Generalizable Brain Tumor Segmentation with Self-Training and Tumor-Aware Deformations

This work presents an approach to the Generalizability Across Tumors (BraTS-GoAT) task of the BraTS 2026 Challenge, which focuses on robust segmentation of brain tumor sub-regions across a heterogeneous patient population. The proposed method employs the nnU-Net framework with a large residual encoder architecture, integrating a semi-supervised learning technique with pseudo-labels generated from the unlabeled training data and a tumor-aware deformable augmentation that locally deforms the lesion while preserving the surrounding anatomy. We evaluate the individual contributions of each component, as well as their combination, using varying proportions of the most confident pseudo-labeled cases. The submitted configuration for the generalization task achieves Dice and NSD scores of 0.881 and 0.473 for Whole Tumor, 0.817 and 0.490 for Tumor Core, and 0.775 and 0.533 for Enhancing Tumor on the BraTS-GoAT validation set, improving over the labeled-only baselines across all tumor regions and confirming that self-training and the proposed augmentation are complementary. Our source code is publicly available at https://github.com/Henrique-zan/brats-goat-2026/.

On the Role of MRI Sequences in Cross-Dataset Generalization for Brain Tumor Segmentation

Brain tumor segmentation in magnetic resonance imaging (MRI) is a critical task for diagnosis and treatment planning. Despite the success of deep learning architectures such as U-Net and its variants, performance degradation across datasets remains a major challenge, particularly under domain shift and limited annotated data. To address this issue, this study systematically evaluates how individual MRI sequences influence model robustness across two well-known datasets. A ResUNet-based framework is employed, where each modality is trained independently to isolate its effect under a controlled cross-dataset evaluation protocol with tumor size stratification, without target-domain training, or with limited domain adaptation. Results show that the T2f/FLAIR sequence achieves the best cross-dataset performance, with Dice scores exceeding 75%. It consistently outperforms other modalities across most tumor size ranges, while multi-sequence training further improves performance. Additionally, even limited target-domain adaptation yields rapid initial gains, reducing the need for extensive annotations and costly retraining. Our source code is publicly available at https://github.com/henrique-zan/brain_tumor_segmentation/.

Multi-Stage Prompt-Guided Feature Modulation for Generalizable Brain Tumor Segmentation

Accurate brain tumor segmentation from magnetic resonance imaging (MRI) is essential for diagnosis, treatment planning, surgical guidance, and disease monitoring. However, developing automated segmentation models that generalize across diverse tumor characteristics, imaging protocols, acquisition sites, and patient populations remains challenging. Variations in tumor morphology and imaging distributions can substantially degrade performance outside the training domain. Consequently, improving the robustness and generalization of deep learning-based segmentation models has become a key objective in medical image analysis. To improve segmentation robustness, we propose Multi-Stage Dynamic Prompt nnU-Net, a prompt-conditioned extension of nnU-Net. Three independent dynamic prompt modules are inserted into the deepest encoder stages. Each module contains a learnable bank of ten 256-dimensional prompt vectors and uses globally pooled encoder features to generate image-specific prompt representations. These representations are projected into feature-wise scaling $(γ)$ and shifting $(β)$ parameters that modulate encoder feature maps through Feature-wise Linear Modulation (FiLM), enabling adaptive feature conditioning at multiple semantic levels. Evaluation on the BraTS GOAT validation dataset demonstrated that the proposed Multi-Stage Dynamic Prompt nnU-Net outperformed the baseline nnU Net across the majority of evaluated metrics and tumor subregions. The proposed model achieved average lesion-wise Dice scores of 76.16% (ET), 80.04% (TC), and 86.42% (WT), compared with 74.38%, 78.14% and 84.01% for the baseline model. The results demonstrate that multi-stage dynamic prompt conditioning improves segmentation accuracy and boundary delineation for brain tumor segmentation.

