Beyond Self-Attention: Deformable Large Kernel Attention for Medical Image Segmentation
RWTH Aachen University（亚琛工业大学）；Iran University of Science and Technology（伊朗科技大学）；Shahid Beheshti University（沙希德·贝赫什提大学）；Northwestern University（西北大学）；University of Regensburg（雷根斯堡大学）；Fraunhofer Institute for Digital Medicine MEVIS（弗劳恩霍夫数字医学研究所MEVIS）
Reza Azad, Leon Niggemeier, Michael Huttemann, Amirhossein Kazerouni, Ehsan Khodapanah Aghdam, Yury Velichko, Ulas Bagci, Dorit Merhof
Medical image segmentation has seen significant improvements with transformer models, which excel in grasping far-reaching contexts and global contextual information. However, the increasing computational demands of these models, proportional to the squared token count, limit their depth and resolution capabilities. Most current methods process D volumetric image data slice-by-slice (called pseudo 3D), missing crucial inter-slice information and thus reducing the model's overall performance. To address these challenges, we introduce the concept of \textbf{Deformable Large Kernel Attention (D-LKA Attention)}, a streamlined attention mechanism employing large convolution kernels to fully appreciate volumetric context. This mechanism operates within a receptive field akin to self-attention while sidestepping the computational overhead. Additionally, our proposed attention mechanism benefits from deformable convolutions to flexibly warp the sampling grid, enabling the model to adapt appropriately to diverse data patterns. We designed both 2D and 3D adaptations of the D-LKA Attention, with the latter excelling in cross-depth data understanding. Together, these components shape our novel hierarchical Vision Transformer architecture, the \textit{D-LKA Net}. Evaluations of our model against leading methods on popular medical segmentation datasets (Synapse, NIH Pancreas, and Skin lesion) demonstrate its superior performance. Our code implementation is publicly available at the: https://github.com/mindflow-institue/deformableLKA
University at Buffalo（布法罗大学）；OPPO US Research Center, InnoPeak Technology Inc.（OPPO美国研究中心，InnoPeak科技公司）
Video instance segmentation (VIS) task requires classifying, segmenting, and tracking object instances over all frames in a video clip. Recently, VisTR has been proposed as end-to-end transformer-based VIS framework, while demonstrating state-of-the-art performance. However, VisTR is slow to converge during training, requiring around 1000 GPU hours due to the high computational cost of its transformer attention module. To improve the training efficiency, we propose Deformable VisTR, leveraging spatio-temporal deformable attention module that only attends to a small fixed set of key spatio-temp…
Peking University（北京大学）；Beijing Institute of Big Data Research（北京大数据研究院）；Massachusetts General Hospital（麻省总医院）
Pap smear testing has been widely used for detecting cervical cancers based on the morphology properties of cell nuclei in microscopic image. An accurate nuclei segmentation could thus improve the success rate of cervical cancer screening. In this work, a method of automated cervical nuclei segmentation using Deformable Multipath Ensemble Model (D-MEM) is proposed. The approach adopts a U-shaped convolutional network as a backbone network, in which dense blocks are used to transfer feature information more effectively. To increase the flexibility of the model, we then use deformable convolutio…
Technical University of Munich（慕尼黑工业大学）；University of Melbourne（墨尔本大学）；German Aerospace Center（德国航空航天中心）
Training semantic segmentation models with few annotated samples has great potential in various real-world applications. For the few-shot segmentation task, the main challenge is how to accurately measure the semantic correspondence between the support and query samples with limited training data. To address this problem, we propose to aggregate the learnable covariance matrices with a deformable 4D Transformer to effectively predict the segmentation map. Specifically, in this work, we first devise a novel hard example mining mechanism to learn covariance kernels for the Gaussian process. The …
College of Computer Science and Technology, Zhejiang University of Technology（浙江工业大学计算机科学与技术学院）
Most instance segmentation models are not end-to-end trainable due to either the incorporation of proposal estimation (RPN) as a pre-processing or non-maximum suppression (NMS) as a post-processing. Here we propose a novel end-to-end instance segmentation method termed ISDA. It reshapes the task into predicting a set of object masks, which are generated via traditional convolution operation with learned position-aware kernels and features of objects. Such kernels and features are learned by leveraging a deformable attention network with multi-scale representation. Thanks to the introduced set-…
