# RAU: Reference-based Anatomical Understanding with Vision Language Models

arXiv: https://arxiv.org/abs/2509.22404 · HTML: https://mlsanity.com/paper/2509.22404/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Placed in Medical vision-language models, one of 16 directions in Multimodal LLMs / vision-language models.
- Builds on 61 of its 100 references that are in the map.
- First posted on arXiv 26 Sep 2025.

## Placed in

- Multimodal LLMs / vision-language models / [Medical vision-language models](https://mlsanity.com/mllm/medical-vision-language-models/)

## Builds on (most cited first, 30 of 61)

- [The Unreasonable Effectiveness of Deep Features as a Perceptual Metric](https://mlsanity.com/paper/1801.03924/) (2018)
- [DeepSeekMath: Pushing the Limits of Mathematical Reasoning in Open Language Models](https://mlsanity.com/paper/2402.03300/) (2024)
- [Segment Anything](https://mlsanity.com/paper/2304.02643/) (2023)
- [DINOv2: Learning Robust Visual Features without Supervision](https://mlsanity.com/paper/2304.07193/) (2023)
- [Visual Instruction Tuning](https://mlsanity.com/paper/2304.08485/) (2023)
- [Qwen Technical Report](https://mlsanity.com/paper/2309.16609/) (2023)
- [Grounding DINO: Marrying DINO with Grounded Pre-Training for Open-Set Object Detection](https://mlsanity.com/paper/2303.05499/) (2023)
- [SAM 2: Segment Anything in Images and Videos](https://mlsanity.com/paper/2408.00714/) (2024)
- [VQA: Visual Question Answering](https://mlsanity.com/paper/1505.00468/) (2015)
- [Sinkhorn Distances: Lightspeed Computation of Optimal Transportation Distances](https://mlsanity.com/paper/1306.0895/) (2013)
- [DINO: DETR with Improved DeNoising Anchor Boxes for End-to-End Object Detection](https://mlsanity.com/paper/2203.03605/) (2022)
- [LLaVA-Med: Training a Large Language-and-Vision Assistant for Biomedicine in One Day](https://mlsanity.com/paper/2306.00890/) (2023)
- [Grounded Language-Image Pre-training](https://mlsanity.com/paper/2112.03857/) (2021)
- [LISA: Reasoning Segmentation via Large Language Model](https://mlsanity.com/paper/2308.00692/) (2023)
- [SpatialVLM: Endowing Vision-Language Models with Spatial Reasoning Capabilities](https://mlsanity.com/paper/2401.12168/) (2024)
- [VoxelMorph: A Learning Framework for Deformable Medical Image Registration](https://mlsanity.com/paper/1809.05231/) (2018)
- [Generalised Dice overlap as a deep learning loss function for highly unbalanced segmentations](https://mlsanity.com/paper/1707.03237/) (2017)
- [TotalSegmentator: robust segmentation of 104 anatomical structures in CT images](https://mlsanity.com/paper/2208.05868/) (2022)
- [MedCLIP: Contrastive Learning from Unpaired Medical Images and Text](https://mlsanity.com/paper/2210.10163/) (2022)
- [Segment Everything Everywhere All at Once](https://mlsanity.com/paper/2304.06718/) (2023)
- [Winoground: Probing Vision and Language Models for Visio-Linguistic Compositionality](https://mlsanity.com/paper/2204.03162/) (2022)
- [Med-Flamingo: a Multimodal Medical Few-shot Learner](https://mlsanity.com/paper/2307.15189/) (2023)
- [A Survey on Hallucination in Large Vision-Language Models](https://mlsanity.com/paper/2402.00253/) (2024)
- [Deep Learning for Segmentation using an Open Large-Scale Dataset in 2D Echocardiography](https://mlsanity.com/paper/1908.06948/) (2019)
- [SugarCrepe: Fixing Hackable Benchmarks for Vision-Language Compositionality](https://mlsanity.com/paper/2306.14610/) (2023)
- [Seg-Zero: Reasoning-Chain Guided Segmentation via Cognitive Reinforcement](https://mlsanity.com/paper/2503.06520/) (2025)
- [Lingshu: A Generalist Foundation Model for Unified Multimodal Medical Understanding and Reasoning](https://mlsanity.com/paper/2506.07044/) (2025)
- [How Abilities in Large Language Models are Affected by Supervised Fine-tuning Data Composition](https://mlsanity.com/paper/2310.05492/) (2023)
- [A survey of loss functions for semantic segmentation](https://mlsanity.com/paper/2006.14822/) (2020)
- [HuatuoGPT-Vision, Towards Injecting Medical Visual Knowledge into Multimodal LLMs at Scale](https://mlsanity.com/paper/2406.19280/) (2024)

## Built on by (most cited first, 3 of 3)

- [Vision-Language Enhanced Foundation Model for Semi-Supervised Medical Image Segmentation](https://mlsanity.com/paper/2511.19759/) (2025)
- [Learning What Helps: Task-Aligned Context Selection for Vision Tasks](https://mlsanity.com/paper/2512.00489/) (2025)
- [Self-Improving Small Object Grounding in LVLMs](https://mlsanity.com/paper/2606.01612/) (2026)

## Abstract (arXiv)

Anatomical understanding, which is the ability to identify, localize, or segment anatomical structures, is critical in medical image analysis; however, its progress is constrained by the scarcity of expert-labeled data. A promising remedy is to leverage an annotated reference image to guide the interpretation of an unlabeled target. Although recent vision-language models (VLMs) exhibit non-trivial visual reasoning, their reference-based understanding and fine-grained localization remain limited. We introduce RAU, a framework for reference-based anatomical understanding with VLMs. We first show that a VLM learns to identify anatomical regions through relative spatial reasoning between reference and target images, trained on a moderately sized dataset. We validate this capability through visual question answering (VQA) and bounding box prediction. Next, we demonstrate that the VLM-derived spatial cues can be seamlessly integrated with the fine-grained segmentation capability of SAM2, enabling localization and pixel-level segmentation of small anatomical regions, such as vessel segments. Across two in-distribution and two out-of-distribution datasets, RAU consistently outperforms a SAM2 fine-tuning baseline using the same memory setup, yielding more accurate segmentations and more reliable localization. More importantly, its generalization ability to unseen modalities makes it scalable to unseen datasets, a property crucial for medical image applications. To the best of our knowledge, RAU is the first to explore the capability of VLMs for reference-based identification, localization, and segmentation of anatomical structures in medical images. Its promising performance highlights the potential of VLM-driven approaches for anatomical understanding in automated clinical workflows.