# ModAn-MulSupCon: Modality-and Anatomy-Aware Multi-Label Supervised Contrastive Pretraining for Medical Imaging

arXiv: https://arxiv.org/abs/2508.18613 · HTML: https://mlsanity.com/paper/2508.18613/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 23 of its 45 references that are in the map.
- First posted on arXiv 26 Aug 2025.

## Builds on (most cited first, 23 of 23)

- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Representation Learning with Contrastive Predictive Coding](https://mlsanity.com/paper/1807.03748/) (2018)
- [Momentum Contrast for Unsupervised Visual Representation Learning](https://mlsanity.com/paper/1911.05722/) (2019)
- [UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction](https://mlsanity.com/paper/1802.03426/) (2018)
- [Supervised Contrastive Learning](https://mlsanity.com/paper/2004.11362/) (2020)
- [CheXpert: A Large Chest Radiograph Dataset with Uncertainty Labels and Expert Comparison](https://mlsanity.com/paper/1901.07031/) (2019)
- [Self-Supervised Pre-Training of Swin Transformers for 3D Medical Image Analysis](https://mlsanity.com/paper/2111.14791/) (2021)
- [Making the Most of Text Semantics to Improve Biomedical Vision--Language Processing](https://mlsanity.com/paper/2204.09817/) (2022)
- [Multi-Label Image Recognition with Graph Convolutional Networks](https://mlsanity.com/paper/1904.03582/) (2019)
- [CNN-RNN: A Unified Framework for Multi-label Image Classification](https://mlsanity.com/paper/1604.04573/) (2016)
- [AttentionXML: Label Tree-based Attention-Aware Deep Model for High-Performance Extreme Multi-Label Text Classification](https://mlsanity.com/paper/1811.01727/) (2018)
- [Learning Spatial Regularization with Image-level Supervisions for Multi-label Image Classification](https://mlsanity.com/paper/1702.05891/) (2017)
- [Self Pre-training with Masked Autoencoders for Medical Image Classification and Segmentation](https://mlsanity.com/paper/2203.05573/) (2022)
- [Use All The Labels: A Hierarchical Multi-Label Contrastive Learning Framework](https://mlsanity.com/paper/2204.13207/) (2022)
- [ImageGCN: Multi-Relational Image Graph Convolutional Networks for Disease Identification with Chest X-rays](https://mlsanity.com/paper/1904.00325/) (2019)
- [Advancing Volumetric Medical Image Segmentation via Global-Local Masked Autoencoder](https://mlsanity.com/paper/2306.08913/) (2023)
- [MiM: Mask in Mask Self-Supervised Pre-Training for 3D Medical Image Analysis](https://mlsanity.com/paper/2404.15580/) (2024)
- [Swin MAE: Masked Autoencoders for Small Datasets](https://mlsanity.com/paper/2212.13805/) (2022)
- [Distributed Contrastive Learning for Medical Image Segmentation](https://mlsanity.com/paper/2208.03808/) (2022)
- [SCALP -- Supervised Contrastive Learning for Cardiopulmonary Disease Classification and Localization in Chest X-rays using Patient Metadata](https://mlsanity.com/paper/2110.14787/) (2021)
- [HEX: Hierarchical Emergence Exploitation in Self-Supervised Algorithms](https://mlsanity.com/paper/2410.23200/) (2024)
- [Hypergraph Tversky-Aware Domain Incremental Learning for Brain Tumor Segmentation with Missing Modalities](https://mlsanity.com/paper/2505.16809/) (2025)
- [VIS-MAE: An Efficient Self-supervised Learning Approach on Medical Image Segmentation and Classification](https://mlsanity.com/paper/2402.01034/) (2024)

## Abstract (arXiv)

Background and objective: Expert annotations limit large-scale supervised pretraining in medical imaging, while ubiquitous metadata (modality, anatomical region) remain underused. We introduce ModAn-MulSupCon, a modality- and anatomy-aware multi-label supervised contrastive pretraining method that leverages such metadata to learn transferable representations. Method: Each image's modality and anatomy are encoded as a multi-hot vector. A ResNet-18 encoder is pretrained on a mini subset of RadImageNet (miniRIN, 16,222 images) with a Jaccard-weighted multi-label supervised contrastive loss, and then evaluated by fine-tuning and linear probing on three binary classification tasks--ACL tear (knee MRI), lesion malignancy (breast ultrasound), and nodule malignancy (thyroid ultrasound). Result: With fine-tuning, ModAn-MulSupCon achieved the best AUC on MRNet-ACL (0.964) and Thyroid (0.763), surpassing all baselines (p<0.05), and ranked second on Breast (0.926) behind SimCLR (0.940; not significant). With the encoder frozen, SimCLR/ImageNet were superior, indicating that ModAn-MulSupCon representations benefit most from task adaptation rather than linear separability. Conclusion: Encoding readily available modality/anatomy metadata as multi-label targets provides a practical, scalable pretraining signal that improves downstream accuracy when fine-tuning is feasible. ModAn-MulSupCon is a strong initialization for label-scarce clinical settings, whereas SimCLR/ImageNet remain preferable for frozen-encoder deployments.