# TubeMLLM: A Foundation Model for Topology Knowledge Exploration in Vessel-like Anatomy

arXiv: https://arxiv.org/abs/2603.09217 · HTML: https://mlsanity.com/paper/2603.09217/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 37 of its 57 references that are in the map.
- First posted on arXiv 10 Mar 2026.

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

- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
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- [SigLIP 2: Multilingual Vision-Language Encoders with Improved Semantic Understanding, Localization, and Dense Features](https://mlsanity.com/paper/2502.14786/) (2025)
- [A Survey on Deep Learning in Medical Image Analysis](https://mlsanity.com/paper/1702.05747/) (2017)
- [SAM 3: Segment Anything with Concepts](https://mlsanity.com/paper/2511.16719/) (2025)
- [Emerging Properties in Unified Multimodal Pretraining](https://mlsanity.com/paper/2505.14683/) (2025)
- [Emu3: Next-Token Prediction is All You Need](https://mlsanity.com/paper/2409.18869/) (2024)
- [LISA: Reasoning Segmentation via Large Language Model](https://mlsanity.com/paper/2308.00692/) (2023)
- [Segment Everything Everywhere All at Once](https://mlsanity.com/paper/2304.06718/) (2023)
- [Domain Adaptation for Medical Image Analysis: A Survey](https://mlsanity.com/paper/2102.09508/) (2021)
- [clDice -- A Novel Topology-Preserving Loss Function for Tubular Structure Segmentation](https://mlsanity.com/paper/2003.07311/) (2020)
- [nnU-Net Revisited: A Call for Rigorous Validation in 3D Medical Image Segmentation](https://mlsanity.com/paper/2404.09556/) (2024)
- [MetaMorph: Multimodal Understanding and Generation via Instruction Tuning](https://mlsanity.com/paper/2412.14164/) (2024)
- [Topology-Preserving Deep Image Segmentation](https://mlsanity.com/paper/1906.05404/) (2019)
- [Mixture-of-Transformers: A Sparse and Scalable Architecture for Multi-Modal Foundation Models](https://mlsanity.com/paper/2411.04996/) (2024)
- [A Topological Loss Function for Deep-Learning based Image Segmentation using Persistent Homology](https://mlsanity.com/paper/1910.01877/) (2019)
- [BiomedParse: a biomedical foundation model for image parsing of everything everywhere all at once](https://mlsanity.com/paper/2405.12971/) (2024)
- [MedSAM2: Segment Anything in 3D Medical Images and Videos](https://mlsanity.com/paper/2504.03600/) (2025)
- [Topology-Aware Segmentation Using Discrete Morse Theory](https://mlsanity.com/paper/2103.09992/) (2021)
- [Large-Vocabulary Segmentation for Medical Images with Text Prompts](https://mlsanity.com/paper/2312.17183/) (2023)
- [Topologically faithful image segmentation via induced matching of persistence barcodes](https://mlsanity.com/paper/2211.15272/) (2022)
- [Skeleton Recall Loss for Connectivity Conserving and Resource Efficient Segmentation of Thin Tubular Structures](https://mlsanity.com/paper/2404.03010/) (2024)
- [Towards a glaucoma risk index based on simulated hemodynamics from fundus images](https://mlsanity.com/paper/1805.10273/) (2018)
- [Centerline Boundary Dice Loss for Vascular Segmentation](https://mlsanity.com/paper/2407.01517/) (2024)
- [MedSAM3: Delving into Segment Anything with Medical Concepts](https://mlsanity.com/paper/2511.19046/) (2025)
- [Medical SAM3: A Foundation Model for Universal Prompt-Driven Medical Image Segmentation](https://mlsanity.com/paper/2601.10880/) (2026)
- [VoxTell: Free-Text Promptable Universal 3D Medical Image Segmentation](https://mlsanity.com/paper/2511.11450/) (2025)

## Abstract (arXiv)

Modeling medical vessel-like anatomy is challenging due to its intricate topology and sensitivity to dataset shifts. Consequently, task-specific models often suffer from topological inconsistencies, including artificial disconnections and spurious merges. Motivated by the promise of multimodal large language models (MLLMs) for zero-shot generalization, we propose TubeMLLM, a unified foundation model that couples structured understanding with controllable generation for medical vessel-like anatomy. By integrating topological priors through explicit natural language prompting and aligning them with visual representations in a shared-attention architecture, TubeMLLM significantly enhances topology-aware perception. Furthermore, we construct TubeMData, a pionner multimodal benchmark comprising comprehensive topology-centric tasks, and introduce an adaptive loss weighting strategy to emphasize topology-critical regions during training. Extensive experiments on fifteen diverse datasets demonstrate our superiority. Quantitatively, TubeMLLM achieves state-of-the-art out-of-distribution performance, substantially reducing global topological discrepancies on color fundus photography (decreasing the β0 number error from 37.42 to 8.58 compared to baselines). Notably, TubeMLLM exhibits exceptional zero-shot cross-modality transferring ability on unseen X-ray angiography, achieving a Dice score of 67.50% while significantly reducing the β0 error to 1.21. TubeMLLM also maintains robustness against degradations such as blur, noise, and low resolution. Furthermore, in topology-aware understanding tasks, the model achieves 97.38% accuracy in evaluating mask topological quality, significantly outperforming standard vision-language baselines.