Locally Rotation Invariant (LRI) operators have shown great potential in biomedical texture analysis where patterns appear at random positions and orientations. LRI operators can be obtained by computing the responses to the discrete rotation of local descriptors, such as Local Binary Patterns (LBP) or the Scale Invariant Feature Transform (SIFT). Other strategies achieve this invariance using Laplacian of Gaussian or steerable wavelets for instance, preventing the introduction of sampling errors during the discretization of the rotations. In this work, we obtain LRI operators via the local projection of the image on the spherical harmonics basis, followed by the computation of the bispectrum, which shares and extends the invariance properties of the spectrum. We investigate the benefits of using the bispectrum over the spectrum in the design of a LRI layer embedded in a shallow Convolutional Neural Network (CNN) for 3D image analysis. The performance of each design is evaluated on two datasets and compared against a standard 3D CNN. The first dataset is made of 3D volumes composed of synthetically generated rotated patterns, while the second contains malignant and benign pulmonary nodules in Computed Tomography (CT) images. The results indicate that bispectrum CNNs allows for a significantly better characterization of 3D textures than both the spectral and standard CNN. In addition, it can efficiently learn with fewer training examples and trainable parameters when compared to a standard convolutional layer.
Signal Intensity-weighted coordinate channels improve learning stability and generalisation in 1D and 2D CNNs in localisation tasks on biomedical signals
Department of Medical Sciences and Technology（医学科学与技术系）；Indian Institute of Technology Madras（印度理工学院马德拉斯）
TU Dresden（德累斯顿工业大学）；AICURA medical GmbH（AICURA医疗有限公司）；National Center of Tumor Diseases (NCT)（国家肿瘤疾病中心）；Max Planck Institute for Human Cognitive and Brain Sciences（马克斯·普朗克人类认知与脑科学研究所）
In recent years, Convolutional Neural Networks (CNNs) have become the state-of-the-art method for biomedical image analysis. However, these networks are usually trained in a supervised manner, requiring large amounts of labelled training data. These labelled data sets are often difficult to acquire in the biomedical domain. In this work, we validate alternative ways to train CNNs with fewer labels for biomedical image segmentation using. We adapt two semi- and self-supervised image classification methods and analyse their performance for semantic segmentation of biomedical microscopy images.
The convolutional neural network (CNN) has become a powerful tool for various biomedical image analysis tasks, but there is a lack of visual explanation for the machinery of CNNs. In this paper, we present a novel algorithm, Respond-weighted Class Activation Mapping (Respond-CAM), for making CNN-based models interpretable by visualizing input regions that are important for predictions, especially for biomedical 3D imaging data inputs. Our method uses the gradients of any target concept (e.g. the score of target class) that flows into a convolutional layer. The weighted feature maps are combine…
Does Bigger Mean Better? Comparitive Analysis of CNNs and Biomedical Vision Language Modles in Medical Diagnosis
University of Texas at Dallas（德克萨斯大学达拉斯分校）；Independent Researcher（独立研究者）；Duke University（杜克大学）；University of Michigan Ann Arbor（密歇根大学安娜堡分校）；Georgia Institute of Technology（佐治亚理工学院）；University of California, Irvine（加州大学 Irvine 分校）
Convolutional neural networks (CNNs) for biomedical image analysis are often of very large size, resulting in high memory requirement and high latency of operations. Searching for an acceptable compressed representation of the base CNN for a specific imaging application typically involves a series of time-consuming training/validation experiments to achieve a good compromise between network size and accuracy. To address this challenge, we propose CC-Net, a new image complexity-guided CNN compression scheme for biomedical image segmentation. Given a CNN model, CC-Net predicts the final accuracy…
University of Kaiserslautern（凯泽斯劳滕大学）；Istituto Dalle Molle di Studi sull’Intelligenza Artificiale (The Swiss AI Lab IDSIA)（达莱莫勒人工智能研究所（瑞士人工智能实验室IDSIA））；Scuola universitaria professionale della Svizzera italiana (SUPSI)（瑞士意大利语区应用科学大学（SUPSI））；Universitá della Svizzera italiana (USI)（瑞士意大利语区大学（USI））；German Research Center for Artificial Intelligence (DFKI)（德国人工智能研究中心（DFKI））
Convolutional Neural Networks (CNNs) can be shifted across 2D images or 3D videos to segment them. They have a fixed input size and typically perceive only small local contexts of the pixels to be classified as foreground or background. In contrast, Multi-Dimensional Recurrent NNs (MD-RNNs) can perceive the entire spatio-temporal context of each pixel in a few sweeps through all pixels, especially when the RNN is a Long Short-Term Memory (LSTM). Despite these theoretical advantages, however, unlike CNNs, previous MD-LSTM variants were hard to parallelize on GPUs. Here we re-arrange the traditi…
TTT-Unet: Enhancing U-Net with Test-Time Training Layers for Biomedical Image Segmentation
