Zengqiang Yan

Tianyi Shi, Xiaohuan Ding, Wei Zhou et al.

Vessel segmentation is crucial in many medical image applications, such as detecting coronary stenoses, retinal vessel diseases and brain aneurysms. However, achieving high pixel-wise accuracy, complete topology structure and robustness to various contrast variations are critical and challenging, and most existing methods focus only on achieving one or two of these aspects. In this paper, we present a novel approach, the affinity feature strengthening network (AFN), which jointly models geometry and refines pixel-wise segmentation features using a contrast-insensitive, multiscale affinity approach. Specifically, we compute a multiscale affinity field for each pixel, capturing its semantic relationships with neighboring pixels in the predicted mask image. This field represents the local geometry of vessel segments of different sizes, allowing us to learn spatial- and scale-aware adaptive weights 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 demonstrate that our AFN outperforms the state-of-the-art methods in terms of both higher accuracy and topological metrics, while also being more robust to various contrast changes. The source code of this work is available at https://github.com/TY-Shi/AFN.

Xian Lin, Yangyang Xiang, Li Yu et al.

End-to-end medical image segmentation is of great value for computer-aided diagnosis dominated by task-specific models, usually suffering from poor generalization. With recent breakthroughs brought by the segment anything model (SAM) for universal image segmentation, extensive efforts have been made to adapt SAM for medical imaging but still encounter two major issues: 1) severe performance degradation and limited generalization without proper adaptation, and 2) semi-automatic segmentation relying on accurate manual prompts for interaction. In this work, we propose SAMUS as a universal model tailored for ultrasound image segmentation and further enable it to work in an end-to-end manner denoted as AutoSAMUS. Specifically, in SAMUS, a parallel CNN branch is introduced to supplement local information through cross-branch attention, and a feature adapter and a position adapter are jointly used to adapt SAM from natural to ultrasound domains while reducing training complexity. AutoSAMUS is realized by introducing an auto prompt generator (APG) to replace the manual prompt encoder of SAMUS to automatically generate prompt embeddings. A comprehensive ultrasound dataset, comprising about 30k images and 69k masks and covering six object categories, is collected for verification. Extensive comparison experiments demonstrate the superiority of SAMUS and AutoSAMUS against the state-of-the-art task-specific and SAM-based foundation models. We believe the auto-prompted SAM-based model has the potential to become a new paradigm for end-to-end medical image segmentation and deserves more exploration. Code and data are available at https://github.com/xianlin7/SAMUS.

Xian Lin, Li Yu, Kwang-Ting Cheng et al.

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.

Nannan Wu, Li Yu, Xin Yang et al.

Federated learning (FL), training deep models from decentralized data without privacy leakage, has shown great potential in medical image computing recently. However, considering the ubiquitous class imbalance in medical data, FL can exhibit performance degradation, especially for minority classes (e.g. rare diseases). Existing methods towards this problem mainly focus on training a balanced classifier to eliminate class prior bias among classes, but neglect to explore better representation to facilitate classification performance. In this paper, we present a privacy-preserving FL method named FedIIC to combat class imbalance from two perspectives: feature learning and classifier learning. In feature learning, two levels of contrastive learning are designed to extract better class-specific features with imbalanced data in FL. In classifier learning, per-class margins are dynamically set according to real-time difficulty and class priors, which helps the model learn classes equally. Experimental results on publicly-available datasets demonstrate the superior performance of FedIIC in dealing with both real-world and simulated multi-source medical imaging data under class imbalance. Code is available at https://github.com/wnn2000/FedIIC.

Xian Lin, Zengqiang Yan, Xianbo Deng et al.

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.

Junjie Shi, Caozhi Shang, Zhaobin Sun et al.

