CarveMix-RC: Addressing Rare-Class Imbalance Through Lesion-Aware Synthetic Augmentation for Brain Metastasis Segmentation
Authors: Md Shibly Sadique, Md Fayaz Bin Hossen, Michael L. Evans, Walia Farzana, Asfaqur Rahman, Ahmed Temtam, Khan M. Iftekharuddin
Organizations: Vision Lab, Department of Electrical and Computer Engineering, Old Dominion University, Norfolk, VA 23529, USA · Interdisciplinary Schools, Old Dominion University, Norfolk, VA 23529, USA
Accurate segmentation of post-treatment brain metastases is essential for treatment planning, longitudinal disease monitoring, and quantitative assessment of therapeutic response. The BraTS-MET 2026 Task 1 challenge introduces a clinically relevant segmentation problem involving four anatomically distinct tumor subregions: non-enhancing tumor core (NETC), surrounding non-enhancing FLAIR hyperintensity (SNFH), enhancing tumor (ET), and the resection cavity (RC). Among these, RC segmentation is particularly challenging because of its low prevalence, heterogeneous postoperative appearance, and lesion-wise evaluation protocol, leading conventional segmentation networks to prioritize dominant tumor classes during optimization. The proposed nnU-Net-based framework explicitly addresses RC segmentation through four complementary components: (i) RC-weighted Dice and Cross-Entropy optimization to alleviate class imbalance, (ii) anatomically consistent cavity augmentation to increase the diversity of postoperative cavity appearances, (iii) a residual encoder architecture for enhanced multi-scale feature learning, and (iv) lesion-aware morphological post-processing to suppress false-positive cavity predictions while preserving anatomically plausible structures. The framework is evaluated on the BraTS-MET 2026 Task 1 online validation benchmark. Among the evaluated configurations, the ensemble model (Residual Encoder nnU-Net + nnU-Net + RC-aware CarveMix) achieves the best performance, with lesion-wise Dice scores of 0.732, 0.752, 0.708, and 0.575 and corresponding NSD scores of 0.794, 0.798, 0.727, and 0.474 for ET, TC, WT, and RC, respectively. These experimental results show that integrating RC-aware optimization, anatomically consistent augmentation, and lesion-aware post-processing provides an effective strategy for improving rare resection cavity segmentation in post-treatment brain metastases.
Brain metastases exhibit high inter-lesion variability in size, enhancement pattern, and post-treatment appearance, making volumetric segmentation of both pre- and post-treatment cases the central challenge of the BraTS 2026 Task 1 (Brain Metastases). We build a pragmatic pipeline on a 5-fold nnU-Net ResEnc-L ensemble, in which each fold is trained independently for 1,000 epochs with the standard Dice + cross-entropy loss on 1,296 four-modality training cases. This ensemble is followed by a rule-based post-processing cascade tuned for the lesion-wise Dice similarity coefficient (LW-DSC), a detection-oriented metric that behaves very differently from the traditional global Dice. The final pipeline reaches an LW-DSC of 0.733 / 0.751 / 0.713 / 0.549 on the enhancing tumour (ET), tumour core (TC), whole tumour (WT), and resection cavity (RC) sub-regions on the official validation leaderboard. Rather than trusting these leaderboard gains, we audit every post-processing stage with a five-fold out-of-fold (OOF) analysis with no model-training leakage over all 1,296 training cases, scored with the official BraTS evaluation code (BraTS_evaluation): it confirms two stages as robust, per-fold-consistent improvements while the third improves only the leaderboard and does not reproduce out-of-fold. We further provide a mechanistic analysis of the LW-DSC metric that explains why recall-recovering post-processing carries low risk whereas component deletion does not, and we report thirteen negative results spanning loss engineering, alternative backbones, and inference-time settings, several of which run counter to widely held intuitions. Source code is released under Apache-2.0 at https://github.com/hornbeamliu/brats2026-met.
Haobin Liu, Xin Wang
College of Software, Jilin University, Changchun, China · Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
Brain metastases are the most common intracranial malignancy, occurring in roughly 30% of patients with primary solid tumors and carrying a median survival near 5.9 months. Automated segmentation is critical for treatment planning and volumetric monitoring, but metastases are frequently small, numerous, and heterogeneous in size within a single patient. We compare a plain nnU-Net baseline, a Residual Encoder Large (ResEncL) variant, region-based training, and a Primus transformer model for BraTS-METS 2026 Task 1, using patient-grouped cross-validation to prevent leakage from the longitudinal UCSD subset. Primus (label-based) is our strongest individual model by aggregate DSC/NSD, achieving 0.710/0.761 (ET), 0.742/0.785 (TC), 0.683/0.689 (WT), and 0.531/0.436 (RC). ResEncL trails Primus on aggregate DSC/NSD but achieves substantially higher lesion-wise F1 (e.g. ET: 0.452 vs. 0.052); a probability-averaging ensemble of the two only partially preserves ResEncL's F1 advantage (ET lesion-wise F1: 0.064). We further report three postprocessing and label-reconstruction pitfalls we believe generalize beyond this challenge. Code is available at https://github.com/mahdiislam79/BraTS_METS_2026.
Mahdi Islam, Musarrat Tabassum
Center for Computational & Data Sciences, Independent University, Bangladesh · Department of Electrical and Electronic Engineering, Independent University, Bangladesh · Independent Researcher
Few-shot brain tumor segmentation remains challenging due to noisy support masks, inter-patient variations between support and query images, and the lack of pixel-wise confidence estimation. This study proposes RUFNet, a Hybrid Mamba-based few-shot framework that combines support mask refinement with uncertainty-aware posterior fusion. To preserve support-query dependencies with manageable cost, RUFNet adopts a Hybrid Mamba interaction backbone with linear complexity. To reduce support-mask noise, an Attention-Guided Mask Refinement module (AGMR) uses query features to recalibrate support masks and improve prototype consistency. To handle ambiguous predictions, an Uncertainty-Aware Posterior Fusion module (UAPF) estimates pixel-wise variance and adaptively balances few-shot predictions with query-aligned priors. On the Brain Tumor Segmentation Challenge (BraTS) 2020 dataset, RUFNet achieves Dice coefficients of 84.3% and 86.1% in the 1-way 1-shot and 1-way 5-shot settings, respectively, outperforming the compared state-of-the-art methods. These results suggest that Hybrid Mamba interaction, mask refinement and uncertainty modelling can improve the robustness of few-shot medical image segmentation. The official implementation code is available at https://github.com/hdy6438/RUFNet.
Dongyi He, Xiangkai Wang, Binbing Xu +5
Department of Language Science and Technology, The Hong Kong Polytechnic University, Hong Kong SAR, China · School of Artificial Intelligence, Chongqing University of Technology, Chongqing, China · Affiliated Lianyungang Hospital of Xuzhou Medical University, Lianyungang, China +1