We propose a new model for digital pathology segmentation, based on the observation that histopathology images are inherently symmetric under rotation and reflection. Utilizing recent findings on rotation equivariant CNNs, the proposed model leverages these symmetries in a principled manner. We present a visual analysis showing improved stability on predictions, and demonstrate that exploiting rotation equivariance significantly improves tumor detection performance on a challenging lymph node metastases dataset. We further present a novel derived dataset to enable principled comparison of machine learning models, in combination with an initial benchmark. Through this dataset, the task of histopathology diagnosis becomes accessible as a challenging benchmark for fundamental machine learning research.
F. Hoffmann-La Roche AG（罗氏制药）；Genentech, Inc.（基因泰克公司）
Recently, vision transformers were shown to be capable of outperforming convolutional neural networks when pretrained on sufficient amounts of data. In comparison to convolutional neural networks, vision transformers have a weaker inductive bias and therefore allow a more flexible feature detection. Due to their promising feature detection, this work explores vision transformers for tumor detection in digital pathology whole slide images in four tissue types, and for tissue type identification. We compared the patch-wise classification performance of the vision transformer DeiT-Tiny to the sta…
Lausanne University Hospital（洛桑大学医院）；University of Applied Sciences Western Switzerland (HES-SO)（瑞士西部应用科学大学（HES-SO））
Convolutional Neural Networks (CNNs) traditionally encode translation equivariance via the convolution operation. Generalization to other transformations has recently received attraction to encode the knowledge of the data geometry in group convolution operations. Equivariance to rotation is particularly important for 3D image analysis due to the large diversity of possible pattern orientations. 3D texture is a particularly important cue for the analysis of medical images such as CT and MRI scans as it describes different types of tissues and lesions. In this paper, we evaluate the use of 3D g…
The field of computational pathology presents many challenges for computer vision algorithms due to the sheer size of pathology images. Histopathology images are large and need to be split up into image tiles or patches so modern convolutional neural networks (CNNs) can process them. In this work, we present a method to generate an interpretable image representation of computational pathology images using quadtrees and a pipeline to use these representations for highly accurate downstream classification. To the best of our knowledge, this is the first attempt to use quadtrees for pathology ima…
Radboud University Medical Center（拉德堡德大学医学中心）；Linköping University（林雪平大学）
Stain variation is a phenomenon observed when distinct pathology laboratories stain tissue slides that exhibit similar but not identical color appearance. Due to this color shift between laboratories, convolutional neural networks (CNNs) trained with images from one lab often underperform on unseen images from the other lab. Several techniques have been proposed to reduce the generalization error, mainly grouped into two categories: stain color augmentation and stain color normalization. The former simulates a wide variety of realistic stain variations during training, producing stain-invarian…
Pathology slides of lung malignancies are classified using resource-frugal convolution neural networks (CNNs) that may be deployed on mobile devices. In particular, the challenging task of distinguishing adenocarcinoma (LUAD) and squamous-cell carcinoma (LUSC) lung cancer subtypes is approached in two stages. First, whole-slide histopathology images are downsampled to a size too large for CNN analysis but large enough to retain key anatomic detail. The downsampled images are decomposed into smaller square tiles, which are sifted based on their image entropies. A lightweight CNN produces tile-l…
Qualcomm AI Research（高通人工智能研究院）；University of Amsterdam（阿姆斯特丹大学）
The principle of equivariance to symmetry transformations enables a theoretically grounded approach to neural network architecture design. Equivariant networks have shown excellent performance and data efficiency on vision and medical imaging problems that exhibit symmetries. Here we show how this principle can be extended beyond global symmetries to local gauge transformations. This enables the development of a very general class of convolutional neural networks on manifolds that depend only on the intrinsic geometry, and which includes many popular methods from equivariant and geometric deep…
