52 research outputs found
Automatic Brain Tumor Segmentation using Cascaded Anisotropic Convolutional Neural Networks
A cascade of fully convolutional neural networks is proposed to segment
multi-modal Magnetic Resonance (MR) images with brain tumor into background and
three hierarchical regions: whole tumor, tumor core and enhancing tumor core.
The cascade is designed to decompose the multi-class segmentation problem into
a sequence of three binary segmentation problems according to the subregion
hierarchy. The whole tumor is segmented in the first step and the bounding box
of the result is used for the tumor core segmentation in the second step. The
enhancing tumor core is then segmented based on the bounding box of the tumor
core segmentation result. Our networks consist of multiple layers of
anisotropic and dilated convolution filters, and they are combined with
multi-view fusion to reduce false positives. Residual connections and
multi-scale predictions are employed in these networks to boost the
segmentation performance. Experiments with BraTS 2017 validation set show that
the proposed method achieved average Dice scores of 0.7859, 0.9050, 0.8378 for
enhancing tumor core, whole tumor and tumor core, respectively. The
corresponding values for BraTS 2017 testing set were 0.7831, 0.8739, and
0.7748, respectively.Comment: 12 pages, 5 figures. MICCAI Brats Challenge 201
An Adaptive Sampling Scheme to Efficiently Train Fully Convolutional Networks for Semantic Segmentation
Deep convolutional neural networks (CNNs) have shown excellent performance in
object recognition tasks and dense classification problems such as semantic
segmentation. However, training deep neural networks on large and sparse
datasets is still challenging and can require large amounts of computation and
memory. In this work, we address the task of performing semantic segmentation
on large data sets, such as three-dimensional medical images. We propose an
adaptive sampling scheme that uses a-posterior error maps, generated throughout
training, to focus sampling on difficult regions, resulting in improved
learning. Our contribution is threefold: 1) We give a detailed description of
the proposed sampling algorithm to speed up and improve learning performance on
large images. We propose a deep dual path CNN that captures information at fine
and coarse scales, resulting in a network with a large field of view and high
resolution outputs. We show that our method is able to attain new
state-of-the-art results on the VISCERAL Anatomy benchmark
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
Hierarchical multi-class segmentation of glioma images using networks with multi-level activation function
For many segmentation tasks, especially for the biomedical image, the
topological prior is vital information which is useful to exploit. The
containment/nesting is a typical inter-class geometric relationship. In the
MICCAI Brain tumor segmentation challenge, with its three hierarchically nested
classes 'whole tumor', 'tumor core', 'active tumor', the nested classes
relationship is introduced into the 3D-residual-Unet architecture. The network
comprises a context aggregation pathway and a localization pathway, which
encodes increasingly abstract representation of the input as going deeper into
the network, and then recombines these representations with shallower features
to precisely localize the interest domain via a localization path. The
nested-class-prior is combined by proposing the multi-class activation function
and its corresponding loss function. The model is trained on the training
dataset of Brats2018, and 20% of the dataset is regarded as the validation
dataset to determine parameters. When the parameters are fixed, we retrain the
model on the whole training dataset. The performance achieved on the validation
leaderboard is 86%, 77% and 72% Dice scores for the whole tumor, enhancing
tumor and tumor core classes without relying on ensembles or complicated
post-processing steps. Based on the same start-of-the-art network architecture,
the accuracy of nested-class (enhancing tumor) is reasonably improved from 69%
to 72% compared with the traditional Softmax-based method which blind to
topological prior.Comment: 12pages first versio
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
Weighted Point Cloud Augmentation for Neural Network Training Data Class-Imbalance
Recent developments in the field of deep learning for 3D data have
demonstrated promising potential for end-to-end learning directly from point
clouds. However, many real-world point clouds contain a large class im-balance
due to the natural class im-balance observed in nature. For example, a 3D scan
of an urban environment will consist mostly of road and facade, whereas other
objects such as poles will be under-represented. In this paper we address this
issue by employing a weighted augmentation to increase classes that contain
fewer points. By mitigating the class im-balance present in the data we
demonstrate that a standard PointNet++ deep neural network can achieve higher
performance at inference on validation data. This was observed as an increase
of F1 score of 19% and 25% on two test benchmark datasets; ScanNet and
Semantic3D respectively where no class im-balance pre-processing had been
performed. Our networks performed better on both highly-represented and
under-represented classes, which indicates that the network is learning more
robust and meaningful features when the loss function is not overly exposed to
only a few classes.Comment: 7 pages, 6 figures, submitted for ISPRS Geospatial Week conference
201
Calibrating the dice loss to handle neural network overconfidence for biomedical image segmentation
The Dice similarity coefficient (DSC) is both a widely used metric and loss function for biomedical image segmentation due to its robustness to class imbalance. However, it is well known that the DSC loss is poorly calibrated, resulting in overconfident predictions that cannot be usefully interpreted in biomedical and clinical practice. Performance is often the only metric used to evaluate segmentations produced by deep neural networks, and calibration is often neglected. However, calibration is important for translation into biomedical and clinical practice, providing crucial contextual information to model predictions for interpretation by scientists and clinicians. In this study, we provide a simple yet effective extension of the DSC loss, named the DSC++ loss, that selectively modulates the penalty associated with overconfident, incorrect predictions. As a standalone loss function, the DSC++ loss achieves significantly improved calibration over the conventional DSC loss across six well-validated open-source biomedical imaging datasets, including both 2D binary and 3D multi-class segmentation tasks. Similarly, we observe significantly improved calibration when integrating the DSC++ loss into four DSC-based loss functions. Finally, we use softmax thresholding to illustrate that well calibrated outputs enable tailoring of recall-precision bias, which is an important post-processing technique to adapt the model predictions to suit the biomedical or clinical task. The DSC++ loss overcomes the major limitation of the DSC loss, providing a suitable loss function for training deep learning segmentation models for use in biomedical and clinical practice. Source code is available at https://github.com/mlyg/DicePlusPlus
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