Incomplete multi-modal image segmentation is a fundamental task in medical imaging to refine deployment efficiency when only partial modalities are available. However, the common practice that complete-modality data is visible during model training is far from realistic, as modalities can have imbalanced missing rates in clinical scenarios. In this paper, we, for the first time, formulate such a challenging setting and propose Preference-Aware Self-diStillatION (PASSION) for incomplete multi-modal medical image segmentation under imbalanced missing rates. Specifically, we first construct pixel-wise and semantic-wise self-distillation to balance the optimization objective of each modality. Then, we define relative preference to evaluate the dominance of each modality during training, based on which to design task-wise and gradient-wise regularization to balance the convergence rates of different modalities. Experimental results on two publicly available multi-modal datasets demonstrate the superiority of PASSION against existing approaches for modality balancing. More importantly, PASSION is validated to work as a plug-and-play module for consistent performance improvement across different backbones. Code is available at https://github.com/Jun-Jie-Shi/PASSION.

Jeffry Wicaksana, Zengqiang Yan, Dong Zhang et al.

The purpose of federated learning is to enable multiple clients to jointly train a machine learning model without sharing data. However, the existing methods for training an image segmentation model have been based on an unrealistic assumption that the training set for each local client is annotated in a similar fashion and thus follows the same image supervision level. To relax this assumption, in this work, we propose a label-agnostic unified federated learning framework, named FedMix, for medical image segmentation based on mixed image labels. In FedMix, each client updates the federated model by integrating and effectively making use of all available labeled data ranging from strong pixel-level labels, weak bounding box labels, to weakest image-level class labels. Based on these local models, we further propose an adaptive weight assignment procedure across local clients, where each client learns an aggregation weight during the global model update. Compared to the existing methods, FedMix not only breaks through the constraint of a single level of image supervision, but also can dynamically adjust the aggregation weight of each local client, achieving rich yet discriminative feature representations. To evaluate its effectiveness, experiments have been carried out on two challenging medical image segmentation tasks, i.e., breast tumor segmentation and skin lesion segmentation. The results validate that our proposed FedMix outperforms the state-of-the-art method by a large margin.

Yangyang Xiang, Nannan Wu, Li Yu et al.

Federated learning has emerged as a compelling paradigm for medical image segmentation, particularly in light of increasing privacy concerns. However, most of the existing research relies on relatively stringent assumptions regarding the uniformity and completeness of annotations across clients. Contrary to this, this paper highlights a prevalent challenge in medical practice: incomplete annotations. Such annotations can introduce incorrectly labeled pixels, potentially undermining the performance of neural networks in supervised learning. To tackle this issue, we introduce a novel solution, named FedIA. Our insight is to conceptualize incomplete annotations as noisy data (i.e., low-quality data), with a focus on mitigating their adverse effects. We begin by evaluating the completeness of annotations at the client level using a designed indicator. Subsequently, we enhance the influence of clients with more comprehensive annotations and implement corrections for incomplete ones, thereby ensuring that models are trained on accurate data. Our method's effectiveness is validated through its superior performance on two extensively used medical image segmentation datasets, outperforming existing solutions. The code is available at https://github.com/HUSTxyy/FedIA.

Xian Lin, Li Yu, Kwang-Ting Cheng et al.

Objective: Transformers, born to remedy the inadequate receptive fields of CNNs, have drawn explosive attention recently. However, the daunting computational complexity of global representation learning, together with rigid window partitioning, hinders their deployment in medical image segmentation. This work aims to address the above two issues in transformers for better medical image segmentation. Methods: We propose a boundary-aware lightweight transformer (BATFormer) that can build cross-scale global interaction with lower computational complexity and generate windows flexibly under the guidance of entropy. Specifically, to fully explore the benefits of transformers in long-range dependency establishment, a cross-scale global transformer (CGT) module is introduced to jointly utilize multiple small-scale feature maps for richer global features with lower computational complexity. Given the importance of shape modeling in medical image segmentation, a boundary-aware local transformer (BLT) module is constructed. Different from rigid window partitioning in vanilla transformers which would produce boundary distortion, BLT adopts an adaptive window partitioning scheme under the guidance of entropy for both computational complexity reduction and shape preservation. Results: BATFormer achieves the best performance in Dice of 92.84%, 91.97%, 90.26%, and 96.30% for the average, right ventricle, myocardium, and left ventricle respectively on the ACDC dataset and the best performance in Dice, IoU, and ACC of 90.76%, 84.64%, and 96.76% respectively on the ISIC 2018 dataset. More importantly, BATFormer requires the least amount of model parameters and the lowest computational complexity compared to the state-of-the-art approaches. Conclusion and Significance: Our results demonstrate the necessity of developing customized transformers for efficient and better medical image segmentation.