The Norwegian University of Science and Technology（挪威科技大学）；St. Olavs Hospital, Trondheim University Hospital（圣奥拉夫斯医院，特隆赫姆大学医院）；SINTEF
Deep convolutional neural networks (CNNs) are the current state-of-the-art for digital analysis of histopathological images. The large size of whole-slide microscopy images (WSIs) requires advanced memory handling to read, display and process these images. There are several open-source platforms for working with WSIs, but few support deployment of CNN models. These applications use third-party solutions for inference, making them less user-friendly and unsuitable for high-performance image analysis. To make deployment of CNNs user-friendly and feasible on low-end machines, we have developed a …
Macquarie University（麦考瑞大学）；University of Technology Sydney（悉尼科技大学）；The University of Sydney（悉尼大学）
Automatic tumor 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 regular CNNs can only exploit translation invariance, ignoring further inherent symmetries existing in medical images such as rotations and reflections. To mitigate this shortcoming, we propose a novel group equivariant segmentation framework by encoding those inherent symmetries for learning mor…
Equivariant Imaging Biomarkers for Robust Unsupervised Segmentation of Histopathology
Department of Biomedical Engineering, Yale University（生物医学工程系，耶鲁大学）；Department of Radiology & Biomedical Imaging, Yale University（放射科与生物医学成像系，耶鲁大学）；Department of Urology, Yale University（泌尿外科系，耶鲁大学）；Medical Scientist Training Program, Yale University（医学科学家培训计划，耶鲁大学）
Université de Strasbourg（斯特拉斯堡大学）；Hannover Medical School（汉诺威医学院）；Université de Haute Alsace（上阿尔萨斯大学）
An important part of Digital Pathology is the analysis of multiple digitised whole slide images from differently stained tissue sections. It is common practice to mount consecutive sections containing corresponding microscopic structures on glass slides, and to stain them differently to highlight specific tissue components. These multiple staining modalities result in very different images but include a significant amount of consistent image information. Deep learning approaches have recently been proposed to analyse these images in order to automatically identify objects of interest for patho…
Sunnybrook Research Institute（森尼布鲁克研究所）；University of Toronto（多伦多大学）；Sunnybrook Health Sciences Centre（森尼布鲁克健康科学中心）
Digital pathology has advanced substantially over the last decade however tumor localization continues to be a challenging problem due to highly complex patterns and textures in the underlying tissue bed. The use of convolutional neural networks (CNNs) to analyze such complex images has been well adopted in digital pathology. However in recent years, the architecture of CNNs have altered with the introduction of inception modules which have shown great promise for classification tasks. In this paper, we propose a modified "transition" module which learns global average pooling layers from filt…
University College London（伦敦大学学院）；Kagenova Limited（Kagenova有限公司）
This paper demonstrates spherical convolutional neural networks (S-CNN) offer distinct advantages over conventional fully-connected networks (FCN) at estimating scalar parameters of tissue microstructure from diffusion MRI (dMRI). Such microstructure parameters are valuable for identifying pathology and quantifying its extent. However, current clinical practice commonly acquires dMRI data consisting of only 6 diffusion weighted images (DWIs), limiting the accuracy and precision of estimated microstructure indices. Machine learning (ML) has been proposed to address this challenge. However, exis…
Qualcomm AI Research（高通AI研究院）；Qualcomm Technologies, Inc.（高通技术公司）；University of Amsterdam（阿姆斯特丹大学）
A common approach to define convolutions on meshes is to interpret them as a graph and apply graph convolutional networks (GCNs). Such GCNs utilize isotropic kernels and are therefore insensitive to the relative orientation of vertices and thus to the geometry of the mesh as a whole. We propose Gauge Equivariant Mesh CNNs which generalize GCNs to apply anisotropic gauge equivariant kernels. Since the resulting features carry orientation information, we introduce a geometric message passing scheme defined by parallel transporting features over mesh edges. Our experiments validate the significan…
