Deep learning models usually suffer from domain shift issues, where models trained on one source domain do not generalize well to other unseen domains. In this work, we investigate the single-source domain generalization problem: training a deep network that is robust to unseen domains, under the condition that training data is only available from one source domain, which is common in medical imaging applications. We tackle this problem in the context of cross-domain medical image segmentation. Under this scenario, domain shifts are mainly caused by different acquisition processes. We propose a simple causality-inspired data augmentation approach to expose a segmentation model to synthesized domain-shifted training examples. Specifically, 1) to make the deep model robust to discrepancies in image intensities and textures, we employ a family of randomly-weighted shallow networks. They augment training images using diverse appearance transformations. 2) Further we show that spurious correlations among objects in an image are detrimental to domain robustness. These correlations might be taken by the network as domain-specific clues for making predictions, and they may break on unseen domains. We remove these spurious correlations via causal intervention. This is achieved by resampling the appearances of potentially correlated objects independently. The proposed approach is validated on three cross-domain segmentation tasks: cross-modality (CT-MRI) abdominal image segmentation, cross-sequence (bSSFP-LGE) cardiac MRI segmentation, and cross-center prostate MRI segmentation. The proposed approach yields consistent performance gains compared with competitive methods when tested on unseen domains.
相關內容
Transformers have made remarkable progress towards modeling long-range dependencies within the medical image analysis domain. However, current transformer-based models suffer from several disadvantages: (1) existing methods fail to capture the important features of the images due to the naive tokenization scheme; (2) the models suffer from information loss because they only consider single-scale feature representations; and (3) the segmentation label maps generated by the models are not accurate enough without considering rich semantic contexts and anatomical textures. In this work, we present CA-GANformer, a novel type of generative adversarial transformers, for medical image segmentation. First, we take advantage of the pyramid structure to construct multi-scale representations and handle multi-scale variations. We then design a novel class-aware transformer module to better learn the discriminative regions of objects with semantic structures. Lastly, we utilize an adversarial training strategy that boosts segmentation accuracy and correspondingly allows a transformer-based discriminator to capture high-level semantically correlated contents and low-level anatomical features. Our experiments demonstrate that CA-GANformer dramatically outperforms previous state-of-the-art transformer-based approaches on three benchmarks, obtaining 2.54%-5.88% absolute improvements in Dice over previous models. Further qualitative experiments provide a more detailed picture of the model's inner workings, shed light on the challenges in improved transparency, and demonstrate that transfer learning can greatly improve performance and reduce the size of medical image datasets in training, making CA-GANformer a strong starting point for downstream medical image analysis tasks. Codes and models will be available to the public.
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.
The focus of disentanglement approaches has been on identifying independent factors of variation in data. However, the causal variables underlying real-world observations are often not statistically independent. In this work, we bridge the gap to real-world scenarios by analyzing the behavior of the most prominent disentanglement approaches on correlated data in a large-scale empirical study (including 4260 models). We show and quantify that systematically induced correlations in the dataset are being learned and reflected in the latent representations, which has implications for downstream applications of disentanglement such as fairness. We also demonstrate how to resolve these latent correlations, either using weak supervision during training or by post-hoc correcting a pre-trained model with a small number of labels.
Enhancing the generalization capability of deep neural networks to unseen domains is crucial for safety-critical applications in the real world such as autonomous driving. To address this issue, this paper proposes a novel instance selective whitening loss to improve the robustness of the segmentation networks for unseen domains. Our approach disentangles the domain-specific style and domain-invariant content encoded in higher-order statistics (i.e., feature covariance) of the feature representations and selectively removes only the style information causing domain shift. As shown in Fig. 1, our method provides reasonable predictions for (a) low-illuminated, (b) rainy, and (c) unseen structures. These types of images are not included in the training dataset, where the baseline shows a significant performance drop, contrary to ours. Being simple yet effective, our approach improves the robustness of various backbone networks without additional computational cost. We conduct extensive experiments in urban-scene segmentation and show the superiority of our approach to existing work. Our code is available at //github.com/shachoi/RobustNet.
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.
We consider the problem of unsupervised domain adaptation for semantic segmentation by easing the domain shift between the source domain (synthetic data) and the target domain (real data) in this work. State-of-the-art approaches prove that performing semantic-level alignment is helpful in tackling the domain shift issue. Based on the observation that stuff categories usually share similar appearances across images of different domains while things (i.e. object instances) have much larger differences, we propose to improve the semantic-level alignment with different strategies for stuff regions and for things: 1) for the stuff categories, we generate feature representation for each class and conduct the alignment operation from the target domain to the source domain; 2) for the thing categories, we generate feature representation for each individual instance and encourage the instance in the target domain to align with the most similar one in the source domain. In this way, the individual differences within thing categories will also be considered to alleviate over-alignment. In addition to our proposed method, we further reveal the reason why the current adversarial loss is often unstable in minimizing the distribution discrepancy and show that our method can help ease this issue by minimizing the most similar stuff and instance features between the source and the target domains. We conduct extensive experiments in two unsupervised domain adaptation tasks, i.e. GTA5 to Cityscapes and SYNTHIA to Cityscapes, and achieve the new state-of-the-art segmentation accuracy.
