Yiwen Ye

Yiwen Ye, Yutong Xie, Jianpeng Zhang et al.

The universal model emerges as a promising trend for medical image segmentation, paving up the way to build medical imaging large model (MILM). One popular strategy to build universal models is to encode each task as a one-hot vector and generate dynamic convolutional layers at the end of the decoder to extract the interested target. Although successful, it ignores the correlations among tasks and meanwhile is too late to make the model 'aware' of the ongoing task. To address both issues, we propose a prompt-driven Universal Segmentation model (UniSeg) for multi-task medical image segmentation using diverse modalities and domains. We first devise a learnable universal prompt to describe the correlations among all tasks and then convert this prompt and image features into a task-specific prompt, which is fed to the decoder as a part of its input. Thus, we make the model 'aware' of the ongoing task early and boost the task-specific training of the whole decoder. Our results indicate that the proposed UniSeg outperforms other universal models and single-task models on 11 upstream tasks. Moreover, UniSeg also beats other pre-trained models on two downstream datasets, providing the community with a high-quality pre-trained model for 3D medical image segmentation. Code and model are available at https://github.com/yeerwen/UniSeg.

Yiwen Ye, Yutong Xie, Jianpeng Zhang et al.

Self-supervised learning is an efficient pre-training method for medical image analysis. However, current research is mostly confined to specific-modality data pre-training, consuming considerable time and resources without achieving universality across different modalities. A straightforward solution is combining all modality data for joint self-supervised pre-training, which poses practical challenges. Firstly, our experiments reveal conflicts in representation learning as the number of modalities increases. Secondly, multi-modal data collected in advance cannot cover all real-world scenarios. In this paper, we reconsider versatile self-supervised learning from the perspective of continual learning and propose MedCoSS, a continuous self-supervised learning approach for multi-modal medical data. Unlike joint self-supervised learning, MedCoSS assigns different modality data to different training stages, forming a multi-stage pre-training process. To balance modal conflicts and prevent catastrophic forgetting, we propose a rehearsal-based continual learning method. We introduce the k-means sampling strategy to retain data from previous modalities and rehearse it when learning new modalities. Instead of executing the pretext task on buffer data, a feature distillation strategy and an intra-modal mixup strategy are applied to these data for knowledge retention. We conduct continuous self-supervised pre-training on a large-scale multi-modal unlabeled dataset, including clinical reports, X-rays, CT scans, MRI scans, and pathological images. Experimental results demonstrate MedCoSS's exceptional generalization ability across nine downstream datasets and its significant scalability in integrating new modality data. Code and pre-trained weight are available at https://github.com/yeerwen/MedCoSS.

Ziyang Chen, Yongsheng Pan, Yiwen Ye et al.

Distribution shift widely exists in medical images acquired from different medical centres and poses a significant obstacle to deploying the pre-trained semantic segmentation model in real-world applications. Test-time adaptation has proven its effectiveness in tackling the cross-domain distribution shift during inference. However, most existing methods achieve adaptation by updating the pre-trained models, rendering them susceptible to error accumulation and catastrophic forgetting when encountering a series of distribution shifts (i.e., under the continual test-time adaptation setup). To overcome these challenges caused by updating the models, in this paper, we freeze the pre-trained model and propose the Visual Prompt-based Test-Time Adaptation (VPTTA) method to train a specific prompt for each test image to align the statistics in the batch normalization layers. Specifically, we present the low-frequency prompt, which is lightweight with only a few parameters and can be effectively trained in a single iteration. To enhance prompt initialization, we equip VPTTA with a memory bank to benefit the current prompt from previous ones. Additionally, we design a warm-up mechanism, which mixes source and target statistics to construct warm-up statistics, thereby facilitating the training process. Extensive experiments demonstrate the superiority of our VPTTA over other state-of-the-art methods on two medical image segmentation benchmark tasks. The code and weights of pre-trained source models are available at https://github.com/Chen-Ziyang/VPTTA.

Ziyang Chen, Yiwen Ye, Yongsheng Pan et al.

