# Topology-Driven Transferability Estimation for 3D Medical Vision Foundation Models

arXiv: https://arxiv.org/abs/2607.04199 · HTML: https://mlsanity.com/paper/2607.04199/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 37 of its 51 references that are in the map.
- First posted on arXiv 5 Jul 2026.

## Builds on (most cited first, 30 of 37)

- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [Delving Deep into Rectifiers: Surpassing Human-Level Performance on ImageNet Classification](https://mlsanity.com/paper/1502.01852/) (2015)
- [DINOv3](https://mlsanity.com/paper/2508.10104/) (2025)
- [Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images](https://mlsanity.com/paper/2201.01266/) (2022)
- [Self-Supervised Pre-Training of Swin Transformers for 3D Medical Image Analysis](https://mlsanity.com/paper/2111.14791/) (2021)
- [AMOS: A Large-Scale Abdominal Multi-Organ Benchmark for Versatile Medical Image Segmentation](https://mlsanity.com/paper/2206.08023/) (2022)
- [nnU-Net Revisited: A Call for Rigorous Validation in 3D Medical Image Segmentation](https://mlsanity.com/paper/2404.09556/) (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)
- [LEEP: A New Measure to Evaluate Transferability of Learned Representations](https://mlsanity.com/paper/2002.12462/) (2020)
- [LogME: Practical Assessment of Pre-trained Models for Transfer Learning](https://mlsanity.com/paper/2102.11005/) (2021)
- [Exploring scalable medical image encoders beyond text supervision](https://mlsanity.com/paper/2401.10815/) (2024)
- [Transferability and Hardness of Supervised Classification Tasks](https://mlsanity.com/paper/1908.08142/) (2019)
- [ISLES 2022: A multi-center magnetic resonance imaging stroke lesion segmentation dataset](https://mlsanity.com/paper/2206.06694/) (2022)
- [An Information-Theoretic Approach to Transferability in Task Transfer Learning](https://mlsanity.com/paper/2212.10082/) (2022)
- [VoCo: A Simple-yet-Effective Volume Contrastive Learning Framework for 3D Medical Image Analysis](https://mlsanity.com/paper/2402.17300/) (2024)
- [Phikon-v2, A large and public feature extractor for biomarker prediction](https://mlsanity.com/paper/2409.09173/) (2024)
- [Masked Image Modeling Advances 3D Medical Image Analysis](https://mlsanity.com/paper/2204.11716/) (2022)
- [Delving into Masked Autoencoders for Multi-Label Thorax Disease Classification](https://mlsanity.com/paper/2210.12843/) (2022)
- [VISTA3D: A Unified Segmentation Foundation Model For 3D Medical Imaging](https://mlsanity.com/paper/2406.05285/) (2024)
- [OTCE: A Transferability Metric for Cross-Domain Cross-Task Representations](https://mlsanity.com/paper/2103.13843/) (2021)
- [LVM-Med: Learning Large-Scale Self-Supervised Vision Models for Medical Imaging via Second-order Graph Matching](https://mlsanity.com/paper/2306.11925/) (2023)
- [Transferability Estimation using Bhattacharyya Class Separability](https://mlsanity.com/paper/2111.12780/) (2021)
- [Ranking Neural Checkpoints](https://mlsanity.com/paper/2011.11200/) (2020)
- [Green Hierarchical Vision Transformer for Masked Image Modeling](https://mlsanity.com/paper/2205.13515/) (2022)
- [Frustratingly Easy Transferability Estimation](https://mlsanity.com/paper/2106.09362/) (2021)
- [A Weighted Correlation Index for Rankings with Ties](https://mlsanity.com/paper/1404.3325/) (2014)
- [Scalable Diverse Model Selection for Accessible Transfer Learning](https://mlsanity.com/paper/2111.06977/) (2021)
- [Deep Learning Enables Automatic Detection and Segmentation of Brain Metastases on Multi-Sequence MRI](https://mlsanity.com/paper/1903.07988/) (2019)
- [PACTran: PAC-Bayesian Metrics for Estimating the Transferability of Pretrained Models to Classification Tasks](https://mlsanity.com/paper/2203.05126/) (2022)

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

- [Benchmarking Self-Supervised 3D Medical Vision Foundation Models and Transferability Estimation](https://mlsanity.com/paper/2610.17573/) (2026)

## Abstract (arXiv)

The growing number of medical vision foundation models highlights the need for effective model selection. However, mainstream selection methods rely on exhaustive fine-tuning, which is computationally expensive. Most of the existing Transferability Estimation (TE) metrics are primarily designed for image-level classification. They fail to preserve spatial relationships and fine-grained boundary details, which are crucial for the segmentation task. Additionally, while image-level tasks typically process a single feature vector per input, dense prediction tasks in 3D medical imaging require voxel-wise evaluation against dense annotations. To bridge these gaps, we propose a textitnon-parametric, topology-driven framework that estimates transferability directly from the alignment between the sparse 1-skeleton graph of dense features and semantic labels via Minimum Spanning Trees (MST). We decouple the alignment into two complementary geometric scales: Local Boundary-Aware Topological Consistency (LBTC) to assess boundary separability, where we prove that the MST leakage rate serves as a finite-sample lower bound on the Bayes error; and Global Representation Topology Divergence (GRTD) to evaluate the overall anatomical layout. Crucially, we formally justify a counterintuitive mechanism: Although without fine-tuning, the randomly initialized segmentation decoder acts as a topology-preserving spatial projector, reducing the variance of pairwise distance estimates and stabilizing global alignment evaluation. Fused via a task-adaptive gating mechanism, these dual metrics adapt to diverse clinical complexities. Evaluated on a large-scale benchmark of 114,000 3D medical volumes across diverse anatomical tasks, our topological framework achieves state-of-the-art transferability estimation with an average weighted Kendall (outperforming by 0.36) while accelerating evaluation by 56 times.