Training Beyond Convergence: Grokking nnU-Net for Glioma Segmentation in Sub-Saharan MRI

Gliomas are placing an increasingly clinical burden on Sub-Saharan Africa (SSA). In the region, the median survival for patients remains under two years, and access to diagnostic imaging is extremely limited. These constraints highlight an urgent need for automated tools that can extract the maximum possible information from each available scan, tools that are specifically trained on local data, rather than adapted from high-income settings where conditions are vastly different. We utilize the Brain Tumor Segmentation (BraTS) Africa 2025 Challenge dataset, an expert annotated collection of glioma MRIs. Our objectives are: (i) establish a strong baseline with nnUNet on this dataset, and (ii) explore whether the celebrated "grokking" phenomenon an abrupt, late training jump from memorization to superior generalization can be triggered to push performance without extra labels. We evaluate two training regimes. The first is a fast, budget-conscious approach that limits optimization to just a few epochs, reflecting the constrained GPU resources typically available in African institutions. Despite this limitation, nnUNet achieves strong Dice scores: 92.3% for whole tumor (WH), 86.6% for tumor core (TC), and 86.3% for enhancing tumor (ET). The second regime extends training well beyond the point of convergence, aiming to trigger a grokking-driven performance leap. With this approach, we were able to achieve grokking and enhanced our results to higher Dice scores: 92.2% for whole tumor (WH), 90.1% for tumor core (TC), and 90.2% for enhancing tumor (ET).

AMGFormer: Adaptive Multi-Granular Transformer for Brain Tumor Segmentation with Missing Modalities

Multimodal MRI is essential for brain tumor segmentation, yet missing modalities in clinical practice cause existing methods to exhibit >40% performance variance across modality combinations, rendering them clinically unreliable. We propose AMGFormer, achieving significantly improved stability through three synergistic modules: (1) QuadIntegrator Bridge (QIB) enabling spatially adaptive fusion maintaining consistent predictions regardless of available modalities, (2) Multi-Granular Attention Orchestrator (MGAO) focusing on pathological regions to reduce background sensitivity, and (3) Modality Quality-Aware Enhancement (MQAE) preventing error propagation from corrupted sequences. On BraTS 2018, our method achieves 89.33% WT, 82.70% TC, 67.23% ET Dice scores with <0.5% variance across 15 modality combinations, solving the stability crisis. Single-modality ET segmentation shows 40-81% relative improvements over state-of-the-art methods. The method generalizes to BraTS 2020/2021, achieving up to 92.44% WT, 89.91% TC, 84.57% ET. The model demonstrates potential for clinical deployment with 1.2s inference. Code: https://github.com/guochengxiangives/AMGFormer.

SegRap2025: A Benchmark of Gross Tumor Volume and Lymph Node Clinical Target Volume Segmentation for Radiotherapy Planning of Nasopharyngeal Carcinoma

Accurate delineation of Gross Tumor Volume (GTV), Lymph Node Clinical Target Volume (LN CTV), and Organ-at-Risk (OAR) from Computed Tomography (CT) scans is essential for precise radiotherapy planning in Nasopharyngeal Carcinoma (NPC). Building upon SegRap2023, which focused on OAR and GTV segmentation using single-center paired non-contrast CT (ncCT) and contrast-enhanced CT (ceCT) scans, the SegRap2025 challenge aims to enhance the generalizability and robustness of segmentation models across imaging centers and modalities. SegRap2025 comprises two tasks: Task01 addresses GTV segmentation using paired CT from the SegRap2023 dataset, with an additional external testing set to evaluate cross-center generalization, and Task02 focuses on LN CTV segmentation using multi-center training data and an unseen external testing set, where each case contains paired CT scans or a single modality, emphasizing both cross-center and cross-modality robustness. This paper presents the challenge setup and provides a comprehensive analysis of the solutions submitted by ten participating teams. For GTV segmentation task, the top-performing models achieved average Dice Similarity Coefficient (DSC) of 74.61% and 56.79% on the internal and external testing cohorts, respectively. For LN CTV segmentation task, the highest average DSC values reached 60.24%, 60.50%, and 57.23% on paired CT, ceCT-only, and ncCT-only subsets, respectively. SegRap2025 establishes a large-scale multi-center, multi-modality benchmark for evaluating the generalization and robustness in radiotherapy target segmentation, providing valuable insights toward clinically applicable automated radiotherapy planning systems. The benchmark is available at: https://hilab-git.github.io/SegRap2025_Challenge.

