Federated learning(FL) is used for distributed scenarios to train artificial intelligence(AI) models while ensuring users' privacy. In federated learning scenario, the server generally never knows about users' data. This type of concept makes the AI training process efficient in terms of data privacy. However, regarding model performance, federated AI models may not sufficiently satisfy AI users' expectations. Furthermore, AI users have a wide range of different needs. It is not easy to satisfy the whole users needs. These types of issues can be addressed through AI model optimization, fine-tuning, or personalization to achieve optimal model performance. To address model optimization challenges, we propose reference model-based federated learning for optimal fine-tuning, which overcomes catastrophic forgetting in each round. This method is derived from Bayesian parameter-efficient transfer learning, which includes an optimal proximal term and enables overcoming the catastrophic forgetting issue in each round by utilizing a reference model that incorporates previous model parameters. As a result, this method achieves both high model performance and low computing cost.
This work introduces a novel framework for brain tumor segmentation leveraging pre-trained GANs and Unet architectures. By combining a global anomaly detection module with a refined mask generation network, the proposed model accurately identifies tumor-sensitive regions and iteratively enhances segmentation precision using adversarial loss constraints. Multi-modal MRI data and synthetic image augmentation are employed to improve robustness and address the challenge of limited annotated datasets. Experimental results on the BraTS dataset demonstrate the effectiveness of the approach, achieving high sensitivity and accuracy in both lesion-wise Dice and HD95 metrics than the baseline. This scalable method minimizes the dependency on fully annotated data, paving the way for practical real-world applications in clinical settings.
Deep learning has demonstrated remarkable success in medical image segmentation and computer-aided diagnosis. In particular, numerous advanced methods have achieved state-of-the-art performance in brain tumor segmentation from MRI scans. While recent studies in other medical imaging domains have revealed that integrating textual reports with visual data can enhance segmentation accuracy, the field of brain tumor analysis lacks a comprehensive dataset that combines radiological images with corresponding textual annotations. This limitation has hindered the exploration of multimodal approaches that leverage both imaging and textual data. To bridge this critical gap, we introduce the TextBraTS dataset, the first publicly available volume-level multimodal dataset that contains paired MRI volumes and rich textual annotations, derived from the widely adopted BraTS2020 benchmark. Building upon this novel dataset, we propose a novel baseline framework and sequential cross-attention method for text-guided volumetric medical image segmentation. Through extensive experiments with various text-image fusion strategies and templated text formulations, our approach demonstrates significant improvements in brain tumor segmentation accuracy, offering valuable insights into effective multimodal integration techniques. Our dataset, implementation code, and pre-trained models are publicly available at https://github.com/Jupitern52/TextBraTS.
Accurate segmentation and classification of brain tumors from Magnetic Resonance Imaging (MRI) remain key challenges in medical image analysis, largely due to the lack of high-quality, balanced, and diverse datasets. In this work, we present a new curated MRI dataset designed specifically for brain tumor segmentation and classification tasks. The dataset comprises 6,000 contrast-enhanced T1-weighted MRI scans annotated by certified radiologists and physicians, spanning three major tumor types-glioma, meningioma, and pituitary-as well as non-tumorous cases. Each sample includes high-resolution labels and is categorized across axial, sagittal, and coronal imaging planes to facilitate robust model development and cross-view generalization. To demonstrate the utility of the dataset, we propose a transformer-based segmentation model and benchmark it against established baselines. Our method achieves the highest weighted mean Intersection-over-Union (IoU) of 82.3%, with improvements observed across all tumor categories. Importantly, this study serves primarily as an introduction to the dataset, establishing foundational benchmarks for future research. We envision this dataset as a valuable resource for advancing machine learning applications in neuro-oncology, supporting both academic research and clinical decision-support development. datasetlink: https://www.kaggle.com/datasets/briscdataset/brisc2025/
The Brain Tumor Segmentation (BraTS) cluster of challenges has significantly advanced brain tumor image analysis by providing large, curated datasets and addressing clinically relevant tasks. However, despite its success and popularity, algorithms and models developed through BraTS have seen limited adoption in both scientific and clinical communities. To accelerate their dissemination, we introduce BraTS orchestrator, an open-source Python package that provides seamless access to state-of-the-art segmentation and synthesis algorithms for diverse brain tumors from the BraTS challenge ecosystem. Available on GitHub (https://github.com/BrainLesion/BraTS), the package features intuitive tutorials designed for users with minimal programming experience, enabling both researchers and clinicians to easily deploy winning BraTS algorithms for inference. By abstracting the complexities of modern deep learning, BraTS orchestrator democratizes access to the specialized knowledge developed within the BraTS community, making these advances readily available to broader neuro-radiology and neuro-oncology audiences.
