# MedSeqFT: Sequential Fine-tuning Foundation Models for 3D Medical Image Segmentation

arXiv: https://arxiv.org/abs/2509.06096 · HTML: https://mlsanity.com/paper/2509.06096/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 34 of its 46 references that are in the map.
- First posted on arXiv 7 Sep 2025.

## Builds on (most cited first, 30 of 34)

- [LoRA: Low-Rank Adaptation of Large Language Models](https://mlsanity.com/paper/2106.09685/) (2021)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [Parameter-Efficient Transfer Learning for NLP](https://mlsanity.com/paper/1902.00751/) (2019)
- [Visualizing the Loss Landscape of Neural Nets](https://mlsanity.com/paper/1712.09913/) (2017)
- [The Medical Segmentation Decathlon](https://mlsanity.com/paper/2106.05735/) (2021)
- [The Liver Tumor Segmentation Benchmark (LiTS)](https://mlsanity.com/paper/1901.04056/) (2019)
- [Self-Supervised Pre-Training of Swin Transformers for 3D Medical Image Analysis](https://mlsanity.com/paper/2111.14791/) (2021)
- [Medical Image Segmentation Review: The success of U-Net](https://mlsanity.com/paper/2211.14830/) (2022)
- [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)
- [Uni-Perceiver: Pre-training Unified Architecture for Generic Perception for Zero-shot and Few-shot Tasks](https://mlsanity.com/paper/2112.01522/) (2021)
- [HydraLoRA: An Asymmetric LoRA Architecture for Efficient Fine-Tuning](https://mlsanity.com/paper/2404.19245/) (2024)
- [Standardized Assessment of Automatic Segmentation of White Matter Hyperintensities and Results of the WMH Segmentation Challenge](https://mlsanity.com/paper/1904.00682/) (2019)
- [ISLES 2022: A multi-center magnetic resonance imaging stroke lesion segmentation dataset](https://mlsanity.com/paper/2206.06694/) (2022)
- [DoDNet: Learning to segment multi-organ and tumors from multiple partially labeled datasets](https://mlsanity.com/paper/2011.10217/) (2020)
- [Conv-Adapter: Exploring Parameter Efficient Transfer Learning for ConvNets](https://mlsanity.com/paper/2208.07463/) (2022)
- [DiRA: Discriminative, Restorative, and Adversarial Learning for Self-supervised Medical Image Analysis](https://mlsanity.com/paper/2204.10437/) (2022)
- [UniSeg: A Prompt-driven Universal Segmentation Model as well as A Strong Representation Learner](https://mlsanity.com/paper/2304.03493/) (2023)
- [MTLoRA: A Low-Rank Adaptation Approach for Efficient Multi-Task Learning](https://mlsanity.com/paper/2403.20320/) (2024)
- [Geometric Visual Similarity Learning in 3D Medical Image Self-supervised Pre-training](https://mlsanity.com/paper/2303.00874/) (2023)
- [Large-Scale 3D Medical Image Pre-training with Geometric Context Priors](https://mlsanity.com/paper/2410.09890/) (2024)
- [Efficient Adaptation of Large Vision Transformer via Adapter Re-Composing](https://mlsanity.com/paper/2310.06234/) (2023)
- [Continual Self-supervised Learning: Towards Universal Multi-modal Medical Data Representation Learning](https://mlsanity.com/paper/2311.17597/) (2023)
- [5%>100%: Breaking Performance Shackles of Full Fine-Tuning on Visual Recognition Tasks](https://mlsanity.com/paper/2408.08345/) (2024)
- [Training Like a Medical Resident: Context-Prior Learning Toward Universal Medical Image Segmentation](https://mlsanity.com/paper/2306.02416/) (2023)
- [AlignDet: Aligning Pre-training and Fine-tuning in Object Detection](https://mlsanity.com/paper/2307.11077/) (2023)
- [Efficient Conditional Pre-training for Transfer Learning](https://mlsanity.com/paper/2011.10231/) (2020)
- [Fine-grained Prompt Tuning: A Parameter and Memory Efficient Transfer Learning Method for High-resolution Medical Image Classification](https://mlsanity.com/paper/2403.07576/) (2024)
- [MedUniSeg: 2D and 3D Medical Image Segmentation via a Prompt-driven Universal Model](https://mlsanity.com/paper/2410.05905/) (2024)
- [DiTASK: Multi-Task Fine-Tuning with Diffeomorphic Transformations](https://mlsanity.com/paper/2502.06029/) (2025)
- [SG-MIM: Structured Knowledge Guided Efficient Pre-training for Dense Prediction](https://mlsanity.com/paper/2409.02513/) (2024)

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

- [C^2GR: Coupled Comprehensive Generative Replay for a Continually Learnable Universal Segmentation Model](https://mlsanity.com/paper/2606.23473/) (2026)

## Abstract (arXiv)

Foundation models have become a promising paradigm for advancing medical image analysis, particularly for segmentation tasks where downstream applications often emerge sequentially. Existing fine-tuning strategies, however, remain limited: parallel fine-tuning isolates tasks and fails to exploit shared knowledge, while multi-task fine-tuning requires simultaneous access to all datasets and struggles with incremental task integration. To address these challenges, we propose MedSeqFT, a sequential fine-tuning framework that progressively adapts pre-trained models to new tasks while refining their representational capacity. MedSeqFT introduces two core components: (1) Maximum Data Similarity (MDS) selection, which identifies downstream samples most representative of the original pre-training distribution to preserve general knowledge, and (2) Knowledge and Generalization Retention Fine-Tuning (K&G RFT), a LoRA-based knowledge distillation scheme that balances task-specific adaptation with the retention of pre-trained knowledge. Extensive experiments on two multi-task datasets covering ten 3D segmentation tasks demonstrate that MedSeqFT consistently outperforms state-of-the-art fine-tuning strategies, yielding substantial performance gains (e.g., an average Dice improvement of 3.0%). Furthermore, evaluations on two unseen tasks (COVID-19-20 and Kidney) verify that MedSeqFT enhances transferability, particularly for tumor segmentation. Visual analyses of loss landscapes and parameter variations further highlight the robustness of MedSeqFT. These results establish sequential fine-tuning as an effective, knowledge-retentive paradigm for adapting foundation models to evolving clinical tasks. Code will be released.