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Abstract Motivation 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 with real experimental data will cause the trained models to perform poorly in predicting classes on real subtomograms.
Results 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.
Availabilityand implementation https://github.com/xulabs/aitom.
Supplementary information Supplementary data are available at Bioinformatics online.
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Active learning methods, like uncertainty sampling, combined with probabilistic prediction techniques have achieved success in various problems like image classification and text classification. For more complex multivariate prediction tasks, the relationships between labels play an important role in designing structured classifiers with better performance. However, computational time complexity limits prevalent probabilistic methods from effectively supporting active learning. Specifically, while non-probabilistic methods based on structured support vector ma-chines can be tractably applied to predicting cuts and bipartite matchings, conditional random fields are intractable for these structures. We propose an adversarial approach for active learning with structured prediction domains that is tractable for cuts and matching. We evaluate this approach algorithmically in two important structured prediction problems: multi-label classification and object tracking in videos. We demonstrate better accuracy and computational efficiency for our proposed method.more » « less
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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.more » « less
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Many important structured prediction problems, including learning to rank items, correspondence-based natural language processing, and multi-object tracking, can be formulated as weighted bipartite matching optimizations. Existing structured prediction approaches have significant drawbacks when applied under the constraints of perfect bipartite matchings. Exponential family probabilistic models, such as the conditional random field (CRF), provide statistical consistency guarantees, but suffer computationally from the need to compute the normalization term of its distribution over matchings, which is a #P-hard matrix permanent computation. In contrast, the structured support vector machine (SSVM) provides computational efficiency, but lacks Fisher consistency, meaning that there are distributions of data for which it cannot learn the optimal matching even under ideal learning conditions (i.e., given the true distribution and selecting from all measurable potential functions). We propose adversarial bipartite matching to avoid both of these limitations. We develop this approach algorithmically, establish its computational efficiency and Fisher consistency properties, and apply it to matching problems that demonstrate its empirical benefitsmore » « less
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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.more » « less
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