3D Modality-Aware Pre-training for Vision-Language Model in MRI Multi-organ Abnormality Detection

Multi-parametric magnetic resonance imaging (mpMRI) is a cornerstone for brain tumor diagnosis and treatment, yet current AI models face critical limitations: their lack of natural language interaction and interpretability impedes spatial information integration and cross-modal reasoning required clinically. Key challenges arise from significant physical meaning differences across modalities, spatial misalignment due to scan intervals, and the need for complex multi-feature interpretation in tasks like glioma grading. While visual-language models (VLMs) show promise in cross-modal understanding, existing methods focus mainly on 2D image modeling, neglecting direct perception of 3D volumetric space. Although 3D VLMs have been proposed for report generation and feature alignment in 3D CT imaging, mpMRI applications demand collaborative inference across multiple imaging modalities-a requirement unmet by current solutions. To address this, we introduce Mr3D-VL, a dedicated visual-language foundation model for multi-parametric 3D MRI. With 4 billion parameters, it employs an unsupervised pre-trained shared 3D encoder and 4D rotational positional embedding for dual modality-spatial integration. Its cross-modal projection layer uses a multi-resolution feature implantation strategy to enhance feature perception across resolutions. Experimental results show significant improvements over existing 4B/7B/30B domain-specific and general-purpose models in text generation tasks, achieving a BERTScore of 0.856 for report generation, with question-answering accuracy at 0.713 and multiple-choice accuracy at 0.912.

Recent advances in large-scale foundation models have enabled strong generalization across a wide range of clinical and research tasks in magnetic resonance imaging (MRI). However, existing vision-language MRI models remain limited in anatomy-specific localization and pathology-aware representation, particularly in real-world settings. We introduce A4-MR, a 3D vision-language foundation model trained on approximately 50,000 MRI studies comprising 491,000 series, roughly half of which are paired with radiology reports. A4-MR is designed to: (1) learn anatomy localization through large-scale pretraining with noisy labels; (2) align image and text representations at the anatomical level; and (3) learn distinct representations of healthy and abnormal anatomy. Across a diverse set of downstream tasks, A4-MR outperforms existing foundation models, including a +1.7 AUROC improvement over MedSigLIP for abnormality detection. Using a frozen encoder, A4-MR also surpasses an end-to-end task-specific MedNeXt model for knee segmentation by +1.4 Dice and performs comparably to the best task-specific model for abdominal organ segmentation on AMOS, within 0.4 Dice. Finally, without anatomical prompts, A4-MR localizes 3D anatomy comparably to MedSAM2 provided with ground-truth bounding boxes. Together, these results demonstrate that anatomy-level multimodal alignment and abnormality-aware representation learning can enable a single MRI foundation model to support localization, segmentation, and pathology-related tasks.

Vision-language pre-training (VLP) holds great promise for general-purpose medical AI by leveraging radiology reports as rich textual supervision, yet existing methods struggle with 3D CT imaging due to inefficient visual backbones and coarse semantic alignment. To address these issues, we propose a tailored VLP framework featuring three key components: (1) a CNN-ViT hybrid encoder that replaces ViT's patch embedding with a 3D CNN backbone to efficiently capture local anatomical details while preserving global attention and compatibility with pre-trained cross-modal priors; (2) a disease-level contrastive learning mechanism using learnable query tokens to dynamically extract disease-specific semantics from full reports and align them with corresponding visual features, thereby disentangling distinct diseases within the same anatomical region; and (3) a diagnosis-aware prompt strategy that employs real clinical phrases and aggregated disease prototypes to bridge the pre-training-inference gap and enhance zero-shot diagnostic reliability. Our model achieves state-of-the-art performance on CT-RATE (84.4% AUC, +5.1%) and Rad-ChestCT (75.4% AUC, +5.4%), with even larger gains (+9.8% AUC) on a challenging 60-disease benchmark, and demonstrates strong transferability to radiology report generation, underscoring the generality and clinical utility of our approach.