DTC: A Deformable Transposed Convolution Module for Medical Image Segmentation
Department of Health Outcomes and Biomedical Informatics, University of Florida（健康结果与生物医学信息学系，佛罗里达大学）；Regenstrief Institue, Indiana University, IU Health（Regenstrief研究所，印第安纳大学，IU健康）
Polyp segmentation is a crucial step towards computer-aided diagnosis of colorectal cancer. However, most of the polyp segmentation methods require pixel-wise annotated datasets. Annotated datasets are tedious and time-consuming to produce, especially for physicians who must dedicate their time to their patients. We tackle this issue by proposing a novel framework that can be trained using only weakly annotated images along with exploiting unlabeled images. To this end, we propose three ideas to address this problem, more specifically our contributions are: 1) a novel sparse foreground loss th…
While robotic manipulation of rigid objects is quite straightforward, coping with deformable objects is an open issue. More specifically, tasks like tying a knot, wiring a connector or even surgical suturing deal with the domain of Deformable Linear Objects (DLOs). In particular the detection of a DLO is a non-trivial problem especially under clutter and occlusions (as well as self-occlusions). The pose estimation of a DLO results into the identification of its parameters related to a designed model, e.g. a basis spline. It follows that the stand-alone segmentation of a DLO might not be suffic…
Shanghai Jiao Tong University（上海交通大学）；SJTU-ParisTech Elite Institute of Technology（上海交通大学-巴黎高科卓越工程学院）
Understanding the surrounding environment of the vehicle is still one of the challenges for autonomous driving. This paper addresses 360-degree road scene semantic segmentation using surround view cameras, which are widely equipped in existing production cars. First, in order to address large distortion problem in the fisheye images, Restricted Deformable Convolution (RDC) is proposed for semantic segmentation, which can effectively model geometric transformations by learning the shapes of convolutional filters conditioned on the input feature map. Second, in order to obtain a large-scale trai…
University of Bern（伯尔尼大学）；Alpen-Adria-Universität Klagenfurt（克拉根福阿尔卑斯-亚德里亚大学）
Semantic segmentation in cataract surgery has a wide range of applications contributing to surgical outcome enhancement and clinical risk reduction. However, the varying issues in segmenting the different relevant structures in these surgeries make the designation of a unique network quite challenging. This paper proposes a semantic segmentation network, termed DeepPyramid, that can deal with these challenges using three novelties: (1) a Pyramid View Fusion module which provides a varying-angle global view of the surrounding region centering at each pixel position in the input convolutional fe…
Harvard Medical School（哈佛医学院）；Massachusetts General Hospital（麻省总医院）；Peking University（北京大学）；Northeastern University（东北大学）
Reliable cell segmentation and classification from biomedical images is a crucial step for both scientific research and clinical practice. A major challenge for more robust segmentation and classification methods is the large variations in the size, shape and viewpoint of the cells, combining with the low image quality caused by noise and artifacts. To address this issue, in this work we propose a learning-based, simultaneous cell segmentation and classification method based on the deep U-Net structure with deformable convolution layers. The U-Net architecture for deep learning has been shown …
Boston University（波士顿大学）；American University in Cairo（开罗美国大学）；Worcester Polytechnic Institute（伍斯特理工学院）；University of Washington（华盛顿大学）；MIT-IBM Watson AI Lab（麻省理工学院-IBM沃森人工智能实验室）
Less than 35% of recyclable waste is being actually recycled in the US, which leads to increased soil and sea pollution and is one of the major concerns of environmental researchers as well as the common public. At the heart of the problem are the inefficiencies of the waste sorting process (separating paper, plastic, metal, glass, etc.) due to the extremely complex and cluttered nature of the waste stream. Recyclable waste detection poses a unique computer vision challenge as it requires detection of highly deformable and often translucent objects in cluttered scenes without the kind of conte…
Twin Deformable Point Convolutions for Point Cloud Semantic Segmentation in Remote Sensing Scenes