Reliability analysis for BraTS-GoAT segmentation: a controlled robustness study of deep-ensemble uncertainty

Deep networks segment brain tumours accurately in-distribution, but can fail silently when the input differs from their training data. That risk is central to clinical deployment and is the premise of the BraTS-GoAT generalizability task. We ask not only how well a model segments, but whether its uncertainty knows when it is wrong. On BraTS-GoAT (Task 3) we train a 5-fold cross-validated nnU-Net baseline (one held-out prediction per case) and a 3-seed deep ensemble. Both are evaluated for calibration and error detection on a per-region relevant mask, aggregated per case. In-distribution the 3-seed ensemble improves modestly over the already strong single model on the same held-out split, with the clearest gain in calibration. The separation appears under shift. In a controlled robustness study using graded synthetic corruptions as a proxy for acquisition shift, the single model's confidence stays flat while its accuracy and calibration degrade. Inter-member disagreement instead rises steeply, about a quarter to a third above the clean condition, several times the single model's response. On the official validation leaderboard the 5-fold ensemble of those folds attains whole-tumour Dice 0.87. The generalization gap is concentrated on the harder regions, with a characteristic failure of missing small, satellite lesions on unseen cohorts. In the synthetic study, disagreement among the 3-seed members is a more sensitive case-level indicator of acquisition shift than single-model confidence. Its per-voxel error localisation weakens as severity grows. The contribution is a rigorous, honest reliability comparison rather than a claim that any one uncertainty method dominates.

Similarity Weighted Aggregation with Global Differential Privacy for Federated Brain Lesion Segmentation

Federated Learning (FL) enables collaborative training of machine learning models across multiple institutions without sharing sensitive data, making it particularly suitable for medical imaging applications. However, heterogeneous data distributions across institutions and potential information leakage through model updates remain important challenges. In this work, we propose DP-SimAgg, a privacy-preserving federated learning framework that integrates similarity-weighted aggregation with a server-side differential privacy mechanism. The proposed method applies L2 clipping to bound collaborator updates, computes similarity-based aggregation weights to mitigate the effects of non-IID data distributions, and injects calibrated Gaussian noise at the central server, providing per-round privacy guarantees under the assumed sensitivity bound. The framework is implemented using Intel's OpenFL platform and evaluated on the FeTS 2022 dataset consisting of 1251 multi-modal MRI scans for brain tumor segmentation. Experimental results demonstrate that DP-SimAgg maintains competitive segmentation performance while providing privacy protection. Under a strict per-round privacy budget (epsilon = 1, cumulative epsilon_total = 20 over 20 rounds), the method achieves Dice scores of 0.6357, 0.5305, and 0.5274 for the enhancing tumor (ET), tumor core (TC), and whole tumor (WT) regions, respectively. With a more relaxed per-round budget (epsilon = 10, cumulative epsilon_total = 200), performance approaches that of the non-private baseline while incorporating a central Gaussian mechanism with per-round (epsilon, delta)-DP accounting under the assumed sensitivity bound. These results highlight the potential of DP-SimAgg for enabling privacy-preserving collaborative learning in medical imaging applications.

A Unified Benchmark of Deep Learning Models for Multi-task 3D Brain Tumor Segmentation from Magnetic Resonance Imaging

Automatic brain tumor segmentation from magnetic resonance imaging (MRI) has become a fundamental task in computer-assisted diagnosis, treatment planning, and disease monitoring. Although numerous deep learning architectures have recently been proposed, objective comparisons remain challenging because published studies often employ different datasets, preprocessing strategies, training protocols, and evaluation procedures. This work presents a unified experimental benchmark for comparing representative convolutional neural networks (CNNs), Transformer-based models, and recent State Space Model (SSM) architectures under homogeneous experimental conditions. Five state-of-the-art three-dimensional segmentation models, including 3D U-Net, SegResNet, Swin UNETR, SegMamba, and SegMambaV2, are evaluated on two brain tumor segmentation datasets representing distinct clinical scenarios: intracranial meningioma segmentation (BraTS 2023) and post-treatment glioma segmentation (BraTS 2024). All architectures are trained using identical preprocessing, data augmentation, optimization strategies, and evaluation protocols to ensure a fair comparison. Performance is assessed using segmentation accuracy metrics together with computational cost indicators, including inference time and the size of each model. The results provide practical insights into the trade-offs between segmentation accuracy and computational efficiency, highlighting the suitability of different architectural paradigms for challenging three-dimensional brain tumor segmentation tasks.

