SAMCT: Segment Any CT Allowing Labor-Free Task-Indicator Prompts

Segment anything model (SAM), a foundation model with superior versatility and generalization across diverse segmentation tasks, has attracted widespread attention in medical imaging. However, it has been proved that SAM would encounter severe performance degradation due to the lack of medical knowledge in training and local feature encoding. Though several SAM-based models have been proposed for tuning SAM in medical imaging, they still suffer from insufficient feature extraction and highly rely on high-quality prompts. In this paper, we construct a large CT dataset consisting of 1.1M CT images and 5M masks from public datasets and propose a powerful foundation model SAMCT allowing labor-free prompts. Specifically, based on SAM, SAMCT is further equipped with a U-shaped CNN image encoder, a cross-branch interaction module, and a task-indicator prompt encoder. The U-shaped CNN image encoder works in parallel with the ViT image encoder in SAM to supplement local features. Cross-branch interaction enhances the feature expression capability of the CNN image encoder and the ViT image encoder by exchanging global perception and local features from one to the other. The task-indicator prompt encoder is a plug-and-play component to effortlessly encode task-related indicators into prompt embeddings. In this way, SAMCT can work in an automatic manner in addition to the semi-automatic interactive strategy in SAM. Extensive experiments demonstrate the superiority of SAMCT against the state-of-the-art task-specific and SAM-based medical foundation models on various tasks. The code, data, and models are released at https://github.com/xianlin7/SAMCT.

FedA3I: Annotation Quality-Aware Aggregation for Federated Medical Image Segmentation Against Heterogeneous Annotation Noise

Federated learning (FL) has emerged as a promising paradigm for training segmentation models on decentralized medical data, owing to its privacy-preserving property. However, existing research overlooks the prevalent annotation noise encountered in real-world medical datasets, which limits the performance ceilings of FL. In this paper, we, for the first time, identify and tackle this problem. For problem formulation, we propose a contour evolution for modeling non-independent and identically distributed (Non-IID) noise across pixels within each client and then extend it to the case of multi-source data to form a heterogeneous noise model (\textit{i.e.}, Non-IID annotation noise across clients). For robust learning from annotations with such two-level Non-IID noise, we emphasize the importance of data quality in model aggregation, allowing high-quality clients to have a greater impact on FL. To achieve this, we propose \textbf{Fed}erated learning with \textbf{A}nnotation qu\textbf{A}lity-aware \textbf{A}ggregat\textbf{I}on, named \textbf{FedA$^3$I}, by introducing a quality factor based on client-wise noise estimation. Specifically, noise estimation at each client is accomplished through the Gaussian mixture model and then incorporated into model aggregation in a layer-wise manner to up-weight high-quality clients. Extensive experiments on two real-world medical image segmentation datasets demonstrate the superior performance of FedA$^3$I against the state-of-the-art approaches in dealing with cross-client annotation noise. The code is available at \color{blue}{https://github.com/wnn2000/FedAAAI}.

SAMUS: Adapting Segment Anything Model for Clinically-Friendly and Generalizable Ultrasound Image Segmentation

Segment anything model (SAM), an eminent universal image segmentation model, has recently gathered considerable attention within the domain of medical image segmentation. Despite the remarkable performance of SAM on natural images, it grapples with significant performance degradation and limited generalization when confronted with medical images, particularly with those involving objects of low contrast, faint boundaries, intricate shapes, and diminutive sizes. In this paper, we propose SAMUS, a universal model tailored for ultrasound image segmentation. In contrast to previous SAM-based universal models, SAMUS pursues not only better generalization but also lower deployment cost, rendering it more suitable for clinical applications. Specifically, based on SAM, a parallel CNN branch is introduced to inject local features into the ViT encoder through cross-branch attention for better medical image segmentation. Then, a position adapter and a feature adapter are developed to adapt SAM from natural to medical domains and from requiring large-size inputs (1024x1024) to small-size inputs (256x256) for more clinical-friendly deployment. A comprehensive ultrasound dataset, comprising about 30k images and 69k masks and covering six object categories, is collected for verification. Extensive comparison experiments demonstrate SAMUS's superiority against the state-of-the-art task-specific models and universal foundation models under both task-specific evaluation and generalization evaluation. Moreover, SAMUS is deployable on entry-level GPUs, as it has been liberated from the constraints of long sequence encoding. The code, data, and models will be released at https://github.com/xianlin7/SAMUS.

