CarveMix-RC: Addressing Rare-Class Imbalance Through Lesion-Aware Synthetic Augmentation for Brain Metastasis Segmentation

Abstract

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.