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Register a new userUser-Guided Domain Adaptation for Rapid Annotation from User Interactions: A Study on Pathological Liver Segmentation
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Added by
Ashwin Raju
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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Mask-based annotation of medical images, especially for 3D data, is a bottleneck in developing reliable machine learning models. Using minimal-labor user interactions (UIs) to guide the annotation is promising, but challenges remain on best harmonizing the mask prediction with the UIs. To address this, we propose the user-guided domain adaptation (UGDA) framework, which uses prediction-based adversarial domain adaptation (PADA) to model the combined distribution of UIs and mask predictions. The UIs are then used as anchors to guide and align the mask prediction. Importantly, UGDA can both learn from unlabelled data and also model the high-level semantic meaning behind different UIs. We test UGDA on annotating pathological livers using a clinically comprehensive dataset of 927 patient studies. Using only extreme-point UIs, we achieve a mean (worst-case) performance of 96.1%(94.9%), compared to 93.0% (87.0%) for deep extreme points (DEXTR). Furthermore, we also show UGDA can retain this state-of-the-art performance even when only seeing a fraction of available UIs, demonstrating an ability for robust and reliable UI-guided segmentation with extremely minimal labor demands.
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Deep neural networks have shown exceptional learning capability and generalizability in the source domain when massive labeled data is provided. However, the well-trained models often fail in the target domain due to the domain shift. Unsupervised domain adaptation aims to improve network performance when applying robust models trained on medical images from source domains to a new target domain. In this work, we present an approach based on the Wasserstein distance guided disentangled representation to achieve 3D multi-domain liver segmentation. Concretely, we embed images onto a shared content space capturing shared feature-level information across domains and domain-specific appearance spaces. The existing mutual information-based representation learning approaches often fail to capture complete representations in multi-domain medical imaging tasks. To mitigate these issues, we utilize Wasserstein distance to learn more complete representation, and introduces a content discriminator to further facilitate the representation disentanglement. Experiments demonstrate that our method outperforms the state-of-the-art on the multi-modality liver segmentation task.
Unsupervised domain adaptation (UDA) becomes more and more popular in tackling real-world problems without ground truth of the target domain. Though a mass of tedious annotation work is not needed, UDA unavoidably faces the problem how to narrow the domain discrepancy to boost the transferring performance. In this paper, we focus on UDA for semantic segmentation task. Firstly, we propose a style-independent content feature extraction mechanism to keep the style information of extracted features in the similar space, since the style information plays a extremely slight role for semantic segmentation compared with the content part. Secondly, to keep the balance of pseudo labels on each category, we propose a category-guided threshold mechanism to choose category-wise pseudo labels for self-supervised learning. The experiments are conducted using GTA5 as the source domain, Cityscapes as the target domain. The results show that our model outperforms the state-of-the-arts with a noticeable gain on cross-domain adaptation tasks.
The main progress for action segmentation comes from densely-annotated data for fully-supervised learning. Since manual annotation for frame-level actions is time-consuming and challenging, we propose to exploit auxiliary unlabeled videos, which are much easier to obtain, by shaping this problem as a domain adaptation (DA) problem. Although various DA techniques have been proposed in recent years, most of them have been developed only for the spatial direction. Therefore, we propose Mixed Temporal Domain Adaptation (MTDA) to jointly align frame- and video-level embedded feature spaces across domains, and further integrate with the domain attention mechanism to focus on aligning the frame-level features with higher domain discrepancy, leading to more effective domain adaptation. Finally, we evaluate our proposed methods on three challenging datasets (GTEA, 50Salads, and Breakfast), and validate that MTDA outperforms the current state-of-the-art methods on all three datasets by large margins (e.g. 6.4% gain on F1@50 and 6.8% gain on the edit score for GTEA).
The microvascular invasion (MVI) is a major prognostic factor in hepatocellular carcinoma, which is one of the malignant tumors with the highest mortality rate. The diagnosis of MVI needs discovering the vessels that contain hepatocellular carcinoma cells and counting their number in each vessel, which depends heavily on experiences of the doctor, is largely subjective and time-consuming. However, there is no algorithm as yet tailored for the MVI detection from pathological images. This paper collects the first pathological liver image dataset containing 522 whole slide images with labels of vessels, MVI, and hepatocellular carcinoma grades. The first and essential step for the automatic diagnosis of MVI is the accurate segmentation of vessels. The unique characteristics of pathological liver images, such as super-large size, multi-scale vessel, and blurred vessel edges, make the accurate vessel segmentation challenging. Based on the collected dataset, we propose an Edge-competing Vessel Segmentation Network (EVS-Net), which contains a segmentation network and two edge segmentation discriminators. The segmentation network, combined with an edge-aware self-supervision mechanism, is devised to conduct vessel segmentation with limited labeled patches. Meanwhile, two discriminators are introduced to distinguish whether the segmented vessel and background contain residual features in an adversarial manner. In the training stage, two discriminators are devised tocompete for the predicted position of edges. Exhaustive experiments demonstrate that, with only limited labeled patches, EVS-Net achieves a close performance of fully supervised methods, which provides a convenient tool for the pathological liver vessel segmentation. Code is publicly available at https://github.com/zju-vipa/EVS-Net.
While fully-supervised deep learning yields good models for urban scene semantic segmentation, these models struggle to generalize to new environments with different lighting or weather conditions for instance. In addition, producing the extensive pixel-level annotations that the task requires comes at a great cost. Unsupervised domain adaptation (UDA) is one approach that tries to address these issues in order to make such systems more scalable. In particular, self-supervised learning (SSL) has recently become an effective strategy for UDA in semantic segmentation. At the core of such methods lies `pseudo-labeling, that is, the practice of assigning high-confident class predictions as pseudo-labels, subsequently used as true labels, for target data. To collect pseudo-labels, previous works often rely on the highest softmax score, which we here argue as an unfavorable confidence measurement. In this work, we propose Entropy-guided Self-supervised Learning (ESL), leveraging entropy as the confidence indicator for producing more accurate pseudo-labels. On different UDA benchmarks, ESL consistently outperforms strong SSL baselines and achieves state-of-the-art results.
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