Institute of Information Systems, HES-SO (University of Applied Sciences and Arts Western Switzerland)（瑞士西部应用科学与艺术大学 信息系统研究所）；Department of Computer Science, University of Geneva（日内瓦大学 计算机科学系）；Department of Neurosciences, University of Padua（帕多瓦大学 神经科学系）；Inselspital, Bern Hospital（伯尔尼大学医院）；Medical Faculty, University of Geneva（日内瓦大学 医学院）
Computational pathology is a domain that aims to develop algorithms to automatically analyze large digitized histopathology images, called whole slide images (WSI). WSIs are produced scanning thin tissue samples that are stained to make specific structures visible. They show stain colour heterogeneity due to different preparation and scanning settings applied across medical centers. Stain colour heterogeneity is a problem to train convolutional neural networks (CNN), the state-of-the-art algorithms for most computational pathology tasks, since CNNs usually underperform when tested on images in…
Unsupervised learning enables modeling complex images without the need for annotations. The representation learned by such models can facilitate any subsequent analysis of large image datasets. However, some generative factors that cause irrelevant variations in images can potentially get entangled in such a learned representation causing the risk of negatively affecting any subsequent use. The orientation of imaged objects, for instance, is often arbitrary/irrelevant, thus it can be desired to learn a representation in which the orientation information is disentangled from all other factors. …
Qualcomm AI Research（高通人工智能研究院）；Qualcomm Technologies Netherlands B.V.（高通科技荷兰有限公司）；EPFL（洛桑联邦理工学院）；U. of Amsterdam（阿姆斯特丹大学）
We present a general theory of Group equivariant Convolutional Neural Networks (G-CNNs) on homogeneous spaces such as Euclidean space and the sphere. Feature maps in these networks represent fields on a homogeneous base space, and layers are equivariant maps between spaces of fields. The theory enables a systematic classification of all existing G-CNNs in terms of their symmetry group, base space, and field type. We also consider a fundamental question: what is the most general kind of equivariant linear map between feature spaces (fields) of given types? Following Mackey, we show that such ma…
Qualcomm Research, Qualcomm Technologies Netherlands B.V.（高通研究，高通技术荷兰有限公司）；EPFL（洛桑联邦理工学院）；University of Amsterdam（阿姆斯特丹大学）
Group equivariant and steerable convolutional neural networks (regular and steerable G-CNNs) have recently emerged as a very effective model class for learning from signal data such as 2D and 3D images, video, and other data where symmetries are present. In geometrical terms, regular G-CNNs represent data in terms of scalar fields ("feature channels"), whereas the steerable G-CNN can also use vector or tensor fields ("capsules") to represent data. In algebraic terms, the feature spaces in regular G-CNNs transform according to a regular representation of the group G, whereas the feature spaces …
DPSeq: A Novel and Efficient Digital Pathology Classifier for Predicting Cancer Biomarkers using Sequencer Architecture
School of Data Science, University of Science and Technology of China（中国科学技术大学数据科学学院）；School of Management, University of Science and Technology of China（中国科学技术大学管理学院）；School of Population Health, UNSW Sydney（新南威尔士大学悉尼分校人口健康学院）；Genmab Inc.（杰特贝公司）
Supporting Mitosis Detection AI Training with Inter-Observer Eye-Gaze Consistencies
University of California, Los Angeles（加利福尼亚大学洛杉矶分校）；University of Illinois, Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）；UCLA David Geffen School of Medicine（加州大学洛杉矶分校大卫·格芬医学院）；Kansas University Medical Center（堪萨斯大学医学中心）
Peking University（北京大学）；The Chinese University of Hong Kong（香港中文大学）；Pazhou Lab（琶洲实验室）
Spherical signals exist in many applications, e.g., planetary data, LiDAR scans and digitalization of 3D objects, calling for models that can process spherical data effectively. It does not perform well when simply projecting spherical data into the 2D plane and then using planar convolution neural networks (CNNs), because of the distortion from projection and ineffective translation equivariance. Actually, good principles of designing spherical CNNs are avoiding distortions and converting the shift equivariance property in planar CNNs to rotation equivariance in the spherical domain. In this …
The big empirical success of group equivariant networks has led in recent years to the sprouting of a great variety of equivariant network architectures. A particular focus has thereby been on rotation and reflection equivariant CNNs for planar images. Here we give a general description of $E(2)$-equivariant convolutions in the framework of Steerable CNNs. The theory of Steerable CNNs thereby yields constraints on the convolution kernels which depend on group representations describing the transformation laws of feature spaces. We show that these constraints for arbitrary group representations…
