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تسجيل مستخدم جديدIdentifying the Best Machine Learning Algorithms for Brain Tumor Segmentation, Progression Assessment, and Overall Survival Prediction in the BRATS Challenge
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Gliomas are the most common primary brain malignancies, with different degrees of aggressiveness, variable prognosis and various heterogeneous histologic sub-regions, i.e., peritumoral edematous/invaded tissue, necrotic core, active and non-enhancing core. This intrinsic heterogeneity is also portrayed in their radio-phenotype, as their sub-regions are depicted by varying intensity profiles disseminated across multi-parametric magnetic resonance imaging (mpMRI) scans, reflecting varying biological properties. Their heterogeneous shape, extent, and location are some of the factors that make these tumors difficult to resect, and in some cases inoperable. The amount of resected tumor is a factor also considered in longitudinal scans, when evaluating the apparent tumor for potential diagnosis of progression. Furthermore, there is mounting evidence that accurate segmentation of the various tumor sub-regions can offer the basis for quantitative image analysis towards prediction of patient overall survival. This study assesses the state-of-the-art machine learning (ML) methods used for brain tumor image analysis in mpMRI scans, during the last seven instances of the International Brain Tumor Segmentation (BraTS) challenge, i.e., 2012-2018. Specifically, we focus on i) evaluating segmentations of the various glioma sub-regions in pre-operative mpMRI scans, ii) assessing potential tumor progression by virtue of longitudinal growth of tumor sub-regions, beyond use of the RECIST/RANO criteria, and iii) predicting the overall survival from pre-operative mpMRI scans of patients that underwent gross total resection. Finally, we investigate the challenge of identifying the best ML algorithms for each of these tasks, considering that apart from being diverse on each instance of the challenge, the multi-institutional mpMRI BraTS dataset has also been a continuously evolving/growing dataset.
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This paper introduces a novel methodology to integrate human brain connectomics and parcellation for brain tumor segmentation and survival prediction. For segmentation, we utilize an existing brain parcellation atlas in the MNI152 1mm space and map t
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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 recen
t 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.
Early and accurate prediction of overall survival (OS) time can help to obtain better treatment planning for brain tumor patients. Although many OS time prediction methods have been developed and obtain promising results, there are still several issu
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The BraTS 2021 challenge celebrates its 10th anniversary and is jointly organized by the Radiological Society of North America (RSNA), the American Society of Neuroradiology (ASNR), and the Medical Image Computing and Computer Assisted Interventions
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