Although recent years have witnessed significant advancements in medical image segmentation, the pervasive issue of domain shift among medical images from diverse centres hinders the effective deployment of pre-trained models. Many Test-time Adaptation (TTA) methods have been proposed to address this issue by fine-tuning pre-trained models with test data during inference. These methods, however, often suffer from less-satisfactory optimization due to suboptimal optimization direction (dictated by the gradient) and fixed step-size (predicated on the learning rate). In this paper, we propose the Gradient alignment-based Test-time adaptation (GraTa) method to improve both the gradient direction and learning rate in the optimization procedure. Unlike conventional TTA methods, which primarily optimize the pseudo gradient derived from a self-supervised objective, our method incorporates an auxiliary gradient with the pseudo one to facilitate gradient alignment. Such gradient alignment enables the model to excavate the similarities between different gradients and correct the gradient direction to approximate the empirical gradient related to the current segmentation task. Additionally, we design a dynamic learning rate based on the cosine similarity between the pseudo and auxiliary gradients, thereby empowering the adaptive fine-tuning of pre-trained models on diverse test data. Extensive experiments establish the effectiveness of the proposed gradient alignment and dynamic learning rate and substantiate the superiority of our GraTa method over other state-of-the-art TTA methods on a benchmark medical image segmentation task. The code and weights of pre-trained source models are available at https://github.com/Chen-Ziyang/GraTa.

Shishuai Hu, Yiwen Ye, Zehui Liao et al.

Kidney structures segmentation is a crucial yet challenging task in the computer-aided diagnosis of surgery-based renal cancer. Although numerous deep learning models have achieved remarkable success in many medical image segmentation tasks, accurate segmentation of kidney structures on computed tomography angiography (CTA) images remains challenging, due to the variable sizes of kidney tumors and the ambiguous boundaries between kidney structures and their surroundings. In this paper, we propose a boundary-aware network (BA-Net) to segment kidneys, kidney tumors, arteries, and veins on CTA scans. This model contains a shared encoder, a boundary decoder, and a segmentation decoder. The multi-scale deep supervision strategy is adopted on both decoders, which can alleviate the issues caused by variable tumor sizes. The boundary probability maps produced by the boundary decoder at each scale are used as attention to enhance the segmentation feature maps. We evaluated the BA-Net on the Kidney PArsing (KiPA) Challenge dataset and achieved an average Dice score of 89.65$\%$ for kidney structure segmentation on CTA scans using 4-fold cross-validation. The results demonstrate the effectiveness of the BA-Net.

Jia Fu, Litingyu Wang, He Li et al.

Accurate delineation of Gross Tumor Volume (GTV), Lymph Node Clinical Target Volume (LN CTV), and Organ-at-Risk (OAR) from Computed Tomography (CT) scans is essential for precise radiotherapy planning in Nasopharyngeal Carcinoma (NPC). Building upon SegRap2023, which focused on OAR and GTV segmentation using single-center paired non-contrast CT (ncCT) and contrast-enhanced CT (ceCT) scans, the SegRap2025 challenge aims to enhance the generalizability and robustness of segmentation models across imaging centers and modalities. SegRap2025 comprises two tasks: Task01 addresses GTV segmentation using paired CT from the SegRap2023 dataset, with an additional external testing set to evaluate cross-center generalization, and Task02 focuses on LN CTV segmentation using multi-center training data and an unseen external testing set, where each case contains paired CT scans or a single modality, emphasizing both cross-center and cross-modality robustness. This paper presents the challenge setup and provides a comprehensive analysis of the solutions submitted by ten participating teams. For GTV segmentation task, the top-performing models achieved average Dice Similarity Coefficient (DSC) of 74.61% and 56.79% on the internal and external testing cohorts, respectively. For LN CTV segmentation task, the highest average DSC values reached 60.24%, 60.50%, and 57.23% on paired CT, ceCT-only, and ncCT-only subsets, respectively. SegRap2025 establishes a large-scale multi-center, multi-modality benchmark for evaluating the generalization and robustness in radiotherapy target segmentation, providing valuable insights toward clinically applicable automated radiotherapy planning systems. The benchmark is available at: https://hilab-git.github.io/SegRap2025_Challenge.

