Semi-supervised learning for medical image segmentation is an important area of research for alleviating the huge cost associated with the construction of reliable large-scale annotations in the medical domain. Recent semi-supervised approaches have demonstrated promising results by employing consistency regularization, pseudo-labeling techniques, and adversarial learning. These methods primarily attempt to learn the distribution of labeled and unlabeled data by enforcing consistency in the predictions or embedding context. However, previous approaches have focused only on local discrepancy minimization or context relations across single classes. In this paper, we introduce a novel adversarial learning-based semi-supervised segmentation method that effectively embeds both local and global features from multiple hidden layers and learns context relations between multiple classes. Our voxel-wise adversarial learning method utilizes a voxel-wise feature discriminator, which considers multilayer voxel-wise features (involving both local and global features) as an input by embedding class-specific voxel-wise feature distribution. Furthermore, we improve our previous representation learning method by overcoming information loss and learning stability problems, which enables rich representations of labeled data. Our method outperforms current best-performing state-of-the-art semi-supervised learning approaches on the image segmentation of the left atrium (single class) and multiorgan datasets (multiclass). Moreover, our visual interpretation of the feature space demonstrates that our proposed method enables a well-distributed and separated feature space from both labeled and unlabeled data, which improves the overall prediction results.
Nanjing University of Aeronautics and Astronautics（南京航空航天大学）；Lingnan University（岭南大学）；Hong Kong Metropolitan University（香港都会大学）；The Education University of Hong Kong（香港教育大学）；Shenzhen Research Institute, Nanjing University of Aeronautics and Astronautics（南京航空航天大学深圳研究院）
Large imbalance often exists between the foreground points (i.e., objects) and the background points in outdoor LiDAR point clouds. It hinders cutting-edge detectors from focusing on informative areas to produce accurate 3D object detection results. This paper proposes a novel object detection network by semantical point-voxel feature interaction, dubbed PV-RCNN++. Unlike most of existing methods, PV-RCNN++ explores the semantic information to enhance the quality of object detection. First, a semantic segmentation module is proposed to retain more discriminative foreground keypoints. Such a mo…
Xiamen University（厦门大学）；Tencent（腾讯）；Xi’an Jiaotong University（西安交通大学）；Macau University of Science and Technology（澳门科技大学）
We introduce a one-shot segmentation method to alleviate the burden of manual annotation for medical images. The main idea is to treat one-shot segmentation as a classical atlas-based segmentation problem, where voxel-wise correspondence from the atlas to the unlabelled data is learned. Subsequently, segmentation label of the atlas can be transferred to the unlabelled data with the learned correspondence. However, since ground truth correspondence between images is usually unavailable, the learning system must be well-supervised to avoid mode collapse and convergence failure. To overcome this …
Geometrical Cross-Attention and Nonvoid Voxelization for Efficient 3D Medical Image Segmentation
organization= Shenzhen Institute for Advanced Study , addressline= University of Electronic Science；organization= School of Electrical；Electronic Engineering , addressline= Nanyang Technological University , city= Singapore , postcode= 639798 , country= Singapore；organization= School of Science；Engineering , addressline= The Chinese University of Hong Kong, Shenzhen , city= Shenzhen , postcode= 518172 , state= Guangdong , country= China；organization= School of Computer Science；Engineering , addressline= Kyungpook National University , city= Daegu , postcode= 37224 , country= South Korea；organization= Department of Electrical；Computer Engineering , addressline= University of Waterloo , city= Waterloo , postcode= N2L3G1 , state= Ontario , country= Canada
Towards Voxel Spacing Consistency for Medical Image Segmentation
Institute of Medical Robotics, Shanghai Jiao Tong University（上海交通大学医疗机器人研究院）；Department of Ultrasound, Shanghai Chest Hospital（上海市胸科医院超声科）；CAMPAR, Technical University of Munich（慕尼黑工业大学CAMPAR）
Tsinghua University（清华大学）；Microsoft Research Asia（微软亚洲研究院）
