A convolutional autoencoder approach for mining features in cellular electron cryo-tomograms and weakly supervised coarse segmentation

Cellular electron cryo-tomography enables the 3D visualization of cellular organization in the near-native state and at submolecular resolution. However, the contents of cellular tomograms are often complex, making it difficult to automatically isolate different in situ cellular components. In this paper, we propose a convolutional autoencoder-based unsupervised approach to provide a coarse grouping of 3D small subvolumes extracted from tomograms. We demonstrate that the autoencoder can be used for efficient and coarse characterization of features of macromolecular complexes and surfaces, such as membranes. In addition, the autoencoder can be used to detect non-cellular features related to sample preparation and data collection, such as carbon edges from the grid and tomogram boundaries. The autoencoder is also able to detect patterns that may indicate spatial interactions between cellular components. Furthermore, we demonstrate that our autoencoder can be used for weakly supervised semantic segmentation of cellular components, requiring a very small amount of manual annotation.Comment: Accepted by Journal of Structural Biolog

MoFA: Model-based Deep Convolutional Face Autoencoder for Unsupervised Monocular Reconstruction

In this work we propose a novel model-based deep convolutional autoencoder that addresses the highly challenging problem of reconstructing a 3D human face from a single in-the-wild color image. To this end, we combine a convolutional encoder network with an expert-designed generative model that serves as decoder. The core innovation is our new differentiable parametric decoder that encapsulates image formation analytically based on a generative model. Our decoder takes as input a code vector with exactly defined semantic meaning that encodes detailed face pose, shape, expression, skin reflectance and scene illumination. Due to this new way of combining CNN-based with model-based face reconstruction, the CNN-based encoder learns to extract semantically meaningful parameters from a single monocular input image. For the first time, a CNN encoder and an expert-designed generative model can be trained end-to-end in an unsupervised manner, which renders training on very large (unlabeled) real world data feasible. The obtained reconstructions compare favorably to current state-of-the-art approaches in terms of quality and richness of representation.Comment: International Conference on Computer Vision (ICCV) 2017 (Oral), 13 page