In this paper, we address the crucial task of brain tumor segmentation in medical imaging and propose innovative approaches to enhance its performance. The current state-of-the-art nnU-Net has shown promising results but suffers from extensive training requirements and underutilization of pre-trained weights. To overcome these limitations, we integrate Axial-Coronal-Sagittal convolutions and pre-trained weights from ImageNet into the nnU-Net framework, resulting in reduced training epochs, reduced trainable parameters, and improved efficiency. Two strategies for transferring 2D pre-trained weights to the 3D domain are presented, ensuring the preservation of learned relationships and feature representations critical for effective information propagation. Furthermore, we explore a joint classification and segmentation model that leverages pre-trained encoders from a brain glioma grade classification proxy task, leading to enhanced segmentation performance, especially for challenging tumor labels. Experimental results demonstrate that our proposed methods in the fast training settings achieve comparable or even outperform the ensemble of cross-validation models, a common practice in the brain tumor segmentation literature.
Precise segmentation of brain tumors, particularly contrast-enhancing regions visible in post-contrast MRI (areas highlighted by contrast agent injection), is crucial for accurate clinical diagnosis and treatment planning but remains challenging. However, current methods exhibit notable performance degradation in segmenting these enhancing brain tumor areas, largely due to insufficient consideration of MRI-specific tumor features such as complex textures and directional variations. To address this, we propose the Harmonized Frequency Fusion Network (HFF-Net), which rethinks brain tumor segmentation from a frequency-domain perspective. To comprehensively characterize tumor regions, we develop a Frequency Domain Decomposition (FDD) module that separates MRI images into low-frequency components, capturing smooth tumor contours and high-frequency components, highlighting detailed textures and directional edges. To further enhance sensitivity to tumor boundaries, we introduce an Adaptive Laplacian Convolution (ALC) module that adaptively emphasizes critical high-frequency details using dynamically updated convolution kernels. To effectively fuse tumor features across multiple scales, we design a Frequency Domain Cross-Attention (FDCA) integrating semantic, positional, and slice-specific information. We further validate and interpret frequency-domain improvements through visualization, theoretical reasoning, and experimental analyses. Extensive experiments on four public datasets demonstrate that HFF-Net achieves an average relative improvement of 4.48\% (ranging from 2.39\% to 7.72\%) in the mean Dice scores across the three major subregions, and an average relative improvement of 7.33% (ranging from 5.96% to 8.64%) in the segmentation of contrast-enhancing tumor regions, while maintaining favorable computational efficiency and clinical applicability. Code: https://github.com/VinyehShaw/HFF.
Accurate 3D medical image segmentation demands architectures capable of reconciling global context modeling with spatial topology preservation. While State Space Models (SSMs) like Mamba show potential for sequence modeling, existing medical SSMs suffer from encoder-decoder incompatibility: the encoder's 1D sequence flattening compromises spatial structures, while conventional decoders fail to leverage Mamba's state propagation. We present DM-SegNet, a Dual-Mamba architecture integrating directional state transitions with anatomy-aware hierarchical decoding. The core innovations include a quadri-directional spatial Mamba module employing four-directional 3D scanning to maintain anatomical spatial coherence, a gated spatial convolution layer that enhances spatially sensitive feature representation prior to state modeling, and a Mamba-driven decoding framework enabling bidirectional state synchronization across scales. Extensive evaluation on two clinically significant benchmarks demonstrates the efficacy of DM-SegNet: achieving state-of-the-art Dice Similarity Coefficient (DSC) of 85.44% on the Synapse dataset for abdominal organ segmentation and 90.22% on the BraTS2023 dataset for brain tumor segmentation.
Existing methods for multimodal MRI segmentation with missing modalities typically assume that all MRI modalities are available during training. However, in clinical practice, some modalities may be missing due to the sequential nature of MRI acquisition, leading to performance degradation. Furthermore, retraining models to accommodate newly available modalities can be inefficient and may cause overfitting, potentially compromising previously learned knowledge. To address these challenges, we propose Replay-based Hypergraph Domain Incremental Learning (ReHyDIL) for brain tumor segmentation with missing modalities. ReHyDIL leverages Domain Incremental Learning (DIL) to enable the segmentation model to learn from newly acquired MRI modalities without forgetting previously learned information. To enhance segmentation performance across diverse patient scenarios, we introduce the Cross-Patient Hypergraph Segmentation Network (CHSNet), which utilizes hypergraphs to capture high-order associations between patients. Additionally, we incorporate Tversky-Aware Contrastive (TAC) loss to effectively mitigate information imbalance both across and within different modalities. Extensive experiments on the BraTS2019 dataset demonstrate that ReHyDIL outperforms state-of-the-art methods, achieving an improvement of over 2% in the Dice Similarity Coefficient across various tumor regions. Our code is available at https://github.com/reeive/ReHyDIL.
