Generating 3D brain tumor regions in MRI using vector-quantization Generative Adversarial Networks.

Comput Biol Med

Department of Computer Science, University of Toronto, 40 St George St., Toronto, M5S 2E4, ON, Canada; Neurosciences & Mental Health Research Program, The Hospital for Sick Children, 686 Bay St., Toronto, M5G 0A4, ON, Canada; Department of Diagnostic and Interventional Radiology, The Hospital for Sick Children, 170 Elizabeth St., Toronto, M5G 1H3, ON, Canada; Institute of Medical Science, University of Toronto, 1 King's College Circle, Toronto, M5S 1A8, ON, Canada; Department of Medical Imaging, University of Toronto, 263 McCaul St., Toronto, M5T 1W7, ON, Canada; Department of Mechanical and Industrial Engineering, University of Toronto, 5 King's College Road, Toronto, M5S 3G8, ON, Canada. Electronic address:

Published: December 2024

Medical image analysis has significantly benefited from advancements in deep learning, particularly in the application of Generative Adversarial Networks (GANs) for generating realistic and diverse images that can augment training datasets. The common GAN-based approach is to generate entire image volumes, rather than the region of interest (ROI). Research on deep learning-based brain tumor classification using MRI has shown that it is easier to classify the tumor ROIs compared to the entire image volumes. In this work, we present a novel framework that uses vector-quantization GAN and a transformer incorporating masked token modeling to generate high-resolution and diverse 3D brain tumor ROIs that can be used as additional data for tumor ROI classification. We apply our method to two imbalanced datasets where we augment the minority class: (1) low-grade glioma (LGG) ROIs from the Multimodal Brain Tumor Segmentation Challenge (BraTS) 2019 dataset; (2) BRAF V600E Mutation genetic marker tumor ROIs from the internal pediatric LGG (pLGG) dataset. We show that the proposed method outperforms various baseline models qualitatively and quantitatively. The generated data was used to balance the data to classify brain tumor types. Our approach demonstrates superior performance, surpassing baseline models by 6.4% in the area under the ROC curve (AUC) on the BraTS 2019 dataset and 4.3% in the AUC on the internal pLGG dataset. The results indicate the generated tumor ROIs can effectively address the imbalanced data problem. Our proposed method has the potential to facilitate an accurate diagnosis of rare brain tumors using MRI scans.

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Source
http://dx.doi.org/10.1016/j.compbiomed.2024.109502DOI Listing

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