SYNAPSE-Net: A Unified Framework with Lesion-Aware Hierarchical Gating for Robust Segmentation of Heterogeneous Brain Lesions

Automatic segmentation of diverse heterogeneous brain lesions using multi-modal MRI is a challenging problem in clinical neuroimaging, mainly because of the lack of generalizability and high prediction variance of pathology-specific deep learning models. In this work, we propose a unified and adaptive multi-stream framework called SYNAPSE-Net to perform robust multi-pathology segmentation with reduced performance variance. The framework is based on multi-stream convolutional encoders with global context modeling and a cross-modal attention fusion strategy to ensure stable and effective multi-modal feature integration. It also employs a variance-aware training strategy to enhance the robustness of the network across diverse tasks. The framework is extensively validated using three public challenge datasets: WMH MICCAI 2017, ISLES 2022, and BraTS 2020. The results show consistent improvements in boundary accuracy, delineation quality, and stability across diverse pathologies. This proposed framework achieved a high Dice similarity coefficient (DSC) of 0.831 and a low Hausdorff distance at the 95th percentile (HD95) of 3.03 on the WMH MICCAI 2017 dataset. It also achieved the lowest HD95 of 9.69 on the ISLES 2022 dataset and the highest tumor core DSC of 0.8651 on the BraTS 2020 dataset. These results validate the robustness of the proposed framework in providing a clinically relevant computer-aided solution for automated brain lesion segmentation. Source code and pretrained models are publicly available at https://github.com/mubid-01/SYNAPSE-Net-pre.