Sparse voxel-based 3D convolutional neural networks (CNNs) are widely used for various 3D vision tasks. Sparse voxel-based 3D CNNs create sparse non-empty voxels from the 3D input and perform 3D convolution operations on them only. We propose a simple yet effective padding scheme --- interpolation-aware padding to pad a few empty voxels adjacent to the non-empty voxels and involve them in the 3D CNN computation so that all neighboring voxels exist when computing point-wise features via the trilinear interpolation. For fine-grained 3D vision tasks where point-wise features are essential, like s…
Seoul National University（首尔国立大学）；Soongsil University（崇实大学）
Recent works in medical image segmentation have actively explored various deep learning architectures or objective functions to encode high-level features from volumetric data owing to limited image annotations. However, most existing approaches tend to ignore cross-volume global context and define context relations in the decision space. In this work, we propose a novel voxel-level Siamese representation learning method for abdominal multi-organ segmentation to improve representation space. The proposed method enforces voxel-wise feature relations in the representation space for leveraging li…
Shanghai Jiao Tong University（上海交通大学）；East China Normal University（华东师范大学）
Existing automatic 3D image segmentation methods usually fail to meet the clinic use. Many studies have explored an interactive strategy to improve the image segmentation performance by iteratively incorporating user hints. However, the dynamic process for successive interactions is largely ignored. We here propose to model the dynamic process of iterative interactive image segmentation as a Markov decision process (MDP) and solve it with reinforcement learning (RL). Unfortunately, it is intractable to use single-agent RL for voxel-wise prediction due to the large exploration space. To reduce …
Artificial Intelligence Research Institute (AIRI)（人工智能研究院（AIRI））；Moscow Institute of Physics and Technology（莫斯科物理技术学院）；Skolkovo Institute of Science and Technology（斯科尔科沃科学技术研究院）
When applying a Deep Learning model to medical images, it is crucial to estimate the model uncertainty. Voxel-wise uncertainty is a useful visual marker for human experts and could be used to improve the model's voxel-wise output, such as segmentation. Moreover, uncertainty provides a solid foundation for out-of-distribution (OOD) detection, improving the model performance on the image-wise level. However, one of the frequent tasks in medical imaging is the segmentation of distinct, local structures such as tumors or lesions. Here, the structure-wise uncertainty allows more precise operations …
Yale University（耶鲁大学）；The University of Texas at Austin（德克萨斯大学奥斯汀分校）
Contrastive learning (CL) aims to learn useful representation without relying on expert annotations in the context of medical image segmentation. Existing approaches mainly contrast a single positive vector (i.e., an augmentation of the same image) against a set of negatives within the entire remainder of the batch by simply mapping all input features into the same constant vector. Despite the impressive empirical performance, those methods have the following shortcomings: (1) it remains a formidable challenge to prevent the collapsing problems to trivial solutions; and (2) we argue that not a…
The Chinese University of Hong Kong（香港中文大学）；The University of Hong Kong（香港大学）；MEGVII Technology（旷视科技）；SmartMore（思谋科技）
In this work, we present a conceptually simple yet effective framework for cross-modality 3D object detection, named voxel field fusion. The proposed approach aims to maintain cross-modality consistency by representing and fusing augmented image features as a ray in the voxel field. To this end, the learnable sampler is first designed to sample vital features from the image plane that are projected to the voxel grid in a point-to-ray manner, which maintains the consistency in feature representation with spatial context. In addition, ray-wise fusion is conducted to fuse features with the supple…
Department of Electrical Engineering, City Univeristy of Hong Kong, Hong Kong
Noisy labels collected with limited annotation cost prevent medical image segmentation algorithms from learning precise semantic correlations. Previous segmentation arts of learning with noisy labels merely perform a pixel-wise manner to preserve semantics, such as pixel-wise label correction, but neglect the pair-wise manner. In fact, we observe that the pair-wise manner capturing affinity relations between pixels can greatly reduce the label noise rate. Motivated by this observation, we present a novel perspective for noisy mitigation by incorporating both pixel-wise and pair-wise manners, w…
Conservatoire National des Arts et Métiers（法国国立工艺学院）；IRCAD（消化癌症研究所）
