We propose adversarial constrained-CNN loss, a new paradigm of constrained-CNN loss methods, for weakly supervised medical image segmentation. In the new paradigm, prior knowledge is encoded and depicted by reference masks, and is further employed to impose constraints on segmentation outputs through adversarial learning with reference masks. Unlike pseudo label methods for weakly supervised segmentation, such reference masks are used to train a discriminator rather than a segmentation network, and thus are not required to be paired with specific images. Our new paradigm not only greatly facilitates imposing prior knowledge on network's outputs, but also provides stronger and higher-order constraints, i.e., distribution approximation, through adversarial learning. Extensive experiments involving different medical modalities, different anatomical structures, different topologies of the object of interest, different levels of prior knowledge and weakly supervised annotations with different annotation ratios is conducted to evaluate our ACCL method. Consistently superior segmentation results over the size constrained-CNN loss method have been achieved, some of which are close to the results of full supervision, thus fully verifying the effectiveness and generalization of our method. Specifically, we report an average Dice score of 75.4% with an average annotation ratio of 0.65%, surpassing the prior art, i.e., the size constrained-CNN loss method, by a large margin of 11.4%. Our codes are made publicly available at https://github.com/PengyiZhang/ACCL.
Tsinghua University（清华大学）；University of San Francisco（旧金山大学）；Boston University（波士顿大学）；University of Southern California（南加州大学）
Convolutional neural networks (CNNs) have been successfully applied to medical image classification, segmentation, and related tasks. Among the many CNNs architectures, U-Net and its improved versions based are widely used and achieve state-of-the-art performance these years. These improved architectures focus on structural improvements and the size of the convolution kernel is generally fixed. In this paper, we propose a module that combines the benefits of multiple kernel sizes and we apply the proposed module to U-Net and its variants. We test our module on three segmentation benchmark data…
Fully-connected Conditional Random Field (CRF) is often used as post-processing to refine voxel classification results by encouraging spatial coherence. In this paper, we propose a new end-to-end training method called Posterior-CRF. In contrast with previous approaches which use the original image intensity in the CRF, our approach applies 3D, fully connected CRF to the posterior probabilities from a CNN and optimizes both CNN and CRF together. The experiments on white matter hyperintensities segmentation demonstrate that our method outperforms CNN, post-processing CRF and different end-to-en…
Convolutional neural network (CNN) based methods have achieved great successes in medical image segmentation, but their capability to learn global representations is still limited due to using small effective receptive fields of convolution operations. Transformer based methods are capable of modelling long-range dependencies of information for capturing global representations, yet their ability to model local context is lacking. Integrating CNN and Transformer to learn both local and global representations while exploring multi-scale features is instrumental in further improving medical image…
University of California, Los Angeles（加利福尼亚大学洛杉矶分校）；NVIDIA（英伟达）
Textures and edges contribute different information to image recognition. Edges and boundaries encode shape information, while textures manifest the appearance of regions. Despite the success of Convolutional Neural Networks (CNNs) in computer vision and medical image analysis applications, predominantly only texture abstractions are learned, which often leads to imprecise boundary delineations. In medical imaging, expert manual segmentation often relies on organ boundaries; for example, to manually segment a liver, a medical practitioner usually identifies edges first and subsequently fills i…