Aerospace Information Research Institute, Chinese Academy of Sciences（中国科学院空天信息创新研究院）；University of Chinese Academy of Sciences（中国科学院大学）；School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences（中国科学院大学电子电气与通信工程学院）
Semantic segmentation in cataract surgery has a wide range of applications contributing to surgical outcome enhancement and clinical risk reduction. However, the varying issues in segmenting the different relevant instances make the designation of a unique network quite challenging. This paper proposes a semantic segmentation network termed as DeepPyram that can achieve superior performance in segmenting relevant objects in cataract surgery videos with varying issues. This superiority mainly originates from three modules: (i) Pyramid View Fusion, which provides a varying-angle global view of t…
Technical University of Catalonia（加泰罗尼亚理工大学）；Technical University of Munich（慕尼黑工业大学）
Video Instance Segmentation (VIS) jointly tackles multi-object detection, tracking, and segmentation in video sequences. In the past, VIS methods mirrored the fragmentation of these subtasks in their architectural design, hence missing out on a joint solution. Transformers recently allowed to cast the entire VIS task as a single set-prediction problem. Nevertheless, the quadratic complexity of existing Transformer-based methods requires long training times, high memory requirements, and processing of low-single-scale feature maps. Deformable attention provides a more efficient alternative but …
Enhanced Deformable Convolution with Center-invariant Offset and Edge-aware Mask
Beihang University（北京航空航天大学）；Shanghai Academy of Spaceflight Technology（上海航天技术研究院）；Shanghai Radio Equipment Research Institute（上海无线电设备研究所）；Cardiff University（卡迪夫大学）；Shenzhen University（深圳大学）；Sun Yat-sen University（中山大学）；Lancaster University（兰卡斯特大学）
University of Leeds（利兹大学）；Leeds Institute for Cardiovascular and Metabolic Medicine（利兹心血管与代谢医学研究所）；KU Leuven（荷语鲁汶大学）；Alan Turing Institute（艾伦·图灵研究所）
Medical image registration is a challenging task involving the estimation of spatial transformations to establish anatomical correspondence between pairs or groups of images. Recently, deep learning-based image registration methods have been widely explored, and demonstrated to enable fast and accurate image registration in a variety of applications. However, most deep learning-based registration methods assume that the deformation fields are smooth and continuous everywhere in the image domain, which is not always true, especially when registering images whose fields of view contain discontin…
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…
In this paper, we propose a novel medical image segmentation using iterative deep learning framework. We have combined an iterative learning approach and an encoder-decoder network to improve segmentation results, which enables to precisely localize the regions of interest (ROIs) including complex shapes or detailed textures of medical images in an iterative manner. The proposed iterative deep convolutional encoder-decoder network consists of two main paths: convolutional encoder path and convolutional decoder path with iterative learning. Experimental results show that the proposed iterative …
CoMiX: Cross-Modal Fusion with Deformable Convolutions for HSI-X Semantic Segmentation
International Institute for Earth System Science, Nanjing University（南京大学国际地球系统科学学院）；Aerospace Information Research Institute, Chinese Academy of Sciences（中国科学院空天信息创新研究院）；University of Trento（特伦托大学）
DAUNet: A Lightweight UNet Variant with Deformable Convolutions and Parameter-Free Attention for Medical Image Segmentation
Department of Electrical Engineering (ISY), Information Coding (ICG), Linköping University（电气工程系（ISY）、信息编码系（ICG）、利厄普大学）；SDAIA-KFUPM Joint Research Center for Artificial Intelligence, King Fahd University of Petroleum & Minerals（SDAIA-KFUPM人工智能联合研究中心、国王法赫德石油大学）；Department of Computer Engineering, College of Computing and Mathematics, King Fahd University of Petroleum & Minerals（计算机工程系、计算与数学学院、国王法赫德石油大学）
Imperial College London（帝国理工学院）；BioMedIA Group, Department of Computing（计算系BioMedIA小组）
Few-shot semantic segmentation (FSS) has great potential for medical imaging applications. Most of the existing FSS techniques require abundant annotated semantic classes for training. However, these methods may not be applicable for medical images due to the lack of annotations. To address this problem we make several contributions: (1) A novel self-supervised FSS framework for medical images in order to eliminate the requirement for annotations during training. Additionally, superpixel-based pseudo-labels are generated to provide supervision; (2) An adaptive local prototype pooling module pl…
