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Cryo-Electron Tomography (cryo-ET) is a 3D imaging technology that enables the visualization of subcellular structures in situ at near-atomic resolution. Cellular cryo-ET images help in resolving the structures of macromolecules and determining their spatial relationship in a single cell, which has broad significance in cell and structural biology. Subtomogram classification and recognition constitute a primary step in the systematic recovery of these macromolecular structures. Supervised deep learning methods have been proven to be highly accurate and efficient for subtomogram classification, but suffer from limited applicability due to scarcity of annotated data. While generating simulated data for training supervised models is a potential solution, a sizeable difference in the image intensity distribution in generated data as compared to real experimental data will cause the trained models to perform poorly in predicting classes on real subtomograms. In this work, we present Cryo-Shift, a fully unsupervised domain adaptation and randomization framework for deep learning-based cross-domain subtomogram classification. We use unsupervised multi-adversarial domain adaption to reduce the domain shift between features of simulated and experimental data. We develop a network-driven domain randomization procedure with `warp' modules to alter the simulated data and help the classifier generalize better on experimental data. We do not use any labeled experimental data to train our model, whereas some of the existing alternative approaches require labeled experimental samples for cross-domain classification. Nevertheless, Cryo-Shift outperforms the existing alternative approaches in cross-domain subtomogram classification in extensive evaluation studies demonstrated herein using both simulated and experimental data., Comment: 14 pages

We propose a novel weakly supervised approach for 3D semantic segmentation on volumetric images. Unlike most existing methods that require voxel-wise densely labeled training data, our weakly-supervised CIVA-Net is the first model that only needs image-level class labels as guidance to learn accurate volumetric segmentation. Our model learns from cross-image co-occurrence for integral region generation, and explores inter-voxel affinity relations to predict segmentation with accurate boundaries. We empirically validate our model on both simulated and real cryo-ET datasets. Our experiments show that CIVA-Net achieves comparable performance to the state-of-the-art models trained with stronger supervision.

The use of random perturbations of ground truth data, such as random translation or scaling of bounding boxes, is a common heuristic used for data augmentation that has been shown to prevent overfitting and improve generalization. Since the design of data augmentation is largely guided by reported best practices, it is difficult to understand if those design choices are optimal. To provide a more principled perspective, we develop a game-theoretic interpretation of data augmentation in the context of object detection. We aim to find an optimal adversarial perturbations of the ground truth data (i.e., the worst case perturbations) that forces the object bounding box predictor to learn from the hardest distribution of perturbed examples for better test-time performance. We establish that the game-theoretic solution (Nash equilibrium) provides both an optimal predictor and optimal data augmentation distribution. We show that our adversarial method of training a predictor can significantly improve test-time performance for the task of object detection. On the ImageNet, Pascal VOC and MS-COCO object detection tasks, our adversarial approach improves performance by about 16%, 5%, and 2% respectively compared to the best performing data augmentation methods.

Many structured prediction tasks arising in computer vision and natural language processing tractably reduce to making minimum cost cuts in graphs with edge weights learned using maximum margin methods. Unfortunately, the hinge loss used to construct these methods often provides a particularly loose bound on the loss function of interest (e.g., the Hamming loss). We develop Adversarial Robust Cuts (ARC), an approach that poses the learning task as a minimax game between predictor and "label approximator" based on minimum cost graph cuts. Unlike maximum margin methods, this game-theoretic perspective always provides meaningful bounds on the Hamming loss. We conduct multi-label and semi-supervised binary prediction experiments that demonstrate the benefits of our approach.