The University of Adelaide（阿德莱德大学）；Northwestern Polytechnical University（西北工业大学）
Convolutional neural networks (CNNs) have been the de facto standard for nowadays 3D medical image segmentation. The convolutional operations used in these networks, however, inevitably have limitations in modeling the long-range dependency due to their inductive bias of locality and weight sharing. Although Transformer was born to address this issue, it suffers from extreme computational and spatial complexities in processing high-resolution 3D feature maps. In this paper, we propose a novel framework that efficiently bridges a {\bf Co}nvolutional neural network and a {\bf Tr}ansformer {\bf (…
MSLAU-Net: A Hybrid CNN-Transformer Network for Medical Image Segmentation
College of Computer Science and Engineering（计算机科学与工程学院）；College of Artificial Intelligence（人工智能学院）；Department of Pharmacy（药学部）；Department of Prosthodontics（修复学部）；Chongqing Key Laboratory of Oral Diseases（重庆口腔疾病重点实验室）；Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education（重庆市口腔生物医学工程高等教育重点实验室）；School of Computer Science and Engineering（计算机科学与工程学院）；Southeast University（东南大学）
University of Electronic Science and Technology of China（电子科技大学）；Shanghai AI Lab（上海人工智能实验室）；SenseTime（商汤科技）
Recently, deep learning with Convolutional Neural Networks (CNNs) and Transformers has shown encouraging results in fully supervised medical image segmentation. However, it is still challenging for them to achieve good performance with limited annotations for training. In this work, we present a very simple yet efficient framework for semi-supervised medical image segmentation by introducing the cross teaching between CNN and Transformer. Specifically, we simplify the classical deep co-training from consistency regularization to cross teaching, where the prediction of a network is used as the …
Deep neural networks have been a prevailing technique in the field of medical image processing. However, the most popular convolutional neural networks (CNNs) based methods for medical image segmentation are imperfect because they model long-range dependencies by stacking layers or enlarging filters. Transformers and the self-attention mechanism are recently proposed to effectively learn long-range dependencies by modeling all pairs of word-to-word attention regardless of their positions. The idea has also been extended to the computer vision field by creating and treating image patches as emb…
CNN-Transformer Rectified Collaborative Learning for Medical Image Segmentation
School of Information and Communication Engineering, Dalian University of Technology（大连理工大学信息与通信工程学院）；Key Laboratory for Ubiquitous Network and Service Software of Liaoning Province（辽宁省泛在网络与服务软件重点实验室）；DUT-RU International School of Information Science and Engineering, Dalian University of Technology（大连理工大学-鲁东大学国际信息科学与工程学院）；Affiliated Zhongshan Hospital of Dalian University（大连大学附属中山医院）
Recent advances of semantic image segmentation greatly benefit from deeper and larger Convolutional Neural Network (CNN) models. Compared to image segmentation in the wild, properties of both medical images themselves and of existing medical datasets hinder training deeper and larger models because of overfitting. To this end, we propose a novel two-stream UNET architecture for automatic end-to-end medical image segmentation, in which intensity value and gradient vector flow (GVF) are two inputs for each stream, respectively. We demonstrate that two-stream CNNs with more low-level features gre…
BEFUnet: A Hybrid CNN-Transformer Architecture for Precise Medical Image Segmentation
School of Electrical Engineering, Iran University of Science and Technology（伊朗科学技术大学电气工程学院）；University College of Nabi Akram（纳比·阿克拉姆大学学院）；Department of Electrical Engineering, Qazvin Branch, Iran（伊朗加兹温分校电气工程系）
Towards Clinician-Preferred Segmentation: Leveraging Human-in-the-Loop for Test Time Adaptation in Medical Image Segmentation
Northwestern Polytechnical University（西北工业大学）；Ningbo Institute of Northwestern Polytechnical University（西北工业大学宁波研究院）；Research and Development Institute of Northwestern Polytechnical University in Shenzhen（西北工业大学深圳研究院）