Pareto-Guided Optimization for Uncertainty-Aware Medical Image Segmentation

Uncertainty in medical image segmentation is inherently non-uniform, with boundary regions exhibiting substantially higher ambiguity than interior areas. Conventional training treats all pixels equally, leading to unstable optimization during early epochs when predictions are unreliable. We argue that this instability hinders convergence toward Pareto-optimal solutions and propose a region-wise curriculum strategy that prioritizes learning from certain regions and gradually incorporates uncertain ones, reducing gradient variance. Methodologically, we introduce a Pareto-consistent loss that balances trade-offs between regional uncertainties by adaptively reshaping the loss landscape and constraining convergence dynamics between interior and boundary regions; this guides the model toward Pareto-approximate solutions. To address boundary ambiguity, we further develop a fuzzy labeling mechanism that maintains binary confidence in non-boundary areas while enabling smooth transitions near boundaries, stabilizing gradients, and expanding flat regions in the loss surface. Experiments on brain metastasis and non-metastatic tumor segmentation show consistent improvements across multiple configurations, with our method outperforming traditional crisp-set approaches in all tumor subregions.

BMDS-Net: A Bayesian Multi-Modal Deep Supervision Network for Robust Brain Tumor Segmentation

Accurate brain tumor segmentation from multi-modal magnetic resonance imaging (MRI) is a prerequisite for precise radiotherapy planning and surgical navigation. While recent Transformer-based models such as Swin UNETR have achieved impressive benchmark performance, their clinical utility is often compromised by two critical issues: sensitivity to missing modalities (common in clinical practice) and a lack of confidence calibration. Merely chasing higher Dice scores on idealized data fails to meet the safety requirements of real-world medical deployment. In this work, we propose BMDS-Net, a unified framework that prioritizes clinical robustness and trustworthiness over simple metric maximization. Our contribution is three-fold. First, we construct a robust deterministic backbone by integrating a Zero-Init Multimodal Contextual Fusion (MMCF) module and a Residual-Gated Deep Decoder Supervision (DDS) mechanism, enabling stable feature learning and precise boundary delineation with significantly reduced Hausdorff Distance, even under modality corruption. Second, and most importantly, we introduce a memory-efficient Bayesian fine-tuning strategy that transforms the network into a probabilistic predictor, providing voxel-wise uncertainty maps to highlight potential errors for clinicians. Third, comprehensive experiments on the BraTS 2021 dataset demonstrate that BMDS-Net not only maintains competitive accuracy but, more importantly, exhibits superior stability in missing-modality scenarios where baseline models fail. The source code is publicly available at https://github.com/RyanZhou168/BMDS-Net.

Reliable Brain Tumor Segmentation Based on Spiking Neural Networks with Efficient Training

We propose a reliable and energy-efficient framework for 3D brain tumor segmentation using spiking neural networks (SNNs). A multi-view ensemble of sagittal, coronal, and axial SNN models provides voxel-wise uncertainty estimation and enhances segmentation robustness. To address the high computational cost in training SNN models for semantic image segmentation, we employ Forward Propagation Through Time (FPTT), which maintains temporal learning efficiency with significantly reduced computational cost. Experiments on the Multimodal Brain Tumor Segmentation Challenges (BraTS 2017 and BraTS 2023) demonstrate competitive accuracy, well-calibrated uncertainty, and an 87% reduction in FLOPs, underscoring the potential of SNNs for reliable, low-power medical IoT and Point-of-Care systems.

Sub-Region-Aware Modality Fusion and Adaptive Prompting for Multi-Modal Brain Tumor Segmentation

The successful adaptation of foundation models to multi-modal medical imaging is a critical yet unresolved challenge. Existing models often struggle to effectively fuse information from multiple sources and adapt to the heterogeneous nature of pathological tissues. To address this, we introduce a novel framework for adapting foundation models to multi-modal medical imaging, featuring two key technical innovations: sub-region-aware modality attention and adaptive prompt engineering. The attention mechanism enables the model to learn the optimal combination of modalities for each tumor sub-region, while the adaptive prompting strategy leverages the inherent capabilities of foundation models to refine segmentation accuracy. We validate our framework on the BraTS 2020 brain tumor segmentation dataset, demonstrating that our approach significantly outperforms baseline methods, particularly in the challenging necrotic core sub-region. Our work provides a principled and effective approach to multi-modal fusion and prompting, paving the way for more accurate and robust foundation model-based solutions in medical imaging.

