This section is organized as follows: Section 2.1 introduces the theory and implementation of AMUSEt. Section 2.2 provides a review of the tICA theory. Section 2.3 presents the theory and implementation of AMUSET-TICA. Finally, Section 2.4 describes the MD simulation datasets and the selection of hyperparameters for applying the AMUSET-TICA, AMUSEt, and tICA methods.