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.
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Supervised learning is constrained by the availability of labeled data, which are especially expensive to acquire in the field of digital pathology. Making use of open-source data for pre-training or using domain adaptation can be a way to overcome this issue. However, pre-trained networks often fail to generalize to new test domains that are not distributed identically due to tissue stainings, types, and textures variations. Additionally, current domain adaptation methods mainly rely on fully-labeled source datasets. In this work, we propose Self-Rule to Multi-Adapt (SRMA), which takes advantage of self-supervised learning to perform domain adaptation, and removes the necessity of fully-labeled source datasets. SRMA can effectively transfer the discriminative knowledge obtained from a few labeled source domain's data to a new target domain without requiring additional tissue annotations. Our method harnesses both domains' structures by capturing visual similarity with intra-domain and cross-domain self-supervision. Moreover, we present a generalized formulation of our approach that allows the framework to learn from multiple source domains. We show that our proposed method outperforms baselines for domain adaptation of colorectal tissue type classification \new{in single and multi-source settings}, and further validate our approach on an in-house clinical cohort. The code and trained models are available open-source: //github.com/christianabbet/SRA.
Mainstream approaches for unsupervised domain adaptation (UDA) learn domain-invariant representations to narrow the domain shift. Recently, self-training has been gaining momentum in UDA, which exploits unlabeled target data by training with target pseudo-labels. However, as corroborated in this work, under distributional shift in UDA, the pseudo-labels can be unreliable in terms of their large discrepancy from target ground truth. Thereby, we propose Cycle Self-Training (CST), a principled self-training algorithm that explicitly enforces pseudo-labels to generalize across domains. CST cycles between a forward step and a reverse step until convergence. In the forward step, CST generates target pseudo-labels with a source-trained classifier. In the reverse step, CST trains a target classifier using target pseudo-labels, and then updates the shared representations to make the target classifier perform well on the source data. We introduce the Tsallis entropy as a confidence-friendly regularization to improve the quality of target pseudo-labels. We analyze CST theoretically under realistic assumptions, and provide hard cases where CST recovers target ground truth, while both invariant feature learning and vanilla self-training fail. Empirical results indicate that CST significantly improves over the state-of-the-arts on visual recognition and sentiment analysis benchmarks.
Unsupervised domain adaptation (UDA) methods for person re-identification (re-ID) aim at transferring re-ID knowledge from labeled source data to unlabeled target data. Although achieving great success, most of them only use limited data from a single-source domain for model pre-training, making the rich labeled data insufficiently exploited. To make full use of the valuable labeled data, we introduce the multi-source concept into UDA person re-ID field, where multiple source datasets are used during training. However, because of domain gaps, simply combining different datasets only brings limited improvement. In this paper, we try to address this problem from two perspectives, \ie{} domain-specific view and domain-fusion view. Two constructive modules are proposed, and they are compatible with each other. First, a rectification domain-specific batch normalization (RDSBN) module is explored to simultaneously reduce domain-specific characteristics and increase the distinctiveness of person features. Second, a graph convolutional network (GCN) based multi-domain information fusion (MDIF) module is developed, which minimizes domain distances by fusing features of different domains. The proposed method outperforms state-of-the-art UDA person re-ID methods by a large margin, and even achieves comparable performance to the supervised approaches without any post-processing techniques.
Domain generalization aims to learn a generalizable model from a known source domain for various unknown target domains. It has been studied widely by domain randomization that transfers source images to different styles in spatial space for learning domain-agnostic features. However, most existing randomization uses GANs that often lack of controls and even alter semantic structures of images undesirably. Inspired by the idea of JPEG that converts spatial images into multiple frequency components (FCs), we propose Frequency Space Domain Randomization (FSDR) that randomizes images in frequency space by keeping domain-invariant FCs (DIFs) and randomizing domain-variant FCs (DVFs) only. FSDR has two unique features: 1) it decomposes images into DIFs and DVFs which allows explicit access and manipulation of them and more controllable randomization; 2) it has minimal effects on semantic structures of images and domain-invariant features. We examined domain variance and invariance property of FCs statistically and designed a network that can identify and fuse DIFs and DVFs dynamically through iterative learning. Extensive experiments over multiple domain generalizable segmentation tasks show that FSDR achieves superior segmentation and its performance is even on par with domain adaptation methods that access target data in training.