Pedro R. A. S. Bassi, Wenxuan Li, Yucheng Tang et al.

How can we test AI performance? This question seems trivial, but it isn't. Standard benchmarks often have problems such as in-distribution and small-size test sets, oversimplified metrics, unfair comparisons, and short-term outcome pressure. As a consequence, good performance on standard benchmarks does not guarantee success in real-world scenarios. To address these problems, we present Touchstone, a large-scale collaborative segmentation benchmark of 9 types of abdominal organs. This benchmark is based on 5,195 training CT scans from 76 hospitals around the world and 5,903 testing CT scans from 11 additional hospitals. This diverse test set enhances the statistical significance of benchmark results and rigorously evaluates AI algorithms across various out-of-distribution scenarios. We invited 14 inventors of 19 AI algorithms to train their algorithms, while our team, as a third party, independently evaluated these algorithms on three test sets. In addition, we also evaluated pre-existing AI frameworks--which, differing from algorithms, are more flexible and can support different algorithms--including MONAI from NVIDIA, nnU-Net from DKFZ, and numerous other open-source frameworks. We are committed to expanding this benchmark to encourage more innovation of AI algorithms for the medical domain.

Zhisong Wang, Yiwen Ye, Ziyang Chen et al.

Scribble-based weakly supervised segmentation methods have shown promising results in medical image segmentation, significantly reducing annotation costs. However, existing approaches often rely on auxiliary tasks to enforce semantic consistency and use hard pseudo labels for supervision, overlooking the unique challenges faced by models trained with sparse annotations. These models must predict pixel-wise segmentation maps from limited data, making it crucial to handle varying levels of annotation richness effectively. In this paper, we propose MaCo, a weakly supervised model designed for medical image segmentation, based on the principle of "from few to more." MaCo leverages Masked Context Modeling (MCM) and Continuous Pseudo Labels (CPL). MCM employs an attention-based masking strategy to perturb the input image, ensuring that the model's predictions align with those of the original image. CPL converts scribble annotations into continuous pixel-wise labels by applying an exponential decay function to distance maps, producing confidence maps that represent the likelihood of each pixel belonging to a specific category, rather than relying on hard pseudo labels. We evaluate MaCo on three public datasets, comparing it with other weakly supervised methods. Our results show that MaCo outperforms competing methods across all datasets, establishing a new record in weakly supervised medical image segmentation.

Xingliang Lei, Yiwen Ye, Zhisong Wang et al.

Parameter-efficient fine-tuning (PEFT) techniques have emerged to address overfitting and high computational costs associated with fully fine-tuning in self-supervised learning. Mainstream PEFT methods add a few trainable parameters while keeping the pre-trained backbone parameters fixed. These methods achieve comparative, and often superior, performance to fully fine-tuning, demonstrating the powerful representation ability of the pre-trained backbone. Despite this success, these methods typically ignore the initialization of the new parameters, often relying solely on random initialization. We argue that if pre-training is significantly beneficial, it should be applied to all parameters requiring representational capacity. Motivated by this, we propose Target Parameter Pre-training (TPP), a simple yet effective fine-tuning framework. TPP pre-trains target parameters, i.e., the new parameters introduced during fine-tuning, in an additional stage before PEFT. During this stage, the pre-trained backbone parameters are frozen, and only the new parameters are trainable. A defined pretext task encourages the new parameters to learn specific representations of downstream data. Subsequently, when PEFT is employed, the pre-trained new parameters are loaded to enhance fine-tuning efficiency. The proposed TPP framework is versatile, allowing integration with various pre-trained backbones, pretext tasks, and PEFT methods. We evaluated the fine-tuning performance of our method on seven public datasets, covering four modalities and two task types. The results demonstrate that TPP can be easily integrated into existing PEFT methods, significantly improving performance.

Ziyang Chen, Yongsheng Pan, Yiwen Ye et al.