Jeffry Wicaksana, Zengqiang Yan, Kwang-Ting Cheng

Limited training data and severe class imbalance pose 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 privacy-sensitive data. However, class imbalance worsens due to variation in inter-client class distribution. We propose federated learning with non-parametric regularization (FedNPR and FedNPR-Per, a personalized version of FedNPR) to regularize the feature extractor and enhance useful and discriminative signal in the feature space. Our extensive experiments show that FedNPR outperform the existing state-of-the art FL approaches in class imbalance skin lesion classification and intracranial hemorrhage identification. Additionally, the non-parametric regularization module consistently improves the performance of existing state-of-the-art FL approaches. We believe that NPR is a valuable tool in FL under clinical settings.

Nannan Wu, Zhaobin Sun, Zengqiang Yan et al.

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 (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 Federated learning with Annotation quAlity-aware AggregatIon, named FedA3I, 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 https://github.com/wnn2000/FedAAAI.

Nannan Wu, Zhuo Kuang, Zengqiang Yan et al.

Due to escalating privacy concerns, federated learning has been recognized as a vital approach for training deep neural networks with decentralized medical data. In practice, it is challenging to ensure consistent imaging quality across various institutions, often attributed to equipment malfunctions affecting a minority of clients. This imbalance in image quality can cause the federated model to develop an inherent bias towards higher-quality images, thus posing a severe fairness issue. In this study, we pioneer the identification and formulation of this new fairness challenge within the context of the imaging quality shift. Traditional methods for promoting fairness in federated learning predominantly focus on balancing empirical risks across diverse client distributions. This strategy primarily facilitates fair optimization across different training data distributions, yet neglects the crucial aspect of generalization. To address this, we introduce a solution termed Federated learning with Inter-client Sharpness Matching (FedISM). FedISM enhances both local training and global aggregation by incorporating sharpness-awareness, aiming to harmonize the sharpness levels across clients for fair generalization. Our empirical evaluations, conducted using the widely-used ICH and ISIC 2019 datasets, establish FedISM's superiority over current state-of-the-art federated learning methods in promoting fairness. Code is available at https://github.com/wnn2000/FFL4MIA.

Xian Lin, Yangyang Xiang, Zhehao Wang et al.

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.

Nannan Wu, Zhuo Kuang, Zengqiang Yan et al.

Despite the potential of federated learning in medical applications, inconsistent imaging quality across institutions-stemming from lower-quality data from a minority of clients-biases federated models toward more common high-quality images. This raises significant fairness concerns. Existing fair federated learning methods have demonstrated some effectiveness in solving this problem by aligning a single 0th- or 1st-order state of convergence (e.g., training loss or sharpness). However, we argue in this work that fairness based on such a single state is still not an adequate surrogate for fairness during testing, as these single metrics fail to fully capture the convergence characteristics, making them suboptimal for guiding fair learning. To address this limitation, we develop a generalized framework. Specifically, we propose assessing convergence using multiple states, defined as sharpness or perturbed loss computed at varying search distances. Building on this comprehensive assessment, we propose promoting fairness for these states across clients to achieve our ultimate fairness objective. This is accomplished through the proposed method, FedISM+. In FedISM+, the search distance evolves over time, progressively focusing on different states. We then incorporate two components in local training and global aggregation to ensure cross-client fairness for each state. This gradually makes convergence equitable for all states, thereby improving fairness during testing. Our empirical evaluations, performed on the well-known RSNA ICH and ISIC 2019 datasets, demonstrate the superiority of FedISM+ over existing state-of-the-art methods for fair federated learning. The code is available at https://github.com/wnn2000/FFL4MIA.

Zhaobin Sun, Nannan Wu, Junjie Shi et al.

