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Diffusing the Blind Spot: Uterine MRI Synthesis with Diffusion Models

Johanna P. Müller, Anika Knupfer, Pedro Blöss, Edoardo Berardi Vittur, Bernhard Kainz, Jana Hutter

arxiv logopreprintAug 11 2025
Despite significant progress in generative modelling, existing diffusion models often struggle to produce anatomically precise female pelvic images, limiting their application in gynaecological imaging, where data scarcity and patient privacy concerns are critical. To overcome these barriers, we introduce a novel diffusion-based framework for uterine MRI synthesis, integrating both unconditional and conditioned Denoising Diffusion Probabilistic Models (DDPMs) and Latent Diffusion Models (LDMs) in 2D and 3D. Our approach generates anatomically coherent, high fidelity synthetic images that closely mimic real scans and provide valuable resources for training robust diagnostic models. We evaluate generative quality using advanced perceptual and distributional metrics, benchmarking against standard reconstruction methods, and demonstrate substantial gains in diagnostic accuracy on a key classification task. A blinded expert evaluation further validates the clinical realism of our synthetic images. We release our models with privacy safeguards and a comprehensive synthetic uterine MRI dataset to support reproducible research and advance equitable AI in gynaecology.

MIND: A Noise-Adaptive Denoising Framework for Medical Images Integrating Multi-Scale Transformer

Tao Tang, Chengxu Yang

arxiv logopreprintAug 11 2025
The core role of medical images in disease diagnosis makes their quality directly affect the accuracy of clinical judgment. However, due to factors such as low-dose scanning, equipment limitations and imaging artifacts, medical images are often accompanied by non-uniform noise interference, which seriously affects structure recognition and lesion detection. This paper proposes a medical image adaptive denoising model (MI-ND) that integrates multi-scale convolutional and Transformer architecture, introduces a noise level estimator (NLE) and a noise adaptive attention module (NAAB), and realizes channel-spatial attention regulation and cross-modal feature fusion driven by noise perception. Systematic testing is carried out on multimodal public datasets. Experiments show that this method significantly outperforms the comparative methods in image quality indicators such as PSNR, SSIM, and LPIPS, and improves the F1 score and ROC-AUC in downstream diagnostic tasks, showing strong prac-tical value and promotional potential. The model has outstanding benefits in structural recovery, diagnostic sensitivity, and cross-modal robustness, and provides an effective solution for medical image enhancement and AI-assisted diagnosis and treatment.

Enhancing Reliability of Medical Image Diagnosis through Top-rank Learning with Rejection Module

Xiaotong Ji, Ryoma Bise, Seiichi Uchida

arxiv logopreprintAug 11 2025
In medical image processing, accurate diagnosis is of paramount importance. Leveraging machine learning techniques, particularly top-rank learning, shows significant promise by focusing on the most crucial instances. However, challenges arise from noisy labels and class-ambiguous instances, which can severely hinder the top-rank objective, as they may be erroneously placed among the top-ranked instances. To address these, we propose a novel approach that enhances toprank learning by integrating a rejection module. Cooptimized with the top-rank loss, this module identifies and mitigates the impact of outliers that hinder training effectiveness. The rejection module functions as an additional branch, assessing instances based on a rejection function that measures their deviation from the norm. Through experimental validation on a medical dataset, our methodology demonstrates its efficacy in detecting and mitigating outliers, improving the reliability and accuracy of medical image diagnoses.

Deep Learning-Based Desikan-Killiany Parcellation of the Brain Using Diffusion MRI

Yousef Sadegheih, Dorit Merhof

arxiv logopreprintAug 11 2025
Accurate brain parcellation in diffusion MRI (dMRI) space is essential for advanced neuroimaging analyses. However, most existing approaches rely on anatomical MRI for segmentation and inter-modality registration, a process that can introduce errors and limit the versatility of the technique. In this study, we present a novel deep learning-based framework for direct parcellation based on the Desikan-Killiany (DK) atlas using only diffusion MRI data. Our method utilizes a hierarchical, two-stage segmentation network: the first stage performs coarse parcellation into broad brain regions, and the second stage refines the segmentation to delineate more detailed subregions within each coarse category. We conduct an extensive ablation study to evaluate various diffusion-derived parameter maps, identifying an optimal combination of fractional anisotropy, trace, sphericity, and maximum eigenvalue that enhances parellation accuracy. When evaluated on the Human Connectome Project and Consortium for Neuropsychiatric Phenomics datasets, our approach achieves superior Dice Similarity Coefficients compared to existing state-of-the-art models. Additionally, our method demonstrates robust generalization across different image resolutions and acquisition protocols, producing more homogeneous parcellations as measured by the relative standard deviation within regions. This work represents a significant advancement in dMRI-based brain segmentation, providing a precise, reliable, and registration-free solution that is critical for improved structural connectivity and microstructural analyses in both research and clinical applications. The implementation of our method is publicly available on github.com/xmindflow/DKParcellationdMRI.

