MedUniSeg: 2D and 3D Medical Image Segmentation via a Prompt-driven Universal Model

Universal segmentation models offer significant potential in addressing a wide range of tasks by effectively leveraging discrete annotations. As the scope of tasks and modalities expands, it becomes increasingly important to generate and strategically position task- and modal-specific priors within the universal model. However, existing universal models often overlook the correlations between different priors, and the optimal placement and frequency of these priors remain underexplored. In this paper, we introduce MedUniSeg, a prompt-driven universal segmentation model designed for 2D and 3D multi-task segmentation across diverse modalities and domains. MedUniSeg employs multiple modal-specific prompts alongside a universal task prompt to accurately characterize the modalities and tasks. To generate the related priors, we propose the modal map (MMap) and the fusion and selection (FUSE) modules, which transform modal and task prompts into corresponding priors. These modal and task priors are systematically introduced at the start and end of the encoding process. We evaluate MedUniSeg on a comprehensive multi-modal upstream dataset consisting of 17 sub-datasets. The results demonstrate that MedUniSeg achieves superior multi-task segmentation performance, attaining a 1.2% improvement in the mean Dice score across the 17 upstream tasks compared to nnUNet baselines, while using less than 1/10 of the parameters. For tasks that underperform during the initial multi-task joint training, we freeze MedUniSeg and introduce new modules to re-learn these tasks. This approach yields an enhanced version, MedUniSeg*, which consistently outperforms MedUniSeg across all tasks. Moreover, MedUniSeg surpasses advanced self-supervised and supervised pre-trained models on six downstream tasks, establishing itself as a high-quality, highly generalizable pre-trained segmentation model.

Pre-training Everywhere: Parameter-Efficient Fine-Tuning for Medical Image Analysis via Target Parameter Pre-training

Parameter-efficient fine-tuning (PEFT) techniques have emerged to address issues of overfitting and high computational costs associated with fully fine-tuning in the paradigm of self-supervised learning. Mainstream methods based on PEFT involve adding a few trainable parameters while keeping the pre-trained parameters of the backbone fixed. These methods achieve comparative, and often superior, performance to fully fine-tuning, demonstrating the powerful representation ability of the pre-trained backbone. Despite its 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 insight, we propose a simple yet effective fine-tuning framework based on Target Parameter Pre-training (TPP). The target parameters refer to the new parameters introduced during fine-tuning. TPP includes an additional stage before PEFT to pre-train these target parameters. During this stage, the pre-trained backbone parameters are frozen, and only the target parameters are trainable. A defined pre-text task is used to encourage the target parameters to learn specific representations of downstream data. When PEFT is subsequently employed, the pre-trained target parameters are loaded to enhance fine-tuning efficiency. The proposed TPP framework is versatile, allowing for the integration of various pretext tasks for pre-training and supporting different PEFT methods as backbones. We evaluated the fine-tining performance of our method using five public datasets, including three modalities and two task types. The results demonstrate that the proposed TPP can be easily integrated into existing PEFT methods, significantly improving performance.

From Few to More: Scribble-based Medical Image Segmentation via Masked Context Modeling and Continuous Pseudo Labels

Scribble-based weakly supervised segmentation techniques offer comparable performance to fully supervised methods while significantly reducing annotation costs, making them an appealing alternative. Existing methods often rely on auxiliary tasks to enforce semantic consistency and use hard pseudo labels for supervision. However, these methods often overlook the unique requirements of models trained with sparse annotations. Since the model must predict pixel-wise segmentation maps with limited annotations, the ability to handle varying levels of annotation richness is critical. In this paper, we adopt the principle of `from few to more' and propose MaCo, a weakly supervised framework designed for medical image segmentation. MaCo employs masked context modeling (MCM) and continuous pseudo labels (CPL). MCM uses an attention-based masking strategy to disrupt the input image, compelling the model's predictions to remain consistent with those of the original image. CPL converts scribble annotations into continuous pixel-wise labels by applying an exponential decay function to distance maps, resulting in continuous maps that represent the confidence of each pixel belonging to a specific category, rather than using hard pseudo labels. We evaluate MaCo against other weakly supervised methods using three public datasets. The results indicate that MaCo outperforms competing methods across all datasets, setting a new record in weakly supervised medical image segmentation.