Generating precise class-aware pseudo ground-truths, a.k.a, class activation maps (CAMs), is essential for weakly-supervised semantic segmentation. The original CAM method usually produces incomplete and inaccurate localization maps. To tackle with this issue, this paper proposes an Expansion and Shrinkage scheme based on the offset learning in the deformable convolution, to sequentially improve the recall and precision of the located object in the two respective stages. In the Expansion stage, an offset learning branch in a deformable convolution layer, referred as "expansion sampler" seeks f…
We propose an attention mechanism for 3D medical image segmentation. The method, named segmentation-by-detection, is a cascade of a detection module followed by a segmentation module. The detection module enables a region of interest to come to attention and produces a set of object region candidates which are further used as an attention model. Rather than dealing with the entire volume, the segmentation module distills the information from the potential region. This scheme is an efficient solution for volumetric data as it reduces the influence of the surrounding noise which is especially im…
Southeast University（东南大学）；Swinburne University of Technology（斯威本科技大学）；Communication University of China（中国传媒大学）
Precise segmentation of organs and tumors plays a crucial role in clinical applications. It is a challenging task due to the irregular shapes and various sizes of organs and tumors as well as the significant class imbalance between the anatomy of interest (AOI) and the background region. In addition, in most situation tumors and normal organs often overlap in medical images, but current approaches fail to delineate both tumors and organs accurately. To tackle such challenges, we propose a position-guided deformable UNet, namely PGD-UNet, which exploits the spatial deformation capabilities of d…
Medical SAM Adapter: Adapting Segment Anything Model for Medical Image Segmentation
University of Oxford（牛津大学）；National University of Singapore（新加坡国立大学）；University of Alberta（阿尔伯塔大学）；A*STAR（新加坡科技研究局）；Carnegie Mellon University（卡内基梅隆大学）；Singapore Eye Research Institute（新加坡眼科研究所）；Mohamed bin Zayed University of Artificial Intelligence（穆罕默德·本·扎耶德人工智能大学）；University of Hongkong（香港大学）
本文提出Medical SAM Adapter（Med-SA），通过轻量适配技术将医学知识融入SAM，利用SD-Trans和HyP-Adpt适配2D模型至3D医学图像，在17个任务上以仅2%参数更新超越SOTA方法。
Université de technologie de Compiègne（贡比涅技术大学）；University of Rouen Normandy（诺曼底鲁昂大学）；Institut universitaire de France（法国大学研究院）
The investigation of uncertainty is of major importance in risk-critical applications, such as medical image segmentation. Belief function theory, a formal framework for uncertainty analysis and multiple evidence fusion, has made significant contributions to medical image segmentation, especially since the development of deep learning. In this paper, we provide an introduction to the topic of medical image segmentation methods using belief function theory. We classify the methods according to the fusion step and explain how information with uncertainty or imprecision is modeled and fused with …
Objective: Deformable image registration is a fundamental problem in medical image analysis, with applications such as longitudinal studies, population modeling, and atlas based image segmentation. Registration is often phrased as an optimization problem, i.e., finding a deformation field that is optimal according to a given objective function. Discrete, combinatorial, optimization techniques have successfully been employed to solve the resulting optimization problem. Specifically, optimization based on $α$-expansion with minimal graph cuts has been proposed as a powerful tool for image regist…
SEG-SAM: Semantic-Guided SAM for Unified Medical Image Segmentation
School of Electronic and Information Engineering, South China University of Technology（华南理工大学电子与信息工程学院）；Pazhou Lab（琶洲实验室）；College of Electronic and Information Engineering, Tongji University（同济大学电子与信息工程学院）
We propose a novel technique to incorporate attention within convolutional neural networks using feature maps generated by a separate convolutional autoencoder. Our attention architecture is well suited for incorporation with deep convolutional networks. We evaluate our model on benchmark segmentation datasets in skin cancer segmentation and lung lesion segmentation. Results show highly competitive performance when compared with U-Net and it's residual variant.
