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Register a new userH2NF-Net for Brain Tumor Segmentation using Multimodal MR Imaging: 2nd Place Solution to BraTS Challenge 2020 Segmentation Task
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In this paper, we propose a Hybrid High-resolution and Non-local Feature Network (H2NF-Net) to segment brain tumor in multimodal MR images. Our H2NF-Net uses the single and cascaded HNF-Nets to segment different brain tumor sub-regions and combines the predictions together as the final segmentation. We trained and evaluated our model on the Multimodal Brain Tumor Segmentation Challenge (BraTS) 2020 dataset. The results on the test set show that the combination of the single and cascaded models achieved average Dice scores of 0.78751, 0.91290, and 0.85461, as well as Hausdorff distances ($95%$) of 26.57525, 4.18426, and 4.97162 for the enhancing tumor, whole tumor, and tumor core, respectively. Our method won the second place in the BraTS 2020 challenge segmentation task out of nearly 80 participants.
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Brain tumor segmentation is a critical task for patients disease management. In order to automate and standardize this task, we trained multiple U-net like neural networks, mainly with deep supervision and stochastic weight averaging, on the Multimodal Brain Tumor Segmentation Challenge (BraTS) 2020 training dataset. Two independent ensembles of models from two different training pipelines were trained, and each produced a brain tumor segmentation map. These two labelmaps per patient were then merged, taking into account the performance of each ensemble for specific tumor subregions. Our performance on the online validation dataset with test time augmentation were as follows: Dice of 0.81, 0.91 and 0.85; Hausdorff (95%) of 20.6, 4,3, 5.7 mm for the enhancing tumor, whole tumor and tumor core, respectively. Similarly, our solution achieved a Dice of 0.79, 0.89 and 0.84, as well as Hausdorff (95%) of 20.4, 6.7 and 19.5mm on the final test dataset, ranking us among the top ten teams. More complicated training schemes and neural network architectures were investigated without significant performance gain at the cost of greatly increased training time. Overall, our approach yielded good and balanced performance for each tumor subregion. Our solution is open sourced at https://github.com/lescientifik/open_brats2020.
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.
Compared with MS-COCO, the dataset for the competition has a larger proportion of large objects which area is greater than 96x96 pixels. As getting fine boundaries is vitally important for large object segmentation, Mask R-CNN with PointRend is selected as the base segmentation framework to output high-quality object boundaries. Besides, a better engine that integrates ResNeSt, FPN and DCNv2, and a range of effective tricks that including multi-scale training and test time augmentation are applied to improve segmentation performance. Our best performance is an ensemble of four models (three PointRend-based models and SOLOv2), which won the 2nd place in IJCAI-PRICAI 3D AI Challenge 2020: Instance Segmentation.
Brain tumor is the most common and deadliest disease that can be found in all age groups. Generally, MRI modality is adopted for identifying and diagnosing tumors by the radiologists. The correct identification of tumor regions and its type can aid to diagnose tumors with the followup treatment plans. However, for any radiologist analysing such scans is a complex and time-consuming task. Motivated by the deep learning based computer-aided-diagnosis systems, this paper proposes multi-task attention guided encoder-decoder network (MAG-Net) to classify and segment the brain tumor regions using MRI images. The MAG-Net is trained and evaluated on the Figshare dataset that includes coronal, axial, and sagittal views with 3 types of tumors meningioma, glioma, and pituitary tumor. With exhaustive experimental trials the model achieved promising results as compared to existing state-of-the-art models, while having least number of training parameters among other state-of-the-art models.
Automatic brain tumor segmentation from multi-modality Magnetic Resonance Images (MRI) using deep learning methods plays an important role in assisting the diagnosis and treatment of brain tumor. However, previous methods mostly ignore the latent relationship among different modalities. In this work, we propose a novel end-to-end Modality-Pairing learning method for brain tumor segmentation. Paralleled branches are designed to exploit different modality features and a series of layer connections are utilized to capture complex relationships and abundant information among modalities. We also use a consistency loss to minimize the prediction variance between two branches. Besides, learning rate warmup strategy is adopted to solve the problem of the training instability and early over-fitting. Lastly, we use average ensemble of multiple models and some post-processing techniques to get final results. Our method is tested on the BraTS 2020 online testing dataset, obtaining promising segmentation performance, with average dice scores of 0.891, 0.842, 0.816 for the whole tumor, tumor core and enhancing tumor, respectively. We won the second place of the BraTS 2020 Challenge for the tumor segmentation task.
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