Automatic Cardiac Pathology Recognition in Echocardiography Images Using Higher Order Dynamic Mode Decomposition and a Vision Transformer for Small Datasets
Universidad Politécnica de Madrid（马德里理工大学）；Centro Nacional de Investigaciones Cardiovasculares (CNIC)（国家心血管研究中心）；Universidad Complutense de Madrid（马德里康普顿斯大学）；Center for Computational Simulation (CCS)（计算仿真中心）
Rotation-invariance is a desired property of machine-learning models for medical image analysis and in particular for computational pathology applications. We propose a framework to encode the geometric structure of the special Euclidean motion group SE(2) in convolutional networks to yield translation and rotation equivariance via the introduction of SE(2)-group convolution layers. This structure enables models to learn feature representations with a discretized orientation dimension that guarantees that their outputs are invariant under a discrete set of rotations. Conventional approaches fo…
University of Amsterdam（阿姆斯特丹大学）；University of Heidelberg（海德堡大学）
In many machine learning tasks it is desirable that a model's prediction transforms in an equivariant way under transformations of its input. Convolutional neural networks (CNNs) implement translational equivariance by construction; for other transformations, however, they are compelled to learn the proper mapping. In this work, we develop Steerable Filter CNNs (SFCNNs) which achieve joint equivariance under translations and rotations by design. The proposed architecture employs steerable filters to efficiently compute orientation dependent responses for many orientations without suffering int…
The fast growing deep learning technologies have become the main solution of many machine learning problems for medical image analysis. Deep convolution neural networks (CNNs), as one of the most important branch of the deep learning family, have been widely investigated for various computer-aided diagnosis tasks including long-term problems and continuously emerging new problems. Image contour detection is a fundamental but challenging task that has been studied for more than four decades. Recently, we have witnessed the significantly improved performance of contour detection thanks to the de…
UvA-Bosch Delta Lab（阿姆斯特丹大学-博世德尔塔实验室）；University of Amsterdam（阿姆斯特丹大学）
The effectiveness of Convolutional Neural Networks (CNNs) has been substantially attributed to their built-in property of translation equivariance. However, CNNs do not have embedded mechanisms to handle other types of transformations. In this work, we pay attention to scale changes, which regularly appear in various tasks due to the changing distances between the objects and the camera. First, we introduce the general theory for building scale-equivariant convolutional networks with steerable filters. We develop scale-convolution and generalize other common blocks to be scale-equivariant. We …
University of Applied Sciences Western Switzerland (HES-SO)（瑞士西部应用科学大学）；Harvard School of Engineering and Applied Sciences（哈佛大学工程与应用科学学院）；Centre Hospitalier Universitaire Vaudois (CHUV)（沃州大学中心医院）；Hopitaux Universitaires de Genève (HUG)（日内瓦大学医院）
Locally Rotation Invariant (LRI) image analysis was shown to be fundamental in many applications and in particular in medical imaging where local structures of tissues occur at arbitrary rotations. LRI constituted the cornerstone of several breakthroughs in texture analysis, including Local Binary Patterns (LBP), Maximum Response 8 (MR8) and steerable filterbanks. Whereas globally rotation invariant Convolutional Neural Networks (CNN) were recently proposed, LRI was very little investigated in the context of deep learning. LRI designs allow learning filters accounting for all orientations, whi…
The convolutional layers of standard convolutional neural networks (CNNs) are equivariant to translation. However, the convolution and fully-connected layers are not equivariant or invariant to other affine geometric transformations. Recently, a new class of CNNs is proposed in which the conventional layers of CNNs are replaced with equivariant convolution, pooling, and batch-normalization layers. The final classification layer in equivariant neural networks is invariant to different affine geometric transformations such as rotation, reflection and translation, and the scalar value is obtained…
