An Explainable AI-Driven Framework for Automated Brain Tumor Segmentation Using an Attention-Enhanced U-Net

Computer-aided segmentation of brain tumors from MRI data is of crucial significance to clinical decision-making in diagnosis, treatment planning, and follow-up disease monitoring. Gliomas, owing to their high malignancy and heterogeneity, represent a very challenging task for accurate and reliable segmentation into intra-tumoral sub-regions. Manual segmentation is typically time-consuming and not reliable, which justifies the need for robust automated techniques.This research resolves this problem by leveraging the BraTS 2020 dataset, where we have labeled MRI scans of glioma patients with four significant classes: background/healthy tissue, necrotic/non-enhancing core, edema, and enhancing tumor. In this work, we present a new segmentation technique based on a U-Net model augmented with executed attention gates to focus on the most significant regions of images. To counter class imbalance, we employ manually designed loss functions like Dice Loss and Categorical Dice Loss, in conjunction with standard categorical cross-entropy. Other evaluation metrics, like sensitivity and specificity, were used to measure discriminability of the model between tumor classes. Besides, we introduce Grad-CAM-based explainable AI to enable visualizing attention regions and improve model interpretability, together with a smooth heatmap generation technique through Gaussian filtering. Our approach achieved superior performance with accuracy of 0.9919, Dice coefficient of 0.9901, mean IoU of 0.9873, sensitivity of 0.9908, and specificity of 0.9974. This study demonstrates that the use of attention mechanisms, personalized loss functions, and explainable AI significantly improves highly complex tumor structure segmentation precision in MRI scans, providing a reliable and explainable method for clinical applications.

PGR-Net: Prior-Guided ROI Reasoning Network for Brain Tumor MRI Segmentation

Brain tumor MRI segmentation is essential for clinical diagnosis and treatment planning, enabling accurate lesion detection and radiotherapy target delineation. However, tumor lesions occupy only a small fraction of the volumetric space, resulting in severe spatial sparsity, while existing segmentation networks often overlook clinically observed spatial priors of tumor occurrence, leading to redundant feature computation over extensive background regions. To address this issue, we propose PGR-Net (Prior-Guided ROI Reasoning Network) - an explicit ROI-aware framework that incorporates a data-driven spatial prior set to capture the distribution and scale characteristics of tumor lesions, providing global guidance for more stable segmentation. Leveraging these priors, PGR-Net introduces a hierarchical Top-K ROI decision mechanism that progressively selects the most confident lesion candidate regions across encoder layers to improve localization precision. We further develop the WinGS-ROI (Windowed Gaussian-Spatial Decay ROI) module, which uses multi-window Gaussian templates with a spatial decay function to produce center-enhanced guidance maps, thus directing feature learning throughout the network. With these ROI features, a windowed RetNet backbone is adopted to enhance localization reliability. Experiments on BraTS-2019/2023 and MSD Task01 show that PGR-Net consistently outperforms existing approaches while using only 8.64M Params, achieving Dice scores of 89.02%, 91.82%, and 89.67% on the Whole Tumor region. Code is available at https://github.com/CNU-MedAI-Lab/PGR-Net.

DGRNet: Disagreement-Guided Refinement for Uncertainty-Aware Brain Tumor Segmentation

Accurate brain tumor segmentation from MRI scans is critical for diagnosis and treatment planning. Despite the strong performance of recent deep learning approaches, two fundamental limitations remain: (1) the lack of reliable uncertainty quantification in single-model predictions, which is essential for clinical deployment because the level of uncertainty may impact treatment decision-making, and (2) the under-utilization of rich information in radiology reports that can guide segmentation in ambiguous regions. In this paper, we propose the Disagreement-Guided Refinement Network (DGRNet), a novel framework that addresses both limitations through multi-view disagreement-based uncertainty estimation and text-conditioned refinement. DGRNet generates diverse predictions via four lightweight view-specific adapters attached to a shared encoder-decoder, enabling efficient uncertainty quantification within a single forward pass. Afterward, we build disagreement maps to identify regions of high segmentation uncertainty, which are then selectively refined according to clinical reports. Moreover, we introduce a diversity-preserving training strategy that combines pairwise similarity penalties and gradient isolation to prevent view collapse. The experimental results on the TextBraTS dataset show that DGRNet favorably improves state-of-the-art segmentation accuracy by 2.4% and 11% in main metrics Dice and HD95, respectively, while providing meaningful uncertainty estimates.

