# Pan-FM: A Pan-Organ Foundation Model with Saliency-Guided Masking for Missing Robustness

arXiv: https://arxiv.org/abs/2605.07055 · HTML: https://mlsanity.com/paper/2605.07055/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 32 of its 60 references that are in the map.
- First posted on arXiv 8 May 2026.

## Builds on (most cited first, 30 of 32)

- [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)
- [Exploring Simple Siamese Representation Learning](https://mlsanity.com/paper/2011.10566/) (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)
- [An Empirical Study of Training Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.02057/) (2021)
- [SimMIM: A Simple Framework for Masked Image Modeling](https://mlsanity.com/paper/2111.09886/) (2021)
- [Self-Supervised Learning from Images with a Joint-Embedding Predictive Architecture](https://mlsanity.com/paper/2301.08243/) (2023)
- [iBOT: Image BERT Pre-Training with Online Tokenizer](https://mlsanity.com/paper/2111.07832/) (2021)
- [V-JEPA 2: Self-Supervised Video Models Enable Understanding, Prediction and Planning](https://mlsanity.com/paper/2506.09985/) (2025)
- [Quantifying Attention Flow in Transformers](https://mlsanity.com/paper/2005.00928/) (2020)
- [MedCLIP: Contrastive Learning from Unpaired Medical Images and Text](https://mlsanity.com/paper/2210.10163/) (2022)
- [BiomedCLIP: a multimodal biomedical foundation model pretrained from fifteen million scientific image-text pairs](https://mlsanity.com/paper/2303.00915/) (2023)
- [Scaling Vision Transformers to Gigapixel Images via Hierarchical Self-Supervised Learning](https://mlsanity.com/paper/2206.02647/) (2022)
- [BiomedGPT: A Generalist Vision-Language Foundation Model for Diverse Biomedical Tasks](https://mlsanity.com/paper/2305.17100/) (2023)
- [Towards Generalist Foundation Model for Radiology by Leveraging Web-scale 2D&3D Medical Data](https://mlsanity.com/paper/2308.02463/) (2023)
- [What to Hide from Your Students: Attention-Guided Masked Image Modeling](https://mlsanity.com/paper/2203.12719/) (2022)
- [SemMAE: Semantic-Guided Masking for Learning Masked Autoencoders](https://mlsanity.com/paper/2206.10207/) (2022)
- [Hard Patches Mining for Masked Image Modeling](https://mlsanity.com/paper/2304.05919/) (2023)
- [Pillar-0: A New Frontier for Radiology Foundation Models](https://mlsanity.com/paper/2511.17803/) (2025)
- [Triad: Vision Foundation Model for 3D Magnetic Resonance Imaging](https://mlsanity.com/paper/2502.14064/) (2025)
- [Towards Generalisable Foundation Models for Brain MRI](https://mlsanity.com/paper/2510.23415/) (2025)
- [A Generalizable Deep Learning System for Cardiac MRI](https://mlsanity.com/paper/2312.00357/) (2023)
- [MM-DINOv2: Adapting Foundation Models for Multi-Modal Medical Image Analysis](https://mlsanity.com/paper/2509.06617/) (2025)
- [Decipher-MR: A Vision-Language Foundation Model for 3D MRI Representations](https://mlsanity.com/paper/2509.21249/) (2025)

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

- [OrganLens: Organ-Specific Representation Learning for CT Foundation Models](https://mlsanity.com/paper/2607.25164/) (2026)

## Abstract (arXiv)

Foundation models (FMs) have shown great promise in medical imaging, but most FMs are trained on unimodal data within isolated domains, such as brain MRI alone. Human aging and disease arise through coordinated biological processes across organs, therefore motivating multimodal FMs that learn whole-body representations. A key challenge, however, is that real-world multimodal biomedical data are often missing not at random, which can reduce power, limit generalizability, and introduce bias. We propose Pan-FM, a pan-organ foundation model pre-trained on imaging from seven organs (Brain, Heart, Adipose, Liver, Kidney, Spleen, and Pancreas) under realistic missing-organ scenarios. Pan-FM uses a unified backbone that handles organ missingness during both training and inference, and is pre-trained with masking-based self-distillation. We find that naive multimodal pre-training leads to dominant-organ shortcut learning bias, with the model over-relying on dominant organs such as adipose and heart. To address this, we introduce Saliency-Guided Masking (SGM), which uses the model attention distribution to adaptively mask dominant organs during pre-training, thus encouraging more balanced cross-organ, whole-body learning. Notably, SGM introduces negligible computational overhead and can be seamlessly integrated into existing self-supervised learning frameworks to improve multi-organ representation learning. On the UK Biobank, Pan-FM achieves stronger prediction across 13 disease categories and 14 single disease entities than single-organ and multi-organ baselines, with improved robustness under missing-organ settings. Pan-FM serves as a scalable solution to realistic modality-missingness in multimodal learning in system neuroscience and as a step toward more generalizable whole-body FMs.