Abstract Recent advances in deep learning methods have redefined the state-of-the-art for many medical imaging applications, surpassing previous approaches and sometimes even competing with human judgment in several tasks. Those models, however, when trained to reduce the empirical risk on a single domain, fail to generalize when applied to other domains, a very common scenario in medical imaging due to the variability of images and anatomical structures, even across the same imaging modality. In this work, we extend the method of unsupervised domain adaptation using self-ensembling for the semantic segmentation task and explore multiple facets of the method on a small and realistic publicly-available magnetic resonance (MRI) dataset. Through an extensive evaluation, we show that self-ensembling can indeed improve the generalization of the models even when using a small amount of unlabeled data.
Deep Domain Adaptation (DDA), which is a field unrelated in essence to medical imaging, has been widely studied in the recent years @cite_35 . We can divide the literature on DDA as follows: (i) methods based on building domain-invariant feature spaces through auto-encoders @cite_19 , adversarial training @cite_29 , GANs @cite_53 @cite_43 , or disentanglement strategies @cite_16 @cite_0 ; (ii) methods based on the analysis of higher-order statistics @cite_26 @cite_48 ; (iii) methods based on explicit discrepancy between source and target domains @cite_20 ; and (iv) methods based on implicit discrepancy between domains, also known as self-ensembling @cite_34 @cite_28 .
@cite_35 @cite_26 @cite_28 @cite_48 @cite_29 @cite_53 @cite_34 @cite_0 @cite_19 @cite_43 @cite_16 @cite_20
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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. We present an adversarial domain adaptation based deep learning approach for automatic tumor segmentation from T2-weighted MRI. Our approach is composed of two steps: (i) a tumor-aware unsupervised cross-domain adaptation (CT to MRI), followed by (ii) semi-supervised tumor segmentation using Unet trained with synthesized and limited number of original MRIs. We introduced a novel target specific loss, called tumor-aware loss, for unsupervised cross-domain adaptation that helps to preserve tumors on synthesized MRIs produced from CT images. In comparison, state-of-the art adversarial networks trained without our tumor-aware loss produced MRIs with ill-preserved or missing tumors. All networks were trained using labeled CT images from 377 patients with non-small cell lung cancer obtained from the Cancer Imaging Archive and unlabeled T2w MRIs from a completely unrelated cohort of 6 patients with pre-treatment and 36 on-treatment scans. Next, we combined 6 labeled pre-treatment MRI scans with the synthesized MRIs to boost tumor segmentation accuracy through semi-supervised learning. Semi-supervised training of cycle-GAN produced a segmentation accuracy of 0.66 computed using Dice Score Coefficient (DSC). Our method trained with only synthesized MRIs produced an accuracy of 0.74 while the same method trained in semi-supervised setting produced the best accuracy of 0.80 on test. Our results show that tumor-aware adversarial domain adaptation helps to achieve reasonably accurate cancer segmentation from limited MRI data by leveraging large CT datasets. In many real-world applications, the domain of model learning (referred as source domain) is usually inconsistent with or even different from the domain of testing (referred as target domain), which makes the learnt model degenerate in target domain, i.e., the test domain. To alleviate the discrepancy between source and target domains, we propose a domain adaptation method, named as Bi-shifting Auto-Encoder network (BAE). The proposed BAE attempts to shift source domain samples to target domain, and also shift the target domain samples to source domain. The non-linear transformation of BAE ensures the feasibility of shifting between domains, and the distribution consistency between the shifted domain and the desirable domain is constrained by sparse reconstruction between them. As a result, the shifted source domain is supervised and follows similar distribution as target domain. Therefore, any supervised method can be applied on the shifted source domain to train a classifier for classification in target domain. The proposed method is evaluated on three domain adaptation scenarios of face recognition, i.e., domain adaptation across view angle, ethnicity, and imaging sensor, and the promising results demonstrate that our proposed BAE can shift samples between domains and thus effectively deal with the domain discrepancy. Domain adaptation is critical for learning in new and unseen environments. With domain adversarial training, deep networks can learn disentangled and transferable features that effectively diminish the dataset shift between the source and target domains for knowledge transfer. In the era of Big Data, the ready availability of large-scale labeled datasets has stimulated wide interest in partial domain adaptation (PDA), which transfers a recognizer from a labeled large domain to an unlabeled small domain. It extends standard domain adaptation to the scenario where target labels are only a subset of source labels. Under the condition that target labels are unknown, the key challenge of PDA is how to transfer relevant examples in the shared classes to promote positive transfer, and ignore irrelevant ones in the specific classes to mitigate negative transfer. In this work, we propose a unified approach to PDA, Example Transfer Network (ETN), which jointly learns domain-invariant representations across the source and target domains, and a progressive weighting scheme that quantifies the transferability of source examples while controlling their importance to the learning task in the target domain. A thorough evaluation on several benchmark datasets shows that our approach achieves state-of-the-art results for partial domain adaptation tasks.