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BrainSymphony: A Transformer-Driven Fusion of fMRI Time Series and Structural Connectivity

Moein Khajehnejad, Forough Habibollahi, Adeel Razi

arxiv logopreprintJun 23 2025
Existing foundation models for neuroimaging are often prohibitively large and data-intensive. We introduce BrainSymphony, a lightweight, parameter-efficient foundation model that achieves state-of-the-art performance while being pre-trained on significantly smaller public datasets. BrainSymphony's strong multimodal architecture processes functional MRI data through parallel spatial and temporal transformer streams, which are then efficiently distilled into a unified representation by a Perceiver module. Concurrently, it models structural connectivity from diffusion MRI using a novel signed graph transformer to encode the brain's anatomical structure. These powerful, modality-specific representations are then integrated via an adaptive fusion gate. Despite its compact design, our model consistently outperforms larger models on a diverse range of downstream benchmarks, including classification, prediction, and unsupervised network identification tasks. Furthermore, our model revealed novel insights into brain dynamics using attention maps on a unique external psilocybin neuroimaging dataset (pre- and post-administration). BrainSymphony establishes that architecturally-aware, multimodal models can surpass their larger counterparts, paving the way for more accessible and powerful research in computational neuroscience.

Ensemble-based Convolutional Neural Networks for brain tumor classification in MRI: Enhancing accuracy and interpretability using explainable AI.

Sánchez-Moreno L, Perez-Peña A, Duran-Lopez L, Dominguez-Morales JP

pubmed logopapersJun 23 2025
Accurate and efficient classification of brain tumors, including gliomas, meningiomas, and pituitary adenomas, is critical for early diagnosis and treatment planning. Magnetic resonance imaging (MRI) is a key diagnostic tool, and deep learning models have shown promise in automating tumor classification. However, challenges remain in achieving high accuracy while maintaining interpretability for clinical use. This study explores the use of transfer learning with pre-trained architectures, including VGG16, DenseNet121, and Inception-ResNet-v2, to classify brain tumors from MRI images. An ensemble-based classifier was developed using a majority voting strategy to improve robustness. To enhance clinical applicability, explainability techniques such as Grad-CAM++ and Integrated Gradients were employed, allowing visualization of model decision-making. The ensemble model outperformed individual Convolutional Neural Network (CNN) architectures, achieving an accuracy of 86.17% in distinguishing gliomas, meningiomas, pituitary adenomas, and benign cases. Interpretability techniques provided heatmaps that identified key regions influencing model predictions, aligning with radiological features and enhancing trust in the results. The proposed ensemble-based deep learning framework improves the accuracy and interpretability of brain tumor classification from MRI images. By combining multiple CNN architectures and integrating explainability methods, this approach offers a more reliable and transparent diagnostic tool to support medical professionals in clinical decision-making.

CT Radiomics-Based Explainable Machine Learning Model for Accurate Differentiation of Malignant and Benign Endometrial Tumors: A Two-Center Study

Tingrui Zhang, Honglin Wu, Zekun Jiang, Yingying Wang, Rui Ye, Huiming Ni, Chang Liu, Jin Cao, Xuan Sun, Rong Shao, Xiaorong Wei, Yingchun Sun