This paper is concerned with a fundamental problem in geometric deep learning that arises in the construction of convolutional neural networks on surfaces. Due to curvature, the transport of filter kernels on surfaces results in a rotational ambiguity, which prevents a uniform alignment of these kernels on the surface. We propose a network architecture for surfaces that consists of vector-valued, rotation-equivariant features. The equivariance property makes it possible to locally align features, which were computed in arbitrary coordinate systems, when aggregating features in a convolution la…
Convolutional neural networks (CNNs) constructed natively on the sphere have been developed recently and shown to be highly effective for the analysis of spherical data. While an efficient framework has been formulated, spherical CNNs are nevertheless highly computationally demanding; typically they cannot scale beyond spherical signals of thousands of pixels. We develop scattering networks constructed natively on the sphere that provide a powerful representational space for spherical data. Spherical scattering networks are computationally scalable and exhibit rotational equivariance, while th…
Symbiosis International University（symbiosis国际大学）；National Institute of Mental Health and Neurosciences（国家精神卫生与神经科学研究院）
We propose a CNN based technique that aggregates feature maps from its multiple layers that can localize abnormalities with greater details as well as predict pathology under consideration. Existing class activation mapping (CAM) techniques extract feature maps from either the final layer or a single intermediate layer to create the discriminative maps and then interpolate to upsample to the original image resolution. In this case, the subject specific localization is coarse and is unable to capture subtle abnormalities. To mitigate this, our method builds a novel CNN based discriminative loca…
Eindhoven University of Technology（埃因霍温理工大学）；University of Amsterdam（阿姆斯特丹大学）
We present a PDE-based framework that generalizes Group equivariant Convolutional Neural Networks (G-CNNs). In this framework, a network layer is seen as a set of PDE-solvers where geometrically meaningful PDE-coefficients become the layer's trainable weights. Formulating our PDEs on homogeneous spaces allows these networks to be designed with built-in symmetries such as rotation in addition to the standard translation equivariance of CNNs. Having all the desired symmetries included in the design obviates the need to include them by means of costly techniques such as data augmentation. We will…
State-of-the-art deep learning systems often require large amounts of data and computation. For this reason, leveraging known or unknown structure of the data is paramount. Convolutional neural networks (CNNs) are successful examples of this principle, their defining characteristic being the shift-equivariance. By sliding a filter over the input, when the input shifts, the response shifts by the same amount, exploiting the structure of natural images where semantic content is independent of absolute pixel positions. This property is essential to the success of CNNs in audio, image and video re…
Explicit encoding of group actions in deep features makes it possible for convolutional neural networks (CNNs) to handle global deformations of images, which is critical to success in many vision tasks. This paper proposes to decompose the convolutional filters over joint steerable bases across the space and the group geometry simultaneously, namely a rotation-equivariant CNN with decomposed convolutional filters (RotDCF). This decomposition facilitates computing the joint convolution, which is proved to be necessary for the group equivariance. It significantly reduces the model size and compu…
University of Washington（华盛顿大学）；Purdue University（普渡大学）；University of Massachusetts Amherst（马萨诸塞大学阿默斯特分校）
Incorporating group symmetry directly into the learning process has proved to be an effective guideline for model design. By producing features that are guaranteed to transform covariantly to the group actions on the inputs, group-equivariant convolutional neural networks (G-CNNs) achieve significantly improved generalization performance in learning tasks with intrinsic symmetry. General theory and practical implementation of G-CNNs have been studied for planar images under either rotation or scaling transformation, but only individually. We present, in this paper, a roto-scale-translation equ…
Kagenova Limited（Kagenova有限公司）；University College London (UCL)（伦敦大学学院）