Convolutional neural networks (CNNs) are inherently limited to model geometric transformations due to the fixed geometric structures in its building modules. In this work, we introduce two new modules to enhance the transformation modeling capacity of CNNs, namely, deformable convolution and deformable RoI pooling. Both are based on the idea of augmenting the spatial sampling locations in the modules with additional offsets and learning the offsets from target tasks, without additional supervision. The new modules can readily replace their plain counterparts in existing CNNs and can be easily …
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…
Interdisciplinary Program in AI, Seoul National University（首尔国立大学人工智能跨学科项目）；Artificial Intelligence Institute, Seoul National University（首尔国立大学人工智能研究所）；Department of Computer Science, Seoul National University（首尔国立大学计算机科学系）
Northwestern Polytechnical University（西北工业大学）；The University of Adelaide（阿德莱德大学）；Australian Institute for Machine Learning（澳大利亚机器学习研究所）
Manual annotation of medical images is highly subjective, leading to inevitable and huge annotation biases. Deep learning models may surpass human performance on a variety of tasks, but they may also mimic or amplify these biases. Although we can have multiple annotators and fuse their annotations to reduce stochastic errors, we cannot use this strategy to handle the bias caused by annotators' preferences. In this paper, we highlight the issue of annotator-related biases on medical image segmentation tasks, and propose a Preference-involved Annotation Distribution Learning (PADL) framework to …
For medical image analysis, segmentation models trained on one or several domains lack generalization ability to unseen domains due to discrepancies between different data acquisition policies. We argue that the degeneration in segmentation performance is mainly attributed to overfitting to source domains and domain shift. To this end, we present a novel generalizable medical image segmentation method. To be specific, we design our approach as a multi-task paradigm by combining the segmentation model with a self-supervision domain-specific image restoration (DSIR) module for model regularizati…
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…
Medical Image Segmentation with Belief Function Theory and Deep Learning
University of Technology of Compiègne（贡比涅技术大学）；Heudiasyc Laboratory（欧洲计算机科学与自动化研究院）；University of Paris-Saclay（巴黎萨克雷大学）；University of Artois（阿图瓦大学）；ENSMM School（国立高等机械与微技术学院）；University of Rouen（鲁昂大学）
Segmentation of images is a long-standing challenge in medical AI. This is mainly due to the fact that training a neural network to perform image segmentation requires a significant number of pixel-level annotated data, which is often unavailable. To address this issue, we propose a semi-supervised image segmentation technique based on the concept of multi-view learning. In contrast to the previous art, we introduce an adversarial form of dual-view training and employ a critic to formulate the learning problem in multi-view training as a min-max problem. Thorough quantitative and qualitative e…
Shanghai Jiao Tong University（上海交通大学）；VoxelCloud, Inc.（体素云公司）；University of California, Los Angeles（加利福尼亚大学洛杉矶分校）
Despite the tremendous success of deep neural networks in medical image segmentation, they typically require a large amount of costly, expert-level annotated data. Few-shot segmentation approaches address this issue by learning to transfer knowledge from limited quantities of labeled examples. Incorporating appropriate prior knowledge is critical in designing high-performance few-shot segmentation algorithms. Since strong spatial priors exist in many medical imaging modalities, we propose a prototype-based method -- namely, the location-sensitive local prototype network -- that leverages spati…