Convolutional Neural Networks (CNNs) have been successful in solving tasks in computer vision including medical image segmentation due to their ability to automatically extract features from unstructured data. However, CNNs are sensitive to rotation and affine transformation and their success relies on huge-scale labeled datasets capturing various input variations. This network paradigm has posed challenges at scale because acquiring annotated data for medical segmentation is expensive, and strict privacy regulations. Furthermore, visual representation learning with CNNs has its own flaws, e.g…
Medical image segmentation - the prerequisite of numerous clinical needs - has been significantly prospered by recent advances in convolutional neural networks (CNNs). However, it exhibits general limitations on modeling explicit long-range relation, and existing cures, resorting to building deep encoders along with aggressive downsampling operations, leads to redundant deepened networks and loss of localized details. Hence, the segmentation task awaits a better solution to improve the efficiency of modeling global contexts while maintaining a strong grasp of low-level details. In this paper, …
ACM-UNet: Adaptive Integration of CNNs and Mamba for Efficient Medical Image Segmentation
Wuhan University of Technology（武汉理工大学）；Chinese Academy of Medical Sciences and Peking Union Medical College（中国医学科学院北京协和医学院）；Zhongnan Hospital of Wuhan University（武汉大学中南医院）
In this article, we look into some essential aspects of convolutional neural networks (CNNs) with the focus on medical image segmentation. First, we discuss the CNN architecture, thereby highlighting the spatial origin of the data, voxel-wise classification and the receptive field. Second, we discuss the sampling of input-output pairs, thereby highlighting the interaction between voxel-wise classification, patch size and the receptive field. Finally, we give a historical overview of crucial changes to CNN architectures for classification and segmentation, giving insights in the relation betwee…
Convolutional Neural Networks (CNNs) have achieved promising results in medical image segmentation. However, CNNs require lots of training data and are incapable of handling pose and deformation of objects. Furthermore, their pooling layers tend to discard important information such as positions as well as CNNs are sensitive to rotation and affine transformation. Capsule network is a recent new architecture that has achieved better robustness in part-whole representation learning by replacing pooling layers with dynamic routing and convolutional strides, which has shown potential results on po…
Macquarie University（麦考瑞大学）；University of Technology Sydney（悉尼科技大学）；Shanghai AI Laboratory（上海人工智能实验室）
Automatic tumor or lesion segmentation is a crucial step in medical image analysis for computer-aided diagnosis. Although the existing methods based on Convolutional Neural Networks (CNNs) have achieved the state-of-the-art performance, many challenges still remain in medical tumor segmentation. This is because, although the human visual system can detect symmetries in 2D images effectively, regular CNNs can only exploit translation invariance, overlooking further inherent symmetries existing in medical images such as rotations and reflections. To solve this problem, we propose a novel group e…
Xiamen University（厦门大学）；Beihang University（北京航空航天大学）；University of Hull（赫尔大学）；Chinese Academy of Sciences（中国科学院）
Medical image segmentation is one of the most fundamental tasks concerning medical information analysis. Various solutions have been proposed so far, including many deep learning-based techniques, such as U-Net, FC-DenseNet, etc. However, high-precision medical image segmentation remains a highly challenging task due to the existence of inherent magnification and distortion in medical images as well as the presence of lesions with similar density to normal tissues. In this paper, we propose TFCNs (Transformers for Fully Convolutional denseNets) to tackle the problem by introducing ResLinear-Tr…
