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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 MRI brain tumor detection using deep learning in conjunction with explainable AI SHAP based diverse and multi feature analysis.

Rahman A, Hayat M, Iqbal N, Alarfaj FK, Alkhalaf S, Alturise F

pubmed logopapersAug 11 2025
Recent innovations in medical imaging have markedly improved brain tumor identification, surpassing conventional diagnostic approaches that suffer from low resolution, radiation exposure, and limited contrast. Magnetic Resonance Imaging (MRI) is pivotal in precise and accurate tumor characterization owing to its high-resolution, non-invasive nature. This study investigates the synergy among multiple feature representation schemes such as local Binary Patterns (LBP), Gabor filters, Discrete Wavelet Transform, Fast Fourier Transform, Convolutional Neural Networks (CNN), and Gray-Level Run Length Matrix alongside five learning algorithms namely: k-nearest Neighbor, Random Forest, Support Vector Classifier (SVC), and probabilistic neural network (PNN), and CNN. Empirical findings indicate that LBP in conjunction with SVC and CNN obtained high specificity and accuracy, rendering it a promising method for MRI-based tumor diagnosis. Further to investigate the contribution of LBP, Statistical analysis chi-square and p-value tests are used to confirm the significant impact of LBP feature space for identification of brain Tumor. In addition, The SHAP analysis was used to identify the most important features in classification. In a small dataset, CNN obtained 97.8% accuracy while SVC yielded 98.06% accuracy. In subsequent analysis, a large benchmark dataset is also utilized to evaluate the performance of learning algorithms in order to investigate the generalization power of the proposed model. CNN achieves the highest accuracy of 98.9%, followed by SVC at 96.7%. These results highlight CNN's effectiveness in automated, high-precision tumor diagnosis. This achievement is ascribed with MRI-based feature extraction by combining high resolution, non-invasive imaging capabilities with the powerful analytical abilities of CNN. CNN demonstrates superiority in medical imaging owing to its ability to learn intricate spatial patterns and generalize effectively. This interaction enhances the accuracy, speed, and consistency of brain tumor detection, ultimately leading to better patient outcomes and more efficient healthcare delivery. https://github.com/asifrahman557/BrainTumorDetection .

Multimodal radiomics in glioma: predicting recurrence in the peritumoural brain zone using integrated MRI.

Li Q, Xiang C, Zeng X, Liao A, Chen K, Yang J, Li Y, Jia M, Song L, Hu X

pubmed logopapersAug 11 2025
Gliomas exhibit a high recurrence rate, particularly in the peritumoural brain zone after surgery. This study aims to develop and validate a radiomics-based model using preoperative fluid-attenuated inversion recovery (FLAIR) and T1-weighted contrast-enhanced (T1-CE) magnetic resonance imaging (MRI) sequences to predict glioma recurrence within specific quadrants of the surgical margin. In this retrospective study, 149 patients with confirmed glioma recurrence were included. 23 cases of data from Guizhou Medical University were used as a test set, and the remaining data were randomly used as a training set (70%) and a validation set (30%). Two radiologists from the research group established a Cartesian coordinate system centred on the tumour, based on FLAIR and T1-CE MRI sequences, dividing the tumour into four quadrants. Recurrence in each quadrant after surgery was assessed, categorising preoperative tumour quadrants as recurrent and non-recurrent. Following the division of tumours into quadrants and the removal of outliers, These quadrants were assigned to a training set (105 non-recurrence quadrants and 226 recurrence quadrants), a verification set (45 non-recurrence quadrants and 97 recurrence quadrants) and a test set (16 non-recurrence quadrants and 68 recurrence quadrants). Imaging features were extracted from preoperative sequences, and feature selection was performed using least absolute shrinkage and selection operator. Machine learning models included support vector machine, random forest, extra trees, and XGBoost. Clinical efficacy was evaluated through model calibration and decision curve analysis. The fusion model, which combines features from FLAIR and T1-CE sequences, exhibited higher predictive accuracy than single-modality models. Among the models, the LightGBM model demonstrated the highest predictive accuracy, with an area under the curve of 0.906 in the training set, 0.832 in the validation set and 0.805 in the test set. The study highlights the potential of a multimodal radiomics approach for predicting glioma recurrence, with the fusion model serving as a robust tool for clinical decision-making.