Hierarchical Text-Guided Brain Tumor Segmentation via Sub-Region-Aware Prompts

Brain tumor segmentation remains challenging because the three standard sub-regions, i.e., whole tumor (WT), tumor core (TC), and enhancing tumor (ET), often exhibit ambiguous visual boundaries. Integrating radiological description texts with imaging has shown promise. However, most multimodal approaches typically compress a report into a single global text embedding shared across all sub-regions, overlooking their distinct clinical characteristics. We propose TextCSP (text-modulated soft cascade architecture), a hierarchical text-guided framework that builds on the TextBraTS baseline with three novel components: (1) a text-modulated soft cascade decoder that predicts WT->TC->ET in a coarse-to-fine manner consistent with their anatomical containment hierarchy. (2) sub-region-aware prompt tuning, which uses learnable soft prompts with a LoRA-adapted BioBERT encoder to generate specialized text representations tailored for each sub-region; (3) text-semantic channel modulators that convert the aforementioned representations into channel-wise refinement signals, enabling the decoder to emphasize features aligned with clinically described patterns. Experiments on the TextBraTS dataset demonstrate consistent improvements across all sub-regions against state-of-the-art methods by 1.7% and 6% on the main metrics Dice and HD95.

Agentic Automation of BT-RADS Scoring: End-to-End Multi-Agent System for Standardized Brain Tumor Follow-up Assessment

The Brain Tumor Reporting and Data System (BT-RADS) standardizes post-treatment MRI response assessment in patients with diffuse gliomas but requires complex integration of imaging trends, medication effects, and radiation timing. This study evaluates an end-to-end multi-agent large language model (LLM) and convolutional neural network (CNN) system for automated BT-RADS classification. A multi-agent LLM system combined with automated CNN-based tumor segmentation was retrospectively evaluated on 509 consecutive post-treatment glioma MRI examinations from a single high-volume center. An extractor agent identified clinical variables (steroid status, bevacizumab status, radiation date) from unstructured clinical notes, while a scorer agent applied BT-RADS decision logic integrating extracted variables with volumetric measurements. Expert reference standard classifications were established by an independent board-certified neuroradiologist. Of 509 examinations, 492 met inclusion criteria. The system achieved 374/492 (76.0%; 95% CI, 72.1%-79.6%) accuracy versus 283/492 (57.5%; 95% CI, 53.1%-61.8%) for initial clinical assessments (+18.5 percentage points; P<.001). Context-dependent categories showed high sensitivity (BT-1b 100%, BT-1a 92.7%, BT-3a 87.5%), while threshold-dependent categories showed moderate sensitivity (BT-3c 74.8%, BT-2 69.2%, BT-4 69.3%, BT-3b 57.1%). For BT-4, positive predictive value was 92.9%. The multi-agent LLM system achieved higher BT-RADS classification agreement with expert reference standard compared to initial clinical scoring, with high accuracy for context-dependent scores and high positive predictive value for BT-4 detection.

Hyper-Connections for Adaptive Multi-Modal MRI Brain Tumor Segmentation

We present the first study of Hyper-Connections (HC) for volumetric multi-modal brain tumor segmentation, integrating them as a drop-in replacement for fixed residual connections across five architectures: nnU-Net, SwinUNETR, VT-UNet, U-Net, and U-Netpp. Dynamic HC consistently improves all 3D models on the BraTS 2021 dataset, yielding up to +1.03 percent mean Dice gain with negligible parameter overhead. Gains are most pronounced in the Enhancing Tumor sub-region, reflecting improved fine-grained boundary delineation. Modality ablation further reveals that HC-equipped models develop sharper sensitivity toward clinically dominant sequences, specifically T1ce for Tumor Core and Enhancing Tumor, and FLAIR for Whole Tumor, a behavior absent in fixed-connection baselines and consistent across all architectures. In 2D settings, improvements are smaller and configuration-sensitive, suggesting that volumetric spatial context amplifies the benefit of adaptive aggregation. These results establish HC as a simple, efficient, and broadly applicable mechanism for multi-modal feature fusion in medical image segmentation.