ConvFormer: Plug-and-Play CNN-Style Transformers for Improving Medical Image Segmentation
Huazhong University of Science and Technology（华中科技大学）；Union Hospital, Tongji Medical College, Huazhong University of Science and Technology（华中科技大学同济医学院附属协和医院）
SegTransVAE: Hybrid CNN -- Transformer with Regularization for medical image segmentation
VinBrain JSC.（VinBrain联合股份公司）；University of Science, Ho Chi Minh City（胡志明市科学大学）；Vietnam National University, Ho Chi Minh City（胡志明市越南国家大学）；Vin University（文大大学）
University College London（伦敦大学学院）；KU Leuven（鲁汶大学）；University Hospitals KU Leuven（鲁汶大学医院）
Convolutional neural networks (CNNs) have achieved state-of-the-art performance for automatic medical image segmentation. However, they have not demonstrated sufficiently accurate and robust results for clinical use. In addition, they are limited by the lack of image-specific adaptation and the lack of generalizability to previously unseen object classes. To address these problems, we propose a novel deep learning-based framework for interactive segmentation by incorporating CNNs into a bounding box and scribble-based segmentation pipeline. We propose image-specific fine-tuning to make a CNN m…
X-Ray image enhancement, along with many other medical image processing applications, requires the segmentation of images into bone, soft tissue, and open beam regions. We apply a machine learning approach to this problem, presenting an end-to-end solution which results in robust and efficient inference. Since medical institutions frequently do not have the resources to process and label the large quantity of X-Ray images usually needed for neural network training, we design an end-to-end solution for small datasets, while achieving state-of-the-art results. Our implementation produces an over…
BRAU-Net++: U-Shaped Hybrid CNN-Transformer Network for Medical Image Segmentation
College of Computer Science and Engineering, Chongqing University of Technology（重庆理工大学计算机科学与工程学院）；College of Computer Science, Chongqing University（重庆大学计算机学院）；College of Artificial Intelligence, Chongqing University of Technology（重庆理工大学人工智能学院）；The First Affiliated Hospital of Chongqing Medical University（重庆医科大学附属第一医院）；Faculty of Computing and Information Technology, King Abdulaziz University（阿卜杜勒阿齐兹大学计算与信息技术学院）
Deep neural network architectures have traditionally been designed and explored with human expertise in a long-lasting trial-and-error process. This process requires huge amount of time, expertise, and resources. To address this tedious problem, we propose a novel algorithm to optimally find hyperparameters of a deep network architecture automatically. We specifically focus on designing neural architectures for medical image segmentation task. Our proposed method is based on a policy gradient reinforcement learning for which the reward function is assigned a segmentation evaluation utility (i.…
HyM-UNet: Synergizing Local Texture and Global Context via Hybrid CNN-Mamba Architecture for Medical Image Segmentation
School of Information and Communication Engineering, Beijing University of Posts and Communications (BUPT)（信息与通信工程学院，北京邮电大学）；Alibaba Cloud AI Labs（阿里云人工智能实验室）
Iran University of Science and Technology（伊朗科技大学）；RWTH Aachen University（亚琛工业大学）；Shahid Beheshti University（沙希德·贝赫什提大学）；University of Montreal（蒙特利尔大学）；Polytechnique Montreal（蒙特利尔理工学院）；Quebec AI Institute（魁北克人工智能研究所）；University of Regensburg（雷根斯堡大学）；Fraunhofer Institute for Digital Medicine MEVIS（弗劳恩霍夫数字医学MEVIS研究所）
Convolutional neural networks (CNNs) have been the consensus for medical image segmentation tasks. However, they suffer from the limitation in modeling long-range dependencies and spatial correlations due to the nature of convolution operation. Although transformers were first developed to address this issue, they fail to capture low-level features. In contrast, it is demonstrated that both local and global features are crucial for dense prediction, such as segmenting in challenging contexts. In this paper, we propose HiFormer, a novel method that efficiently bridges a CNN and a transformer fo…
MedPrompt: LLM-CNN Fusion with Weight Routing for Medical Image Segmentation and Classification
