The quality of the teacher label has a dramatic impact on the outcome of the machine learning process. Medical image segmentation often suffers from a noisy ground truth (GT) mask due to difficulties in consistent annotation. Although a recent study has proposed a promising method to curate the noisy GT mask, this requires additional well-curated GT masks that are not always accessible without the aid of multiple medical experts. As an alternative, we propose SAM-Correction, which utilizes a foundation model to correct the noisy GT mask in a fully adaptive manner instead of manually preparing well-curated masks. In our approach, we progressively mitigate label noise via the segment anything model (SAM), where prompts are given from another segmentation network that we train concurrently. Experiments with various types of label noise derived from actual human annotations demonstrate that SAM-C achieves precise noise reduction and high-performing segmentation models trained thereby. Our method paves the way for robust model training even when clean labels are entirely unavailable.
Figures & tables
Figure 1: Proposed framework and data utilized in this study. (a) Overview of SAM-C (see the main text for details). B-mix excludes the bounding box from a noisy prediction that does not overlap with any of those in Ycpre . The B-mix gate can be disabled to directly use prompts from the noisy prediction. The post-correction is not shown here. (b) Examples from LIDC-IDRI (top) and Cityscapes (bottom).
Table 1: DSC between the prediction of f and the clean GT. The average and the standard error over five independent trials are shown. (a) Comparison of our method with others. (b) Ablation study for pre-, mid-, and post-correction processes.
Figure 2: Comparison of predictions by DNN. (Left) Results for LIDC-IDRI. All methods except the oracle used GTs with “or noise”. Colored contours represent individual annotations. (Right) Results for Cityscapes.
Table 2: Comparison between Yn and Yc regarding DSC with clean GT in the training dataset. In the numerals, blue, red, and black represent increase, decrease, and unchanged, respectively.
Medical image segmentation delineates organs, lesions, and other structures in scans to support measurement, diagnosis, treatment planning, and research.
Medical image segmentation models built on Segment Anything Model (SAM) achieve strong performance on clean benchmarks, yet their reliability often degrades under realistic image corruptions such as noise, blur, motion artifacts, and modality-specific distortions. Existing approaches address either medical-domain adaptation or corruption robustness, but not both jointly. In SAM, we find that these capabilities are concentrated in complementary modules: the image encoder preserves medical priors, while the mask decoder governs corruption robustness. Motivated by this observation, we propose RobustMedSAM, which adopts module-wise checkpoint fusion by initializing the image encoder from MedSAM and the mask decoder from RobustSAM under a shared ViT-B architecture. We then fine-tune only the mask decoder on 35 medical datasets from MedSegBench, spanning six imaging modalities and 12 corruption types, while freezing the remaining components to preserve pretrained medical representations. We additionally investigate an SVD-based parameter-efficient variant for limited encoder adaptation. Experiments on both in-distribution and out-of-distribution benchmarks show that RobustMedSAM improves degraded-image Dice from 0.613 to 0.719 (+0.106) over SAM, demonstrating that structured fusion of complementary pretrained models is an effective and practical approach for robust medical image segmentation.
Label noise is common in medical imaging datasets due to factors such as inter-rater variability, annotation errors, and ambiguous cases. This can severely undermine the reliability and clinical effectiveness of machine learning models trained using those datasets. To address this challenge, we introduce Lightweight Noise Correction (LiNC), which adds a single trainable trust parameter per training sample and learns when to use the observed label and when to defer to the model during a standard training loop. The key idea is to train using a convex combination of the observed label and the model's own predictive distribution, controlled by a per-sample trust parameter. We show that the gradient of this objective drives trust values in opposite directions for clean versus noisy samples in the early training phase, yielding separable trust distributions. We use a 3-component Gaussian Mixture Model over the trust values to separate them into clean, ambiguous, and noisy cases and then execute a short soft-correction phase on the noisy cases and a final hard correction phase. Experiments on ten 2D datasets from MedMNISTv2 under label noise of up to 50% show consistent gains in accuracy and strong mislabel detection. LiNC adds negligible asymptotic overhead: the training-time complexity remains dominated by the base network, with additional memory growing linearly with the size of the training set.
Abhishek Moturu, Babak Taati, Anna Goldenberg
Department of Computer Science University of Toronto The Hospital for Sick Children UHN KITE Research Institute T-CAIREM Vector Institute · Department of Computer Science Institute of Biomedical Engineering University of Toronto Rehabilitation Sciences Institute UHN KITE Research Institute Vector Institute · Department of Computer Science Department of Laboratory Medicine and Pathobiology University of Toronto The Hospital for Sick Children T-CAIREM Vector Institute
Segmentation is central to clinical diagnosis and monitoring, yet the reliability of modern foundation models in medical imaging still depends on the availability of precise prompts. The Segment Anything Model (SAM) offers powerful zero-shot capabilities, although it collapses under the weak, generic, and noisy prompts that dominate real clinical workflows. In practice, annotations such as centerline points are coarse and ambiguous, often drifting across neighboring anatomy and misguiding SAM toward inconsistent or incomplete masks. We introduce SPD, a Saliency-Guided Prompt Distillation framework that converts these unreliable cues into robust guidance. SPD first learns data-driven anatomical priors through a lightweight saliency head to obtain confident localization maps. These priors then drive Contextual Prompt Distillation, which validates and enriches noisy prompts using cues from anatomically adjacent slices, producing a consensus prompt set that matches the behavior of expert reasoning. A Pairwise Slice Consistency objective further enforces local anatomical coherence during segmentation. Experiments on four challenging MRI and CT benchmarks demonstrate that SPD consistently outperforms existing SAM adaptations and supervised baselines, delivering large gains in both region-based and boundary-based metrics. SPD provides a practical and principled path toward reliable foundation model deployment in clinical environments where only imperfect prompts are available.
Jingxuan Kang, Ziqi Zhang, Shaoming Zheng +9
Imperial College London · Beihang University · National Health Service +1