Lehigh University（里海大学）；Northeastern University（东北大学）；University of Notre Dame（圣母大学）；University of Georgia（佐治亚大学）；Massachusetts General Hospital（麻省总医院）；Harvard Medical School（哈佛医学院）
Sun Yat-sen University（中山大学）；The University of Hong Kong（香港大学）；Deepwise AI Lab（深智云人工智能实验室）
Recent progress in biomedical image segmentation based on deep convolutional neural networks (CNNs) has drawn much attention. However, its vulnerability towards adversarial samples cannot be overlooked. This paper is the first one that discovers that all the CNN-based state-of-the-art biomedical image segmentation models are sensitive to adversarial perturbations. This limits the deployment of these methods in safety-critical biomedical fields. In this paper, we discover that global spatial dependencies and global contextual information in a biomedical image can be exploited to defend against …
University at Buffalo（布法罗大学）；Beihang University（北京航空航天大学）；Kwai Inc.（快手公司）
In recent years, deep learning has dominated progress in the field of medical image analysis. We find however, that the ability of current deep learning approaches to represent the complex geometric structures of many medical images is insufficient. One limitation is that deep learning models require a tremendous amount of data, and it is very difficult to obtain a sufficient amount with the necessary detail. A second limitation is that there are underlying features of these medical images that are well established, but the black-box nature of existing convolutional neural networks (CNNs) do n…
Cancers are the leading cause of death in many countries. Early diagnosis plays a crucial role in having proper treatment for this debilitating disease. The automated classification of the type of cancer is a challenging task since pathologists must examine a huge number of histopathological images to detect infinitesimal abnormalities. In this study, we propose a novel convolutional neural network (CNN) architecture composed of a Concatenation of multiple Networks, called C-Net, to classify biomedical images. The model incorporates multiple CNNs including Outer, Middle, and Inner. The first t…
Compression is a standard procedure for making convolutional neural networks (CNNs) adhere to some specific computing resource constraints. However, searching for a compressed architecture typically involves a series of time-consuming training/validation experiments to determine a good compromise between network size and performance accuracy. To address this, we propose an image complexity-guided network compression technique for biomedical image segmentation. Given any resource constraints, our framework utilizes data complexity and network architecture to quickly estimate a compressed model …
In recent years, significant progress has been made in developing more accurate and efficient machine learning algorithms for segmentation of medical and natural images. In this review article, we highlight the imperative role of machine learning algorithms in enabling efficient and accurate segmentation in the field of medical imaging. We specifically focus on several key studies pertaining to the application of machine learning methods to biomedical image segmentation. We review classical machine learning algorithms such as Markov random fields, k-means clustering, random forest, etc. Althou…
U-Mamba: Enhancing Long-range Dependency for Biomedical Image Segmentation
Peter Munk Cardiac Centre, University Health Network（彼得·蒙克心脏中心，大学健康网络）；University of Toronto（多伦多大学）；Vector Institute for Artificial Intelligence（向量人工智能研究所）
University of Padua（帕多瓦大学）；Missouri State University（密苏里州立大学）；Tampere University（坦佩雷大学）
Recently, much attention has been devoted to finding highly efficient and powerful activation functions for CNN layers. Because activation functions inject different nonlinearities between layers that affect performance, varying them is one method for building robust ensembles of CNNs. The objective of this study is to examine the performance of CNN ensembles made with different activation functions, including six new ones presented here: 2D Mexican ReLU, TanELU, MeLU+GaLU, Symmetric MeLU, Symmetric GaLU, and Flexible MeLU. The highest performing ensemble was built with CNNs having different a…
Qatar University（卡塔尔大学）；Izmir University of Economics（伊兹密尔经济大学）；Tampere University of Technology（坦佩雷理工大学）
Computer-aided diagnosis (CAD) based on histopathological imaging has progressed rapidly in recent years with the rise of machine learning based methodologies. Traditional approaches consist of training a classification model using features extracted from the images, based on textures or morphological properties. Recently, deep-learning based methods have been applied directly to the raw (unprocessed) data. However, their usability is impacted by the paucity of annotated data in the biomedical sector. In order to leverage the learning capabilities of deep Convolutional Neural Nets (CNNs) withi…
From $\mathcal{O}(n^{2})$ to $\mathcal{O}(n)$ Parameters: Quantum Self-Attention in Vision Transformers for Biomedical Image Classification
