a network-based method to reduce the dimensionality of a clinical dataset, while capturing the interaction among variables. The results show that the proposed methods are efficient and easy to use in comparison to the current machine learning methods.