MIND: Multimodal Intent-Driven Network via Diffusion Transformers for Medical Image Fusion

Medical image fusion aims to integrate complementary information from diverse imaging modalities to support clinical diagnosis. Existing methods typically apply uniform fusion rules globally, lacking a deep understanding of diagnostic intents and pathological structures. To address these limitations, we propose MIND, a Multimodal Intent-Driven Network via Diffusion Transformers (DiTs) for medical image fusion. Specifically, we utilize BioMedGPT to generate intent-driven fusion texts from source images, guiding the fusion process with pathology-aware diagnostic intents. To combat the loss of 2D spatial continuity caused by 1D sequence flattening in DiTs, we design a Multi-scale Latent Adapter. This module explicitly extracts source image features before serialization, injecting them into the network via strict dimensional alignment to effectively supplement image features. To resolve the semantic shift caused by decoupling image outputs from diagnostic intents, we design a medical semantic consistency loss. This loss ensures deep semantic locking between fused images and fusion texts while maintaining the stability of the underlying physical manifold reconstruction. Comprehensive experiments on the Harvard, BraTS, and GFP datasets reveal that MIND delivers superior fusion quality, significantly improves downstream brain tumor segmentation accuracy, and enables flexible interactive fusion, holding significant promise for intent-driven intelligent clinical decision support systems.

Set-Inclusive Uncertainty Modeling for Robust Brain Tumor Segmentation

Multimodal MRI is essential for accurate brain tumor segmentation. However, acquiring all modalities at inference is often challenging in practice, which causes intrinsic uncertainty due to unavoidable information loss. Without modeling this uncertainty, existing methods encode incomplete evidence into deterministic representations that appear plausible but lack reliability. In this regime, we propose a probabilistic representation framework that models representations as Gaussian distributions, where their mean captures task information and their variance measures uncertainty from missing evidence. To make variance reflect information deficiency, we regularize the mean from each partial configuration toward its full-modality counterpart, while scaling the variance with the discrepancy between their aligned means. We further introduce a set-inclusive strategy that exploits the hierarchical structure of modality subsets and enforces an ordering constraint to maintain their consistent uncertainty relationships. Extensive experiments on BraTS 2018 and 2020 demonstrate that our approach offers superior performance over baselines across diverse missing-modality scenarios. Code and model checkpoint are available at https://github.com/atlas-sky/SIUM.

When Average Calibration Fails: Site-Conditional Federated Conformal Risk Control

Conformal risk control (CRC) provides distribution-free segmentation guarantees by calibrating a prediction-set threshold on held-out data. In federated deployments, the standard approach pools calibration scores into a single threshold. We quantify, on real multi-institutional brain tumor data (FeTS-2022, 1,251 subjects, 20 institutions), a critical failure: naive pooled CRC protects the average hospital but violates coverage at 40% of individual institutions, with the worst site exceeding the target false-negative rate by 7.8 percentage points. We trace this failure to a hidden design choice: the aggregation weights implicitly determine whose coverage is protected. Sample-size weighting optimizes patient-level validity but can sacrifice institution-level reliability; equal-site weighting improves institution-level reliability on this benchmark at comparable efficiency, using only a single scalar per site. We propose risk-curve shrinkage as a principled mechanism: each site transmits its empirical risk curve (G scalars) and a single hyperparameter n0 smoothly interpolates between site-specific local calibration and sample-size-weighted pooled calibration. Leave-one-site-out sensitivity analysis identifies n0=19, achieving 2.7/20 violations at 2.0x stretch. Direct Lagrangian budget optimization fails by concentrating risk on vulnerable hospitals; the finite-sample correction term is essential: removing it triples violations. No patient-level images, masks, or per-volume scores leave any site.