Accurate segmentation of brain images typically requires the integration of complementary information from multiple image modalities. However, clinical data for all modalities may not be available for every patient, creating a significant challenge. To address this, previous studies encode multiple modalities into a shared latent space. While somewhat effective, it remains suboptimal, as each modality contains distinct and valuable information. In this study, we propose DC-Seg (Disentangled Contrastive Learning for Segmentation), a new method that explicitly disentangles images into modality-invariant anatomical representation and modality-specific representation, by using anatomical contrastive learning and modality contrastive learning respectively. This solution improves the separation of anatomical and modality-specific features by considering the modality gaps, leading to more robust representations. Furthermore, we introduce a segmentation-based regularizer that enhances the model's robustness to missing modalities. Extensive experiments on the BraTS 2020 and a private white matter hyperintensity(WMH) segmentation dataset demonstrate that DC-Seg outperforms state-of-the-art methods in handling incomplete multimodal brain tumor segmentation tasks with varying missing modalities, while also demonstrate strong generalizability in WMH segmentation. The code is available at https://github.com/CuCl-2/DC-Seg.
Self-supervised pretrain techniques have been widely used to improve the downstream tasks' performance. However, real-world magnetic resonance (MR) studies usually consist of different sets of contrasts due to different acquisition protocols, which poses challenges for the current deep learning methods on large-scale pretrain and different downstream tasks with different input requirements, since these methods typically require a fixed set of input modalities or, contrasts. To address this challenge, we propose variable-input ViT (VIViT), a transformer-based framework designed for self-supervised pretraining and segmentation finetuning for variable contrasts in each study. With this ability, our approach can maximize the data availability in pretrain, and can transfer the learned knowledge from pretrain to downstream tasks despite variations in input requirements. We validate our method on brain infarct and brain tumor segmentation, where our method outperforms current CNN and ViT-based models with a mean Dice score of 0.624 and 0.883 respectively. These results highlight the efficacy of our design for better adaptability and performance on tasks with real-world heterogeneous MR data.
Background: Brain tumor segmentation has a significant impact on the diagnosis and treatment of brain tumors. Accurate brain tumor segmentation remains challenging due to their irregular shapes, vague boundaries, and high variability. Objective: We propose a brain tumor segmentation method that combines deep learning with prior knowledge derived from a region-growing algorithm. Methods: The proposed method utilizes a multi-scale feature fusion (MSFF) module and adaptive attention mechanisms (AAM) to extract multi-scale features and capture global contextual information. To enhance the model's robustness in low-confidence regions, the Monte Carlo Dropout (MC Dropout) strategy is employed for uncertainty estimation. Results: Extensive experiments demonstrate that the proposed method achieves superior performance on Brain Tumor Segmentation (BraTS) datasets, significantly outperforming various state-of-the-art methods. On the BraTS2021 dataset, the test Dice scores are 89.18% for Enhancing Tumor (ET) segmentation, 93.67% for Whole Tumor (WT) segmentation, and 91.23% for Tumor Core (TC) segmentation. On the BraTS2019 validation set, the validation Dice scores are 87.43%, 90.92%, and 90.40% for ET, WT, and TC segmentation, respectively. Ablation studies further confirmed the contribution of each module to segmentation accuracy, indicating that each component played a vital role in overall performance improvement. Conclusion: This study proposed a novel 3D brain tumor segmentation network based on the U-Net architecture. By incorporating the prior knowledge and employing the uncertainty estimation method, the robustness and performance were improved. The code for the proposed method is available at https://github.com/chenzhao2023/UPMAD_Net_BrainSeg.