Transformer models achieve state-of-the-art results for image segmentation. However, achieving long-range attention, necessary to capture global context, with high-resolution 3D images is a fundamental challenge. This paper introduces the Full resolutIoN mEmory (FINE) transformer to overcome this issue. The core idea behind FINE is to learn memory tokens to indirectly model full range interactions while scaling well in both memory and computational costs. FINE introduces memory tokens at two levels: the first one allows full interaction between voxels within local image regions (patches), the …
We present a novel lightweight convolutional neural network for point cloud analysis. In contrast to many current CNNs which increase receptive field by downsampling point cloud, our method directly operates on the entire point sets without sampling and achieves good performances efficiently. Our network consists of point voxel convolution (PVC) layer as building block. Each layer has two parallel branches, namely the voxel branch and the point branch. For the voxel branch specifically, we aggregate local features on non-empty voxel centers to reduce geometric information loss caused by voxeli…
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…
Yale University（耶鲁大学）；The University of Texas at Austin（德克萨斯大学奥斯汀分校）
Automated segmentation in medical image analysis is a challenging task that requires a large amount of manually labeled data. However, most existing learning-based approaches usually suffer from limited manually annotated medical data, which poses a major practical problem for accurate and robust medical image segmentation. In addition, most existing semi-supervised approaches are usually not robust compared with the supervised counterparts, and also lack explicit modeling of geometric structure and semantic information, both of which limit the segmentation accuracy. In this work, we present S…
Uncertainty-aware Evidential Fusion-based Learning for Semi-supervised Medical Image Segmentation
Key Laboratory of High Confidence Software Technologies (Peking University)（高可信软件技术重点实验室（北京大学））；Department of Computer and Information Science, University of Macau（澳门大学计算机与信息科学系）
Recently, a variety of vision transformers have been developed as their capability of modeling long-range dependency. In current transformer-based backbones for medical image segmentation, convolutional layers were replaced with pure transformers, or transformers were added to the deepest encoder to learn global context. However, there are mainly two challenges in a scale-wise perspective: (1) intra-scale problem: the existing methods lacked in extracting local-global cues in each scale, which may impact the signal propagation of small objects; (2) inter-scale problem: the existing methods fai…
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…
Despite the success of deep learning methods in medical image segmentation tasks, the human-level performance relies on massive training data with high-quality annotations, which are expensive and time-consuming to collect. The fact is that there exist low-quality annotations with label noise, which leads to suboptimal performance of learned models. Two prominent directions for segmentation learning with noisy labels include pixel-wise noise robust training and image-level noise robust training. In this work, we propose a novel framework to address segmenting with noisy labels by distilling ef…
Recently deep residual learning with residual units for training very deep neural networks advanced the state-of-the-art performance on 2D image recognition tasks, e.g., object detection and segmentation. However, how to fully leverage contextual representations for recognition tasks from volumetric data has not been well studied, especially in the field of medical image computing, where a majority of image modalities are in volumetric format. In this paper we explore the deep residual learning on the task of volumetric brain segmentation. There are at least two main contributions in our work.…
We present Hybrid Voxel Network (HVNet), a novel one-stage unified network for point cloud based 3D object detection for autonomous driving. Recent studies show that 2D voxelization with per voxel PointNet style feature extractor leads to accurate and efficient detector for large 3D scenes. Since the size of the feature map determines the computation and memory cost, the size of the voxel becomes a parameter that is hard to balance. A smaller voxel size gives a better performance, especially for small objects, but a longer inference time. A larger voxel can cover the same area with a smaller f…
Fully convolutional networks (FCNs), including UNet and VNet, are widely-used network architectures for semantic segmentation in recent studies. However, conventional FCN is typically trained by the cross-entropy or Dice loss, which only calculates the error between predictions and ground-truth labels for pixels individually. This often results in non-smooth neighborhoods in the predicted segmentation. To address this problem, we propose a two-stage framework, with the first stage to quickly localize the prostate region and the second stage to precisely segment the prostate by a multi-task UNe…