Although recent years have witnessed the great success of convolutional neural networks (CNNs) in medical image segmentation, the domain shift issue caused by the highly variable image quality of medical images hinders the deployment of CNNs in real-world clinical applications. Domain generalization (DG) methods aim to address this issue by training a robust model on the source domain, which has a strong generalization ability. Previously, many DG methods based on feature-space domain randomization have been proposed, which, however, suffer from the limited and unordered search space of feature styles. In this paper, we propose a multi-source DG method called Treasure in Distribution (TriD), which constructs an unprecedented search space to obtain the model with strong robustness by randomly sampling from a uniform distribution. To learn the domain-invariant representations explicitly, we further devise a style-mixing strategy in our TriD, which mixes the feature styles by randomly mixing the augmented and original statistics along the channel wise and can be extended to other DG methods. Extensive experiments on two medical segmentation tasks with different modalities demonstrate that our TriD achieves superior generalization performance on unseen target-domain data. Code is available at https://github.com/Chen-Ziyang/TriD.

Xiangde Luo, Jia Fu, Yunxin Zhong et al.

Radiation therapy is a primary and effective NasoPharyngeal Carcinoma (NPC) treatment strategy. The precise delineation of Gross Tumor Volumes (GTVs) and Organs-At-Risk (OARs) is crucial in radiation treatment, directly impacting patient prognosis. Previously, the delineation of GTVs and OARs was performed by experienced radiation oncologists. Recently, deep learning has achieved promising results in many medical image segmentation tasks. However, for NPC OARs and GTVs segmentation, few public datasets are available for model development and evaluation. To alleviate this problem, the SegRap2023 challenge was organized in conjunction with MICCAI2023 and presented a large-scale benchmark for OAR and GTV segmentation with 400 Computed Tomography (CT) scans from 200 NPC patients, each with a pair of pre-aligned non-contrast and contrast-enhanced CT scans. The challenge's goal was to segment 45 OARs and 2 GTVs from the paired CT scans. In this paper, we detail the challenge and analyze the solutions of all participants. The average Dice similarity coefficient scores for all submissions ranged from 76.68\% to 86.70\%, and 70.42\% to 73.44\% for OARs and GTVs, respectively. We conclude that the segmentation of large-size OARs is well-addressed, and more efforts are needed for GTVs and small-size or thin-structure OARs. The benchmark will remain publicly available here: https://segrap2023.grand-challenge.org

Yihang Fu, Ziyang Chen, Yiwen Ye et al.

Medical images often exhibit distribution shifts due to variations in imaging protocols and scanners across different medical centers. Domain Generalization (DG) methods aim to train models on source domains that can generalize to unseen target domains. Recently, the segment anything model (SAM) has demonstrated strong generalization capabilities due to its prompt-based design, and has gained significant attention in image segmentation tasks. Existing SAM-based approaches attempt to address the need for manual prompts by introducing prompt generators that automatically generate these prompts. However, we argue that auto-generated prompts may not be sufficiently accurate under distribution shifts, potentially leading to incorrect predictions that still require manual verification and correction by clinicians. To address this challenge, we propose a method for 2D medical image segmentation called Self-Correcting SAM (CoSAM). Our approach begins by generating coarse masks using SAM in a prompt-free manner, providing prior prompts for the subsequent stages, and eliminating the need for prompt generators. To automatically refine these coarse masks, we introduce a generalized error decoder that simulates the correction process typically performed by clinicians. Furthermore, we generate diverse prompts as feedback based on the corrected masks, which are used to iteratively refine the predictions within a self-correcting loop, enhancing the generalization performance of our model. Extensive experiments on two medical image segmentation benchmarks across multiple scenarios demonstrate the superiority of CoSAM over state-of-the-art SAM-based methods.

Ziyang Chen, Yiwen Ye, Feilong Tang et al.