ConvFormer: Plug-and-Play CNN-Style Transformers for Improving Medical Image Segmentation

Transformers have been extensively studied in medical image segmentation to build pairwise long-range dependence. Yet, relatively limited well-annotated medical image data makes transformers struggle to extract diverse global features, resulting in attention collapse where attention maps become similar or even identical. Comparatively, convolutional neural networks (CNNs) have better convergence properties on small-scale training data but suffer from limited receptive fields. Existing works are dedicated to exploring the combinations of CNN and transformers while ignoring attention collapse, leaving the potential of transformers under-explored. In this paper, we propose to build CNN-style Transformers (ConvFormer) to promote better attention convergence and thus better segmentation performance. Specifically, ConvFormer consists of pooling, CNN-style self-attention (CSA), and convolutional feed-forward network (CFFN) corresponding to tokenization, self-attention, and feed-forward network in vanilla vision transformers. In contrast to positional embedding and tokenization, ConvFormer adopts 2D convolution and max-pooling for both position information preservation and feature size reduction. In this way, CSA takes 2D feature maps as inputs and establishes long-range dependency by constructing self-attention matrices as convolution kernels with adaptive sizes. Following CSA, 2D convolution is utilized for feature refinement through CFFN. Experimental results on multiple datasets demonstrate the effectiveness of ConvFormer working as a plug-and-play module for consistent performance improvement of transformer-based frameworks. Code is available at https://github.com/xianlin7/ConvFormer.

FedNoRo: Towards Noise-Robust Federated Learning by Addressing Class Imbalance and Label Noise Heterogeneity

Federated noisy label learning (FNLL) is emerging as a promising tool for privacy-preserving multi-source decentralized learning. Existing research, relying on the assumption of class-balanced global data, might be incapable to model complicated label noise, especially in medical scenarios. In this paper, we first formulate a new and more realistic federated label noise problem where global data is class-imbalanced and label noise is heterogeneous, and then propose a two-stage framework named FedNoRo for noise-robust federated learning. Specifically, in the first stage of FedNoRo, per-class loss indicators followed by Gaussian Mixture Model are deployed for noisy client identification. In the second stage, knowledge distillation and a distance-aware aggregation function are jointly adopted for noise-robust federated model updating. Experimental results on the widely-used ICH and ISIC2019 datasets demonstrate the superiority of FedNoRo against the state-of-the-art FNLL methods for addressing class imbalance and label noise heterogeneity in real-world FL scenarios.

FCA: Taming Long-tailed Federated Medical Image Classification by Classifier Anchoring

Limited training data and severe class imbalance impose significant challenges to developing clinically robust deep learning models. Federated learning (FL) addresses the former by enabling different medical clients to collaboratively train a deep model without sharing data. However, the class imbalance problem persists due to inter-client class distribution variations. To overcome this, we propose federated classifier anchoring (FCA) by adding a personalized classifier at each client to guide and debias the federated model through consistency learning. Additionally, FCA debiases the federated classifier and each client's personalized classifier based on their respective class distributions, thus mitigating divergence. With FCA, the federated feature extractor effectively learns discriminative features suitably globally for federation as well as locally for all participants. In clinical practice, the federated model is expected to be both generalized, performing well across clients, and specialized, benefiting each individual client from collaboration. According to this, we propose a novel evaluation metric to assess models' generalization and specialization performance globally on an aggregated public test set and locally at each client. Through comprehensive comparison and evaluation, FCA outperforms the state-of-the-art methods with large margins for federated long-tailed skin lesion classification and intracranial hemorrhage classification, making it a more feasible solution in clinical settings.

Affinity Feature Strengthening for Accurate, Complete and Robust Vessel Segmentation

Vessel segmentation is essential in many medical image applications, such as the detection of coronary stenoses, retinal vessel diseases and brain aneurysms. A high pixel-wise accuracy, complete topology structure and robustness to various contrast variations are three critical aspects of vessel segmentation. However, most existing methods only focus on achieving part of them via dedicated designs while few of them can concurrently achieve the three goals. In this paper, we present a novel affinity feature strengthening network (AFN) which adopts a contrast-insensitive approach based on multiscale affinity to jointly model topology and refine pixel-wise segmentation features. Specifically, for each pixel we derive a multiscale affinity field which captures the semantic relationships of the pixel with its neighbors on the predicted mask image. Such a multiscale affinity field can effectively represent the local topology of a vessel segment of different sizes. Meanwhile, it does not depend on image intensities and hence is robust to various illumination and contrast changes. We further learn spatial- and scale-aware adaptive weights for the corresponding affinity fields to strengthen vessel features. We evaluate our AFN on four different types of vascular datasets: X-ray angiography coronary vessel dataset (XCAD), portal vein dataset (PV), digital subtraction angiography cerebrovascular vessel dataset (DSA) and retinal vessel dataset (DRIVE). Extensive experimental results on the four datasets demonstrate that our AFN outperforms the state-of-the-art methods in terms of both higher accuracy and topological metrics, and meanwhile is more robust to various contrast changes than existing methods. Codes will be made public.