Optimal surface segmentation is a state-of-the-art method used for segmentation of multiple globally optimal surfaces in volumetric datasets. The method is widely used in numerous medical image segmentation applications. However, nodes in the graph based optimal surface segmentation method typically encode uniformly distributed orthogonal voxels of the volume. Thus the segmentation cannot attain an accuracy greater than a single unit voxel, i.e. the distance between two adjoining nodes in graph space. Segmentation accuracy higher than a unit voxel is achievable by exploiting partial volume inf…
The autonomous car must recognize the driving environment quickly for safe driving. As the Light Detection And Range (LiDAR) sensor is widely used in the autonomous car, fast semantic segmentation of LiDAR point cloud, which is the point-wise classification of the point cloud within the sensor framerate, has attracted attention in recognition of the driving environment. Although the voxel and fusion-based semantic segmentation models are the state-of-the-art model in point cloud semantic segmentation recently, their real-time performance suffer from high computational load due to high voxel re…
Illinois Institute of Technology（伊利诺伊理工学院）；University of Michigan（密歇根大学）
Recently, due to the increasing requirements of medical imaging applications and the professional requirements of annotating medical images, few-shot learning has gained increasing attention in the medical image semantic segmentation field. To perform segmentation with limited number of labeled medical images, most existing studies use Proto-typical Networks (PN) and have obtained compelling success. However, these approaches overlook the query image features extracted from the proposed representation network, failing to preserving the spatial connection between query and support images. In th…
EPL: Evidential Prototype Learning for Semi-supervised Medical Image Segmentation
Key Laboratory of High Confidence Software Technologies (Peking University)（高可信软件技术重点实验室（北京大学））；School of Computer Science, Peking University（北京大学计算机学院）
Sun Yat-Sen University（中山大学）；Xidian University（西安电子科技大学）；The Sixth Affiliated Hospital, Sun Yat-sen University（中山大学附属第六医院）
Semi-supervised learning (SSL), which aims at leveraging a few labeled images and a large number of unlabeled images for network training, is beneficial for relieving the burden of data annotation in medical image segmentation. According to the experience of medical imaging experts, local attributes such as texture, luster and smoothness are very important factors for identifying target objects like lesions and polyps in medical images. Motivated by this, we propose a cross-level contrastive learning scheme to enhance representation capacity for local features in semi-supervised medical image …
Medical image segmentation, or computing voxelwise semantic masks, is a fundamental yet challenging task to compute a voxel-level semantic mask. To increase the ability of encoder-decoder neural networks to perform this task across large clinical cohorts, contrastive learning provides an opportunity to stabilize model initialization and enhance encoders without labels. However, multiple target objects (with different semantic meanings) may exist in a single image, which poses a problem for adapting traditional contrastive learning methods from prevalent 'image-level classification' to 'pixel-l…
Deep learning highly relies on the quantity of annotated data. However, the annotations for 3D volumetric medical data require experienced physicians to spend hours or even days for investigation. Self-supervised learning is a potential solution to get rid of the strong requirement of training data by deeply exploiting raw data information. In this paper, we propose a novel self-supervised learning framework for volumetric medical images. Specifically, we propose a context restoration task, i.e., Rubik's cube++, to pre-train 3D neural networks. Different from the existing context-restoration-b…
Segmentation of findings in the gastrointestinal tract is a challenging but also an important task which is an important building stone for sufficient automatic decision support systems. In this work, we present our solution for the Medico 2020 task, which focused on the problem of colon polyp segmentation. We present our simple but efficient idea of using an augmentation method that uses grids in a pyramid-like manner (large to small) for segmentation. Our results show that the proposed methods work as indented and can also lead to comparable results when competing with other methods.
