Volumetric medical VQA requires reasoning over long and redundant 3D visual token sequences, especially in multi-sequence MRI where complementary modalities provide diverse diagnostic cues but expose the decoder to many repeated anatomical regions. To investigate reasoning under multi-sequence visual redundancy, we first introduce BreMRIs-VQA, a clinically curated breast MRI benchmark with 1.19M QA pairs from 71.0K sequences and 12.9K patients, covering both free-text and multiple-choice questions. We further propose SeVeR, a selective visual exposure framework that compresses dense volumes into modality-wise prototypes and retrieves complementary multi-level evidence with change-aware gated attention during decoding, trained with a marginal-utility self-consistency objective that suppresses unhelpful retrieval. Experiments on BreMRIs-VQA and public benchmarks show that SeVeR improves both discriminative and generative performance while exposing substantially fewer visual tokens.
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 language models (LLMs) and their extension to vision-language models (VLMs) have made it easier to combine text and images for tasks such as report generation. Existing VLMs in medicine typically focus on 2D images (chest X-rays), and their extension to 3D imaging has been difficult because of the lack of paired 3D imaging-text data. Thus, we introduce a new method for creating a 3D image-text dataset for brain oncology using 3D MRI scans of glioma and meningioma cases. We use a cooperative system in which several LLMs work together to generate and check reports, ensuring that they are accurate and clear. By leveraging the new 3D MRI-text dataset, we further build a VLM that converts MRI scans into tokens and aligns them with text instructions. Our VLM performed better in report generation and visual question answering tasks than other 2D and 3D methods. Our method not only improves the quality of reports but also helps with better diagnosis and treatment in brain oncology.
Induk Um, Youngung Han, Kyeonghun Kim +14cs.CV cs.LG
Perineural invasion (PNI) is associated with poor prognosis in cholangiocarcinoma (CCA). However, its detection from 3D MRI remains challenging due to the subtle and spatially heterogeneous imaging signatures at the tumor periphery. Capturing such spatially sparse cues necessitates volumetric analysis of 3D MRI, but existing deep learning approaches incur prohibitive computational costs on volumetric medical images, limiting their clinical deployment. We propose Dual Sparsity Spikformer (SpikeDS), a spiking neural network architecture that jointly exploits activation sparsity from binary spike communication and spatial sparsity from window pruning based on firing rates. SpikeDS introduces Dual Sparsity Spiking Attention (DSSA), which combines two complementary mechanisms. The first is Window-based Expert Mixture Spiking Attention (W-EMSA), which selectively applies attention only to salient windows identified by their firing rates. The second is Cross-Window Spiking Self-Attention (CW-SSA), which enables global context exchange through an asymmetric scheme in which pruned windows still contribute as key-value sources. Evaluated on a clinical cohort of 139 CCA patients via 5-fold cross-validation, SpikeDS achieves an AUC of 0.753 while consuming only 14.4 mJ, surpassing the best baseline in both AUC and energy efficiency. These results suggest that dual sparsity provides an effective hardware-aware strategy for improving the efficiency of 3D spiking transformers without compromising diagnostic performance.
Youngung Han, Hyunsu Go, Kyeonghun Kim +9cs.CV cs.AI
Perineural invasion (PNI) is a clinically relevant indicator of tumor aggressiveness and can influence surgical decision-making, motivating interest in reliable preoperative assessment. The subtle MRI features of PNI, however, often resemble nearby anatomy, complicating noninvasive prediction. These fine perineural cues are easily attenuated by routine downsampling or overly global feature aggregation, reducing the effectiveness of conventional volumetric models. We present LoSA-Net, a localized and scale-adaptive architecture for boundary-sensitive PNI prediction in 3D MRI. Talking Neighborhood Attention (TNA) preserves nerve-aligned detail through localized self-attention with head-wise mixing, and Scale-Adaptive Feature Mixing (SAFM) modulates the receptive field using multi-scale depthwise processing. Cross-Scale Refinement and Alignment (CSRA) maintains consistency between semantic context and high-resolution boundaries across stages. In contrast-enhanced MRI scans from 168 patients with cholangiocarcinoma, LoSA-Net achieves an AUC of 0.7567 and outperforms representative convolutional and transformer baselines under matched preprocessing and optimization settings.
Youngung Han, Induk Um, Kyeonghun Kim +9cs.CV cs.AI
Perineural invasion (PNI) is a critical prognostic factor in cholangiocarcinoma. Non-invasive prediction from 3D MRI is challenging, demanding models that efficiently capture both fine-grained details and global context. We propose the Multi-window Mixture-of-Head Attention Transformer (MMA-Former), a novel end-to-end 3D architecture featuring a Coarse-Fine Transformer (CFT) structure for parallel multi-scale feature extraction. We advance this structure by integrating a novel Window-Specific Mixture-of-Head attention (WS-MoH) mechanism. Unlike standard Multi-Head Self Attention (MSA), WS-MoH generates a representation for each 3D window and dynamically routes the entire window to specialized or common attention heads. This enables spatially adaptive feature extraction tailored to the local context of each window, enhancing specialization and reducing redundancy without increasing parameters. Evaluated on a retrospective dataset of 168 T1-weighted MRI scans, MMA-Former achieved an AUC of 0.752, outperforming other 3D architectures, including the best CNN (AUC of 0.708) and Transformer baselines (AUC of 0.681).
Manual reporting of 3D MRI studies is time-consuming, yet end-to-end structured report generation for 3D liver MRI remains underexplored due to volumetric complexity and scarce paired data. We propose MRI2Rep, an autoregressive framework for liver MRI report generation. From 3,929 real-world MRI-report pairs acquired over a 10-year single-institution cohort, a Report-to-Label Canonicalization (RLC) module converts free-text reports into structured, closed-vocabulary diagnostic sequences without lesion-level annotations. On a held-out test set, MRI2Rep achieves 76.0% case-level sensitivity, 29.4% lesion-level F1, compared with no more than 8.3% for adapted medical vision-language baselines, and 82.4% liver-level accuracy. In a blinded reader study, two radiologists rated 75% and 70% of AI-generated reports as clinically acceptable, compared with 95% and 100% for original reports. Our automated LLM-based judge, LLM-Eval, rated 61.8% of AI-generated reports as acceptable, applying a stricter standard and supporting its use as a conservative proxy. To our knowledge, this is the first end-to-end LI-RADS-structured reporting system for 3D liver MRI.