Anatomy-Aware Low-Dose CT Denoising via Pretrained Vision Models and Semantic-Guided Contrastive Learning

Runze Wang, Zeli Chen, Zhiyun Song, Wei Fang, Jiajin Zhang, Danyang Tu, Yuxing Tang, Minfeng Xu, Xianghua Ye, Le Lu, Dakai Jin

arxiv logopreprintAug 11 2025
To reduce radiation exposure and improve the diagnostic efficacy of low-dose computed tomography (LDCT), numerous deep learning-based denoising methods have been developed to mitigate noise and artifacts. However, most of these approaches ignore the anatomical semantics of human tissues, which may potentially result in suboptimal denoising outcomes. To address this problem, we propose ALDEN, an anatomy-aware LDCT denoising method that integrates semantic features of pretrained vision models (PVMs) with adversarial and contrastive learning. Specifically, we introduce an anatomy-aware discriminator that dynamically fuses hierarchical semantic features from reference normal-dose CT (NDCT) via cross-attention mechanisms, enabling tissue-specific realism evaluation in the discriminator. In addition, we propose a semantic-guided contrastive learning module that enforces anatomical consistency by contrasting PVM-derived features from LDCT, denoised CT and NDCT, preserving tissue-specific patterns through positive pairs and suppressing artifacts via dual negative pairs. Extensive experiments conducted on two LDCT denoising datasets reveal that ALDEN achieves the state-of-the-art performance, offering superior anatomy preservation and substantially reducing over-smoothing issue of previous work. Further validation on a downstream multi-organ segmentation task (encompassing 117 anatomical structures) affirms the model's ability to maintain anatomical awareness.

SOFA: Deep Learning Framework for Simulating and Optimizing Atrial Fibrillation Ablation

Yunsung Chung, Chanho Lim, Ghassan Bidaoui, Christian Massad, Nassir Marrouche, Jihun Hamm

arxiv logopreprintAug 11 2025
Atrial fibrillation (AF) is a prevalent cardiac arrhythmia often treated with catheter ablation procedures, but procedural outcomes are highly variable. Evaluating and improving ablation efficacy is challenging due to the complex interaction between patient-specific tissue and procedural factors. This paper asks two questions: Can AF recurrence be predicted by simulating the effects of procedural parameters? How should we ablate to reduce AF recurrence? We propose SOFA (Simulating and Optimizing Atrial Fibrillation Ablation), a novel deep-learning framework that addresses these questions. SOFA first simulates the outcome of an ablation strategy by generating a post-ablation image depicting scar formation, conditioned on a patient's pre-ablation LGE-MRI and the specific procedural parameters used (e.g., ablation locations, duration, temperature, power, and force). During this simulation, it predicts AF recurrence risk. Critically, SOFA then introduces an optimization scheme that refines these procedural parameters to minimize the predicted risk. Our method leverages a multi-modal, multi-view generator that processes 2.5D representations of the atrium. Quantitative evaluations show that SOFA accurately synthesizes post-ablation images and that our optimization scheme leads to a 22.18\% reduction in the model-predicted recurrence risk. To the best of our knowledge, SOFA is the first framework to integrate the simulation of procedural effects, recurrence prediction, and parameter optimization, offering a novel tool for personalizing AF ablation.

Enhanced Liver Tumor Detection in CT Images Using 3D U-Net and Bat Algorithm for Hyperparameter Optimization

Nastaran Ghorbani, Bitasadat Jamshidi, Mohsen Rostamy-Malkhalifeh

arxiv logopreprintAug 11 2025
Liver cancer is one of the most prevalent and lethal forms of cancer, making early detection crucial for effective treatment. This paper introduces a novel approach for automated liver tumor segmentation in computed tomography (CT) images by integrating a 3D U-Net architecture with the Bat Algorithm for hyperparameter optimization. The method enhances segmentation accuracy and robustness by intelligently optimizing key parameters like the learning rate and batch size. Evaluated on a publicly available dataset, our model demonstrates a strong ability to balance precision and recall, with a high F1-score at lower prediction thresholds. This is particularly valuable for clinical diagnostics, where ensuring no potential tumors are missed is paramount. Our work contributes to the field of medical image analysis by demonstrating that the synergy between a robust deep learning architecture and a metaheuristic optimization algorithm can yield a highly effective solution for complex segmentation tasks.