Gradient Alignment Improves Test-Time Adaptation for Medical Image Segmentation

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 will be available.

Unleashing the Potential of Open-set Noisy Samples Against Label Noise for Medical Image Classification

The challenge of addressing mixed closed-set and open-set label noise in medical image classification remains largely unexplored. Unlike natural image classification where there is a common practice of segregation and separate processing of closed-set and open-set noisy samples from clean ones, medical image classification faces difficulties due to high inter-class similarity which complicates the identification of open-set noisy samples. Moreover, prevailing methods do not leverage the full potential of open-set noisy samples for label noise mitigation, often leading to their exclusion or application of uniform soft labels. To address these issues, we propose an Extended Noise-robust Contrastive and Open-set Feature Augmentation (ENCOFA) framework. ENCOFA includes the Extended Noise-robust Supervised Contrastive (ENSC) Loss, which aids in distinguishing features across classes. The ENSC loss regards open-set noisy samples as an extended class and mitigates label noise by weighting contrastive pairs with label reliability. Furthermore, we develop an Open-set Feature Augmentation (OSFeatAug) module that enriches the features of open-set samples, utilizing the model's extra capacity to prevent overfitting to noisy data. We conducted experiments on a synthetic noisy dataset and a real-world noisy dataset. Our results indicate the superiority of ENCOFA and the effectiveness of leveraging the open-set noisy samples to combat label noise.

Towards Clinician-Preferred Segmentation: Leveraging Human-in-the-Loop for Test Time Adaptation in Medical Image Segmentation

Deep learning-based medical image segmentation models often face performance degradation when deployed across various medical centers, largely due to the discrepancies in data distribution. Test Time Adaptation (TTA) methods, which adapt pre-trained models to test data, have been employed to mitigate such discrepancies. However, existing TTA methods primarily focus on manipulating Batch Normalization (BN) layers or employing prompt and adversarial learning, which may not effectively rectify the inconsistencies arising from divergent data distributions. In this paper, we propose a novel Human-in-the-loop TTA (HiTTA) framework that stands out in two significant ways. First, it capitalizes on the largely overlooked potential of clinician-corrected predictions, integrating these corrections into the TTA process to steer the model towards predictions that coincide more closely with clinical annotation preferences. Second, our framework conceives a divergence loss, designed specifically to diminish the prediction divergence instigated by domain disparities, through the careful calibration of BN parameters. Our HiTTA is distinguished by its dual-faceted capability to acclimatize to the distribution of test data whilst ensuring the model's predictions align with clinical expectations, thereby enhancing its relevance in a medical context. Extensive experiments on a public dataset underscore the superiority of our HiTTA over existing TTA methods, emphasizing the advantages of integrating human feedback and our divergence loss in enhancing the model's performance and adaptability across diverse medical centers.

PairAug: What Can Augmented Image-Text Pairs Do for Radiology?

Current vision-language pre-training (VLP) methodologies predominantly depend on paired image-text datasets, a resource that is challenging to acquire in radiology due to privacy considerations and labelling complexities. Data augmentation provides a practical solution to overcome the issue of data scarcity, however, most augmentation methods exhibit a limited focus, prioritising either image or text augmentation exclusively. Acknowledging this limitation, our objective is to devise a framework capable of concurrently augmenting medical image and text data. We design a Pairwise Augmentation (PairAug) approach that contains an Inter-patient Augmentation (InterAug) branch and an Intra-patient Augmentation (IntraAug) branch. Specifically, the InterAug branch of our approach generates radiology images using synthesised yet plausible reports derived from a Large Language Model (LLM). The generated pairs can be considered a collection of new patient cases since they are artificially created and may not exist in the original dataset. In contrast, the IntraAug branch uses newly generated reports to manipulate images. This process allows us to create new paired data for each individual with diverse medical conditions. Our extensive experiments on various downstream tasks covering medical image classification zero-shot and fine-tuning analysis demonstrate that our PairAug, concurrently expanding both image and text data, substantially outperforms image-/text-only expansion baselines and advanced medical VLP baselines. Our code is released at \url{https://github.com/YtongXie/PairAug}.

