# A4-MR: Abnormality-aware Anatomical Alignment for MR

arXiv: https://arxiv.org/abs/2610.13056 · HTML: https://mlsanity.com/paper/2610.13056/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 44 of its 56 references that are in the map.
- First posted on arXiv 9 Oct 2026.

## Builds on (most cited first, 30 of 44)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [DINOv2: Learning Robust Visual Features without Supervision](https://mlsanity.com/paper/2304.07193/) (2023)
- [End-to-End Object Detection with Transformers](https://mlsanity.com/paper/2005.12872/) (2020)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [Qwen2.5-VL Technical Report](https://mlsanity.com/paper/2502.13923/) (2025)
- [You Only Look Once: Unified, Real-Time Object Detection](https://mlsanity.com/paper/1506.02640/) (2015)
- [Sigmoid Loss for Language Image Pre-Training](https://mlsanity.com/paper/2303.15343/) (2023)
- [UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction](https://mlsanity.com/paper/1802.03426/) (2018)
- [FlashAttention-2: Faster Attention with Better Parallelism and Work Partitioning](https://mlsanity.com/paper/2307.08691/) (2023)
- [V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation](https://mlsanity.com/paper/1606.04797/) (2016)
- [Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing](https://mlsanity.com/paper/2007.15779/) (2020)
- [MDETR -- Modulated Detection for End-to-End Multi-Modal Understanding](https://mlsanity.com/paper/2104.12763/) (2021)
- [Contrastive Learning of Medical Visual Representations from Paired Images and Text](https://mlsanity.com/paper/2010.00747/) (2020)
- [TotalSegmentator: robust segmentation of 104 anatomical structures in CT images](https://mlsanity.com/paper/2208.05868/) (2022)
- [ClipCap: CLIP Prefix for Image Captioning](https://mlsanity.com/paper/2111.09734/) (2021)
- [BiomedCLIP: a multimodal biomedical foundation model pretrained from fifteen million scientific image-text pairs](https://mlsanity.com/paper/2303.00915/) (2023)
- [MONAI: An open-source framework for deep learning in healthcare](https://mlsanity.com/paper/2211.02701/) (2022)
- [MedGemma Technical Report](https://mlsanity.com/paper/2507.05201/) (2025)
- [AMOS: A Large-Scale Abdominal Multi-Organ Benchmark for Versatile Medical Image Segmentation](https://mlsanity.com/paper/2206.08023/) (2022)
- [3D MRI brain tumor segmentation using autoencoder regularization](https://mlsanity.com/paper/1810.11654/) (2018)
- [MedNeXt: Transformer-driven Scaling of ConvNets for Medical Image Segmentation](https://mlsanity.com/paper/2303.09975/) (2023)
- [SAM-Med3D: Towards General-purpose Segmentation Models for Volumetric Medical Images](https://mlsanity.com/paper/2310.15161/) (2023)
- [Merlin: A Computed Tomography Vision-Language Foundation Model and Dataset](https://mlsanity.com/paper/2406.06512/) (2024)
- [MedSAM2: Segment Anything in 3D Medical Images and Videos](https://mlsanity.com/paper/2504.03600/) (2025)
- [VISTA3D: A Unified Segmentation Foundation Model For 3D Medical Imaging](https://mlsanity.com/paper/2406.05285/) (2024)
- [Vision Foundation Models for Computed Tomography](https://mlsanity.com/paper/2501.09001/) (2025)
- [MedImageInsight: An Open-Source Embedding Model for General Domain Medical Imaging](https://mlsanity.com/paper/2410.06542/) (2024)
- [X-DETR: A Versatile Architecture for Instance-wise Vision-Language Tasks](https://mlsanity.com/paper/2204.05626/) (2022)

## Abstract (arXiv)

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.