A Physics-Driven Neural Network with Parameter Embedding for Generating Quantitative MR Maps from Weighted Images

Lingjing Chen, Chengxiu Zhang, Yinqiao Yi, Yida Wang, Yang Song, Xu Yan, Shengfang Xu, Dalin Zhu, Mengqiu Cao, Yan Zhou, Chenglong Wang, Guang Yang

arxiv logopreprintAug 11 2025
We propose a deep learning-based approach that integrates MRI sequence parameters to improve the accuracy and generalizability of quantitative image synthesis from clinical weighted MRI. Our physics-driven neural network embeds MRI sequence parameters -- repetition time (TR), echo time (TE), and inversion time (TI) -- directly into the model via parameter embedding, enabling the network to learn the underlying physical principles of MRI signal formation. The model takes conventional T1-weighted, T2-weighted, and T2-FLAIR images as input and synthesizes T1, T2, and proton density (PD) quantitative maps. Trained on healthy brain MR images, it was evaluated on both internal and external test datasets. The proposed method achieved high performance with PSNR values exceeding 34 dB and SSIM values above 0.92 for all synthesized parameter maps. It outperformed conventional deep learning models in accuracy and robustness, including data with previously unseen brain structures and lesions. Notably, our model accurately synthesized quantitative maps for these unseen pathological regions, highlighting its superior generalization capability. Incorporating MRI sequence parameters via parameter embedding allows the neural network to better learn the physical characteristics of MR signals, significantly enhancing the performance and reliability of quantitative MRI synthesis. This method shows great potential for accelerating qMRI and improving its clinical utility.

Neonatal neuroimaging: from research to bedside practice.

Cizmeci MN, El-Dib M, de Vries LS

pubmed logopapersAug 11 2025
Neonatal neuroimaging is essential in research and clinical practice, offering important insights into brain development and neurologic injury mechanisms. Visualizing the brain enables researchers and clinicians to improve neonatal care and parental counselling through better diagnosis and prognostication of disease. Common neuroimaging modalities used in the neonatal intensive care unit (NICU) are cranial ultrasonography (cUS) and magnetic resonance imaging (MRI). Between these modalities, conventional MRI provides the optimal image resolution and detail about the developing brain, while advanced MRI techniques allow for the evaluation of tissue microstructure and functional networks. Over the last two decades, medical imaging techniques using brain MRI have rapidly progressed, and these advances have facilitated high-quality extraction of quantitative features as well as the implementation of novel devices for use in neurological disorders. Major advancements encompass the use of low-field dedicated MRI systems within the NICU and trials of ultralow-field portable MRI systems at the bedside. Additionally, higher-field magnets are utilized to enhance image quality, and ultrafast brain MRI is employed to decrease image acquisition time. Furthermore, the implementation of advanced MRI sequences, the application of machine learning algorithms, multimodal neuroimaging techniques, motion correction techniques, and novel modalities are used to visualize pathologies that are not visible to the human eye. In this narrative review, we will discuss the fundamentals of these neuroimaging modalities, and their clinical applications to explore the present landscape of neonatal neuroimaging from bench to bedside.

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.

PrIINeR: Towards Prior-Informed Implicit Neural Representations for Accelerated MRI

Ziad Al-Haj Hemidi, Eytan Kats, Mattias P. Heinrich

arxiv logopreprintAug 11 2025
Accelerating Magnetic Resonance Imaging (MRI) reduces scan time but often degrades image quality. While Implicit Neural Representations (INRs) show promise for MRI reconstruction, they struggle at high acceleration factors due to weak prior constraints, leading to structural loss and aliasing artefacts. To address this, we propose PrIINeR, an INR-based MRI reconstruction method that integrates prior knowledge from pre-trained deep learning models into the INR framework. By combining population-level knowledge with instance-based optimization and enforcing dual data consistency, PrIINeR aligns both with the acquired k-space data and the prior-informed reconstruction. Evaluated on the NYU fastMRI dataset, our method not only outperforms state-of-the-art INR-based approaches but also improves upon several learning-based state-of-the-art methods, significantly improving structural preservation and fidelity while effectively removing aliasing artefacts.PrIINeR bridges deep learning and INR-based techniques, offering a more reliable solution for high-quality, accelerated MRI reconstruction. The code is publicly available on https://github.com/multimodallearning/PrIINeR.

Improving early detection of Alzheimer's disease through MRI slice selection and deep learning techniques.