Karhunen-Loève Expansion-Based Residual Anomaly Map for Resource-Efficient Glioma MRI Segmentation

Accurate segmentation of brain tumors is essential for clinical diagnosis and treatment planning. Deep learning is currently the state-of-the-art for brain tumor segmentation, yet it requires either large datasets or extensive computational resources that are inaccessible in most areas. This makes the problem increasingly difficult: state-of-the-art models use thousands of training cases and vast computational power, where performance drops sharply when either is limited. The top performer in the Brats GLI 2023 competition relied on supercomputers trained on over 92,000 augmented MRI scans using an AMD EPYC 7402 CPU, six NVIDIA RTX 6000 GPUs (48GB VRAM each), and 1024GB of RAM over multiple weeks. To address this, the Karhunen--Loève Expansion (KLE) was implemented as a feature extraction step on downsampled, z-score normalized MRI volumes. Each 240$\times$240$\times$155 multi-modal scan is reduced to four $48^3$ channels and compressed into 32 KL coefficients. The resulting approximate reconstruction enables a residual-based anomaly map, which is upsampled and added as a fifth channel to a compact 3D U-Net. All experiments were run on a consumer workstation (AMD Ryzen 5 7600X CPU, RTX 4060Ti (8GB VRAM), and 64GB RAM while using far fewer training cases. This model achieves post-processed Dice scores of 0.929 (WT), 0.856 (TC), and 0.821 (ET), with HD95 distances of 2.93, 6.78, and 10.35 voxels. These results are significantly better than the winning BraTS 2023 methodology for HD95 distances and WT dice scores. This demonstrates that a KLE-based residual anomaly map can dramatically reduce computational cost and data requirements while retaining state-of-the-art performance.

VISTA-PATH: An interactive foundation model for pathology image segmentation and quantitative analysis in computational pathology

Accurate semantic segmentation for histopathology image is crucial for quantitative tissue analysis and downstream clinical modeling. Recent segmentation foundation models have improved generalization through large-scale pretraining, yet remain poorly aligned with pathology because they treat segmentation as a static visual prediction task. Here we present VISTA-PATH, an interactive, class-aware pathology segmentation foundation model designed to resolve heterogeneous structures, incorporate expert feedback, and produce pixel-level segmentation that are directly meaningful for clinical interpretation. VISTA-PATH jointly conditions segmentation on visual context, semantic tissue descriptions, and optional expert-provided spatial prompts, enabling precise multi-class segmentation across heterogeneous pathology images. To support this paradigm, we curate VISTA-PATH Data, a large-scale pathology segmentation corpus comprising over 1.6 million image-mask-text triplets spanning 9 organs and 93 tissue classes. Across extensive held-out and external benchmarks, VISTA-PATH consistently outperforms existing segmentation foundation models. Importantly, VISTA-PATH supports dynamic human-in-the-loop refinement by propagating sparse, patch-level bounding-box annotation feedback into whole-slide segmentation. Finally, we show that the high-fidelity, class-aware segmentation produced by VISTA-PATH is a preferred model for computational pathology. It improve tissue microenvironment analysis through proposed Tumor Interaction Score (TIS), which exhibits strong and significant associations with patient survival. Together, these results establish VISTA-PATH as a foundation model that elevates pathology image segmentation from a static prediction to an interactive and clinically grounded representation for digital pathology. Source code and demo can be found at https://github.com/zhihuanglab/VISTA-PATH.

A Generalist Foundation Model for Total-body PET/CT Enables Diagnostic Reporting and System-wide Metabolic Profiling

Total-body PET/CT enables system-wide molecular imaging, but heterogeneous anatomical and metabolic signals, approximately 2 m axial coverage, and structured radiology semantics challenge existing medical AI models that assume single-modality inputs, localized fields of view, and coarse image-text alignment. We introduce SDF-HOLO (Systemic Dual-stream Fusion Holo Model), a multimodal foundation model for holistic total-body PET/CT, pre-trained on more than 10,000 patients. SDF-HOLO decouples CT and PET representation learning with dual-stream encoders and couples them through a cross-modal interaction module, allowing anatomical context to refine PET aggregation while metabolic saliency guides subtle morphological reasoning. To model long-range dependencies across the body, hierarchical context modeling combines efficient local windows with global attention. To bridge voxels and clinical language, we use anatomical segmentation masks as explicit semantic anchors and perform voxel-mask-text alignment during pre-training. Across tumor segmentation, low-dose lesion detection, and multilingual diagnostic report generation, SDF-HOLO outperforms strong task-specific and clinical-reference baselines while reducing localization errors and hallucinated findings. Beyond focal interpretation, the model enables system-wide metabolic profiling and reveals tumor-associated fingerprints of inter-organ metabolic network interactions, providing a scalable computational foundation for total-body PET/CT diagnostics and system-level precision oncology.