No existing spherical convolutional neural network (CNN) framework is both computationally scalable and rotationally equivariant. Continuous approaches capture rotational equivariance but are often prohibitively computationally demanding. Discrete approaches offer more favorable computational performance but at the cost of equivariance. We develop a hybrid discrete-continuous (DISCO) group convolution that is simultaneously equivariant and computationally scalable to high-resolution. While our framework can be applied to any compact group, we specialize to the sphere. Our DISCO spherical convo…
Chalmers University of Technology（查尔姆斯理工大学）；Berlin Institute of Technology（柏林工业大学）；Berlin Institute for the Foundations of Learning and Data (BIFOLD)（柏林学习与数据基础研究所（BIFOLD））；University of Gothenburg（哥德堡大学）；Umeå University（于默奥大学）；Zenseact（Zenseact（智己汽车科技有限公司））
We analyze the role of rotational equivariance in convolutional neural networks (CNNs) applied to spherical images. We compare the performance of the group equivariant networks known as S2CNNs and standard non-equivariant CNNs trained with an increasing amount of data augmentation. The chosen architectures can be considered baseline references for the respective design paradigms. Our models are trained and evaluated on single or multiple items from the MNIST or FashionMNIST dataset projected onto the sphere. For the task of image classification, which is inherently rotationally invariant, we f…
Technical University of Munich（慕尼黑工业大学）；Munich Center for Machine Learning（慕尼黑机器学习中心）；Friedrich-Alexander University Erlangen-Nuremberg（埃尔朗根-纽伦堡弗里德里希-亚历山大大学）
We address the problem of 3D rotation equivariance in convolutional neural networks. 3D rotations have been a challenging nuisance in 3D classification tasks requiring higher capacity and extended data augmentation in order to tackle it. We model 3D data with multi-valued spherical functions and we propose a novel spherical convolutional network that implements exact convolutions on the sphere by realizing them in the spherical harmonic domain. Resulting filters have local symmetry and are localized by enforcing smooth spectra. We apply a novel pooling on the spectral domain and our operations…
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…
Efficient 3D affinely equivariant CNNs with adaptive fusion of augmented spherical Fourier-Bessel bases
School of Computer and Artificial Intelligence, Nanjing University of Finance and Economics（南京金融学院计算机与人工智能学院）；Interdisciplinary Center for Scientific Computing, Mannheim Institute for Intelligent Systems in Medicine, Medical Faculty Mannheim, Heidelberg University（科学计算交叉中心、医学智能系统研究所、曼海姆医学院、海德堡大学）；Computer Assisted Clinical Medicine, Mannheim Institute for Intelligent Systems in Medicine, Medical Faculty Mannheim, Heidelberg University（临床医学辅助计算机、医学智能系统研究所、曼海姆医学院、海德堡大学）；Department of Diagnostic and Interventional Radiology, University Hospital Bonn（诊断与介入放射科、波恩大学医院）；Interdisciplinary Center for Scientific Computing, Central Institute for Computer Engineering, CSZ Heidelberg Center for Model-Based AI, Data Analysis and Modeling in Medicine, Mannheim Institute for Intelligent Systems in Medicine, Medical Faculty Mannheim, Heidelberg University（科学计算交叉中心、计算机工程中央研究所、海德堡模型驱动AI中心、医学数据与建模中心、曼海姆医学智能系统研究所、曼海姆医学院、海德堡大学）
Many problems across computer vision and the natural sciences require the analysis of spherical data, for which representations may be learned efficiently by encoding equivariance to rotational symmetries. We present a generalized spherical CNN framework that encompasses various existing approaches and allows them to be leveraged alongside each other. The only existing non-linear spherical CNN layer that is strictly equivariant has complexity $\mathcal{O}(C^2L^5)$, where $C$ is a measure of representational capacity and $L$ the spherical harmonic bandlimit. Such a high computational cost often…
Pohang University of Science and Technology (POSTECH)（浦项科技大学）
Detecting robust keypoints from an image is an integral part of many computer vision problems, and the characteristic orientation and scale of keypoints play an important role for keypoint description and matching. Existing learning-based methods for keypoint detection rely on standard translation-equivariant CNNs but often fail to detect reliable keypoints against geometric variations. To learn to detect robust oriented keypoints, we introduce a self-supervised learning framework using rotation-equivariant CNNs. We propose a dense orientation alignment loss by an image pair generated by synth…
