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Register a new userCombating Uncertainty with Novel Losses for Automatic Left Atrium Segmentation
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Xin Yang
Publication date
2018
fields
Informatics Engineering
and research's language is
English
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Segmenting left atrium in MR volume holds great potentials in promoting the treatment of atrial fibrillation. However, the varying anatomies, artifacts and low contrasts among tissues hinder the advance of both manual and automated solutions. In this paper, we propose a fully-automated framework to segment left atrium in gadolinium-enhanced MR volumes. The region of left atrium is firstly automatically localized by a detection module. Our framework then originates with a customized 3D deep neural network to fully explore the spatial dependency in the region for segmentation. To alleviate the risk of low training efficiency and potential overfitting, we enhance our deep network with the transfer learning and deep supervision strategy. Main contribution of our network design lies in the composite loss function to combat the boundary ambiguity and hard examples. We firstly adopt the Overlap loss to encourage network reduce the overlap between the foreground and background and thus sharpen the predictions on boundary. We then propose a novel Focal Positive loss to guide the learning of voxel-specific threshold and emphasize the foreground to improve classification sensitivity. Further improvement is obtained with an recursive training scheme. With ablation studies, all the introduced modules prove to be effective. The proposed framework achieves an average Dice of 92.24 in segmenting left atrium with pulmonary veins on 20 testing volumes.
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Training deep convolutional neural networks usually requires a large amount of labeled data. However, it is expensive and time-consuming to annotate data for medical image segmentation tasks. In this paper, we present a novel uncertainty-aware semi-supervised framework for left atrium segmentation from 3D MR images. Our framework can effectively leverage the unlabeled data by encouraging consistent predictions of the same input under different perturbations. Concretely, the framework consists of a student model and a teacher model, and the student model learns from the teacher model by minimizing a segmentation loss and a consistency loss with respect to the targets of the teacher model. We design a novel uncertainty-aware scheme to enable the student model to gradually learn from the meaningful and reliable targets by exploiting the uncertainty information. Experiments show that our method achieves high performance gains by incorporating the unlabeled data. Our method outperforms the state-of-the-art semi-supervised methods, demonstrating the potential of our framework for the challenging semi-supervised problems.
Semi-supervised learning has attracted great attention in the field of machine learning, especially for medical image segmentation tasks, since it alleviates the heavy burden of collecting abundant densely annotated data for training. However, most of existing methods underestimate the importance of challenging regions (e.g. small branches or blurred edges) during training. We believe that these unlabeled regions may contain more crucial information to minimize the uncertainty prediction for the model and should be emphasized in the training process. Therefore, in this paper, we propose a novel Mutual Consistency Network (MC-Net) for semi-supervised left atrium segmentation from 3D MR images. Particularly, our MC-Net consists of one encoder and two slightly different decoders, and the prediction discrepancies of two decoders are transformed as an unsupervised loss by our designed cycled pseudo label scheme to encourage mutual consistency. Such mutual consistency encourages the two decoders to have consistent and low-entropy predictions and enables the model to gradually capture generalized features from these unlabeled challenging regions. We evaluate our MC-Net on the public Left Atrium (LA) database and it obtains impressive performance gains by exploiting the unlabeled data effectively. Our MC-Net outperforms six recent semi-supervised methods for left atrium segmentation, and sets the new state-of-the-art performance on the LA database.
Deep learning has achieved promising segmentation performance on 3D left atrium MR images. However, annotations for segmentation tasks are expensive, costly and difficult to obtain. In this paper, we introduce a novel hierarchical consistency regularized mean teacher framework for 3D left atrium segmentation. In each iteration, the student model is optimized by multi-scale deep supervision and hierarchical consistency regularization, concurrently. Extensive experiments have shown that our method achieves competitive performance as compared with full annotation, outperforming other state-of-the-art semi-supervised segmentation methods.
Late Gadolinium Enhanced Cardiac MRI (LGE-CMRI) for detecting atrial scars in atrial fibrillation (AF) patients has recently emerged as a promising technique to stratify patients, guide ablation therapy and predict treatment success. Visualisation and quantification of scar tissues require a segmentation of both the left atrium (LA) and the high intensity scar regions from LGE-CMRI images. These two segmentation tasks are challenging due to the cancelling of healthy tissue signal, low signal-to-noise ratio and often limited image quality in these patients. Most approaches require manual supervision and/or a second bright-blood MRI acquisition for anatomical segmentation. Segmenting both the LA anatomy and the scar tissues automatically from a single LGE-CMRI acquisition is highly in demand. In this study, we proposed a novel fully automated multiview two-task (MVTT) recursive attention model working directly on LGE-CMRI images that combines a sequential learning and a dilated residual learning to segment the LA (including attached pulmonary veins) and delineate the atrial scars simultaneously via an innovative attention model. Compared to other state-of-the-art methods, the proposed MVTT achieves compelling improvement, enabling to generate a patient-specific anatomical and atrial scar assessment model.
Weakly-supervised learning based on, e.g., partially labelled images or image-tags, is currently attracting significant attention in CNN segmentation as it can mitigate the need for full and laborious pixel/voxel annotations. Enforcing high-order (global) inequality constraints on the network output (for instance, to constrain the size of the target region) can leverage unlabeled data, guiding the training process with domain-specific knowledge. Inequality constraints are very flexible because they do not assume exact prior knowledge. However, constrained Lagrangian dual optimization has been largely avoided in deep networks, mainly for computational tractability reasons. To the best of our knowledge, the method of [Pathak et al., 2015] is the only prior work that addresses deep CNNs with linear constraints in weakly supervised segmentation. It uses the constraints to synthesize fully-labeled training masks (proposals) from weak labels, mimicking full supervision and facilitating dual optimization. We propose to introduce a differentiable penalty, which enforces inequality constraints directly in the loss function, avoiding expensive Lagrangian dual iterates and proposal generation. From constrained-optimization perspective, our simple penalty-based approach is not optimal as there is no guarantee that the constraints are satisfied. However, surprisingly, it yields substantially better results than the Lagrangian-based constrained CNNs in [Pathak et al., 2015], while reducing the computational demand for training. By annotating only a small fraction of the pixels, the proposed approach can reach a level of segmentation performance that is comparable to full supervision on three separate tasks. While our experiments focused on basic linear constraints such as the target-region size and image tags, our framework can be easily extended to other non-linear constraints.
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