# OrganLens: Organ-Specific Representation Learning for CT Foundation Models

arXiv: https://arxiv.org/abs/2607.25164 · HTML: https://mlsanity.com/paper/2607.25164/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 25 of its 58 references that are in the map.
- First posted on arXiv 28 Jul 2026.

## Builds on (most cited first, 25 of 25)

- [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)
- [Emerging Properties in Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.14294/) (2021)
- [On the Opportunities and Risks of Foundation Models](https://mlsanity.com/paper/2108.07258/) (2021)
- [V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation](https://mlsanity.com/paper/1606.04797/) (2016)
- [iBOT: Image BERT Pre-Training with Online Tokenizer](https://mlsanity.com/paper/2111.07832/) (2021)
- [ClinicalBERT: Modeling Clinical Notes and Predicting Hospital Readmission](https://mlsanity.com/paper/1904.05342/) (2019)
- [Knowledge-enhanced Visual-Language Pre-training on Chest Radiology Images](https://mlsanity.com/paper/2302.14042/) (2023)
- [Spreading vectors for similarity search](https://mlsanity.com/paper/1806.03198/) (2018)
- [Merlin: A Computed Tomography Vision-Language Foundation Model and Dataset](https://mlsanity.com/paper/2406.06512/) (2024)
- [Machine-Learning-Based Multiple Abnormality Prediction with Large-Scale Chest Computed Tomography Volumes](https://mlsanity.com/paper/2002.04752/) (2020)
- [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)
- [Models Genesis](https://mlsanity.com/paper/2004.07882/) (2020)
- [Representing Part-Whole Hierarchies in Foundation Models by Learning Localizability, Composability, and Decomposability from Anatomy via Self-Supervision](https://mlsanity.com/paper/2404.15672/) (2024)
- [ONCOPILOT: A Promptable CT Foundation Model For Solid Tumor Evaluation](https://mlsanity.com/paper/2410.07908/) (2024)
- [TotalFM: An Organ-Separated 3D-CT Foundation Model Leveraging Large-Scale Routine Clinical Radiology Data](https://mlsanity.com/paper/2601.00260/) (2026)
- [EXACT: an explainable anomaly-aware vision foundation model for analysis of 3D chest CT](https://mlsanity.com/paper/2604.24146/) (2026)
- [Universal CT Representations from Anatomy to Disease Phenotype through Agglomerative Pretraining](https://mlsanity.com/paper/2605.21906/) (2026)
- [SigVLP: Sigmoid Volume-Language Pre-Training for Self-Supervised CT-Volume Adaptive Representation Learning](https://mlsanity.com/paper/2602.21735/) (2026)
- [CoralBay: A Self-Supervised CT Foundation Model](https://mlsanity.com/paper/2606.03888/) (2026)
- [Learning Anatomy-Grounded CT Vision-Language Representations with Organ-Hierarchical Report Knowledge](https://mlsanity.com/paper/2607.10953/) (2026)
- [OWT: A Foundational Organ-Wise Tokenization Framework for Medical Imaging](https://mlsanity.com/paper/2505.04899/) (2025)
- [Pan-FM: A Pan-Organ Foundation Model with Saliency-Guided Masking for Missing Robustness](https://mlsanity.com/paper/2605.07055/) (2026)
- [ORACLE-CT: Anatomy-Aware Support Pooling for CT Classification](https://mlsanity.com/paper/2606.05460/) (2026)

## Abstract (arXiv)

A CT examination captures multiple organs, but many biomedical questions concern abnormalities, prognosis, or longitudinal change in a specific organ. These questions require a separate representation for each organ within the same CT volume. Existing CT foundation models commonly produce a single volume-level representation, while recent anatomy-aware methods either encode pre-separated organ volumes or explicitly disentangle images into organ token groups. The former may remove clinically relevant surrounding context, while the latter does not condition a shared encoder on a selected organ before its features are formed. We introduce OrganLens for organ-specific representation learning through self-supervision. An organ identity conditions a shared CT encoder, while organ-specific distillation and anatomy-mask supervision shape features for anatomy-weighted pooling into organ-specific representations. At inference, the shared model produces 11 organ-specific representations without external segmentation masks. We evaluate OrganLens on CT-RATE, RAD-ChestCT, INSPECT, and NLST across diverse acquisitions and downstream evaluations. Relative to CT-pretrained DINOv2, heart representations raise CT-RATE cardiomegaly AUROC from 0.910 to 0.953, while lung representations improve the Harrell C-index for NLST lung-cancer mortality by 14.2%. The global representation reaches INSPECT Recall@10 of 33.09% and 32.04% for text-to-image and image-to-text retrieval, respectively. Across organ-related tasks, anatomically matched representations provide stronger task-relevant signal, while the global representation retains broad utility. OrganLens offers a scalable approach to organ-specific CT representation learning with a shared encoder. More broadly, it provides the medical research community with a reusable framework for studying organ-specific disease across cohorts and clinical endpoints.