CytoSyn: a Foundation Diffusion Model for Histopathology -- Tech Report

Computational pathology has made significant progress in recent years, fueling advances in both fundamental disease understanding and clinically ready tools. This evolution is driven by the availability of large amounts of digitized slides and specialized deep learning methods and models. Multiple self-supervised foundation feature extractors have been developed, enabling downstream predictive applications from cell segmentation to tumor sub-typing and survival analysis. In contrast, generative foundation models designed specifically for histopathology remain scarce. Such models could address tasks that are beyond the capabilities of feature extractors, such as virtual staining. In this paper, we introduce CytoSyn, a state-of-the-art foundation latent diffusion model that enables the guided generation of highly realistic and diverse histopathology H&E-stained images, as shown in an extensive benchmark. We explored methodological improvements, training set scaling, sampling strategies and slide-level overfitting, culminating in the improved CytoSyn-v2, and compared our work to PixCell, a state-of-the-art model, in an in-depth manner. This comparison highlighted the strong sensitivity of both diffusion models and performance metrics to preprocessing-specific details such as JPEG compression. Our model has been trained on a dataset obtained from more than 10,000 TCGA diagnostic whole-slide images of 32 different cancer types. Despite being trained only on oncology slides, it maintains state-of-the-art performance generating inflammatory bowel disease images. To support the research community, we publicly release CytoSyn's weights, its training and validation datasets, and a sample of synthetic images in this repository: https://huggingface.co/Owkin-Bioptimus/CytoSyn.

LoGSAM: Parameter-Efficient Cross-Modal Grounding for MRI Segmentation

Precise localization and delineation of brain tumors using Magnetic Resonance Imaging (MRI) are essential for planning therapy and guiding surgical decisions. However, most existing approaches rely on task-specific supervised models and are constrained by the limited availability of annotated data. To address this, we propose LoGSAM, a parameter-efficient, detection-driven framework that transforms radiologist dictation into text prompts for foundation-model-based localization and segmentation. Radiologist speech is first transcribed and translated using a pretrained Whisper ASR model, followed by negation-aware clinical NLP to extract tumor-specific textual prompts. These prompts guide text-conditioned tumor localization via a LoRA-adapted vision-language detection model, Grounding DINO (GDINO). The LoRA adaptation updates using 5% of the model parameters, thereby enabling computationally efficient domain adaptation while preserving pretrained cross-modal knowledge. The predicted bounding boxes are used as prompts for MedSAM to generate pixel-level tumor masks without any additional fine-tuning. Conditioning the frozen MedSAM on LoGSAM-derived priors yields a state-of-the-art dice score of 80.32% on BRISC 2025. In addition, we evaluate the full pipeline using German dictations from a board-certified radiologist on 12 unseen MRI scans, achieving 91.7% case-level accuracy. These results highlight the feasibility of constructing a modular, speech-to-segmentation pipeline by intelligently leveraging pretrained foundation models with minimal parameter updates.

Evidential learning driven Breast Tumor Segmentation with Stage-divided Vision-Language Interaction

Breast cancer is one of the most common causes of death among women worldwide, with millions of fatalities annually. Magnetic Resonance Imaging (MRI) can provide various sequences for characterizing tumor morphology and internal patterns, and becomes an effective tool for detection and diagnosis of breast tumors. However, previous deep-learning based tumor segmentation methods have limitations in accurately locating tumor contours due to the challenge of low contrast between cancer and normal areas and blurred boundaries. Leveraging text prompt information holds promise in ameliorating tumor segmentation effect by delineating segmentation regions. Inspired by this, we propose text-guided Breast Tumor Segmentation model (TextBCS) with stage-divided vision-language interaction and evidential learning. Specifically, the proposed stage-divided vision-language interaction facilitates information mutual between visual and text features at each stage of down-sampling, further exerting the advantages of text prompts to assist in locating lesion areas in low contrast scenarios. Moreover, the evidential learning is adopted to quantify the segmentation uncertainty of the model for blurred boundary. It utilizes the variational Dirichlet to characterize the distribution of the segmentation probabilities, addressing the segmentation uncertainties of the boundaries. Extensive experiments validate the superiority of our TextBCS over other segmentation networks, showcasing the best breast tumor segmentation performance on publicly available datasets.

Decoding Matters: Efficient Mamba-Based Decoder with Distribution-Aware Deep Supervision for Medical Image Segmentation

Deep learning has achieved remarkable success in medical image segmentation, often reaching expert-level accuracy in delineating tumors and tissues. However, most existing approaches remain task-specific, showing strong performance on individual datasets but limited generalization across diverse imaging modalities. Moreover, many methods focus primarily on the encoder, relying on large pretrained backbones that increase computational complexity. In this paper, we propose a decoder-centric approach for generalized 2D medical image segmentation. The proposed Deco-Mamba follows a U-Net-like structure with a Transformer-CNN-Mamba design. The encoder combines a CNN block and Transformer backbone for efficient feature extraction, while the decoder integrates our novel Co-Attention Gate (CAG), Vision State Space Module (VSSM), and deformable convolutional refinement block to enhance multi-scale contextual representation. Additionally, a windowed distribution-aware KL-divergence loss is introduced for deep supervision across multiple decoding stages. Extensive experiments on diverse medical image segmentation benchmarks yield state-of-the-art performance and strong generalization capability while maintaining moderate model complexity. The source code will be released upon acceptance.