Biomedical image segmentation is an important task in many medical applications. Segmentation methods based on convolutional neural networks attain state-of-the-art accuracy; however, they typically rely on supervised training with large labeled datasets. Labeling datasets of medical images requires significant expertise and time, and is infeasible at large scales. To tackle the lack of labeled data, researchers use techniques such as hand-engineered preprocessing steps, hand-tuned architectures, and data augmentation. However, these techniques involve costly engineering efforts, and are typically dataset-specific. We present an automated data augmentation method for medical images. We demonstrate our method on the task of segmenting magnetic resonance imaging (MRI) brain scans, focusing on the one-shot segmentation scenario -- a practical challenge in many medical applications. Our method requires only a single segmented scan, and leverages other unlabeled scans in a semi-supervised approach. We learn a model of transforms from the images, and use the model along with the labeled example to synthesize additional labeled training examples for supervised segmentation. Each transform is comprised of a spatial deformation field and an intensity change, enabling the synthesis of complex effects such as variations in anatomy and image acquisition procedures. Augmenting the training of a supervised segmenter with these new examples provides significant improvements over state-of-the-art methods for one-shot biomedical image segmentation. Our code is available at //github.com/xamyzhao/brainstorm.
We study object recognition under the constraint that each object class is only represented by very few observations. In such cases, naive supervised learning would lead to severe over-fitting in deep neural networks due to limited training data. We tackle this problem by creating much more training data through label propagation from the few labeled examples to a vast collection of unannotated images. Our main insight is that such a label propagation scheme can be highly effective when the similarity metric used for propagation is learned and transferred from other related domains with lots of data. We test our approach on semi-supervised learning, transfer learning and few-shot recognition, where we learn our similarity metric using various supervised/unsupervised pretraining methods, and transfer it to unlabeled data across different data distributions. By taking advantage of unlabeled data in this way, we achieve significant improvements on all three tasks. Notably, our approach outperforms current state-of-the-art techniques by an absolute $20\%$ for semi-supervised learning on CIFAR10, $10\%$ for transfer learning from ImageNet to CIFAR10, and $6\%$ for few-shot recognition on mini-ImageNet, when labeled examples are limited.
3D image segmentation plays an important role in biomedical image analysis. Many 2D and 3D deep learning models have achieved state-of-the-art segmentation performance on 3D biomedical image datasets. Yet, 2D and 3D models have their own strengths and weaknesses, and by unifying them together, one may be able to achieve more accurate results. In this paper, we propose a new ensemble learning framework for 3D biomedical image segmentation that combines the merits of 2D and 3D models. First, we develop a fully convolutional network based meta-learner to learn how to improve the results from 2D and 3D models (base-learners). Then, to minimize over-fitting for our sophisticated meta-learner, we devise a new training method that uses the results of the base-learners as multiple versions of "ground truths". Furthermore, since our new meta-learner training scheme does not depend on manual annotation, it can utilize abundant unlabeled 3D image data to further improve the model. Extensive experiments on two public datasets (the HVSMR 2016 Challenge dataset and the mouse piriform cortex dataset) show that our approach is effective under fully-supervised, semi-supervised, and transductive settings, and attains superior performance over state-of-the-art image segmentation methods.
Data augmentation has been widely used for training deep learning systems for medical image segmentation and plays an important role in obtaining robust and transformation-invariant predictions. However, it has seldom been used at test time for segmentation and not been formulated in a consistent mathematical framework. In this paper, we first propose a theoretical formulation of test-time augmentation for deep learning in image recognition, where the prediction is obtained through estimating its expectation by Monte Carlo simulation with prior distributions of parameters in an image acquisition model that involves image transformations and noise. We then propose a novel uncertainty estimation method based on the formulated test-time augmentation. Experiments with segmentation of fetal brains and brain tumors from 2D and 3D Magnetic Resonance Images (MRI) showed that 1) our test-time augmentation outperforms a single-prediction baseline and dropout-based multiple predictions, and 2) it provides a better uncertainty estimation than calculating the model-based uncertainty alone and helps to reduce overconfident incorrect predictions.
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