Beijing Institute of Technology（北京理工大学）；Renmin University of China（中国人民大学）；University of Minnesota（明尼苏达大学）
Deep learning methods have contributed substantially to the rapid advancement of medical image segmentation, the quality of which relies on the suitable design of loss functions. Popular loss functions, including the cross-entropy and dice losses, often fall short of boundary detection, thereby limiting high-resolution downstream applications such as automated diagnoses and procedures. We developed a novel loss function that is tailored to reflect the boundary information to enhance the boundary detection. As the contrast between segmentation and background regions along the classification bou…
Leveraging Labelled Data Knowledge: A Cooperative Rectification Learning Network for Semi-supervised 3D Medical Image Segmentation
School of Mechanical Engineering and Automation, Northeastern University（东北大学机械工程与自动化学院）；Australian Institute for Machine Learning, University of Adelaide（阿德莱德大学澳大利亚机器学习研究所）；Centre for Vision, Speech and Signal Processing (CVSSP), University of Surrey（萨里大学视觉、语音与信号处理中心）
Deep neural network models used for medical image segmentation are large because they are trained with high-resolution three-dimensional (3D) images. Graphics processing units (GPUs) are widely used to accelerate the trainings. However, the memory on a GPU is not large enough to train the models. A popular approach to tackling this problem is patch-based method, which divides a large image into small patches and trains the models with these small patches. However, this method would degrade the segmentation quality if a target object spans multiple patches. In this paper, we propose a novel app…
College of Computer Science and Technology, Huaqiao University（华侨大学计算机科学与技术学院）；School of Economics and Finance, Huaqiao University（华侨大学经济与金融学院）
Despite the remarkable performance of deep learning methods on various tasks, most cutting-edge models rely heavily on large-scale annotated training examples, which are often unavailable for clinical and health care tasks. The labeling costs for medical images are very high, especially in medical image segmentation, which typically requires intensive pixel/voxel-wise labeling. Therefore, the strong capability of learning and generalizing from limited supervision, including a limited amount of annotations, sparse annotations, and inaccurate annotations, is crucial for the successful applicatio…
City University of Hong Kong（香港城市大学）；University College London（伦敦大学学院）
Dice similarity coefficient (DSC) and Hausdorff distance (HD) are widely used for evaluating medical image segmentation. They have also been criticised, when reported alone, for their unclear or even misleading clinical interpretation. DSCs may also differ substantially from HDs, due to boundary smoothness or multiple regions of interest (ROIs) within a subject. More importantly, either metric can also have a nonlinear, non-monotonic relationship with outcomes based on Type 1 and 2 errors, designed for specific clinical decisions that use the resulting segmentation. Whilst cases causing disagr…
vox2vec: A Framework for Self-supervised Contrastive Learning of Voxel-level Representations in Medical Images
Skolkovo Institute of Science and Technology（斯科尔科沃科学技术研究院）；Artificial Intelligence Research Institute (AIRI)（人工智能研究院（AIRI））；Institute for Information Transmission Problems（信息传输问题研究所）；IRA-Labs（IRA实验室）
Computer Science and Artificial Intelligence Lab, MIT（麻省理工学院计算机科学与人工智能实验室）；Meinig School of Biomedical Engineering, Cornell University（康奈尔大学迈尼格生物医学工程学院）；Martinos Center for Biomedical Imaging, MGH, HMS（麻省总医院哈佛医学院马蒂诺生物医学成像中心）
We present VoxelMorph, a fast learning-based framework for deformable, pairwise medical image registration. Traditional registration methods optimize an objective function for each pair of images, which can be time-consuming for large datasets or rich deformation models. In contrast to this approach, and building on recent learning-based methods, we formulate registration as a function that maps an input image pair to a deformation field that aligns these images. We parameterize the function via a convolutional neural network (CNN), and optimize the parameters of the neural network on a set of…
We present an edge preserving and denoising filter for enhancing the features in images, which contain an ROI having a narrow spatial extent. Typical examples include angiograms, or ROI spatially distributed in multiple locations and contained within an outlying region, such as in multiple-sclerosis. The filtering involves determination of multiplicative weights in the spatial domain using an extended set of neighborhood directions. Equivalently, the filtering operation may be interpreted as a combination of directional filters in the frequency domain, with selective weighting for spatial freq…
