Pulling back symmetric Riemannian geometry for data analysis

Data sets tend to live in low-dimensional non-linear subspaces. Ideal data analysis tools for such data sets should therefore account for such non-linear geometry. The symmetric Riemannian geometry setting can be suitable for a variety of reasons. First, it comes with a rich mathematical structure to account for a wide range of non-linear geometries that has been shown to be able to capture the data geometry through empirical evidence from classical non-linear embedding. Second, many standard data analysis tools initially developed for data in Euclidean space can also be generalised efficiently to data on a symmetric Riemannian manifold. A conceptual challenge comes from the lack of guidelines for constructing a symmetric Riemannian structure on the data space itself and the lack of guidelines for modifying successful algorithms on symmetric Riemannian manifolds for data analysis to this setting. This work considers these challenges in the setting of pullback Riemannian geometry through a diffeomorphism. The first part of the paper characterises diffeomorphisms that result in proper, stable and efficient data analysis. The second part then uses these best practices to guide construction of such diffeomorphisms through deep learning. As a proof of concept, different types of pullback geometries -- among which the proposed construction -- are tested on several data analysis tasks and on several toy data sets. The numerical experiments confirm the predictions from theory, i.e., that the diffeomorphisms generating the pullback geometry need to map the data manifold into a geodesic subspace of the pulled back Riemannian manifold while preserving local isometry around the data manifold for proper, stable and efficient data analysis, and that pulling back positive curvature can be problematic in terms of stability.

Spectral decomposition of atomic structures in heterogeneous cryo-EM

We consider the problem of recovering the three-dimensional atomic structure of a flexible macromolecule from a heterogeneous cryo-EM dataset. The dataset contains noisy tomographic projections of the electrostatic potential of the macromolecule, taken from different viewing directions, and in the heterogeneous case, each image corresponds to a different conformation of the macromolecule. Under the assumption that the macromolecule can be modelled as a chain, or discrete curve (as it is for instance the case for a protein backbone with a single chain of amino-acids), we introduce a method to estimate the deformation of the atomic model with respect to a given conformation, which is assumed to be known a priori. Our method consists on estimating the torsion and bond angles of the atomic model in each conformation as a linear combination of the eigenfunctions of the Laplace operator in the manifold of conformations. These eigenfunctions can be approximated by means of a well-known technique in manifold learning, based on the construction of a graph Laplacian using the cryo-EM dataset. Finally, we test our approach with synthetic datasets, for which we recover the atomic model of two-dimensional and three-dimensional flexible structures from noisy tomographic projections.