The Lighter The Better: Rethinking Transformers in Medical Image Segmentation Through Adaptive Pruning

Vision transformers have recently set off a new wave in the field of medical image analysis due to their remarkable performance on various computer vision tasks. However, recent hybrid-/transformer-based approaches mainly focus on the benefits of transformers in capturing long-range dependency while ignoring the issues of their daunting computational complexity, high training costs, and redundant dependency. In this paper, we propose to employ adaptive pruning to transformers for medical image segmentation and propose a lightweight and effective hybrid network APFormer. To our best knowledge, this is the first work on transformer pruning for medical image analysis tasks. The key features of APFormer mainly are self-supervised self-attention (SSA) to improve the convergence of dependency establishment, Gaussian-prior relative position embedding (GRPE) to foster the learning of position information, and adaptive pruning to eliminate redundant computations and perception information. Specifically, SSA and GRPE consider the well-converged dependency distribution and the Gaussian heatmap distribution separately as the prior knowledge of self-attention and position embedding to ease the training of transformers and lay a solid foundation for the following pruning operation. Then, adaptive transformer pruning, both query-wise and dependency-wise, is performed by adjusting the gate control parameters for both complexity reduction and performance improvement. Extensive experiments on two widely-used datasets demonstrate the prominent segmentation performance of APFormer against the state-of-the-art methods with much fewer parameters and lower GFLOPs. More importantly, we prove, through ablation studies, that adaptive pruning can work as a plug-n-play module for performance improvement on other hybrid-/transformer-based methods. Code is available at https://github.com/xianlin7/APFormer.

C2FTrans: Coarse-to-Fine Transformers for Medical Image Segmentation

Convolutional neural networks (CNN), the most prevailing architecture for deep-learning based medical image analysis, are still functionally limited by their intrinsic inductive biases and inadequate receptive fields. Transformer, born to address this issue, has drawn explosive attention in natural language processing and computer vision due to its remarkable ability in capturing long-range dependency. However, most recent transformer-based methods for medical image segmentation directly apply vanilla transformers as an auxiliary module in CNN-based methods, resulting in severe detail loss due to the rigid patch partitioning scheme in transformers. To address this problem, we propose C2FTrans, a novel multi-scale architecture that formulates medical image segmentation as a coarse-to-fine procedure. C2FTrans mainly consists of a cross-scale global transformer (CGT) which addresses local contextual similarity in CNN and a boundary-aware local transformer (BLT) which overcomes boundary uncertainty brought by rigid patch partitioning in transformers. Specifically, CGT builds global dependency across three different small-scale feature maps to obtain rich global semantic features with an acceptable computational cost, while BLT captures mid-range dependency by adaptively generating windows around boundaries under the guidance of entropy to reduce computational complexity and minimize detail loss based on large-scale feature maps. Extensive experimental results on three public datasets demonstrate the superior performance of C2FTrans against state-of-the-art CNN-based and transformer-based methods with fewer parameters and lower FLOPs. We believe the design of C2FTrans would further inspire future work on developing efficient and lightweight transformers for medical image segmentation. The source code of this paper is publicly available at https://github.com/xianlin7/C2FTrans.

FedRare: Federated Learning with Intra- and Inter-Client Contrast for Effective Rare Disease Classification

Federated learning (FL), enabling different medical institutions or clients to train a model collaboratively without data privacy leakage, has drawn great attention in medical imaging communities recently. Though inter-client data heterogeneity has been thoroughly studied, the class imbalance problem due to the existence of rare diseases still is under-explored. In this paper, we propose a novel FL framework FedRare for medical image classification especially on dealing with data heterogeneity with the existence of rare diseases. In FedRare, each client trains a model locally to extract highly-separable latent features for classification via intra-client supervised contrastive learning. Considering the limited data on rare diseases, we build positive sample queues for augmentation (i.e. data re-sampling). The server in FedRare would collect the latent features from clients and automatically select the most reliable latent features as guidance sent back to clients. Then, each client is jointly trained by an inter-client contrastive loss to align its latent features to the federated latent features of full classes. In this way, the parameter/feature variances across clients are effectively minimized, leading to better convergence and performance improvements. Experimental results on the publicly-available dataset for skin lesion diagnosis demonstrate FedRare's superior performance. Under the 10-client federated setting where four clients have no rare disease samples, FedRare achieves an average increase of 9.60% and 5.90% in balanced accuracy compared to the baseline framework FedAvg and the state-of-the-art approach FedIRM respectively. Considering the board existence of rare diseases in clinical scenarios, we believe FedRare would benefit future FL framework design for medical image classification. The source code of this paper is publicly available at https://github.com/wnn2000/FedRare.