SO(3)-invariant PCA with application to molecular data

Principal component analysis (PCA) is a fundamental technique for dimensionality reduction and denoising; however, its application to three-dimensional data with arbitrary orientations -- common in structural biology -- presents significant challenges. A naive approach requires augmenting the dataset with many rotated copies of each sample, incurring prohibitive computational costs. In this paper, we extend PCA to 3D volumetric datasets with unknown orientations by developing an efficient and principled framework for SO(3)-invariant PCA that implicitly accounts for all rotations without explicit data augmentation. By exploiting underlying algebraic structure, we demonstrate that the computation involves only the square root of the total number of covariance entries, resulting in a substantial reduction in complexity. We validate the method on real-world molecular datasets, demonstrating its effectiveness and opening up new possibilities for large-scale, high-dimensional reconstruction problems.

Diffusion Maps for Group-Invariant Manifolds

In this article, we consider the manifold learning problem when the data set is invariant under the action of a compact Lie group $K$. Our approach consists in augmenting the data-induced graph Laplacian by integrating over the $K$-orbits of the existing data points, which yields a $K$-invariant graph Laplacian $L$. We prove that $L$ can be diagonalized by using the unitary irreducible representation matrices of $K$, and we provide an explicit formula for computing its eigenvalues and eigenfunctions. In addition, we show that the normalized Laplacian operator $L_N$ converges to the Laplace-Beltrami operator of the data manifold with an improved convergence rate, where the improvement grows with the dimension of the symmetry group $K$. This work extends the steerable graph Laplacian framework of Landa and Shkolnisky from the case of $\operatorname{SO}(2)$ to arbitrary compact Lie groups.