# Universal CT Representations from Anatomy to Disease Phenotype through Agglomerative Pretraining

arXiv: https://arxiv.org/abs/2605.21906 · HTML: https://mlsanity.com/paper/2605.21906/

## Key facts

- Cited by 4 papers in the map (data through 14 Oct 2026).
- Builds on 28 of its 50 references that are in the map.
- First posted on arXiv 21 May 2026.

## Builds on (most cited first, 28 of 28)

- [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)
- [Qwen3 Technical Report](https://mlsanity.com/paper/2505.09388/) (2025)
- [DINOv2: Learning Robust Visual Features without Supervision](https://mlsanity.com/paper/2304.07193/) (2023)
- [Emerging Properties in Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.14294/) (2021)
- [DINOv3](https://mlsanity.com/paper/2508.10104/) (2025)
- [Qwen3 Embedding: Advancing Text Embedding and Reranking Through Foundation Models](https://mlsanity.com/paper/2506.05176/) (2025)
- [iBOT: Image BERT Pre-Training with Online Tokenizer](https://mlsanity.com/paper/2111.07832/) (2021)
- [Vision Transformers Need Registers](https://mlsanity.com/paper/2309.16588/) (2023)
- [VoxelMorph: A Learning Framework for Deformable Medical Image Registration](https://mlsanity.com/paper/1809.05231/) (2018)
- [TotalSegmentator: robust segmentation of 104 anatomical structures in CT images](https://mlsanity.com/paper/2208.05868/) (2022)
- [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)
- [AMOS: A Large-Scale Abdominal Multi-Organ Benchmark for Versatile Medical Image Segmentation](https://mlsanity.com/paper/2206.08023/) (2022)
- [Validation, comparison, and combination of algorithms for automatic detection of pulmonary nodules in computed tomography images: the LUNA16 challenge](https://mlsanity.com/paper/1612.08012/) (2016)
- [Generalist Foundation Models from a Multimodal Dataset for 3D Computed Tomography](https://mlsanity.com/paper/2403.17834/) (2024)
- [The state of the art in kidney and kidney tumor segmentation in contrast-enhanced CT imaging: Results of the KiTS19 Challenge](https://mlsanity.com/paper/1912.01054/) (2019)
- [FlexiViT: One Model for All Patch Sizes](https://mlsanity.com/paper/2212.08013/) (2022)
- [Merlin: A Computed Tomography Vision-Language Foundation Model and Dataset](https://mlsanity.com/paper/2406.06512/) (2024)
- [Vision Foundation Models for Computed Tomography](https://mlsanity.com/paper/2501.09001/) (2025)
- [TIPS: Text-Image Pretraining with Spatial awareness](https://mlsanity.com/paper/2410.16512/) (2024)
- [Large-Scale 3D Medical Image Pre-training with Geometric Context Priors](https://mlsanity.com/paper/2410.09890/) (2024)
- [COVID-Net CT-2: Enhanced Deep Neural Networks for Detection of COVID-19 from Chest CT Images Through Bigger, More Diverse Learning](https://mlsanity.com/paper/2101.07433/) (2021)
- [Primus: Enforcing Attention Usage for 3D Medical Image Segmentation](https://mlsanity.com/paper/2503.01835/) (2025)
- [Automatic Organ and Pan-cancer Segmentation in Abdomen CT: the FLARE 2023 Challenge](https://mlsanity.com/paper/2408.12534/) (2024)
- [Comprehensive language-image pre-training for 3D medical image understanding](https://mlsanity.com/paper/2510.15042/) (2025)
- [Curia: A Multi-Modal Foundation Model for Radiology](https://mlsanity.com/paper/2509.06830/) (2025)
- [Scaling Self-Supervised and Cross-Modal Pretraining for Volumetric CT Transformers](https://mlsanity.com/paper/2511.17209/) (2025)

## Built on by (most cited first, 4 of 4)

- [Big, Bright, or Invisible: A Frozen-Feature Benchmark of 3D CT Foundation Models](https://mlsanity.com/paper/2608.05960/) (2026)
- [A digital-twin framework for forecasting treatment-day imaging with contour uncertainty in adaptive proton radiotherapy](https://mlsanity.com/paper/2609.24725/) (2026)
- [OrganLens: Organ-Specific Representation Learning for CT Foundation Models](https://mlsanity.com/paper/2607.25164/) (2026)
- [An Uncertainty-Guided Digital Twin Framework for Online Adaptive Proton Therapy in Head and Neck Cancer: A Feasibility Study](https://mlsanity.com/paper/2609.39010/) (2026)

## Abstract (arXiv)

Computed tomography (CT) is a central to three-dimensional medical imaging, yet CT-based artificial intelligence remains fragmented across task-specific models for segmentation, classification, registration, and report analysis. Here we present FlexiCT, a family of CT foundation models trained by agglomerative continual pretraining on 266,227 CT volumes from 56 publicly available datasets, forming a large-scale public resource for CT representation learning. FlexiCT uses agglomerative pretraining across three stages: two-dimensional axial pretraining, three-dimensional anatomical pretraining and report-guided semantic alignment. This training strategy supports slice-level, volume-level and vision-language analysis. Across five downstream task families (segmentation, classification, registration, vision-language understanding and clinical retrieval), FlexiCT matches or exceeds prior task-specific approaches on multiple benchmarks. Its embeddings further organize CT scans along gradients associated with various tumor stages, suggesting that CT foundation models can capture imaging features relevant to disease phenotype characterization. Project page and code are available at: https://ricklisz.github.io/flexict.github.io and https://github.com/ricklisz/FlexiCT.