Juan Iñaki Larrea, Lucas Mansilla, Enzo Ferrantecs.CV
Foundation models are increasingly deployed for medical image analysis. However, under the inter-institutional distribution shift typical of deployment, their performance varies widely and cannot be known without target-domain labels, which are rarely available. This leaves a practical question unresolved: given several candidate foundational models and labeled-data from a source domain, which one to deploy in an unlabeled target domain? We propose a label-free selection criterion built on SUDO, a framework for evaluating clinical AI systems without ground-truth annotations. SUDO partitions the unlabeled target data by predicted probability and, for each region, measures a pseudo-label discrepancy reflecting class contamination; aggregated across regions, this yields a score (AURCC) requiring neither target annotation nor fine-tuning. We show that AURCC can be used to rank a variety of vision-language models (BioMedCLIP, CXR-CLIP, CheXzero, MedCLIP, MedImageInsight, CLIP) on chest X-ray classification across three inter-hospital shift scenarios, under zero-shot and MLP-probe regimes. The AURCC ranking recovers the ground-truth ranking with Spearman rho up to 0.943 (p<0.05). Against the natural baseline of ranking by held-out source accuracy, AURCC is competitive when the labeled source is large and yields a more accurate ranking once it is small; the regime of interest in resource-constrained settings.
Domain shift across imaging modalities and acquisition sites remains a significant barrier to the clinical deployment of segmentation models. Source-free unsupervised domain adaptation (SFUDA) addresses this by adapting a pretrained model to an unlabeled target domain without requiring access to sensitive source data. We introduce a novel SFUDA framework built on Symmetrical Flow Matching, a unified generative model that segments an input image and synthesizes a source-like image from a mask within the same learned flow. By initializing inference from a domain-agnostic Gaussian origin, the model preserves structural consistency across domains and grounds predictions in learned anatomy rather than shifted texture statistics. Our pipeline leverages this symmetry to generate reliable pseudo-labels and corresponding source-like synthetic images from unlabeled target data, creating a generative replay buffer that anchors source knowledge during a generative self-training stage that fine-tunes on a joint set of real target and synthetic source-like images. We evaluate on abdominal multi-organ and cardiac segmentation, covering cross-modality MRI<->CT shifts, and multi-site prostate segmentation. Our approach outperforms SFUDA baselines and is competitive with conventional UDA methods.
Md Ashraful Hossen Akash, Shyla Afroge, Abdullah Al Mamun +2cs.CV
The advanced retinal disease diagnosing imaging modality, optical coherence tomography (OCT), encounters a lack of automation because of the high expenses for annotations performed by specialists. The use of SSL solves the problem of insufficient annotations using unlabeled B-scans; however, most of the current techniques for generating pseudo-labels are based on prediction confidence without considering the asymmetry between different types of errors. This paper proposes TRIAGE, a risk-controlled semi-supervised framework for OCT scans classification, which uses the concept of a patient-level conformal risk controller with an asymmetric cost matrix. TRIAGE unites three crucial modules: a hierarchical classifier that is capable of working with partially abnormal supervision of the disease subtypes, a patient-grouped conformal risk controller with primal-dual coverage control, and a context-aware Transformer teacher for cross-slice verification. On the dataset from Noor Eye Hospital (16,822 B-scans, 161 patients, and 554 volumes) with a test set of unseen patients, TRIAGE demonstrates 89.66% scan-level accuracy, 0.8805 macro-F1, 0.9641 macro-AUC, and an 8.34% under-grading rate when using only 20% of the labeled data. With only 5% of the labeled data, TRIAGE keeps 76.88% accuracy and a 0.1656 under-grading rate. Compared with the other six state-of-the-art semi-supervised methods, TRIAGE significantly outperforms them with ablation study demonstrating the contribution of each module in the overall framework performance (by 42.7% in terms of under-grading rate comparing to fixed threshold methods). TRIAGE demonstrates 98.00% accuracy for 3-class classification with 1% labeled data and 95.94% accuracy for 8-class classification with 10% labeled data on the OCT-C8 dataset.
Scribble annotations offer an efficient alternative to costly pixel-wise labeling for medical image segmentation, yet in real clinical scenarios, scribble-annotated samples are often still limited, imposing the dual challenges of sparse supervision and annotated sample scarcity. These compounded constraints severely deprive models of the structural evidence needed for complete region recovery and precise boundary delineation. To break this bottleneck, we propose a bi-level collaborative learning framework for few-shot scribble-supervised medical image segmentation. Specifically, an upper-level learnable superpixel model is introduced to provide region-structural priors for lower-level segmentation, while superpixel-based region-wise pseudo-label propagation and a spatial-prior-guided filtering strategy are performed to generate reliable dense pseudo-labels for segmentation learning. Meanwhile, the anatomical semantics learned by the lower-level segmentation model under the guidance of the current superpixels are fed back to the upper level, further driving it to learn region-structural representations better aligned with the segmentation task. Through bidirectional interaction and collaborative learning between the upper and lower levels, the proposed framework significantly outperforms existing state-of-the-art scribble-supervised methods on the ACDC and Prostate datasets under the few-shot scribble-supervised setting.
Learning from minimal human supervision is a long-standing goal in medical image analysis, where dense expert annotations are costly. We study retinal vessel segmentation in an extreme semi-supervised setting with one annotated image and a pool of unlabeled images. We propose ESRVS, which selects a representative reference image for manual annotation and transfers vessel cues using target-domain-adapted DINOv3 features. ESRVS constructs a multi granular vessel prototype, combines prototype-similarity maps with a physics-inspired prior to generate initial pseudo-labels, and refines the transferred supervision through weighted pseudo-label training and adversarial refinement. Across eight public datasets, ESRVS achieves the best Dice and clDice on six datasets, and the best HD95 on all eight datasets among the compared semi-supervised methods, although those methods use 10 to 20% labeled data. With Mask2Former, ESRVS retains on average 93.7% of fully supervised Dice and 95.1% of fully supervised clDice. These results demonstrate the potential of foundation-model label propagation for highly label-efficient retinal vessel segmentation. Code is available at https://github.com/IAANNH/ESRVS.