arxiv logopreprintJun 22 2025
Aimed to develop and validate a CT radiomics-based explainable machine learning model for diagnosing malignancy and benignity specifically in endometrial cancer (EC) patients. A total of 83 EC patients from two centers, including 46 with malignant and 37 with benign conditions, were included, with data split into a training set (n=59) and a testing set (n=24). The regions of interest (ROIs) were manually segmented from pre-surgical CT scans, and 1132 radiomic features were extracted from the pre-surgical CT scans using Pyradiomics. Six explainable machine learning modeling algorithms were implemented respectively, for determining the optimal radiomics pipeline. The diagnostic performance of the radiomic model was evaluated by using sensitivity, specificity, accuracy, precision, F1 score, confusion matrices, and ROC curves. To enhance clinical understanding and usability, we separately implemented SHAP analysis and feature mapping visualization, and evaluated the calibration curve and decision curve. By comparing six modeling strategies, the Random Forest model emerged as the optimal choice for diagnosing EC, with a training AUC of 1.00 and a testing AUC of 0.96. SHAP identified the most important radiomic features, revealing that all selected features were significantly associated with EC (P < 0.05). Radiomics feature maps also provide a feasible assessment tool for clinical applications. DCA indicated a higher net benefit for our model compared to the "All" and "None" strategies, suggesting its clinical utility in identifying high-risk cases and reducing unnecessary interventions. In conclusion, the CT radiomics-based explainable machine learning model achieved high diagnostic performance, which could be used as an intelligent auxiliary tool for the diagnosis of endometrial cancer.

From "time is brain" to "time is collaterals": updates on the role of cerebral collateral circulation in stroke.

Marilena M, Romana PF, Guido A, Gianluca R, Sebastiano F, Enrico P, Sabrina A

pubmed logopapersJun 22 2025
Acute ischemic stroke (AIS) remains the leading cause of mortality and disability worldwide. While revascularization therapies-such as intravenous thrombolysis (IVT) and endovascular thrombectomy (EVT)-have significantly improved outcomes, their success is strongly influenced by the status of cerebral collateral circulation. Collateral vessels sustain cerebral perfusion during vascular occlusion, limiting infarct growth and extending therapeutic windows. Despite this recognized importance, standardized methods for assessing collateral status and integrating it into treatment strategies are still evolving. This narrative review synthesizes current evidence on the role of collateral circulation in AIS, focusing on its impact on infarct dynamics, treatment efficacy, and functional recovery. We highlight findings from major clinical trials-including MR CLEAN, DAWN, DEFUSE-3, and SWIFT PRIME which consistently demonstrate that robust collateral networks are associated with improved outcomes and expanded eligibility for reperfusion therapies. Advances in neuroimaging, such as multiphase CTA and perfusion MRI, alongside emerging AI-driven automated collateral grading, are reshaping patients' selection and clinical decision-making. We also discuss novel therapeutic strategies aimed at enhancing collateral flow, such as vasodilators, neuroprotective agents, statins, and stem cell therapies. Despite growing evidence supporting collateral-based treatment approaches, real-time clinical implementation remains limited by challenges in standardization and access. Cerebral collateral circulation is a critical determinant of stroke prognosis and treatment response. Incorporating collateral assessment into acute stroke workflows-supported by advanced imaging, artificial intelligence, and personalized medicine-offers a promising pathway to optimize outcomes. As the field moves beyond a strict "time is brain" model, the emerging paradigm of "time is collaterals" may better reflect the dynamic interplay between perfusion, tissue viability, and therapeutic opportunity in AIS management.

Pre-Trained LLM is a Semantic-Aware and Generalizable Segmentation Booster

Fenghe Tang, Wenxin Ma, Zhiyang He, Xiaodong Tao, Zihang Jiang, S. Kevin Zhou

arxiv logopreprintJun 22 2025
With the advancement of Large Language Model (LLM) for natural language processing, this paper presents an intriguing finding: a frozen pre-trained LLM layer can process visual tokens for medical image segmentation tasks. Specifically, we propose a simple hybrid structure that integrates a pre-trained, frozen LLM layer within the CNN encoder-decoder segmentation framework (LLM4Seg). Surprisingly, this design improves segmentation performance with a minimal increase in trainable parameters across various modalities, including ultrasound, dermoscopy, polypscopy, and CT scans. Our in-depth analysis reveals the potential of transferring LLM's semantic awareness to enhance segmentation tasks, offering both improved global understanding and better local modeling capabilities. The improvement proves robust across different LLMs, validated using LLaMA and DeepSeek.