Şener B, Açıcı K, Sümer E

pubmed logopapersAug 10 2025
Alzheimer's disease is a progressive neurodegenerative disorder marked by cognitive decline, memory loss, and behavioral changes. Early diagnosis, particularly identifying Early Mild Cognitive Impairment (EMCI), is vital for managing the disease and improving patient outcomes. Detecting EMCI is challenging due to the subtle structural changes in the brain, making precise slice selection from MRI scans essential for accurate diagnosis. In this context, the careful selection of specific MRI slices that provide distinct anatomical details significantly enhances the ability to identify these early changes. The chief novelty of the study is that instead of selecting all slices, an approach for identifying the important slices is developed. The ADNI-3 dataset was used as the dataset when running the models for early detection of Alzheimer's disease. Satisfactory results have been obtained by classifying with deep learning models, vision transformers (ViT) and by adding new structures to them, together with the model proposal. In the results obtained, while an accuracy of 99.45% was achieved with EfficientNetB2 + FPN in AD vs. LMCI classification from the slices selected with SSIM, an accuracy of 99.19% was achieved in AD vs. EMCI classification, in fact, the study significantly advances early detection by demonstrating improved diagnostic accuracy of the disease at the EMCI stage. The results obtained with these methods emphasize the importance of developing deep learning models with slice selection integrated with the Vision Transformers architecture. Focusing on accurate slice selection enables early detection of Alzheimer's at the EMCI stage, allowing for timely interventions and preventive measures before the disease progresses to more advanced stages. This approach not only facilitates early and accurate diagnosis, but also lays the groundwork for timely intervention and treatment, offering hope for better patient outcomes in Alzheimer's disease. The study is finally evaluated by a statistical significance test.

Large-scale Multi-sequence Pretraining for Generalizable MRI Analysis in Versatile Clinical Applications

Zelin Qiu, Xi Wang, Zhuoyao Xie, Juan Zhou, Yu Wang, Lingjie Yang, Xinrui Jiang, Juyoung Bae, Moo Hyun Son, Qiang Ye, Dexuan Chen, Rui Zhang, Tao Li, Neeraj Ramesh Mahboobani, Varut Vardhanabhuti, Xiaohui Duan, Yinghua Zhao, Hao Chen

arxiv logopreprintAug 10 2025
Multi-sequence Magnetic Resonance Imaging (MRI) offers remarkable versatility, enabling the distinct visualization of different tissue types. Nevertheless, the inherent heterogeneity among MRI sequences poses significant challenges to the generalization capability of deep learning models. These challenges undermine model performance when faced with varying acquisition parameters, thereby severely restricting their clinical utility. In this study, we present PRISM, a foundation model PRe-trained with large-scale multI-Sequence MRI. We collected a total of 64 datasets from both public and private sources, encompassing a wide range of whole-body anatomical structures, with scans spanning diverse MRI sequences. Among them, 336,476 volumetric MRI scans from 34 datasets (8 public and 26 private) were curated to construct the largest multi-organ multi-sequence MRI pretraining corpus to date. We propose a novel pretraining paradigm that disentangles anatomically invariant features from sequence-specific variations in MRI, while preserving high-level semantic representations. We established a benchmark comprising 44 downstream tasks, including disease diagnosis, image segmentation, registration, progression prediction, and report generation. These tasks were evaluated on 32 public datasets and 5 private cohorts. PRISM consistently outperformed both non-pretrained models and existing foundation models, achieving first-rank results in 39 out of 44 downstream benchmarks with statistical significance improvements. These results underscore its ability to learn robust and generalizable representations across unseen data acquired under diverse MRI protocols. PRISM provides a scalable framework for multi-sequence MRI analysis, thereby enhancing the translational potential of AI in radiology. It delivers consistent performance across diverse imaging protocols, reinforcing its clinical applicability.

The eyelid and pupil dynamics underlying stress levels in awake mice.

Zeng, H.

biorxiv logopreprintAug 10 2025
Stress is a natural response of the body to perceived threats, and it can have both positive and negative effects on brain hemodynamics. Stress-induced changes in pupil and eyelid size/shape have been used as a biomarker in several fMRI studies. However, there were limited knowledges regarding changes in behavior of pupil and eyelid dynamics, particularly on animal models. In the present study, the pupil and eyelid dynamics were carefully investigated and characterized in a newly developed awake rodent fMRI protocol. Leveraging deep learning techniques, the mouse pupil and eyelid diameters were extracted and analyzed during different training and imaging phases in the present project. Our findings demonstrate a consistent downwards trend in pupil and eyelid dynamics under a meticulously designed training protocol, suggesting that the behaviors of the pupil and eyelid can be served as reliable indicators of stress levels and motion artifacts in awake fMRI studies. The current recording platform not only enables the facilitation of awake animal MRI studies but also highlights its potential applications to numerous other research areas, owing to the non-invasive nature and straightforward implementation.
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