A Unified Benchmark of Deep Learning Models for Multi-task 3D Brain Tumor Segmentation from Magnetic Resonance Imaging
Authors: Diego J. Torrejón, Luna Y. Hernández, Javier Sánchez
Organizations: Centro de Tecnologías de la Imagen (CTIM) Instituto Universitario de Cibernética, Empresas y Sociedad (IUCES) University of Las Palmas de Gran Canaria 35017 Las Palmas de Gran Canaria, Spain · Centro de Tecnologías de la Imagen (CTIM) Instituto Universitario de Cibernética, Empresas y Sociedad (IUCES) University of Las Palmas de Gran Canaria2026 35017 Las Palmas de Gran Canaria, Spain
Abstract
Automatic brain tumor segmentation from magnetic resonance imaging (MRI) has become a fundamental task in computer-assisted diagnosis, treatment planning, and disease monitoring. Although numerous deep learning architectures have recently been proposed, objective comparisons remain challenging because published studies often employ different datasets, preprocessing strategies, training protocols, and evaluation procedures. This work presents a unified experimental benchmark for comparing representative convolutional neural networks (CNNs), Transformer-based models, and recent State Space Model (SSM) architectures under homogeneous experimental conditions. Five state-of-the-art three-dimensional segmentation models, including 3D U-Net, SegResNet, Swin UNETR, SegMamba, and SegMambaV2, are evaluated on two brain tumor segmentation datasets representing distinct clinical scenarios: intracranial meningioma segmentation (BraTS 2023) and post-treatment glioma segmentation (BraTS 2024). All architectures are trained using identical preprocessing, data augmentation, optimization strategies, and evaluation protocols to ensure a fair comparison. Performance is assessed using segmentation accuracy metrics together with computational cost indicators, including inference time and the size of each model. The results provide practical insights into the trade-offs between segmentation accuracy and computational efficiency, highlighting the suitability of different architectural paradigms for challenging three-dimensional brain tumor segmentation tasks.
Brain tumors exhibit high heterogeneity in morphology and multimodal contrast, making manual slice-by-slice de lineation time-consuming and experience-dependent, thus necessitating efficient and stable automated segmentation methods. To address the limitations of CNNs in modeling long-range dependencies, and the heavy computational and memory overhead and inter-block contextual in coherence of Transformers in 3D MRI, this paper proposes Multi-Head Mamba (MHMamba). This method combines a U-shaped architecture with a multi-head state-space model (Mamba), splitting the channel dimension into parallel SSM heads and aggregating them with residuals. This enhances long-range representation and improves the stability of multimodal training while maintaining linear complexity. To further align statistics and enhance lesion response, we designed a channel-space calibration module for multi-head outputs and introduced an adaptive fusion mechanism at skip connections to dynamically connect global semantics with local details, thereby improving boundary consistency and the detection of small-volume lesions. We conducted experiments and ablations on BraTS2021 and BraTS2023. The results showed that MHMamba achieved stable and significant improvements in overall accuracy, boundary smoothness, and sensitivity to tumor core and small-volume enhancement areas, while preserving the linear-complexity advantage of Mamba-based modeling, thus verifying the effectiveness and versatility of the method.
Automatic brain tumor segmentation from multi-modal MRI remains challenging because volumetric models often incur substantial computational cost. This paper presents DALight-3D, a compact 3D U-Net variant that combines depthwise separable 3D convolutions, identifier-conditioned normalization, cross-slice attention, and adaptive skip fusion. The method is evaluated on the Medical Segmentation Decathlon Task01 BrainTumour benchmark under matched optimization settings against standard 3D U-Net, Attention U-Net, Residual 3D U-Net, and V-Net baselines. In the reported 50-epoch comparison, DALight-3D achieves a mean Dice of 0.727 with 2.22M parameters, compared with 0.710 Dice and 3.20M parameters for Residual 3D U-Net. Component-wise ablations show consistent performance degradation when SepConv, identifier-conditioned normalization, CSA, or SSFB is removed. These results indicate that DALight-3D offers a favorable accuracy-efficiency trade-off within the present benchmark setting.
Nand Kumar Mishra, Dhruv Mishra, Dr Manu Pratap Singh
Accurate 3D brain tumour segmentation from multi-modal Magnetic Resonance Imaging (MRI) is essential for clinical diagnosis and treatment planning. Existing brain tumour segmentation methods often suffer from heavy computational demands, while current lightweight architectures frequently lack the capacity to maintain segmentation fidelity in complex tumour regions. To address these issues, we propose a novel ultra-lightweight framework (Uni-Light) that achieves high-fidelity segmentation with substantially reduced computational overhead. It combines multi-scale convolutions with an uncertainty-aware knowledge distillation scheme that directs the student model toward hard-to-classify regions, complemented by a Signed Distance Field boundary loss for geometric constraints. Experimental results on BraTS2023-GLI and MSD-BTS datasets demonstrate that Uni-Light reduces parameters by 97.56%, floating-point operations (FLOPs) by 73.03%, and inference memory footprint by 81.58%, while surpassing the state-of-the-art model by an average of 1.47% in Dice score, offering a highly competitive trade-off between segmentation accuracy and computational efficiency in resource-constrained clinical settings. This work also advances data engineering for medical imaging by demonstrating that teacher model uncertainty can be exploited as a data-driven supervisory signal, re-prioritising the training data distribution without requiring additional annotation.