1 ,2 Department of Electrical；Electronic Engineering,\ University of Engineering；3Department of Computer Science \& Engineering,\ University of Engineering \& Technology, Rajshahi-6204, Bangladesh
TEC-Net: Vision Transformer Embrace Convolutional Neural Networks for Medical Image Segmentation
Shaanxi University of Science and Technology（陕西科技大学）；Xi’an Jiaotong University（西安交通大学）；Griffith University（格里菲斯大学）；Northwestern Polytechnical University（西北工业大学）；Brunel University London（伦敦布鲁内尔大学）
ScribFormer: Transformer Makes CNN Work Better for Scribble-based Medical Image Segmentation
Xiamen University（厦门大学）；University of Washington（华盛顿大学）；Peking University（北京大学）；University of Hull（赫尔大学）；Chinese University of Hong Kong（香港中文大学）；Hong Kong Institute of Medical Engineering（香港医学工程研究所）；Hong Kong Centre for Cerebro-cardiovascular Health Engineering（香港心脑血管健康工程中心）；ShanghaiTech University（上海科技大学）；Shanghai United Imaging Intelligence Co., Ltd.（上海联影智能医疗科技有限公司）；Shanghai Clinical Research and Trial Center（上海临床研究与试验中心）
Eindhoven University of Technology（埃因霍温理工大学）；Philips GmbH Innovative Technologies（飞利浦创新技术有限公司）
Automatic segmentation of anatomical structures with convolutional neural networks (CNNs) constitutes a large portion of research in medical image analysis. The majority of CNN-based methods rely on an abundance of labeled data for proper training. Labeled medical data is often scarce, but unlabeled data is more widely available. This necessitates approaches that go beyond traditional supervised learning and leverage unlabeled data for segmentation tasks. This work investigates the potential of autoencoder-extracted features to improve segmentation with a CNN. Two strategies were considered. F…
Beijing University of Posts and Telecommunications（北京邮电大学）；Dalian University of Technology（大连理工大学）；Guilin University of Electronic Technology（桂林电子科技大学）；Guangdong Provincial People’s Hospital（广东省人民医院）；Guangdong Academy of Medical Sciences（广东省医学科学院）
The success of Transformer in computer vision has attracted increasing attention in the medical imaging community. Especially for medical image segmentation, many excellent hybrid architectures based on convolutional neural networks (CNNs) and Transformer have been presented and achieve impressive performance. However, most of these methods, which embed modular Transformer into CNNs, struggle to reach their full potential. In this paper, we propose a novel hybrid architecture for medical image segmentation called PHTrans, which parallelly hybridizes Transformer and CNN in main building blocks …
Like other applications in computer vision, medical image segmentation has been most successfully addressed using deep learning models that rely on the convolution operation as their main building block. Convolutions enjoy important properties such as sparse interactions, weight sharing, and translation equivariance. These properties give convolutional neural networks (CNNs) a strong and useful inductive bias for vision tasks. In this work we show that a different method, based entirely on self-attention between neighboring image patches and without any convolution operations, can achieve comp…
University of California, Los Angeles（加州大学洛杉矶分校）；NVIDIA（英伟达）
Fully convolutional neural networks (CNNs) have proven to be effective at representing and classifying textural information, thus transforming image intensity into output class masks that achieve semantic image segmentation. In medical image analysis, however, expert manual segmentation often relies on the boundaries of anatomical structures of interest. We propose boundary aware CNNs for medical image segmentation. Our networks are designed to account for organ boundary information, both by providing a special network edge branch and edge-aware loss terms, and they are trainable end-to-end. W…
MaxViT-UNet: Multi-Axis Attention for Medical Image Segmentation
Pakistan Institute of Engineering & Applied Sciences（巴基斯坦工程与应用科学学院）；PIEAS Artificial Intelligence Center (PAIC)（PIEAS人工智能中心）；Center for Mathematical Sciences（数学科学中心）
Are Vision xLSTM Embedded UNet More Reliable in Medical 3D Image Segmentation?