Cancer remains one of the leading causes of mortality worldwide, and among its many forms, brain tumors are particularly notorious due to their aggressive nature and the critical challenges involved in early diagnosis. Recent advances in artificial intelligence have shown great promise in assisting medical professionals with precise tumor segmentation, a key step in timely diagnosis and treatment planning. However, many state-of-the-art segmentation methods require extensive computational resources and prolonged training times, limiting their practical application in resource-constrained settings. In this work, we present a novel dual-decoder U-Net architecture enhanced with attention-gated skip connections, designed specifically for brain tumor segmentation from MRI scans. Our approach balances efficiency and accuracy by achieving competitive segmentation performance while significantly reducing training demands. Evaluated on the BraTS 2020 dataset, the proposed model achieved Dice scores of 85.06% for Whole Tumor (WT), 80.61% for Tumor Core (TC), and 71.26% for Enhancing Tumor (ET) in only 50 epochs, surpassing several commonly used U-Net variants. Our model demonstrates that high-quality brain tumor segmentation is attainable even under limited computational resources, thereby offering a viable solution for researchers and clinicians operating with modest hardware. This resource-efficient model has the potential to improve early detection and diagnosis of brain tumors, ultimately contributing to better patient outcomes
Despite continuous advancements in cancer treatment, brain metastatic disease remains a significant complication of primary cancer and is associated with an unfavorable prognosis. One approach for improving diagnosis, management, and outcomes is to implement algorithms based on artificial intelligence for the automated segmentation of both pre- and post-treatment MRI brain images. Such algorithms rely on volumetric criteria for lesion identification and treatment response assessment, which are still not available in clinical practice. Therefore, it is critical to establish tools for rapid volumetric segmentations methods that can be translated to clinical practice and that are trained on high quality annotated data. The BraTS-METS 2025 Lighthouse Challenge aims to address this critical need by establishing inter-rater and intra-rater variability in dataset annotation by generating high quality annotated datasets from four individual instances of segmentation by neuroradiologists while being recorded on video (two instances doing "from scratch" and two instances after AI pre-segmentation). This high-quality annotated dataset will be used for testing phase in 2025 Lighthouse challenge and will be publicly released at the completion of the challenge. The 2025 Lighthouse challenge will also release the 2023 and 2024 segmented datasets that were annotated using an established pipeline of pre-segmentation, student annotation, two neuroradiologists checking, and one neuroradiologist finalizing the process. It builds upon its previous edition by including post-treatment cases in the dataset. Using these high-quality annotated datasets, the 2025 Lighthouse challenge plans to test benchmark algorithms for automated segmentation of pre-and post-treatment brain metastases (BM), trained on diverse and multi-institutional datasets of MRI images obtained from patients with brain metastases.
Due to the success of CNN-based and Transformer-based models in various computer vision tasks, recent works study the applicability of CNN-Transformer hybrid architecture models in 3D multi-modality medical segmentation tasks. Introducing Transformer brings long-range dependent information modeling ability in 3D medical images to hybrid models via the self-attention mechanism. However, these models usually employ fixed receptive fields of 3D volumetric features within each self-attention layer, ignoring the multi-scale volumetric lesion features. To address this issue, we propose a CNN-Transformer hybrid 3D medical image segmentation model, named TMA-TransBTS, based on an encoder-decoder structure. TMA-TransBTS realizes simultaneous extraction of multi-scale 3D features and modeling of long-distance dependencies by multi-scale division and aggregation of 3D tokens in a self-attention layer. Furthermore, TMA-TransBTS proposes a 3D multi-scale cross-attention module to establish a link between the encoder and the decoder for extracting rich volume representations by exploiting the mutual attention mechanism of cross-attention and multi-scale aggregation of 3D tokens. Extensive experimental results on three public 3D medical segmentation datasets show that TMA-TransBTS achieves higher averaged segmentation results than previous state-of-the-art CNN-based 3D methods and CNN-Transform hybrid 3D methods for the segmentation of 3D multi-modality brain tumors.
Deep learning has been successfully applied to medical image segmentation, enabling accurate identification of regions of interest such as organs and lesions. This approach works effectively across diverse datasets, including those with single-image contrast, multi-contrast, and multimodal imaging data. To improve human understanding of these black-box models, there is a growing need for Explainable AI (XAI) techniques for model transparency and accountability. Previous research has primarily focused on post hoc pixel-level explanations, using methods gradient-based and perturbation-based apporaches. These methods rely on gradients or perturbations to explain model predictions. However, these pixel-level explanations often struggle with the complexity inherent in multi-contrast magnetic resonance imaging (MRI) segmentation tasks, and the sparsely distributed explanations have limited clinical relevance. In this study, we propose using contrast-level Shapley values to explain state-of-the-art models trained on standard metrics used in brain tumor segmentation. Our results demonstrate that Shapley analysis provides valuable insights into different models' behavior used for tumor segmentation. We demonstrated a bias for U-Net towards over-weighing T1-contrast and FLAIR, while Swin-UNETR provided a cross-contrast understanding with balanced Shapley distribution.