CoMNet: A MedNeXt-CorrDiff Framework for Multi-Site Brain Tumor Segmentation

Accurate brain tumor segmentation from multiparametric magnetic resonance imaging (MRI) is critical for treatment planning, response assessment, and neuro-oncology research. However, automated segmentation remains a difficult task in computer vision because of variation in tumor appearance and MRI protocols across patient scans. Moreover, clinically important regions such as enhancing tumor and tumor core are often small relative to the full brain volume, further increasing the difficulty of achieving high voxel-level precision. These challenges are amplified in multi-site datasets, where differences in scanner hardware and acquisition parameters can introduce non-biological variation. To address this, networks must learn tumor-specific features while remaining robust to site-dependent noise. In this paper, we show that an ensemble of multi-fold predictions from a modern 3D convolutional segmentation network with corrective diffusion (CorrDiff) post-processing improves brain tumor segmentation across datasets. We propose CoMNet, an ensembled MedNeXt-CorrDiff framework for accurate multi-site brain tumor segmentation. In this framework, we use MedNeXt as the primary segmentation model for feature learning, while a corrective diffusion block learns to refine the residual errors in the individual prediction maps before probabilistic thresholding. This process reduces the variance across fold predictions by correcting fold-specific residual errors and aggregating them into a consensus mask that is less sensitive to site-dependent imaging variability. Our proposed framework achieved the highest Dice score compared to two baseline models on the UTSW-Glioma and BraTS-SSA datasets. Experimental results support the use of corrective diffusion and fold-level probability ensembling as meaningful additions to existing state-of-the-art models for accurate glioma segmentation on multi-site datasets.

Diffusion-Refined Segmentation and Vision-Language Interpretation for Pediatric Brain Tumor MRI

Accurate pediatric brain tumor segmentation remains challenging due to limited annotated data, heterogeneous imaging phenotypes, diffuse tumor boundaries, and class imbalance across tumor subregions. Here, we present a two-stage deep learning framework for improving multi-modal pediatric brain MRI segmentation and clinical interpretation. First, we evaluate 3D Res U-Net and Swin-UNETR baselines on BraTS-PEDs MRI scans, using four co-registered modalities to predict tumor core, whole tumor, and enhancing tumor regions. Second, we introduce diffusion-based refinement models conditioned on coarse Swin-UNETR predictions, including a 3D DDPM refiner and MedSegDiff. Conditioning substantially improves diffusion stability and performance, particularly for enhancing tumor boundary segmentation. Conditioned MedSegDiff achieves the strongest boundary agreement with the lowest HD95. Finally, predicted tumor volumes and representative segmentation overlays are integrated with a multimodal language model to generate structured radiology-style reports. Together, our results suggest that coarse-to-refined diffusion segmentation can improve pediatric tumor boundary delineation and support end-to-end interpretable AI-assisted neuro-oncology workflows.

SegGuidedNet: Sub-Region-Aware Attention Supervision for Interpretable Brain Tumor Segmentation

Accurate segmentation of brain tumour sub-regions from multi-parametric MRI is critical for treatment planning yet remains challenging due to morphological variability, class imbalance, and overlapping appearances of tumour regions across imaging sequences. We propose SegGuidedNet, a three-dimensional residual encoder--decoder network introducing a novel SegAttentionGate module that explicitly supervises the decoder to produce spatially discriminative attention maps for each tumour sub-region necrotic core, peritumoral oedema, and enhancing tumour via a lightweight auxiliary loss, adding less than 0.2% parameter overhead. This sub-region supervision maintains decoder discriminability between visually ambiguous classes while providing free-of-cost spatial interpretability at inference without any post-hoc explanation method. Evaluated independently on BraTS2021 and BraTS2023 GLI across 251 held-out subjects each, SegGuidedNet achieves mean Dice of 0.905 (ET= 0.873, TC=0.906, WT=0.935) and 0.897 (ET=0.859, TC=0.902, WT=0.931) respectively, surpassing ensemble-based nnU-Net and HNF-Netv2 as a single model and approaching Swin UNETR a 10-model ensemble within 2--4 Dice points at a fraction of the inference cost. The consistency of results across two benchmark editions further confirms the generalisability of the proposed approach, offering competitive accuracy with built-in interpretability in a lightweight, clinically practical framework.