LLM-driven Medical Report Generation via Communication-efficient Heterogeneous Federated Learning

Haoxuan Che, Haibo Jin, Zhengrui Guo, Yi Lin, Cheng Jin, Hao Chen

arxiv logopreprintJun 21 2025
LLMs have demonstrated significant potential in Medical Report Generation (MRG), yet their development requires large amounts of medical image-report pairs, which are commonly scattered across multiple centers. Centralizing these data is exceptionally challenging due to privacy regulations, thereby impeding model development and broader adoption of LLM-driven MRG models. To address this challenge, we present FedMRG, the first framework that leverages Federated Learning (FL) to enable privacy-preserving, multi-center development of LLM-driven MRG models, specifically designed to overcome the critical challenge of communication-efficient LLM training under multi-modal data heterogeneity. To start with, our framework tackles the fundamental challenge of communication overhead in FL-LLM tuning by employing low-rank factorization to efficiently decompose parameter updates, significantly reducing gradient transmission costs and making LLM-driven MRG feasible in bandwidth-constrained FL settings. Furthermore, we observed the dual heterogeneity in MRG under the FL scenario: varying image characteristics across medical centers, as well as diverse reporting styles and terminology preferences. To address this, we further enhance FedMRG with (1) client-aware contrastive learning in the MRG encoder, coupled with diagnosis-driven prompts, which capture both globally generalizable and locally distinctive features while maintaining diagnostic accuracy; and (2) a dual-adapter mutual boosting mechanism in the MRG decoder that harmonizes generic and specialized adapters to address variations in reporting styles and terminology. Through extensive evaluation of our established FL-MRG benchmark, we demonstrate the generalizability and adaptability of FedMRG, underscoring its potential in harnessing multi-center data and generating clinically accurate reports while maintaining communication efficiency.

Generative deep-learning-model based contrast enhancement for digital subtraction angiography using a text-conditioned image-to-image model.

Takata T, Yamada K, Yamamoto M, Kondo H

pubmed logopapersJun 20 2025
Digital subtraction angiography (DSA) is an essential imaging technique in interventional radiology, enabling detailed visualization of blood vessels by subtracting pre- and post-contrast images. However, reduced contrast, either accidental or intentional, can impair the clarity of vascular structures. This issue becomes particularly critical in patients with chronic kidney disease (CKD), where minimizing iodinated contrast is necessary to reduce the risk of contrast-induced nephropathy (CIN). This study explored the potential of using a generative deep-learning-model based contrast enhancement technique for DSA. A text-conditioned image-to-image model was developed using Stable Diffusion, augmented with ControlNet to reduce hallucinations and Low-Rank Adaptation for model fine-tuning. A total of 1207 DSA series were used for training and testing, with additional low-contrast images generated through data augmentation. The model was trained using tagged text labels and evaluated using metrics such as Root Mean Square (RMS) contrast, Michelson contrast, signal-to-noise ratio (SNR), and entropy. Evaluation results indicated significant improvements, with RMS contrast, Michelson contrast, and entropy respectively increased from 7.91 to 17.7, 0.875 to 0.992, and 3.60 to 5.60, reflecting enhanced detail. However, SNR decreased from 21.3 to 8.50, indicating increased noise. This study demonstrated the feasibility of deep learning-based contrast enhancement for DSA images and highlights the potential for generative deep-learning-model to improve angiographic imaging. Further refinements, particularly in artifact suppression and clinical validation, are necessary for practical implementation in medical settings.

Evaluating ChatGPT's performance across radiology subspecialties: A meta-analysis of board-style examination accuracy and variability.