Pretrain techniques, whether supervised or self-supervised, are widely used in deep learning to enhance model performance. In real-world clinical scenarios, different sets of magnetic resonance (MR) contrasts are often acquired for different subjects/cases, creating challenges for deep learning models assuming consistent input modalities among all the cases and between pretrain and finetune. Existing methods struggle to maintain performance when there is an input modality/contrast set mismatch with the pretrained model, often resulting in degraded accuracy. We propose an adaptive Vision Transformer (AdaViT) framework capable of handling variable set of input modalities for each case. We utilize a dynamic tokenizer to encode different input image modalities to tokens and take advantage of the characteristics of the transformer to build attention mechanism across variable length of tokens. Through extensive experiments, we demonstrate that this architecture effectively transfers supervised pretrained models to new datasets with different input modality/contrast sets, resulting in superior performance on zero-shot testing, few-shot finetuning, and backward transferring in brain infarct and brain tumor segmentation tasks. Additionally, for self-supervised pretrain, the proposed method is able to maximize the pretrain data and facilitate transferring to diverse downstream tasks with variable sets of input modalities.
Leveraging multi-center data for medical analytics presents challenges due to privacy concerns and data heterogeneity. While distributed approaches such as federated learning has gained traction, they remain vulnerable to privacy breaches, particularly in sensitive domains like medical imaging. Generative models, such as diffusion models, enhance privacy by synthesizing realistic data. However, they are prone to memorization, especially when trained on small datasets. This study proposes a decentralized few-shot generative model (DFGM) to synthesize brain tumor images while fully preserving privacy. DFGM harmonizes private tumor data with publicly shareable healthy images from multiple medical centers, constructing a new dataset by blending tumor foregrounds with healthy backgrounds. This approach ensures stringent privacy protection and enables controllable, high-quality synthesis by preserving both the healthy backgrounds and tumor foregrounds. We assess DFGM's effectiveness in brain tumor segmentation using a UNet, achieving Dice score improvements of 3.9% for data augmentation and 4.6% for fairness on a separate dataset.
Accurate segmentation of glioma brain tumors is crucial for diagnosis and treatment planning. Deep learning techniques offer promising solutions, but optimal model architectures remain under investigation. We used the BraTS 2021 dataset, selecting T1 with contrast enhancement (T1CE), T2, and Fluid-Attenuated Inversion Recovery (FLAIR) sequences for model development. The proposed Attention Xception UNet (AXUNet) architecture integrates an Xception backbone with dot-product self-attention modules, inspired by state-of-the-art (SOTA) large language models such as Google Bard and OpenAI ChatGPT, within a UNet-shaped model. We compared AXUNet with SOTA models. Comparative evaluation on the test set demonstrated improved results over baseline models. Inception-UNet and Xception-UNet achieved mean Dice scores of 90.88 and 93.24, respectively. Attention ResUNet (AResUNet) attained a mean Dice score of 92.80, with the highest score of 84.92 for enhancing tumor (ET) among all models. Attention Gate UNet (AGUNet) yielded a mean Dice score of 90.38. AXUNet outperformed all models with a mean Dice score of 93.73. It demonstrated superior Dice scores across whole tumor (WT) and tumor core (TC) regions, achieving 92.59 for WT, 86.81 for TC, and 84.89 for ET. The integration of the Xception backbone and dot-product self-attention mechanisms in AXUNet showcases enhanced performance in capturing spatial and contextual information. The findings underscore the potential utility of AXUNet in facilitating precise tumor delineation.
Medical image segmentation, particularly for brain tumor analysis, demands precise and computationally efficient models due to the complexity of multimodal MRI datasets and diverse tumor morphologies. This study introduces PSO-UNet, which integrates Particle Swarm Optimization (PSO) with the U-Net architecture for dynamic hyperparameter optimization. Unlike traditional manual tuning or alternative optimization approaches, PSO effectively navigates complex hyperparameter search spaces, explicitly optimizing the number of filters, kernel size, and learning rate. PSO-UNet substantially enhances segmentation performance, achieving Dice Similarity Coefficients (DSC) of 0.9578 and 0.9523 and Intersection over Union (IoU) scores of 0.9194 and 0.9097 on the BraTS 2021 and Figshare datasets, respectively. Moreover, the method reduces computational complexity significantly, utilizing only 7.8 million parameters and executing in approximately 906 seconds, markedly faster than comparable U-Net-based frameworks. These outcomes underscore PSO-UNet's robust generalization capabilities across diverse MRI modalities and tumor classifications, emphasizing its clinical potential and clear advantages over conventional hyperparameter tuning methods. Future research will explore hybrid optimization strategies and validate the framework against other bio-inspired algorithms to enhance its robustness and scalability.