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Register a new userUncertainty-aware Incremental Learning for Multi-organ Segmentation
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Yuhang Zhou
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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Most existing approaches to train a unified multi-organ segmentation model from several single-organ datasets require simultaneously access multiple datasets during training. In the real scenarios, due to privacy and ethics concerns, the training data of the organs of interest may not be publicly available. To this end, we investigate a data-free incremental organ segmentation scenario and propose a novel incremental training framework to solve it. We use the pretrained model instead of its own training data for privacy protection. Specifically, given a pretrained $K$ organ segmentation model and a new single-organ dataset, we train a unified $K+1$ organ segmentation model without accessing any data belonging to the previous training stages. Our approach consists of two parts: the background label alignment strategy and the uncertainty-aware guidance strategy. The first part is used for knowledge transfer from the pretained model to the training model. The second part is used to extract the uncertainty information from the pretrained model to guide the whole knowledge transfer process. By combing these two strategies, more reliable information is extracted from the pretrained model without original training data. Experiments on multiple publicly available pretrained models and a multi-organ dataset MOBA have demonstrated the effectiveness of our framework.
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Accurate and robust segmentation of abdominal organs on CT is essential for many clinical applications such as computer-aided diagnosis and computer-aided surgery. But this task is challenging due to the weak boundaries of organs, the complexity of the background, and the variable sizes of different organs. To address these challenges, we introduce a novel framework for multi-organ segmentation by using organ-attention networks with reverse connections (OAN-RCs) which are applied to 2D views, of the 3D CT volume, and output estimates which are combined by statistical fusion exploiting structural similarity. OAN is a two-stage deep convolutional network, where deep network features from the first stage are combined with the original image, in a second stage, to reduce the complex background and enhance the discriminative information for the target organs. RCs are added to the first stage to give the lower layers semantic information thereby enabling them to adapt to the sizes of different organs. Our networks are trained on 2D views enabling us to use holistic information and allowing efficient computation. To compensate for the limited cross-sectional information of the original 3D volumetric CT, multi-sectional images are reconstructed from the three different 2D view directions. Then we combine the segmentation results from the different views using statistical fusion, with a novel term relating the structural similarity of the 2D views to the original 3D structure. To train the network and evaluate results, 13 structures were manually annotated by four human raters and confirmed by a senior expert on 236 normal cases. We tested our algorithm and computed Dice-Sorensen similarity coefficients and surface distances for evaluating our estimates of the 13 structures. Our experiments show that the proposed approach outperforms 2D- and 3D-patch based state-of-the-art methods.
In this paper, we present a novel unsupervised domain adaptation (UDA) method, named Domain Adaptive Relational Reasoning (DARR), to generalize 3D multi-organ segmentation models to medical data collected from different scanners and/or protocols (domains). Our method is inspired by the fact that the spatial relationship between internal structures in medical images is relatively fixed, e.g., a spleen is always located at the tail of a pancreas, which serves as a latent variable to transfer the knowledge shared across multiple domains. We formulate the spatial relationship by solving a jigsaw puzzle task, i.e., recovering a CT scan from its shuffled patches, and jointly train it with the organ segmentation task. To guarantee the transferability of the learned spatial relationship to multiple domains, we additionally introduce two schemes: 1) Employing a super-resolution network also jointly trained with the segmentation model to standardize medical images from different domain to a certain spatial resolution; 2) Adapting the spatial relationship for a test image by test-time jigsaw puzzle training. Experimental results show that our method improves the performance by 29.60% DSC on target datasets on average without using any data from the target domain during training.
Multi-organ segmentation has extensive applications in many clinical applications. To segment multiple organs of interest, it is generally quite difficult to collect full annotations of all the organs on the same images, as some medical centers might only annotate a portion of the organs due to their own clinical practice. In most scenarios, one might obtain annotations of a single or a few organs from one training set, and obtain annotations of the the other organs from another set of training images. Existing approaches mostly train and deploy a single model for each subset of organs, which are memory intensive and also time inefficient. In this paper, we propose to co-train weight-averaged models for learning a unified multi-organ segmentation network from few-organ datasets. We collaboratively train two networks and let the coupled networks teach each other on un-annotated organs. To alleviate the noisy teaching supervisions between the networks, the weighted-averaged models are adopted to produce more reliable soft labels. In addition, a novel region mask is utilized to selectively apply the consistent constraint on the un-annotated organ regions that require collaborative teaching, which further boosts the performance. Extensive experiments on three public available single-organ datasets LiTS, KiTS, Pancreas and manually-constructed single-organ datasets from MOBA show that our method can better utilize the few-organ datasets and achieves superior performance with less inference computational cost.
Unsupervised domain adaptation (UDA) aims to adapt existing models of the source domain to a new target domain with only unlabeled data. Most existing methods suffer from noticeable negative transfer resulting from either the error-prone discriminator network or the unreasonable teacher model. Besides, the local regional consistency in UDA has been largely neglected, and only extracting the global-level pattern information is not powerful enough for feature alignment due to the abuse use of contexts. To this end, we propose an uncertainty-aware consistency regularization method for cross-domain semantic segmentation. Firstly, we introduce an uncertainty-guided consistency loss with a dynamic weighting scheme by exploiting the latent uncertainty information of the target samples. As such, more meaningful and reliable knowledge from the teacher model can be transferred to the student model. We further reveal the reason why the current consistency regularization is often unstable in minimizing the domain discrepancy. Besides, we design a ClassDrop mask generation algorithm to produce strong class-wise perturbations. Guided by this mask, we propose a ClassOut strategy to realize effective regional consistency in a fine-grained manner. Experiments demonstrate that our method outperforms the state-of-the-art methods on four domain adaptation benchmarks, i.e., GTAV $rightarrow $ Cityscapes and SYNTHIA $rightarrow $ Cityscapes, Virtual KITTI $rightarrow$ KITTI and Cityscapes $rightarrow$ KITTI.
Although having achieved great success in medical image segmentation, deep learning-based approaches usually require large amounts of well-annotated data, which can be extremely expensive in the field of medical image analysis. Unlabeled data, on the other hand, is much easier to acquire. Semi-supervised learning and unsupervised domain adaptation both take the advantage of unlabeled data, and they are closely related to each other. In this paper, we propose uncertainty-aware multi-view co-training (UMCT), a unified framework that addresses these two tasks for volumetric medical image segmentation. Our framework is capable of efficiently utilizing unlabeled data for better performance. We firstly rotate and permute the 3D volumes into multiple views and train a 3D deep network on each view. We then apply co-training by enforcing multi-view consistency on unlabeled data, where an uncertainty estimation of each view is utilized to achieve accurate labeling. Experiments on the NIH pancreas segmentation dataset and a multi-organ segmentation dataset show state-of-the-art performance of the proposed framework on semi-supervised medical image segmentation. Under unsupervised domain adaptation settings, we validate the effectiveness of this work by adapting our multi-organ segmentation model to two pathological organs from the Medical Segmentation Decathlon Datasets. Additionally, we show that our UMCT-DA model can even effectively handle the challenging situation where labeled source data is inaccessible, demonstrating strong potentials for real-world applications.
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