# SAM Meets VLM: Parameter-Decoupled Full-Parameter Training for Unified Medical Reasoning and Segmentation

arXiv: https://arxiv.org/abs/2609.37283 · HTML: https://mlsanity.com/paper/2609.37283/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Clinical and biomedical applications, one of 17 directions in LLM reasoning.
- Builds on 28 of its 91 references that are in the map.
- First posted on arXiv 29 Sep 2026.

## Placed in

- LLM reasoning / [Clinical and biomedical applications](https://mlsanity.com/lr/clinical-and-biomedical-applications/)
- Multimodal LLMs / vision-language models / [Medical vision-language models](https://mlsanity.com/mllm/medical-vision-language-models/)

## Builds on (most cited first, 28 of 28)

- [Qwen2.5-VL Technical Report](https://mlsanity.com/paper/2502.13923/) (2025)
- [Improved Baselines with Visual Instruction Tuning](https://mlsanity.com/paper/2310.03744/) (2023)
- [SAM 2: Segment Anything in Images and Videos](https://mlsanity.com/paper/2408.00714/) (2024)
- [FlashAttention-2: Faster Attention with Better Parallelism and Work Partitioning](https://mlsanity.com/paper/2307.08691/) (2023)
- [OK-VQA: A Visual Question Answering Benchmark Requiring External Knowledge](https://mlsanity.com/paper/1906.00067/) (2019)
- [A-OKVQA: A Benchmark for Visual Question Answering using World Knowledge](https://mlsanity.com/paper/2206.01718/) (2022)
- [MedGemma Technical Report](https://mlsanity.com/paper/2507.05201/) (2025)
- [PMC-VQA: Visual Instruction Tuning for Medical Visual Question Answering](https://mlsanity.com/paper/2305.10415/) (2023)
- [Molmo and PixMo: Open Weights and Open Data for State-of-the-Art Vision-Language Models](https://mlsanity.com/paper/2409.17146/) (2024)
- [ChatDoctor: A Medical Chat Model Fine-Tuned on a Large Language Model Meta-AI (LLaMA) Using Medical Domain Knowledge](https://mlsanity.com/paper/2303.14070/) (2023)
- [HuatuoGPT-o1, Towards Medical Complex Reasoning with LLMs](https://mlsanity.com/paper/2412.18925/) (2024)
- [Lingshu: A Generalist Foundation Model for Unified Multimodal Medical Understanding and Reasoning](https://mlsanity.com/paper/2506.07044/) (2025)
- [MedXpertQA: Benchmarking Expert-Level Medical Reasoning and Understanding](https://mlsanity.com/paper/2501.18362/) (2025)
- [PMC-CLIP: Contrastive Language-Image Pre-training using Biomedical Documents](https://mlsanity.com/paper/2303.07240/) (2023)
- [ALLaVA: Harnessing GPT4V-Synthesized Data for Lite Vision-Language Models](https://mlsanity.com/paper/2402.11684/) (2024)
- [HuatuoGPT-Vision, Towards Injecting Medical Visual Knowledge into Multimodal LLMs at Scale](https://mlsanity.com/paper/2406.19280/) (2024)
- [MedReason: Eliciting Factual Medical Reasoning Steps in LLMs via Knowledge Graphs](https://mlsanity.com/paper/2504.00993/) (2025)
- [CheXpert Plus: Augmenting a Large Chest X-ray Dataset with Text Radiology Reports, Patient Demographics and Additional Image Formats](https://mlsanity.com/paper/2405.19538/) (2024)
- [MosMedData: Chest CT Scans With COVID-19 Related Findings Dataset](https://mlsanity.com/paper/2005.06465/) (2020)
- [HuatuoGPT-II, One-stage Training for Medical Adaption of LLMs](https://mlsanity.com/paper/2311.09774/) (2023)
- [AlpaCare:Instruction-tuned Large Language Models for Medical Application](https://mlsanity.com/paper/2310.14558/) (2023)
- [PMC-LLaMA: Towards Building Open-source Language Models for Medicine](https://mlsanity.com/paper/2304.14454/) (2023)
- [DenseNet: Implementing Efficient ConvNet Descriptor Pyramids](https://mlsanity.com/paper/1404.1869/) (2014)
- [SA-Med2D-20M Dataset: Segment Anything in 2D Medical Imaging with 20 Million masks](https://mlsanity.com/paper/2311.11969/) (2023)
- [Towards a Multimodal Large Language Model with Pixel-Level Insight for Biomedicine](https://mlsanity.com/paper/2412.09278/) (2024)
- [MedGround-R1: Advancing Medical Image Grounding via Spatial-Semantic Rewarded Group Relative Policy Optimization](https://mlsanity.com/paper/2507.02994/) (2025)
- [Citrus: Leveraging Expert Cognitive Pathways in a Medical Language Model for Advanced Medical Decision Support](https://mlsanity.com/paper/2502.18274/) (2025)
- [Citrus-V: Advancing Medical Foundation Models with Unified Medical Image Grounding for Clinical Reasoning](https://mlsanity.com/paper/2509.19090/) (2025)

## Abstract (arXiv)

Medical multimodal large language models (MLLMs) are increasingly expected not only to answer clinical questions, but also to localize the visual evidence behind their predictions. A common strategy connects a vision--language model (VLM) with SAM-style segmentation through a special <SEG> token, yet full-parameter training of this unified architecture is difficult because image-level reasoning and pixel-level segmentation impose different requirements on the shared representation space. To address this issue, we propose a parameter-decoupled training framework for unified medical reasoning and segmentation. The framework treats the <SEG> hidden state as a semantic-to-spatial prompt for the mask decoder and encourages it to become separable from generic language states, reducing ambiguous segmentation prompts and potential disruption to reasoning representations. It first performs medical shallow alignment to adapt visual features to clinical language without disturbing the LLM; then controlled instruction tuning shapes separable <SEG> prompt states, monitored by the Davies--Bouldin Index (DBI), while scaling segmentation gradients entering the language backbone; finally, the SAM branch is specialized with the VLM frozen to improve mask precision without altering reasoning parameters. Experiments on medical referring segmentation, grounding, visual QA, and textual QA benchmarks show that our framework achieves strong language-conditioned segmentation while preserving competitive reasoning ability. Ablations show that two-phase instruction tuning, gradient scaling, and segmentation specialization all contribute to the model.