MIND: A Noise-Adaptive Denoising Framework for Medical Images Integrating Multi-Scale Transformer

Tao Tang, Chengxu Yang

arxiv logopreprintAug 11 2025
The core role of medical images in disease diagnosis makes their quality directly affect the accuracy of clinical judgment. However, due to factors such as low-dose scanning, equipment limitations and imaging artifacts, medical images are often accompanied by non-uniform noise interference, which seriously affects structure recognition and lesion detection. This paper proposes a medical image adaptive denoising model (MI-ND) that integrates multi-scale convolutional and Transformer architecture, introduces a noise level estimator (NLE) and a noise adaptive attention module (NAAB), and realizes channel-spatial attention regulation and cross-modal feature fusion driven by noise perception. Systematic testing is carried out on multimodal public datasets. Experiments show that this method significantly outperforms the comparative methods in image quality indicators such as PSNR, SSIM, and LPIPS, and improves the F1 score and ROC-AUC in downstream diagnostic tasks, showing strong prac-tical value and promotional potential. The model has outstanding benefits in structural recovery, diagnostic sensitivity, and cross-modal robustness, and provides an effective solution for medical image enhancement and AI-assisted diagnosis and treatment.

Improving discriminative ability in mammographic microcalcification classification using deep learning: a novel double transfer learning approach validated with an explainable artificial intelligence technique

Arlan, K., Bjornstrom, M., Makela, T., Meretoja, T. J., Hukkinen, K.

medrxiv logopreprintAug 11 2025
BackgroundBreast microcalcification diagnostics are challenging due to their subtle presentation, overlapping with benign findings, and high inter-reader variability, often leading to unnecessary biopsies. While deep learning (DL) models - particularly deep convolutional neural networks (DCNNs) - have shown potential to improve diagnostic accuracy, their clinical application remains limited by the need for large annotated datasets and the "black box" nature of their decision-making. PurposeTo develop and validate a deep learning model (DCNN) using a double transfer learning (d-TL) strategy for classifying suspected mammographic microcalcifications, with explainable AI (XAI) techniques to support model interpretability. Material and methodsA retrospective dataset of 396 annotated regions of interest (ROIs) from full-field digital mammography (FFDM) images of 194 patients who underwent stereotactic vacuum-assisted biopsy at the Womens Hospital radiological department, Helsinki University Hospital, was collected. The dataset was randomly split into training and test sets (24% test set, balanced for benign and malignant cases). A ResNeXt-based DCNN was developed using a d-TL approach: first pretrained on ImageNet, then adapted using an intermediate mammography dataset before fine-tuning on the target microcalcification data. Saliency maps were generated using Gradient-weighted Class Activation Mapping (Grad-CAM) to evaluate the visual relevance of model predictions. Diagnostic performance was compared to a radiologists BI-RADS-based assessment, using final histopathology as the reference standard. ResultsThe ensemble DCNN achieved an area under the ROC curve (AUC) of 0.76, with 65% sensitivity, 83% specificity, 79% positive predictive value (PPV), and 70% accuracy. The radiologist achieved an AUC of 0.65 with 100% sensitivity but lower specificity (30%) and PPV (59%). Grad-CAM visualizations showed consistent activation of the correct ROIs, even in misclassified cases where confidence scores fell below the threshold. ConclusionThe DCNN model utilizing d-TL achieved performance comparable to radiologists, with higher specificity and PPV than BI-RADS. The approach addresses data limitation issues and may help reduce additional imaging and unnecessary biopsies.

Adapting Biomedical Foundation Models for Predicting Outcomes of Anti Seizure Medications

Pham, D. K., Mehta, D., Jiang, Y., Thom, D., Chang, R. S.-k., Foster, E., Fazio, T., Holper, S., Verspoor, K., Liu, J., Nhu, D., Barnard, S., O'Brien, T., Chen, Z., French, J., Kwan, P., Ge, Z.

medrxiv logopreprintAug 11 2025
Epilepsy affects over 50 million people worldwide, with anti-seizure medications (ASMs) as the primary treatment for seizure control. However, ASM selection remains a "trial and error" process due to the lack of reliable predictors of effectiveness and tolerability. While machine learning approaches have been explored, existing models are limited to predicting outcomes only for ASMs encountered during training and have not leveraged recent biomedical foundation models for this task. This work investigates ASM outcome prediction using only patient MRI scans and reports. Specifically, we leverage biomedical vision-language foundation models and introduce a novel contextualized instruction-tuning framework that integrates expert-built knowledge trees of MRI entities to enhance their performance. Additionally, by training only on the four most commonly prescribed ASMs, our framework enables generalization to predicting outcomes and effectiveness for unseen ASMs not present during training. We evaluate our instruction-tuning framework on two retrospective epilepsy patient datasets, achieving an average AUC of 71.39 and 63.03 in predicting outcomes for four primary ASMs and three completely unseen ASMs, respectively. Our approach improves the AUC by 5.53 and 3.51 compared to standard report-based instruction tuning for seen and unseen ASMs, respectively. Our code, MRI knowledge tree, prompting templates, and TREE-TUNE generated instruction-answer tuning dataset are available at the link.
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