Learning with Diversification from Block Sparse Signal

This paper introduces a novel prior called Diversified Block Sparse Prior to characterize the widespread block sparsity phenomenon in real-world data. By allowing diversification on variance and correlation matrix, we effectively address the sensitivity issue of existing block sparse learning methods to pre-defined block information, which enables adaptive block estimation while mitigating the risk of overfitting. Based on this, a diversified block sparse Bayesian learning method (DivSBL) is proposed, utilizing EM algorithm and dual ascent method for hyperparameter estimation. Moreover, we establish the global and local optimality theory of our model. Experiments validate the advantages of DivSBL over existing algorithms.

MAST: Video Polyp Segmentation with a Mixture-Attention Siamese Transformer

Accurate segmentation of polyps from colonoscopy videos is of great significance to polyp treatment and early prevention of colorectal cancer. However, it is challenging due to the difficulties associated with modelling long-range spatio-temporal relationships within a colonoscopy video. In this paper, we address this challenging task with a novel Mixture-Attention Siamese Transformer (MAST), which explicitly models the long-range spatio-temporal relationships with a mixture-attention mechanism for accurate polyp segmentation. Specifically, we first construct a Siamese transformer architecture to jointly encode paired video frames for their feature representations. We then design a mixture-attention module to exploit the intra-frame and inter-frame correlations, enhancing the features with rich spatio-temporal relationships. Finally, the enhanced features are fed to two parallel decoders for predicting the segmentation maps. To the best of our knowledge, our MAST is the first transformer model dedicated to video polyp segmentation. Extensive experiments on the large-scale SUN-SEG benchmark demonstrate the superior performance of MAST in comparison with the cutting-edge competitors. Our code is publicly available at https://github.com/Junqing-Yang/MAST.

Part to Whole: Collaborative Prompting for Surgical Instrument Segmentation

Foundation models like the Segment Anything Model (SAM) have demonstrated promise in generic object segmentation. However, directly applying SAM to surgical instrument segmentation presents key challenges. First, SAM relies on per-frame point-or-box prompts which complicate surgeon-computer interaction. Also, SAM yields suboptimal performance on segmenting surgical instruments, owing to insufficient surgical data in its pre-training as well as the complex structure and fine-grained details of various surgical instruments. To address these challenges, in this paper, we investigate text promptable surgical instrument segmentation and propose SP-SAM (SurgicalPart-SAM), a novel efficient-tuning approach that integrates surgical instrument structure knowledge with the generic segmentation knowledge of SAM. Specifically, we achieve this by proposing (1) collaborative prompts in the text form "[part name] of [instrument category name]" that decompose instruments into fine-grained parts; (2) a Cross-Modal Prompt Encoder that encodes text prompts jointly with visual embeddings into discriminative part-level representations; and (3) a Part-to-Whole Selective Fusion and a Hierarchical Decoding strategy that selectively assemble the part-level representations into a whole for accurate instrument segmentation. Built upon them, SP-SAM acquires a better capability to comprehend surgical instrument structures and distinguish between various categories. Extensive experiments on both the EndoVis2018 and EndoVis2017 datasets demonstrate SP-SAM's state-of-the-art performance with minimal tunable parameters. Code is at https://github.com/wenxi-yue/SurgicalPart-SAM.