Domain generalization (DG) aims to enhance the ability of models trained on source domains to generalize effectively to unseen domains. Recently, Sharpness-Aware Minimization (SAM) has shown promise in this area by reducing the sharpness of the loss landscape to obtain more generalized models. However, SAM and its variants sometimes fail to guide the model toward a flat minimum, and their training processes exhibit limitations, hindering further improvements in model generalization. In this paper, we first propose an improved model training process aimed at encouraging the model to converge to a flat minima. To achieve this, we design a curvature metric that has a minimal effect when the model is far from convergence but becomes increasingly influential in indicating the curvature of the minima as the model approaches a local minimum. Then we derive a novel algorithm from this metric, called Meta Curvature-Aware Minimization (MeCAM), to minimize the curvature around the local minima. Specifically, the optimization objective of MeCAM simultaneously minimizes the regular training loss, the surrogate gap of SAM, and the surrogate gap of meta-learning. We provide theoretical analysis on MeCAM's generalization error and convergence rate, and demonstrate its superiority over existing DG methods through extensive experiments on five benchmark DG datasets, including PACS, VLCS, OfficeHome, TerraIncognita, and DomainNet. Code will be available on GitHub.

Linhao Li, Yiwen Ye, Ziyang Chen et al.

3D medical image segmentation often faces heavy resource and time consumption, limiting its scalability and rapid deployment in clinical environments. Existing efficient segmentation models are typically static and manually designed prior to training, which restricts their adaptability across diverse tasks and makes it difficult to balance performance with resource efficiency. In this paper, we propose PSP-Seg, a progressive pruning framework that enables dynamic and efficient 3D segmentation. PSP-Seg begins with a redundant model and iteratively prunes redundant modules through a combination of block-wise pruning and a functional decoupling loss. We evaluate PSP-Seg on five public datasets, benchmarking it against seven state-of-the-art models and six efficient segmentation models. Results demonstrate that the lightweight variant, PSP-Seg-S, achieves performance on par with nnU-Net while reducing GPU memory usage by 42-45%, training time by 29-48%, and parameter number by 83-87% across all datasets. These findings underscore PSP-Seg's potential as a cost-effective yet high-performing alternative for widespread clinical application.

Yiwen Ye, Yicheng Wu, Xiangde Luo et al.

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.

Zhisong Wang, Yiwen Ye, Ziyang Chen et al.

Weakly supervised semantic segmentation (WSSS) in medical imaging struggles with effectively using sparse annotations. One promising direction for WSSS leverages gaze annotations, captured via eye trackers that record regions of interest during diagnostic procedures. However, existing gaze-based methods, such as GazeMedSeg, do not fully exploit the rich information embedded in gaze data. In this paper, we propose GradTrack, a framework that utilizes physicians' gaze track, including fixation points, durations, and temporal order, to enhance WSSS performance. GradTrack comprises two key components: Gaze Track Map Generation and Track Attention, which collaboratively enable progressive feature refinement through multi-level gaze supervision during the decoding process. Experiments on the Kvasir-SEG and NCI-ISBI datasets demonstrate that GradTrack consistently outperforms existing gaze-based methods, achieving Dice score improvements of 3.21\% and 2.61\%, respectively. Moreover, GradTrack significantly narrows the performance gap with fully supervised models such as nnUNet.

Ziyang Chen, Yiwen Ye, Yongsheng Pan et al.

Distribution shifts widely exist in medical images acquired from different medical centres, hindering the deployment of semantic segmentation models trained on one centre (source domain) to another (target domain). While unsupervised domain adaptation has shown significant promise in mitigating these shifts, it poses privacy risks due to sharing data between centres. To facilitate adaptation while preserving data privacy, source-free domain adaptation (SFDA) and test-time adaptation (TTA) have emerged as effective paradigms, relying solely on target domain data. However, SFDA requires a pre-collected target domain dataset before deployment. TTA insufficiently exploit the potential value of test data, as it processes the test data only once. Considering that most medical centres operate during the day and remain inactive at night in clinical practice, we propose a novel adaptation framework called Day-Night Adaptation (DyNA) with above insights, which performs adaptation through day-night cycles without requiring access to source data. During the day, a low-frequency prompt is trained to adapt the frozen model to each test sample. We construct a memory bank for prompt initialization and develop a warm-up mechanism to enhance prompt training. During the night, we reuse test data collected from the day and introduce a global student model to bridge the knowledge between teacher and student models, facilitating model fine-tuning while ensuring training stability. Extensive experiments demonstrate that our DyNA outperforms existing TTA and SFDA methods on two benchmark medical image segmentation tasks. Code will be available after the paper is published.