In this paper, we tackle the unsupervised domain adaptation (UDA) for semantic segmentation, which aims to segment the unlabeled real data using labeled synthetic data. The main problem of UDA for semantic segmentation relies on reducing the domain gap between the real image and synthetic image. To solve this problem, we focused on separating information in an image into content and style. Here, only the content has cues for semantic segmentation, and the style makes the domain gap. Thus, precise separation of content and style in an image leads to effect as supervision of real data even when learning with synthetic data. To make the best of this effect, we propose a zero-style loss. Even though we perfectly extract content for semantic segmentation in the real domain, another main challenge, the class imbalance problem, still exists in UDA for semantic segmentation. We address this problem by transferring the contents of tail classes from synthetic to real domain. Experimental results show that the proposed method achieves the state-of-the-art performance in semantic segmentation on the major two UDA settings.
Recent works showed that Generative Adversarial Networks (GANs) can be successfully applied in unsupervised domain adaptation, where, given a labeled source dataset and an unlabeled target dataset, the goal is to train powerful classifiers for the target samples. In particular, it was shown that a GAN objective function can be used to learn target features indistinguishable from the source ones. In this work, we extend this framework by (i) forcing the learned feature extractor to be domain-invariant, and (ii) training it through data augmentation in the feature space, namely performing feature augmentation. While data augmentation in the image space is a well established technique in deep learning, feature augmentation has not yet received the same level of attention. We accomplish it by means of a feature generator trained by playing the GAN minimax game against source features. Results show that both enforcing domain-invariance and performing feature augmentation lead to superior or comparable performance to state-of-the-art results in several unsupervised domain adaptation benchmarks.
Convolutional networks (ConvNets) have achieved great successes in various challenging vision tasks. However, the performance of ConvNets would degrade when encountering the domain shift. The domain adaptation is more significant while challenging in the field of biomedical image analysis, where cross-modality data have largely different distributions. Given that annotating the medical data is especially expensive, the supervised transfer learning approaches are not quite optimal. In this paper, we propose an unsupervised domain adaptation framework with adversarial learning for cross-modality biomedical image segmentations. Specifically, our model is based on a dilated fully convolutional network for pixel-wise prediction. Moreover, we build a plug-and-play domain adaptation module (DAM) to map the target input to features which are aligned with source domain feature space. A domain critic module (DCM) is set up for discriminating the feature space of both domains. We optimize the DAM and DCM via an adversarial loss without using any target domain label. Our proposed method is validated by adapting a ConvNet trained with MRI images to unpaired CT data for cardiac structures segmentations, and achieved very promising results.
Novel neural models have been proposed in recent years for learning under domain shift. Most models, however, only evaluate on a single task, on proprietary datasets, or compare to weak baselines, which makes comparison of models difficult. In this paper, we re-evaluate classic general-purpose bootstrapping approaches in the context of neural networks under domain shifts vs. recent neural approaches and propose a novel multi-task tri-training method that reduces the time and space complexity of classic tri-training. Extensive experiments on two benchmarks are negative: while our novel method establishes a new state-of-the-art for sentiment analysis, it does not fare consistently the best. More importantly, we arrive at the somewhat surprising conclusion that classic tri-training, with some additions, outperforms the state of the art. We conclude that classic approaches constitute an important and strong baseline.
Can we detect common objects in a variety of image domains without instance-level annotations? In this paper, we present a framework for a novel task, cross-domain weakly supervised object detection, which addresses this question. For this paper, we have access to images with instance-level annotations in a source domain (e.g., natural image) and images with image-level annotations in a target domain (e.g., watercolor). In addition, the classes to be detected in the target domain are all or a subset of those in the source domain. Starting from a fully supervised object detector, which is pre-trained on the source domain, we propose a two-step progressive domain adaptation technique by fine-tuning the detector on two types of artificially and automatically generated samples. We test our methods on our newly collected datasets containing three image domains, and achieve an improvement of approximately 5 to 20 percentage points in terms of mean average precision (mAP) compared to the best-performing baselines.
In this paper, we propose to tackle the problem of reducing discrepancies between multiple domains referred to as multi-source domain adaptation and consider it under the target shift assumption: in all domains we aim to solve a classification problem with the same output classes, but with labels' proportions differing across them. We design a method based on optimal transport, a theory that is gaining momentum to tackle adaptation problems in machine learning due to its efficiency in aligning probability distributions. Our method performs multi-source adaptation and target shift correction simultaneously by learning the class probabilities of the unlabeled target sample and the coupling allowing to align two (or more) probability distributions. Experiments on both synthetic and real-world data related to satellite image segmentation task show the superiority of the proposed method over the state-of-the-art.
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