Dimensionality Reduction

Four decomposition methods are available:

  • PCA

  • Kernel PCA

  • Contact Kernel PCA

  • Diffusion Maps

# Standard PCA
pipeline.decomposition.add.pca(
    n_components=10, selection_name="my_selection"
)

# Kernel PCA with RBF kernel
pipeline.decomposition.add.kernel_pca(
    n_components=10, kernel='rbf', gamma=0.01,
    selection_name="my_selection"
)

# Contact Kernel PCA (optimized for binary contact data)
pipeline.decomposition.add.contact_kernel_pca(
    n_components=10, gamma=0.001, selection_name="contacts_only"
)

# Diffusion Maps
pipeline.decomposition.add.diffusion_maps(
    n_components=10, selection_name="my_selection"
)