9,934 research outputs found
Brain Tumor Segmentation with Deep Neural Networks
In this paper, we present a fully automatic brain tumor segmentation method
based on Deep Neural Networks (DNNs). The proposed networks are tailored to
glioblastomas (both low and high grade) pictured in MR images. By their very
nature, these tumors can appear anywhere in the brain and have almost any kind
of shape, size, and contrast. These reasons motivate our exploration of a
machine learning solution that exploits a flexible, high capacity DNN while
being extremely efficient. Here, we give a description of different model
choices that we've found to be necessary for obtaining competitive performance.
We explore in particular different architectures based on Convolutional Neural
Networks (CNN), i.e. DNNs specifically adapted to image data.
We present a novel CNN architecture which differs from those traditionally
used in computer vision. Our CNN exploits both local features as well as more
global contextual features simultaneously. Also, different from most
traditional uses of CNNs, our networks use a final layer that is a
convolutional implementation of a fully connected layer which allows a 40 fold
speed up. We also describe a 2-phase training procedure that allows us to
tackle difficulties related to the imbalance of tumor labels. Finally, we
explore a cascade architecture in which the output of a basic CNN is treated as
an additional source of information for a subsequent CNN. Results reported on
the 2013 BRATS test dataset reveal that our architecture improves over the
currently published state-of-the-art while being over 30 times faster
Automatic Brain Tumor Segmentation by Deep Convolutional Networks and Graph Cuts
Brain tumor segmentation in magnetic resonance imaging (MRI) is helpful for diagnostics, growth rate prediction, tumor volume measurements and treatment planning of brain tumor. The difficulties for brain tumor segmentation are mainly due to high variation of brain tumors in size, shape, regularity, location, and their heterogeneous appearance (e.g., contrast, intensity and texture variation for different tumors). Due to recent advances in deep convolutional neural networks for semantic image segmentation, automatic brain tumor segmentation is a promising research direction.
This thesis investigates automatic brain tumor segmentation by combining deep convolutional neural network with regularization by a graph cut. We investigate several deep convolutional network structures that have been successful in semantic and medical image segmentation. Since the tumor pixels account for a very small portion in the whole brain slice, segmenting the tumor from the background is a highly imbalanced dense prediction task. We use a loss function that takes the imbalance of the training data into consideration. In the second part of the thesis, we improve the segmentation results of a deep neural network by using optimization framework with graph cuts. The graph cut framework can improve segmentation boundaries by making them more smooth and regular. The main issue when using the segmentation results of convolutional neural networks for the graph cut optimization framework is to convert tumor probabilities learned by a convolutional network into data terms. We investigate several possible ways that take into consideration the segmentation artifacts by convolutional neural networks.
In experiments, we present the segmentation results by different deep convolutional neural network structures, e.g., fully convolutional neural network, dilated residual network and UNet. Also, we compare the combination of U-Net with different data terms for graph cut regularization to improve the neural network segmentation results. Experimental results show that the U-Net performs best with the intersection over union (IoU) for tumors of 0.7286. The IoU for tumors is improved to 0.7530 by training on three slices. Also, the IoU for tumors is improved to 0.7713 by U-Net with balanced loss function. The IoU for tumors is further improved to 0.8078 by graph cut regularization
Automatic Brain Tumor Segmentation using Convolutional Neural Networks with Test-Time Augmentation
Automatic brain tumor segmentation plays an important role for diagnosis,
surgical planning and treatment assessment of brain tumors. Deep convolutional
neural networks (CNNs) have been widely used for this task. Due to the
relatively small data set for training, data augmentation at training time has
been commonly used for better performance of CNNs. Recent works also
demonstrated the usefulness of using augmentation at test time, in addition to
training time, for achieving more robust predictions. We investigate how
test-time augmentation can improve CNNs' performance for brain tumor
segmentation. We used different underpinning network structures and augmented
the image by 3D rotation, flipping, scaling and adding random noise at both
training and test time. Experiments with BraTS 2018 training and validation set
show that test-time augmentation helps to improve the brain tumor segmentation
accuracy and obtain uncertainty estimation of the segmentation results.Comment: 12 pages, 3 figures, MICCAI BrainLes 201
Generalized Wasserstein Dice Score, Distributionally Robust Deep Learning, and Ranger for brain tumor segmentation: BraTS 2020 challenge
Training a deep neural network is an optimization problem with four main
ingredients: the design of the deep neural network, the per-sample loss
function, the population loss function, and the optimizer. However, methods
developed to compete in recent BraTS challenges tend to focus only on the
design of deep neural network architectures, while paying less attention to the
three other aspects. In this paper, we experimented with adopting the opposite
approach. We stuck to a generic and state-of-the-art 3D U-Net architecture and
experimented with a non-standard per-sample loss function, the generalized
Wasserstein Dice loss, a non-standard population loss function, corresponding
to distributionally robust optimization, and a non-standard optimizer, Ranger.
Those variations were selected specifically for the problem of multi-class
brain tumor segmentation. The generalized Wasserstein Dice loss is a per-sample
loss function that allows taking advantage of the hierarchical structure of the
tumor regions labeled in BraTS. Distributionally robust optimization is a
generalization of empirical risk minimization that accounts for the presence of
underrepresented subdomains in the training dataset. Ranger is a generalization
of the widely used Adam optimizer that is more stable with small batch size and
noisy labels. We found that each of those variations of the optimization of
deep neural networks for brain tumor segmentation leads to improvements in
terms of Dice scores and Hausdorff distances. With an ensemble of three deep
neural networks trained with various optimization procedures, we achieved
promising results on the validation dataset of the BraTS 2020 challenge. Our
ensemble ranked fourth out of the 693 registered teams for the segmentation
task of the BraTS 2020 challenge.Comment: MICCAI 2020 BrainLes Workshop. Our method ranked fourth out of the
693 registered teams for the segmentation task of the BraTS 2020 challenge.
v2: Added some clarifications following reviewers' feedback (camera-ready
version
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