D3Seg: Dependency-Aware Diffusion for Brain Tumor Segmentation with Missing Modalities

Accurate brain tumor segmentation using multiparametric MRI is critical for effective treatment planning. However, in clinical settings, complete acquisition of all MRI sequences is not always possible. The absence of certain MRI modalities results in substantial performance degradation in existing segmentation methods, which typically rely on naive feature concatenation or direct fusion strategies. To address this limitation, we propose a novel segmentation model D3Seg which is designed to maintain stable performance under missing-modality settings. D3Seg introduces Multi-hop Modality Graph Fusion (MMGF) to model higher order inter-modality dependencies, a lightweight diffusion-based imputation mechanism to compensate for missing T1ce representations in latent space, and probability-space decision refinement to mitigate dominant class overconfidence and improve delineation of underrepresented tumor subregions. Extensive evaluation on BraTS 2023 dataset demonstrates that our D3Seg model consistently improves segmentation performance under missing modality configurations. The proposed model achieves approximately 1.5-2.0% Dice improvement on enhancing tumor (ET) and around 1.0% on tumor core (TC) across multiple missing modality configurations compared to the current state-of-the-art model, while maintaining computational efficiency.

DALight-3D: A Lightweight 3D U-Net for Brain Tumor Segmentation from Multi-Modal MRI

Automatic brain tumor segmentation from multi-modal MRI remains challenging because volumetric models often incur substantial computational cost. This paper presents DALight-3D, a compact 3D U-Net variant that combines depthwise separable 3D convolutions, identifier-conditioned normalization, cross-slice attention, and adaptive skip fusion. The method is evaluated on the Medical Segmentation Decathlon Task01 BrainTumour benchmark under matched optimization settings against standard 3D U-Net, Attention U-Net, Residual 3D U-Net, and V-Net baselines. In the reported 50-epoch comparison, DALight-3D achieves a mean Dice of 0.727 with 2.22M parameters, compared with 0.710 Dice and 3.20M parameters for Residual 3D U-Net. Component-wise ablations show consistent performance degradation when SepConv, identifier-conditioned normalization, CSA, or SSFB is removed. These results indicate that DALight-3D offers a favorable accuracy-efficiency trade-off within the present benchmark setting.

M\textsuperscript{4}Fuse: Lightweight State-Space MoE with a Cross-Scale Gating Bridge for Brain Tumor Segmentation

Encoder-decoder imbalance and the reliance on large input volumes make many 3D brain tumor segmentation models both compute-heavy and brittle. We present M\textsuperscript{4}Fuse, a lightweight network that prioritizes discriminative brain tumor cues over exhaustive appearance reconstruction. Our method balances encoder and decoder capacity and replaces depth expansion with a synergistic design: it propagates long-range context with linear complexity via a grouped state space mixer, denoises and aligns skip features using a cross-scale dual-stage gating bridge, and absorbs cross-site acquisition shifts with a sample-level mixture-of-experts. On the BraTS2019 and BraTS2021 benchmarks, M\textsuperscript{4}Fuse outperforms other lightweight excellent methods in both parameter count and performance. Even at a challenging input resolution of \(64\times128\times128\) (half that of existing excellent models), M\textsuperscript{4}Fuse reduces parameters by 62.63\% and improves average performance by 0.09\%. Ablations of key components validate the method's exceptional parameter-to-accuracy efficiency and robustness across diverse data centers.