Jiyu Wei, Di Hong, Zhanjie Zhang +3cs.AI cs.HC cs.RO eess.SP
Brain-Machine Interfaces (BMIs), which link the brain to external devices, hold great potential in rehabilitation, human performance augmentation, and human-centered robotics. However, invasive BMIs face a critical challenge for long-term deployment due to neural drift, which degrades decoding performance over time and necessitates frequent recalibration. Existing methods designed to mitigate neural drift typically rely on either domain adaptation (DA) or domain generalization (DG) alone and often fail to capture fine-grained distribution shifts across neural subdomains, resulting in limited performance. To overcome these limitations, we propose Uncertainty-guided Self-paced Cycling (UnSPC), a robust framework that synergizes DA and DG for target domain refining under an Uncertainty-guided Self-paced Pseudo-labeling (UnSPL) mechanism. To handle subdomain neural drift across domains, UNSPL is proposed to iteratively mine reliable pseudo-labeled samples with a noise-robust ranking strategy for further fine-tuning. Leveraging these high-quality samples, we introduce a novel Cycling Adaptation and Generalization (CycAG) strategy, which integrates DA and DG within an iterative cycle to progressively mitigate both global and subdomain drift. This cyclic process enables effective alignment to evolving target distributions while preserving robust and transferable representations, thereby mitigating performance degradation under long-term neural drifts. Extensive experiments on multiple neural decoding datasets demonstrate the effectiveness and robustness of UnSPC. To our knowledge, our proposed UnSPC is the first to cyclically integrate DA and DG with pseudo-labeling, paving the way toward stable long-term BMI controls.
Vision Language Model (VLM) has great potential to enhance the quality of pseudo labels in semi-supervised spine segmentation by leveraging textual class prompts to generate segmentation map, but no one has studied it yet. Although promising, it lacks explicit constraints to ensure consistency between spine class prompts and spine unit region, resulting in unsatisfactory performance in multi-class segmentation map generation. In this paper, we propose CPS4, the first text-guided semi-supervised spine segmentation network using class prompts to enhance the quality of spine pseudo labels. Specifically, CPS4 is implemented through two training stages. (i) Class-specific consistency constrained VLM pretraining stage: we propose token- and pixel-level attention loss to optimize the consistency between class prompts and spine units, forcing the textual class prompt to be closely coupled with the target spine unit in the semantic space. (ii) Class Prompt driven semi-supervised spine segmentation stage: using the pretrained vision-text encoder, we derive each class-specific binary segmentation map for the unlabeled spine image and integrate them into an unified multi-class segmentation map, improving the quality of the spine pseudo label generated by the semi-supervised spine segmentation network. Experimental results show that our CPS4 achieves superior spine segmentation performance with Dice of 80.44%, only using 5% labeled data on the public spine segmentation dataset, surpassing popular semi-supervised learning and VLM methods. Our code will be available.
The integration of deep learning approaches in biomedical research has been transformative, enabling breakthroughs in various applications. Despite these strides, its application in protein inference is impeded by the scarcity of extensively labeled datasets, a challenge compounded by the high costs and complexities of accurate protein annotation. In this study, we introduce GraphPI, a novel framework that treats protein inference as a node classification problem. We treat proteins as interconnected nodes within a protein-peptide-PSM graph, utilizing a Graph Neural Network-based architecture to elucidate their interrelations. To address label scarcity, we train the model on a set of unlabeled public protein datasets with pseudo-labels derived from an existing protein inference algorithm, enhanced by self-training to iteratively refine labels based on confidence scores. Contrary to prevalent methodologies necessitating dataset-specific training, our research illustrates that GraphPI, due to the well normalized nature of Percolator features, exhibits universal applicability without dataset-specific fine-tuning, a feature that not only mitigates the risk of overfitting but also enhances computational efficiency. Our empirical experiments reveal notable performance on various test datasets and deliver significantly reduced computation times compared to common protein inference algorithms.
Semi-supervised learning (SSL) has become a promising solution to alleviate the annotation burden of deep learning-based medical image segmentation models. While recent advances in foundation model-driven SSL have pushed the boundary to extremely limited annotation scenarios, they fail to maintain robust competitive performance in complex imaging modalities. In this paper, we propose SemiSAM-O1, an annotation-efficient framework using only one annotated template image for segmentation. SemiSAM-O1 extends the specialist-generalist collaborative learning framework to the extreme one-label setting by fully exploiting the foundation model's feature representation capability beyond its prompting interface. SemiSAM-O1 operates in two stages. In the first stage, the foundation model's encoder extracts dense features from all volumes, and class prototypes derived from the single annotated template are propagated to the unlabeled pool via feature similarity to produce coarse initial pseudo-labels. In the second stage, an iterative training-and-refinement loop progressively improves both the segmentation model and the pseudo-labels over multiple rounds, where each round trains the model from scratch on current pseudo-labels and generates updated predictions with voxel-wise uncertainty estimates. An uncertainty-guided refinement step further leverages the foundation model's global feature space to correct high-uncertainty regions by aggregating labels from their most similar confident neighbors, establishing a virtuous cycle of mutual improvement. Extensive experiments on a wide range of segmentation tasks across different modalities and anatomical targets demonstrate that SemiSAM-O1 significantly narrows the performance gap between one-label semi-supervised learning and full supervision, while significantly reducing the computational overhead of online foundation model inference.