Differentiable Probabilistic Models of Scientific Imaging with the Fourier Slice Theorem

Karen Ullrich, Rianne van den Berg, Marcus Brubaker, David Fleet, Max Welling
Proceedings of The 35th Uncertainty in Artificial Intelligence Conference, PMLR 115:399-411, 2020.

Abstract

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.

Cite this Paper

BibTeX
@InProceedings{pmlr-v115-ullrich20a, title = {Differentiable Probabilistic Models of Scientific Imaging with the Fourier Slice Theorem}, author = {Ullrich, Karen and van den Berg, Rianne and Brubaker, Marcus and Fleet, David and Welling, Max}, booktitle = {Proceedings of The 35th Uncertainty in Artificial Intelligence Conference}, pages = {399--411}, year = {2020}, editor = {Adams, Ryan P. and Gogate, Vibhav}, volume = {115}, series = {Proceedings of Machine Learning Research}, month = {22--25 Jul}, publisher = {PMLR}, pdf = {http://proceedings.mlr.press/v115/ullrich20a/ullrich20a.pdf}, url = {https://proceedings.mlr.press/v115/ullrich20a.html}, abstract = {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. } }
Endnote
%0 Conference Paper %T Differentiable Probabilistic Models of Scientific Imaging with the Fourier Slice Theorem %A Karen Ullrich %A Rianne van den Berg %A Marcus Brubaker %A David Fleet %A Max Welling %B Proceedings of The 35th Uncertainty in Artificial Intelligence Conference %C Proceedings of Machine Learning Research %D 2020 %E Ryan P. Adams %E Vibhav Gogate %F pmlr-v115-ullrich20a %I PMLR %P 399--411 %U https://proceedings.mlr.press/v115/ullrich20a.html %V 115 %X 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.
APA
Ullrich, K., van den Berg, R., Brubaker, M., Fleet, D. & Welling, M.. (2020). Differentiable Probabilistic Models of Scientific Imaging with the Fourier Slice Theorem. Proceedings of The 35th Uncertainty in Artificial Intelligence Conference, in Proceedings of Machine Learning Research 115:399-411 Available from https://proceedings.mlr.press/v115/ullrich20a.html.

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