Data Efficient Variational Inference


I explore the interplay of group theory, harmonic analysis, deep learning, probabilistic models and variational inference in the data sparse regime. Learning is hard here due to scarse signals and lots of biases. I am currently collaborating with David Fleet and Marcus A. Brubaker on a project in cryo-electron microscopy. I am also working on a project related to systems biology.

Differentiable probabilistic models of scientific imaging with the Fourier slice theorem (2019)

Karen Ullrich, Rianne van den Berg, Marcus Brubaker, David Fleet, Max Welling [PDF] [BIBTEX]
Accepted paper at the Conference on Uncertainty in Artificial Intelligence (UAI) 2019, Tel Aviv, Israel.

Scientific imaging techniques such as optical and electron microscopy and computed tomography (CT) scanning are used to study the 3D structure of an object through 2D observations. These observations are related to the original 3D object through orthogonal integral projections. For common 3D reconstruction algorithms, computational efficiency requires the modeling of the 3D structures to take place in Fourier space by applying the Fourier slice theorem. At present, it is unclear how to differentiate through the projection operator, and hence current learning algorithms can not rely on gradient based methods to optimize 3D structure models. In this paper we show how back-propagation through the projection operator in Fourier space can be achieved. We demonstrate the validity of the approach with experiments on 3D reconstruction of proteins. We further extend our approach to learning probabilistic models of 3D objects. This allows us to predict regions of low sampling rates or estimate noise. A higher sample efficiency can be reached by utilizing the learned uncertainties of the 3D structure as an unsupervised estimate of the model fit. Finally, we demonstrate how the reconstruction algorithm can be extended with an amortized inference scheme on unknown attributes such as object pose. Through empirical studies we show that joint inference of the 3D structure and the object pose becomes more difficult when the ground truth object contains more symmetries. Due to the presence of for instance (approximate) rotational symmetries, the pose estimation can easily get stuck in local optima, inhibiting a fine-grained high-quality estimate of the 3D structure.