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Register a new userA New Ensemble Learning Framework for 3D Biomedical Image Segmentation
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Added by
Hao Zheng
Publication date
2018
fields
Informatics Engineering
and research's language is
English
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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 multip
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Despite the astonishing performance of deep-learning based approaches for visual tasks such as semantic segmentation, they are known to produce miscalibrated predictions, which could be harmful for critical decision-making processes. Ensemble learning has shown to not only boost the performance of individual models but also reduce their miscalibration by averaging independent predictions. In this scenario, model diversity has become a key factor, which facilitates individual models converging to different functional solutions. In this work, we introduce Orthogonal Ensemble Networks (OEN), a novel framework to explicitly enforce model diversity by means of orthogonal constraints. The proposed method is based on the hypothesis that inducing orthogonality among the constituents of the ensemble will increase the overall model diversity. We resort to a new pairwise orthogonality constraint which can be used to regularize a sequential ensemble training process, resulting on improved predictive performance and better calibrated model outputs. We benchmark the proposed framework in two challenging brain lesion segmentation tasks --brain tumor and white matter hyper-intensity segmentation in MR images. The experimental results show that our approach produces more robust and well-calibrated ensemble models and can deal with challenging tasks in the context of biomedical image segmentation.
Segmentation of 3D images is a fundamental problem in biomedical image analysis. Deep learning (DL) approaches have achieved state-of-the-art segmentation perfor- mance. To exploit the 3D contexts using neural networks, known DL segmentation methods, including 3D convolution, 2D convolution on planes orthogonal to 2D image slices, and LSTM in multiple directions, all suffer incompatibility with the highly anisotropic dimensions in common 3D biomedical images. In this paper, we propose a new DL framework for 3D image segmentation, based on a com- bination of a fully convolutional network (FCN) and a recurrent neural network (RNN), which are responsible for exploiting the intra-slice and inter-slice contexts, respectively. To our best knowledge, this is the first DL framework for 3D image segmentation that explicitly leverages 3D image anisotropism. Evaluating using a dataset from the ISBI Neuronal Structure Segmentation Challenge and in-house image stacks for 3D fungus segmentation, our approach achieves promising results comparing to the known DL-based 3D segmentation approaches.
In this paper, we adopt 3D Convolutional Neural Networks to segment volumetric medical images. Although deep neural networks have been proven to be very effective on many 2D vision tasks, it is still challenging to apply them to 3D tasks due to the limited amount of annotated 3D data and limited computational resources. We propose a novel 3D-based coarse-to-fine framework to effectively and efficiently tackle these challenges. The proposed 3D-based framework outperforms the 2D counterpart to a large margin since it can leverage the rich spatial infor- mation along all three axes. We conduct experiments on two datasets which include healthy and pathological pancreases respectively, and achieve the current state-of-the-art in terms of Dice-S{o}rensen Coefficient (DSC). On the NIH pancreas segmentation dataset, we outperform the previous best by an average of over 2%, and the worst case is improved by 7% to reach almost 70%, which indicates the reliability of our framework in clinical applications.
With the increase in available large clinical and experimental datasets, there has been substantial amount of work being done on addressing the challenges in the area of biomedical image analysis. Image segmentation, which is crucial for any quantitative analysis, has especially attracted attention. Recent hardware advancement has led to the success of deep learning approaches. However, although deep learning models are being trained on large datasets, existing methods do not use the information from different learning epochs effectively. In this work, we leverage the information of each training epoch to prune the prediction maps of the subsequent epochs. We propose a novel architecture called feedback attention network (FANet) that unifies the previous epoch mask with the feature map of the current training epoch. The previous epoch mask is then used to provide a hard attention to the learnt feature maps at different convolutional layers. The network also allows to rectify the predictions in an iterative fashion during the test time. We show that our proposed feedback attention model provides a substantial improvement on most segmentation metrics tested on seven publicly available biomedical imaging datasets demonstrating the effectiveness of the proposed FANet.
Convolutional neural networks (CNNs) for biomedical image analysis are often of very large size, resulting in high memory requirement and high latency of operations. Searching for an acceptable compressed representation of the base CNN for a specific imaging application typically involves a series of time-consuming training/validation experiments to achieve a good compromise between network size and accuracy. To address this challenge, we propose CC-Net, a new image complexity-guided CNN compression scheme for biomedical image segmentation. Given a CNN model, CC-Net predicts the final accuracy of networks of different sizes based on the average image complexity computed from the training data. It then selects a multiplicative factor for producing a desired network with acceptable network accuracy and size. Experiments show that CC-Net is effective for generating compressed segmentation networks, retaining up to 95% of the base network segmentation accuracy and utilizing only 0.1% of trainable parameters of the full-sized networks in the best case.
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