# Anatomy Contextualized Adaptation of CT Foundation Models

arXiv: https://arxiv.org/abs/2607.27154 · HTML: https://mlsanity.com/paper/2607.27154/

## Key facts

- Cited by 1 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 33 of its 40 references that are in the map.
- First posted on arXiv 29 Jul 2026.

## 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 33)

- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [LoRA: Low-Rank Adaptation of Large Language Models](https://mlsanity.com/paper/2106.09685/) (2021)
- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Qwen3 Technical Report](https://mlsanity.com/paper/2505.09388/) (2025)
- [Momentum Contrast for Unsupervised Visual Representation Learning](https://mlsanity.com/paper/1911.05722/) (2019)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [Emerging Properties in Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.14294/) (2021)
- [Quo Vadis, Action Recognition? A New Model and the Kinetics Dataset](https://mlsanity.com/paper/1705.07750/) (2017)
- [BEiT: BERT Pre-Training of Image Transformers](https://mlsanity.com/paper/2106.08254/) (2021)
- [SimMIM: A Simple Framework for Masked Image Modeling](https://mlsanity.com/paper/2111.09886/) (2021)
- [Quantifying Attention Flow in Transformers](https://mlsanity.com/paper/2005.00928/) (2020)
- [AdaptFormer: Adapting Vision Transformers for Scalable Visual Recognition](https://mlsanity.com/paper/2205.13535/) (2022)
- [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)
- [Generalist Foundation Models from a Multimodal Dataset for 3D Computed Tomography](https://mlsanity.com/paper/2403.17834/) (2024)
- [Multi-Granularity Cross-modal Alignment for Generalized Medical Visual Representation Learning](https://mlsanity.com/paper/2210.06044/) (2022)
- [MedKLIP: Medical Knowledge Enhanced Language-Image Pre-Training in Radiology](https://mlsanity.com/paper/2301.02228/) (2023)
- [Merlin: A Computed Tomography Vision-Language Foundation Model and Dataset](https://mlsanity.com/paper/2406.06512/) (2024)
- [Joint Learning of Localized Representations from Medical Images and Reports](https://mlsanity.com/paper/2112.02889/) (2021)
- [Parameter-efficient Model Adaptation for Vision Transformers](https://mlsanity.com/paper/2203.16329/) (2022)
- [VoCo: A Simple-yet-Effective Volume Contrastive Learning Framework for 3D Medical Image Analysis](https://mlsanity.com/paper/2402.17300/) (2024)
- [GenerateCT: Text-Conditional Generation of 3D Chest CT Volumes](https://mlsanity.com/paper/2305.16037/) (2023)
- [VISTA3D: A Unified Segmentation Foundation Model For 3D Medical Imaging](https://mlsanity.com/paper/2406.05285/) (2024)
- [UniMiSS: Universal Medical Self-Supervised Learning via Breaking Dimensionality Barrier](https://mlsanity.com/paper/2112.09356/) (2021)
- [Large-scale and Fine-grained Vision-language Pre-training for Enhanced CT Image Understanding](https://mlsanity.com/paper/2501.14548/) (2025)
- [Polyhistor: Parameter-Efficient Multi-Task Adaptation for Dense Vision Tasks](https://mlsanity.com/paper/2210.03265/) (2022)
- [Vision Foundation Models for Computed Tomography](https://mlsanity.com/paper/2501.09001/) (2025)
- [A generalizable 3D framework and model for self-supervised learning in medical imaging](https://mlsanity.com/paper/2501.11755/) (2025)
- [CT-GLIP: 3D Grounded Language-Image Pretraining with CT Scans and Radiology Reports for Full-Body Scenarios](https://mlsanity.com/paper/2404.15272/) (2024)
- [Models Genesis](https://mlsanity.com/paper/2004.07882/) (2020)

## Built on by (most cited first, 1 of 1)

- [Instance-Guided Report Anchoring for Text-Free 3D Abnormality Segmentation in Chest CT](https://mlsanity.com/paper/2609.00447/) (2026)

## Abstract (arXiv)

CT vision-language foundation models have demonstrated promising performance across downstream tasks, but are typically trained with whole-volume representations that dilute fine-grained anatomical signals. Fine-grained vision-language pre-training addresses this by aligning anatomy-level visual features with anatomy-specific text, but in doing so discards the global context that whole-volume models provide. Furthermore, existing fine-grained approaches train from scratch, making them computationally expensive. We introduce Anatomy Contextualized Adaptation (ACA), a lightweight framework that adapts frozen CT foundation model representations for anatomy-level vision-language alignment while enhancing global contextualization. ACA uses TotalSegmentator to decompose CT volumes into anatomy-level embeddings, which are refined via a transformer that captures cross-anatomy relationships, and aligned to both per-anatomy and scan-level text extracted from radiology reports. Evaluated on Merlin and CT-RATE, ACA consistently outperforms both the frozen foundation model baselines and existing fine-grained methods in zero-shot finding classification, while requiring less than one hour of training once embeddings are cached. The attention weights learned by ACA's inter-anatomy transformer additionally indicate plausible cross-anatomy context routing. Altogether, these results support ACA as a lightweight approach for adapting CT foundation models to anatomically grounded vision-language alignment while preserving and enhancing global anatomical context.