Nguyen D, Kim GHJ, Bedayat A

pubmed logopapersJun 20 2025
Large language models (LLMs) like ChatGPT are increasingly used in medicine due to their ability to synthesize information and support clinical decision-making. While prior research has evaluated ChatGPT's performance on medical board exams, limited data exist on radiology-specific exams especially considering prompt strategies and input modalities. This meta-analysis reviews ChatGPT's performance on radiology board-style questions, assessing accuracy across radiology subspecialties, prompt engineering methods, GPT model versions, and input modalities. Searches in PubMed and SCOPUS identified 163 articles, of which 16 met inclusion criteria after excluding irrelevant topics and non-board exam evaluations. Data extracted included subspecialty topics, accuracy, question count, GPT model, input modality, prompting strategies, and access dates. Statistical analyses included two-proportion z-tests, a binomial generalized linear model (GLM), and meta-regression with random effects (Stata v18.0, R v4.3.1). Across 7024 questions, overall accuracy was 58.83 % (95 % CI, 55.53-62.13). Performance varied widely by subspecialty, highest in emergency radiology (73.00 %) and lowest in musculoskeletal radiology (49.24 %). GPT-4 and GPT-4o significantly outperformed GPT-3.5 (p < .001), but visual inputs yielded lower accuracy (46.52 %) compared to textual inputs (67.10 %, p < .001). Prompting strategies showed significant improvement (p < .01) with basic prompts (66.23 %) compared to no prompts (59.70 %). A modest but significant decline in performance over time was also observed (p < .001). ChatGPT demonstrates promising but inconsistent performance in radiology board-style questions. Limitations in visual reasoning, heterogeneity across studies, and prompt engineering variability highlight areas requiring targeted optimization.

Large models in medical imaging: Advances and prospects.

Fang M, Wang Z, Pan S, Feng X, Zhao Y, Hou D, Wu L, Xie X, Zhang XY, Tian J, Dong D

pubmed logopapersJun 20 2025
Recent advances in large models demonstrate significant prospects for transforming the field of medical imaging. These models, including large language models, large visual models, and multimodal large models, offer unprecedented capabilities in processing and interpreting complex medical data across various imaging modalities. By leveraging self-supervised pretraining on vast unlabeled datasets, cross-modal representation learning, and domain-specific medical knowledge adaptation through fine-tuning, large models can achieve higher diagnostic accuracy and more efficient workflows for key clinical tasks. This review summarizes the concepts, methods, and progress of large models in medical imaging, highlighting their potential in precision medicine. The article first outlines the integration of multimodal data under large model technologies, approaches for training large models with medical datasets, and the need for robust evaluation metrics. It then explores how large models can revolutionize applications in critical tasks such as image segmentation, disease diagnosis, personalized treatment strategies, and real-time interactive systems, thus pushing the boundaries of traditional imaging analysis. Despite their potential, the practical implementation of large models in medical imaging faces notable challenges, including the scarcity of high-quality medical data, the need for optimized perception of imaging phenotypes, safety considerations, and seamless integration with existing clinical workflows and equipment. As research progresses, the development of more efficient, interpretable, and generalizable models will be critical to ensuring their reliable deployment across diverse clinical environments. This review aims to provide insights into the current state of the field and provide directions for future research to facilitate the broader adoption of large models in clinical practice.

Research hotspots and development trends in molecular imaging of glioma (2014-2024): A bibliometric review.

Zhou H, Luo Y, Li S, Zhang G, Zeng X

pubmed logopapersJun 20 2025
This study aims to explore research hotspots and development trends in molecular imaging of glioma from 2014 to 2024. A total of 2957 publications indexed in the web of science core collection (WoSCC) were analyzed using bibliometric techniques. To visualize the research landscape, co-citation clustering, keyword analysis, and technological trend mapping were performed using CiteSpace and Excel. Publication output peaked in 2021. Emerging research trends included the integration of radiomics and artificial intelligence and the application of novel imaging modalities such as positron emission tomography and magnetic resonance spectroscopy. Significant progress was observed in blood-brain barrier disruption techniques and the development of molecular probes, especially those targeting IDH and MGMT mutations. Molecular imaging has been pivotal in advancing glioma research, contributing to improved diagnostic accuracy and personalized treatment strategies. However, challenges such as clinical translation and standardization remain. Future studies should focus on integrating advanced technologies into routine clinical practice to enhance patient care.
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