Machine Intelligence Unit Indian Statistical Institute（机器智能单位印度统计研究所）；Department of Computer Science and Engineering Jadavpur University（计算机科学与工程系贾梵布尔大学）；Department of Computer Science and Engineering Alipurduar Government Engineering and Management College（计算机科学与工程系阿里普杜尔政府工程与管理学院）
VinAI Research（VinAI研究院）；University of Arkansas（阿肯色大学）
Medical image segmentation has been so far achieving promising results with Convolutional Neural Networks (CNNs). However, it is arguable that in traditional CNNs, its pooling layer tends to discard important information such as positions. Moreover, CNNs are sensitive to rotation and affine transformation. Capsule network is a data-efficient network design proposed to overcome such limitations by replacing pooling layers with dynamic routing and convolutional strides, which aims to preserve the part-whole relationships. Capsule network has shown a great performance in image recognition and nat…
Department of Statistics and Applied Probability National University of Singapore（新加坡国立大学统计与应用概率系）
In recent years, convolutional neural networks (CNNs) have revolutionized medical image analysis. One of the most well-known CNN architectures in semantic segmentation is the U-net, which has achieved much success in several medical image segmentation applications. Also more recently, with the rise of autoML ad advancements in neural architecture search (NAS), methods like NAS-Unet have been proposed for NAS in medical image segmentation. In this paper, with inspiration from LadderNet, U-Net, autoML and NAS, we propose an ensemble deep neural network with an underlying U-Net framework consisti…
Convolutional Neural Networks (CNNs) work very well for supervised learning problems when the training dataset is representative of the variations expected to be encountered at test time. In medical image segmentation, this premise is violated when there is a mismatch between training and test images in terms of their acquisition details, such as the scanner model or the protocol. Remarkable performance degradation of CNNs in this scenario is well documented in the literature. To address this problem, we design the segmentation CNN as a concatenation of two sub-networks: a relatively shallow i…
TBConvL-Net: A Hybrid Deep Learning Architecture for Robust Medical Image Segmentation
COMSATS University Islamabad (CUI)（COMSATS大学伊斯兰堡校区）；University of New South Wales（新南威尔士大学）；University of Engineering and Technology (UET) Lahore（拉合尔工程技术大学）
本文提出混合架构 TBConvL-Net，融合 CNN、双卷积 LSTM 与 ViT 建模局部、长程及时序上下文，并采用复合损失提升边界与鲁棒性，在十种公开数据集上优于现有方法。
Umeå University（于默奥大学）；Eindhoven University of Technology（埃因霍温理工大学）
When using Convolutional Neural Networks (CNNs) for segmentation of organs and lesions in medical images, the conventional approach is to work with inputs and outputs either as single slice (2D) or whole volumes (3D). One common alternative, in this study denoted as pseudo-3D, is to use a stack of adjacent slices as input and produce a prediction for at least the central slice. This approach gives the network the possibility to capture 3D spatial information, with only a minor additional computational cost. In this study, we systematically evaluate the segmentation performance and computationa…
Convolutional neural networks (CNNs) are the current state-of-the-art meta-algorithm for volumetric segmentation of medical data, for example, to localize COVID-19 infected tissue on computer tomography scans or the detection of tumour volumes in magnetic resonance imaging. A key limitation of 3D CNNs on voxelised data is that the memory consumption grows cubically with the training data resolution. Occupancy networks (O-Nets) are an alternative for which the data is represented continuously in a function space and 3D shapes are learned as a continuous decision boundary. While O-Nets are signi…
Multi-Modal Brain Tumor Segmentation via 3D Multi-Scale Self-attention and Cross-attention
University of Electronic Science and Technology of China（电子科技大学）；School of Computer Science and Engineering, University of Electronic Science and Technology of China（电子科技大学计算机科学与工程学院）；School of Information and Software Engineering, University of Electronic Science and Technology of China（电子科技大学信息与软件工程学院）
Southeast University（东南大学）；Jiangsu Provincial Joint International Research Laboratory of Medical Information Processing（江苏省医学信息处理联合国际研究实验室）；Centre de Recherche en Information Biomédicale Sino-Français (CRIBs)（中法生物医学信息研究中心（CRIBs））
The nature of thick-slice scanning causes severe inter-slice discontinuities of 3D medical images, and the vanilla 2D/3D convolutional neural networks (CNNs) fail to represent sparse inter-slice information and dense intra-slice information in a balanced way, leading to severe underfitting to inter-slice features (for vanilla 2D CNNs) and overfitting to noise from long-range slices (for vanilla 3D CNNs). In this work, a novel mesh network (MNet) is proposed to balance the spatial representation inter axes via learning. 1) Our MNet latently fuses plenty of representation processes by embedding …
