The mapping between the atomic coordinates x and the basis states we call f (x; θ) = χ where θ is a vector of parameters of that mapping. For example, f may involve projecting coordinates onto the backbone dihedral angles of a protein, followed by clustering into 100 discrete states using k-means clustering. The MSM is then specified with a lag time of 10 ns. The parameters of the MSM are the 100 × 100 = 10000 elements of T, while the hyperparameters are θ = (backbone dihedrals, K-Means, 100) where the elements correspond to the feature, clustering method, number of basis states respectively.