Deep learning techniques have successfully been employed in numerous computer vision tasks including image segmentation. The techniques have also been applied to medical image segmentation, one of the most critical tasks in computer-aided diagnosis. Compared with natural images, the medical image is a gray-scale image with low-contrast (even with some invisible parts). Because some organs have similar intensity and texture with neighboring organs, there is usually a need to refine automatic segmentation results. In this paper, we propose an interactive deep refinement framework to improve the …
International Institute of Information Technology, Hyderabad（海得拉巴国际信息技术学院）
Handwritten documents are often characterized by dense and uneven layout. Despite advances, standard deep network based approaches for semantic layout segmentation are not robust to complex deformations seen across semantic regions. This phenomenon is especially pronounced for the low-resource Indic palm-leaf manuscript domain. To address the issue, we first introduce Indiscapes2, a new large-scale diverse dataset of Indic manuscripts with semantic layout annotations. Indiscapes2 contains documents from four different historical collections and is 150% larger than its predecessor, Indiscapes. …
Due to the limitation of available labeled data, medical image segmentation is a challenging task for deep learning. Traditional data augmentation techniques have been shown to improve segmentation network performances by optimizing the usage of few training examples. However, current augmentation approaches for segmentation do not tackle the strong texture bias of convolutional neural networks, observed in several studies. This work shows on the MoNuSeg dataset that style augmentation, which is already used in classification tasks, helps reducing texture over-fitting and improves segmentation…
Nanjing University of Science and Technology（南京理工大学）
Segmentation is one of the most important and popular tasks in medical image analysis, which plays a critical role in disease diagnosis, surgical planning, and prognosis evaluation. During the past five years, on the one hand, thousands of medical image segmentation methods have been proposed for various organs and lesions in different medical images, which become more and more challenging to fairly compare different methods. On the other hand, international segmentation challenges can provide a transparent platform to fairly evaluate and compare different methods. In this paper, we present a …
Generalizability is seen as one of the major challenges in deep learning, in particular in the domain of medical imaging, where a change of hospital or in imaging routines can lead to a complete failure of a model. To tackle this, we introduce Consistency Training, a training procedure and alternative to data augmentation based on maximizing models' prediction consistency across augmented and unaugmented data in order to facilitate better out-of-distribution generalization. To this end, we develop a novel region-based segmentation loss function called Segmentation Inconsistency Loss (SIL), whi…
Image segmentation is often performed on medical images for identifying diseases in clinical evaluation. Hence it has become one of the major research areas. Conventional image segmentation techniques are unable to provide satisfactory segmentation results for medical images as they contain irregularities. They need to be pre-processed before segmentation. In order to obtain the most suitable method for medical image segmentation, we propose a two stage algorithm. The first stage automatically generates a binary marker image of the region of interest using mathematical morphology. This marker …
South China University of Technology（华南理工大学）；University of Utah（犹他大学）
We introduce the idea of inter-slice image augmentation whereby the numbers of the medical images and the corresponding segmentation labels are increased between two consecutive images in order to boost medical image segmentation accuracy. Unlike conventional data augmentation methods in medical imaging, which only increase the number of training samples directly by adding new virtual samples using simple parameterized transformations such as rotation, flipping, scaling, etc., we aim to augment data based on the relationship between two consecutive images, which increases not only the number b…