Cross-silo federated learning (FL) enables decentralized organizations to collaboratively train models while preserving data privacy and has made significant progress in medical image classification. One common assumption is task homogeneity where each client has access to all classes during training. However, in clinical practice, given a multi-label classification task, constrained by the level of medical knowledge and the prevalence of diseases, each institution may diagnose only partial categories, resulting in task heterogeneity. How to pursue effective multi-label medical image classification under task heterogeneity is under-explored. In this paper, we first formulate such a realistic label missing setting in the multi-label FL domain and propose a two-stage method FedMLP to combat class missing from two aspects: pseudo label tagging and global knowledge learning. The former utilizes a warmed-up model to generate class prototypes and select samples with high confidence to supplement missing labels, while the latter uses a global model as a teacher for consistency regularization to prevent forgetting missing class knowledge. Experiments on two publicly-available medical datasets validate the superiority of FedMLP against the state-of-the-art both federated semi-supervised and noisy label learning approaches under task heterogeneity. Code is available at https://github.com/szbonaldo/FedMLP.

Nannan Wu, Zengqiang Yan, Nong Sang et al.

Training a model that effectively handles both common and rare data-i.e., achieving performance fairness-is crucial in federated learning (FL). While existing fair FL methods have shown effectiveness, they remain vulnerable to mislabeled data. Ensuring robustness in fair FL is therefore essential. However, fairness and robustness inherently compete, which causes robust strategies to hinder fairness. In this paper, we attribute this competition to the homogeneity in loss patterns exhibited by rare and mislabeled data clients, preventing existing loss-based fair and robust FL methods from effectively distinguishing and handling these two distinct client types. To address this, we propose performance-capacity analysis, which jointly considers model performance on each client and its capacity to handle the dataset, measured by loss and a newly introduced feature dispersion score. This allows mislabeled clients to be identified by their significantly deviated performance relative to capacity while preserving rare data clients. Building on this, we introduce FedPCA, an FL method that robustly achieves fairness. FedPCA first identifies mislabeled clients via a Gaussian Mixture Model on loss-dispersion pairs, then applies fairness and robustness strategies in global aggregation and local training by adjusting client weights and selectively using reliable data. Extensive experiments on three datasets demonstrate FedPCA's effectiveness in tackling this complex challenge. Code will be publicly available upon acceptance.

Nannan Wu, Li Yu, Xuefeng Jiang et al.

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.

Jeffry Wicaksana, Zengqiang Yan, Kwang-Ting Cheng

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.

Shichao Li, Zengqiang Yan, Hongyang Li et al.

We present a new learning-based framework to recover vehicle pose in SO(3) from a single RGB image. In contrast to previous works that map from local appearance to observation angles, we explore a progressive approach by extracting meaningful Intermediate Geometrical Representations (IGRs) to estimate egocentric vehicle orientation. This approach features a deep model that transforms perceived intensities to IGRs, which are mapped to a 3D representation encoding object orientation in the camera coordinate system. Core problems are what IGRs to use and how to learn them more effectively. We answer the former question by designing IGRs based on an interpolated cuboid that derives from primitive 3D annotation readily. The latter question motivates us to incorporate geometry knowledge with a new loss function based on a projective invariant. This loss function allows unlabeled data to be used in the training stage to improve representation learning. Without additional labels, our system outperforms previous monocular RGB-based methods for joint vehicle detection and pose estimation on the KITTI benchmark, achieving performance even comparable to stereo methods. Code and pre-trained models are available at this https URL.

Katsushi Ikeuchi, Zengqiang Yan, Zhaoyuan Ma et al.

We have been developing a paradigm, which we refer to as Learning-from-observation, for a robot to automatically acquire what-to-do through observation of human performance. Since a simple mimicking method to repeat exact joint angles does not work due to the kinematic and dynamic difference between a human and a robot, the method introduces an intermediate symbolic representation, task models, to conceptually represent what-to-do through observation. Then, these task models are mapped appropriate robot motions depending on each robot hardware. This paper presents task models, designed based on the Labanotation, for upper body movements of humanoid robots. Given a human motion sequence, we first analyze the motions of the upper body, and extract certain fixed poses at certain key frames. These key poses are translated into states represented by Labanotation symbols. Then, task models, identified from the state transitions, are mapped to robot movements on a particular robot hardware. Since the task models based on Labanotation are independent from different robot hardware, we can share the same observation module; we only need task mapping modules depending on different robot hardware. The system was implemented and demonstrated that three different robots can automatically mimic human upper body motions with satisfactory level of resemblance.