Magnetic Resonance Imaging Feature-Based Subtyping and Model Ensemble for Enhanced Brain Tumor Segmentation

Accurate and automatic segmentation of brain tumors in multi-parametric magnetic resonance imaging (mpMRI) is essential for quantitative measurements, which play an increasingly important role in clinical diagnosis and prognosis. The International Brain Tumor Segmentation (BraTS) Challenge 2024 offers a unique benchmarking opportunity, including various types of brain tumors in both adult and pediatric populations, such as pediatric brain tumors (PED), meningiomas (MEN-RT) and brain metastases (MET), among others. Compared to previous editions, BraTS 2024 has implemented changes to substantially increase clinical relevance, such as refined tumor regions for evaluation. We propose a deep learning-based ensemble approach that integrates state-of-the-art segmentation models. Additionally, we introduce innovative, adaptive pre- and post-processing techniques that employ MRI-based radiomic analyses to differentiate tumor subtypes. Given the heterogeneous nature of the tumors present in the BraTS datasets, this approach enhances the precision and generalizability of segmentation models. On the final testing sets, our method achieved mean lesion-wise Dice similarity coefficients of 0.926, 0.801, and 0.688 for the whole tumor in PED, MEN-RT, and MET, respectively. These results demonstrate the effectiveness of our approach in improving segmentation performance and generalizability for various brain tumor types.

Adult Glioma Segmentation in Sub-Saharan Africa using Transfer Learning on Stratified Finetuning Data

Gliomas, a kind of brain tumor characterized by high mortality, present substantial diagnostic challenges in low- and middle-income countries, particularly in Sub-Saharan Africa. This paper introduces a novel approach to glioma segmentation using transfer learning to address challenges in resource-limited regions with minimal and low-quality MRI data. We leverage pre-trained deep learning models, nnU-Net and MedNeXt, and apply a stratified fine-tuning strategy using the BraTS2023-Adult-Glioma and BraTS-Africa datasets. Our method exploits radiomic analysis to create stratified training folds, model training on a large brain tumor dataset, and transfer learning to the Sub-Saharan context. A weighted model ensembling strategy and adaptive post-processing are employed to enhance segmentation accuracy. The evaluation of our proposed method on unseen validation cases on the BraTS-Africa 2024 task resulted in lesion-wise mean Dice scores of 0.870, 0.865, and 0.926, for enhancing tumor, tumor core, and whole tumor regions and was ranked first for the challenge. Our approach highlights the ability of integrated machine-learning techniques to bridge the gap between the medical imaging capabilities of resource-limited countries and established developed regions. By tailoring our methods to a target population's specific needs and constraints, we aim to enhance diagnostic capabilities in isolated environments. Our findings underscore the importance of approaches like local data integration and stratification refinement to address healthcare disparities, ensure practical applicability, and enhance impact.

Model Ensemble for Brain Tumor Segmentation in Magnetic Resonance Imaging

Segmenting brain tumors in multi-parametric magnetic resonance imaging enables performing quantitative analysis in support of clinical trials and personalized patient care. This analysis provides the potential to impact clinical decision-making processes, including diagnosis and prognosis. In 2023, the well-established Brain Tumor Segmentation (BraTS) challenge presented a substantial expansion with eight tasks and 4,500 brain tumor cases. In this paper, we present a deep learning-based ensemble strategy that is evaluated for newly included tumor cases in three tasks: pediatric brain tumors (PED), intracranial meningioma (MEN), and brain metastases (MET). In particular, we ensemble outputs from state-of-the-art nnU-Net and Swin UNETR models on a region-wise basis. Furthermore, we implemented a targeted post-processing strategy based on a cross-validated threshold search to improve the segmentation results for tumor sub-regions. The evaluation of our proposed method on unseen test cases for the three tasks resulted in lesion-wise Dice scores for PED: 0.653, 0.809, 0.826; MEN: 0.876, 0.867, 0.849; and MET: 0.555, 0.6, 0.58; for the enhancing tumor, tumor core, and whole tumor, respectively. Our method was ranked first for PED, third for MEN, and fourth for MET, respectively.

Data Alchemy: Mitigating Cross-Site Model Variability Through Test Time Data Calibration

Deploying deep learning-based imaging tools across various clinical sites poses significant challenges due to inherent domain shifts and regulatory hurdles associated with site-specific fine-tuning. For histopathology, stain normalization techniques can mitigate discrepancies, but they often fall short of eliminating inter-site variations. Therefore, we present Data Alchemy, an explainable stain normalization method combined with test time data calibration via a template learning framework to overcome barriers in cross-site analysis. Data Alchemy handles shifts inherent to multi-site data and minimizes them without needing to change the weights of the normalization or classifier networks. Our approach extends to unseen sites in various clinical settings where data domain discrepancies are unknown. Extensive experiments highlight the efficacy of our framework in tumor classification in hematoxylin and eosin-stained patches. Our explainable normalization method boosts classification tasks' area under the precision-recall curve(AUPR) by 0.165, 0.545 to 0.710. Additionally, Data Alchemy further reduces the multisite classification domain gap, by improving the 0.710 AUPR an additional 0.142, elevating classification performance further to 0.852, from 0.545. Our Data Alchemy framework can popularize precision medicine with minimal operational overhead by allowing for the seamless integration of pre-trained deep learning-based clinical tools across multiple sites.