# 3D Foundation Model for Generalizable Disease Detection in Head Computed Tomography

arXiv: https://arxiv.org/abs/2502.02779 · HTML: https://mlsanity.com/paper/2502.02779/

## Key facts

- Cited by 12 papers in the map (data through 14 Oct 2026).
- Builds on 42 of its 70 references that are in the map.
- First posted on arXiv 4 Feb 2025.

## Builds on (most cited first, 30 of 42)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [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)
- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [DINOv2: Learning Robust Visual Features without Supervision](https://mlsanity.com/paper/2304.07193/) (2023)
- [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)
- [On the Opportunities and Risks of Foundation Models](https://mlsanity.com/paper/2108.07258/) (2021)
- [Prototypical Networks for Few-shot Learning](https://mlsanity.com/paper/1703.05175/) (2017)
- [SAM 2: Segment Anything in Images and Videos](https://mlsanity.com/paper/2408.00714/) (2024)
- [Unsupervised Learning of Visual Features by Contrasting Cluster Assignments](https://mlsanity.com/paper/2006.09882/) (2020)
- [BEiT: BERT Pre-Training of Image Transformers](https://mlsanity.com/paper/2106.08254/) (2021)
- [Barlow Twins: Self-Supervised Learning via Redundancy Reduction](https://mlsanity.com/paper/2103.03230/) (2021)
- [VideoMAE: Masked Autoencoders are Data-Efficient Learners for Self-Supervised Video Pre-Training](https://mlsanity.com/paper/2203.12602/) (2022)
- [CoCa: Contrastive Captioners are Image-Text Foundation Models](https://mlsanity.com/paper/2205.01917/) (2022)
- [Attention-based Deep Multiple Instance Learning](https://mlsanity.com/paper/1802.04712/) (2018)
- [Scaling Vision Transformers](https://mlsanity.com/paper/2106.04560/) (2021)
- [iBOT: Image BERT Pre-Training with Online Tokenizer](https://mlsanity.com/paper/2111.07832/) (2021)
- [Scaling Vision Transformers to 22 Billion Parameters](https://mlsanity.com/paper/2302.05442/) (2023)
- [Can Spatiotemporal 3D CNNs Retrace the History of 2D CNNs and ImageNet?](https://mlsanity.com/paper/1711.09577/) (2017)
- [Self-Supervised Pre-Training of Swin Transformers for 3D Medical Image Analysis](https://mlsanity.com/paper/2111.14791/) (2021)
- [SatMAE: Pre-training Transformers for Temporal and Multi-Spectral Satellite Imagery](https://mlsanity.com/paper/2207.08051/) (2022)
- [Big Self-Supervised Models Advance Medical Image Classification](https://mlsanity.com/paper/2101.05224/) (2021)
- [Context Autoencoder for Self-Supervised Representation Learning](https://mlsanity.com/paper/2202.03026/) (2022)
- [Masked Autoencoders that Listen](https://mlsanity.com/paper/2207.06405/) (2022)
- [Segment Anything in Medical Images](https://mlsanity.com/paper/2304.12306/) (2023)
- [BiomedGPT: A Generalist Vision-Language Foundation Model for Diverse Biomedical Tasks](https://mlsanity.com/paper/2305.17100/) (2023)
- [SimpleShot: Revisiting Nearest-Neighbor Classification for Few-Shot Learning](https://mlsanity.com/paper/1911.04623/) (2019)
- [Merlin: A Computed Tomography Vision-Language Foundation Model and Dataset](https://mlsanity.com/paper/2406.06512/) (2024)

## Built on by (most cited first, 12 of 12)

- [Towards Scalable Language-Image Pre-training for 3D Medical Imaging](https://mlsanity.com/paper/2505.21862/) (2025)
- [Revisiting 2D Foundation Models for Scalable 3D Medical Image Classification](https://mlsanity.com/paper/2512.12887/) (2025)
- [A Non-contrast Head CT Foundation Model for Comprehensive Neuro-Trauma Triage](https://mlsanity.com/paper/2502.21106/) (2025)
- [X2CT-CLIP: Enable Multi-Abnormality Detection in Computed Tomography from Chest Radiography via Tri-Modal Contrastive Learning](https://mlsanity.com/paper/2503.02162/) (2025)
- [Learning complete and explainable visual representations from itemized text supervision](https://mlsanity.com/paper/2512.11141/) (2025)
- [Multimodal, Multi-Disease Medical Imaging Foundation Model (MerMED-FM)](https://mlsanity.com/paper/2507.00185/) (2025)
- [Adapting Medical Vision Foundation Models for Volumetric Medical Image Segmentation via Active Learning and Selective Semi-supervised Fine-tuning](https://mlsanity.com/paper/2509.10784/) (2025)
- [Specializing Foundation Models via Mixture of Low-Rank Experts for Comprehensive Head CT Analysis](https://mlsanity.com/paper/2603.00675/) (2026)
- [Volumetric Radiology AI in the Era of Multimodal Large Language Models](https://mlsanity.com/paper/2608.20549/) (2026)
- [Comparative Study of Anatomical and Learned Features in AI Models for Structural Brain MRI](https://mlsanity.com/paper/2609.06807/) (2026)
- [A4-MR: Abnormality-aware Anatomical Alignment for MR](https://mlsanity.com/paper/2610.13056/) (2026)
- [Benchmarking Self-Supervised 3D Medical Vision Foundation Models and Transferability Estimation](https://mlsanity.com/paper/2610.17573/) (2026)

## Abstract (arXiv)

Head computed tomography (CT) imaging is a widely-used imaging modality with multitudes of medical indications, particularly in assessing pathology of the brain, skull, and cerebrovascular system. It is commonly the first-line imaging in neurologic emergencies given its rapidity of image acquisition, safety, cost, and ubiquity. Deep learning models may facilitate detection of a wide range of diseases. However, the scarcity of high-quality labels and annotations, particularly among less common conditions, significantly hinders the development of powerful models. To address this challenge, we introduce FM-CT: a Foundation Model for Head CT for generalizable disease detection, trained using self-supervised learning. Our approach pre-trains a deep learning model on a large, diverse dataset of 361,663 non-contrast 3D head CT scans without the need for manual annotations, enabling the model to learn robust, generalizable features. To investigate the potential of self-supervised learning in head CT, we employed both discrimination with self-distillation and masked image modeling, and we construct our model in 3D rather than at the slice level (2D) to exploit the structure of head CT scans more comprehensively and efficiently. The model's downstream classification performance is evaluated using internal and three external datasets, encompassing both in-distribution (ID) and out-of-distribution (OOD) data. Our results demonstrate that the self-supervised foundation model significantly improves performance on downstream diagnostic tasks compared to models trained from scratch and previous 3D CT foundation models on scarce annotated datasets. This work highlights the effectiveness of self-supervised learning in medical imaging and sets a new benchmark for head CT image analysis in 3D, enabling broader use of artificial intelligence for head CT-based diagnosis.