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

Deep learning in remote sensing: a review

Standing at the paradigm shift towards data-intensive science, machine learning techniques are becoming increasingly important. In particular, as a major breakthrough in the field, deep learning has proven as an extremely powerful tool in many fields. Shall we embrace deep learning as the key to all? Or, should we resist a 'black-box' solution? There are controversial opinions in the remote sensing community. In this article, we analyze the challenges of using deep learning for remote sensing data analysis, review the recent advances, and provide resources to make deep learning in remote sensing ridiculously simple to start with. More importantly, we advocate remote sensing scientists to bring their expertise into deep learning, and use it as an implicit general model to tackle unprecedented large-scale influential challenges, such as climate change and urbanization.Comment: Accepted for publication IEEE Geoscience and Remote Sensing Magazin

AnchorNet: A Weakly Supervised Network to Learn Geometry-sensitive Features For Semantic Matching

Despite significant progress of deep learning in recent years, state-of-the-art semantic matching methods still rely on legacy features such as SIFT or HoG. We argue that the strong invariance properties that are key to the success of recent deep architectures on the classification task make them unfit for dense correspondence tasks, unless a large amount of supervision is used. In this work, we propose a deep network, termed AnchorNet, that produces image representations that are well-suited for semantic matching. It relies on a set of filters whose response is geometrically consistent across different object instances, even in the presence of strong intra-class, scale, or viewpoint variations. Trained only with weak image-level labels, the final representation successfully captures information about the object structure and improves results of state-of-the-art semantic matching methods such as the deformable spatial pyramid or the proposal flow methods. We show positive results on the cross-instance matching task where different instances of the same object category are matched as well as on a new cross-category semantic matching task aligning pairs of instances each from a different object class.Comment: Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition. 201