UCL Hawkes Institute（UCL哈维斯研究所）；Department of Medical Physics and Biomedical Engineering（医学物理与生物医学工程系）；University College London（伦敦大学学院）；University College London Hospitals NHS Foundation Trust（伦敦大学学院医院国家健康服务信托基金会）；Human Physiology and Performance Laboratory (HPPL)（人体生理与表现实验室）；Centre for Peri-operative Medicine（围手术期医学中心）；Department of Targeted Intervention（精准干预系）；Division of Surgery and Interventional Science（外科与介入科学 division）
Objective: Multiple Sclerosis (MS) is an autoimmune, and demyelinating disease that leads to lesions in the central nervous system. This disease can be tracked and diagnosed using Magnetic Resonance Imaging (MRI). Up to now a multitude of multimodality automatic biomedical approaches is used to segment lesions which are not beneficial for patients in terms of cost, time, and usability. The authors of the present paper propose a method employing just one modality (FLAIR image) to segment MS lesions accurately. Methods: A patch-based Convolutional Neural Network (CNN) is designed, inspired by 3D…
Warsaw University of Technology（华沙理工大学）；Poznan University of Medical Sciences（波兹南医科大学）；Medical Centre Leeuwarden（吕伐登医疗中心）；Tooploox
Convolutional neural networks (CNNs) are used in many areas of computer vision, such as object tracking and recognition, security, military, and biomedical image analysis. This review presents the application of convolutional neural networks in one of the fields of dentistry - orthodontics. Advances in medical imaging technologies and methods allow CNNs to be used in orthodontics to shorten the planning time of orthodontic treatment, including an automatic search of landmarks on cephalometric X-ray images, tooth segmentation on Cone-Beam Computed Tomography (CBCT) images or digital models, and…
We present a new method for image reconstruction which replaces the projector in a projected gradient descent (PGD) with a convolutional neural network (CNN). CNNs trained as high-dimensional (image-to-image) regressors have recently been used to efficiently solve inverse problems in imaging. However, these approaches lack a feedback mechanism to enforce that the reconstructed image is consistent with the measurements. This is crucial for inverse problems, and more so in biomedical imaging, where the reconstructions are used for diagnosis. In our scheme, the gradient descent enforces measureme…
HybridMamba: A Dual-domain Mamba for 3D Medical Image Segmentation
The Hong Kong University of Science and Technology (Guangzhou)（香港科学与技术大学（广州））；Department of Radiology, Fudan University Shanghai Cancer Center（复旦大学上海肿瘤中心放射科）；Department of Oncology, Shanghai Medical College, Fudan University（复旦大学上海医学院肿瘤科）；The Hong Kong University of Science and Technology（香港科学与技术大学）
Segmentation of histological images is one of the most crucial tasks for many biomedical analyses including quantification of certain tissue type. However, challenges are posed by high variability and complexity of structural features in such images, in addition to imaging artifacts. Further, the conventional approach of manual thresholding is labor-intensive, and highly sensitive to inter- and intra-image intensity variations. An accurate and robust automated segmentation method is of high interest. We propose and evaluate an elegant convolutional neural network (CNN) designed for segmentatio…
xLSTM-UNet can be an Effective 2D & 3D Medical Image Segmentation Backbone with Vision-LSTM (ViL) better than its Mamba Counterpart
College of Computer Science and Technology, Zhejiang University（浙江大学计算机科学与技术学院）；KOKONI, Moxin (Huzhou) Tech. Co., LTD.（墨芯（湖州）科技有限公司KOKONI）；School of Information Engineering, Huzhou University（湖州师范学院信息工程学院）；Information Systems Technology and Design Pillar, Singapore University of Technology and Design（新加坡科技设计大学信息系统技术与设计 pillar）；School of Information Science and Technology, University of Science and Technology of China（中国科学技术大学信息科学技术学院）；School of Software Technology, Zhejiang University（浙江大学软件学院）
Recently, deep learning methods have achieved state-of-the-art performance in many medical image segmentation tasks. Many of these are based on convolutional neural networks (CNNs). For such methods, the encoder is the key part for global and local information extraction from input images; the extracted features are then passed to the decoder for predicting the segmentations. In contrast, several recent works show a superior performance with the use of transformers, which can better model long-range spatial dependencies and capture low-level details. However, transformer as sole encoder underp…
National Technical University of Athens（雅典国立技术大学）；National and Kapodistrian University of Athens（雅典国立卡波迪斯特里安大学）；Aretaieion Hospital（阿雷泰翁医院）
Deep Convolutional Neural Networks (CNNs) for image classification successively alternate convolutions and downsampling operations, such as pooling layers or strided convolutions, resulting in lower resolution features the deeper the network gets. These downsampling operations save computational resources and provide some translational invariance as well as a bigger receptive field at the next layers. However, an inherent side-effect of this is that high-level features, produced at the deep end of the network, are always captured in low resolution feature maps. The inverse is also true, as sha…
