Using deep learning models to diagnose cancer from histology data presents several challenges. Cancer grading and localization of regions of interest (ROIs) in these images normally relies on both image- and pixel-level labels, the latter requiring a costly annotation process. Deep weakly-supervised object localization (WSOL) methods provide different strategies for low-cost training of deep learning models. Using only image-class annotations, these methods can be trained to classify an image, and yield class activation maps (CAMs) for ROI localization. This paper provides a review of state-of-art DL methods for WSOL. We propose a taxonomy where these methods are divided into bottom-up and top-down methods according to the information flow in models. Although the latter have seen limited progress, recent bottom-up methods are currently driving much progress with deep WSOL methods. Early works focused on designing different spatial pooling functions. However, these methods reached limited localization accuracy, and unveiled a major limitation -- the under-activation of CAMs which leads to high false negative localization. Subsequent works aimed to alleviate this issue and recover complete object. Representative methods from our taxonomy are evaluated and compared in terms of classification and localization accuracy on two challenging histology datasets. Overall, the results indicate poor localization performance, particularly for generic methods that were initially designed to process natural images. Methods designed to address the challenges of histology data yielded good results. However, all methods suffer from high false positive/negative localization. Four key challenges are identified for the application of deep WSOL methods in histology -- under/over activation of CAMs, sensitivity to thresholding, and model selection.
Trained using only image class label, deep weakly supervised methods allow image classification and ROI segmentation for interpretability. Despite their success on natural images, they face several challenges over histology data where ROI are visually similar to background making models vulnerable to high pixel-wise false positives. These methods lack mechanisms for modeling explicitly non-discriminative regions which raises false-positive rates. We propose novel regularization terms, which enable the model to seek both non-discriminative and discriminative regions, while discouraging unbalanc…
École de Technologie Superieure, Université du Québec（魁北克大学高等技术学院）
Weakly supervised object localization is a challenging task in which the object of interest should be localized while learning its appearance. State-of-the-art methods recycle the architecture of a standard CNN by using the activation maps of the last layer for localizing the object. While this approach is simple and works relatively well, object localization relies on different features than classification, thus, a specialized localization mechanism is required during training to improve performance. In this paper, we propose a convolutional, multi-scale spatial localization network that prov…
State Key Laboratory of Software Development Environment, Beihang University（北京航空航天大学软件开发环境国家重点实验室）；College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics（南京航空航天大学计算机科学与技术学院）
Weakly-supervised temporal action localization (WTAL) in untrimmed videos has emerged as a practical but challenging task since only video-level labels are available. Existing approaches typically leverage off-the-shelf segment-level features, which suffer from spatial incompleteness and temporal incoherence, thus limiting their performance. In this paper, we tackle this problem from a new perspective by enhancing segment-level representations with a simple yet effective graph convolutional network, namely action complement graph network (ACGNet). It facilitates the current video segment to pe…
To enable a deep learning-based system to be used in the medical domain as a computer-aided diagnosis system, it is essential to not only classify diseases but also present the locations of the diseases. However, collecting instance-level annotations for various thoracic diseases is expensive. Therefore, weakly supervised localization methods have been proposed that use only image-level annotation. While the previous methods presented the disease location as the most discriminative part for classification, this causes a deep network to localize wrong areas for indistinguishable X-ray images. T…
In this study, the effects of different class labels created as a result of multiple conceptual meanings on localization using Weakly Supervised Learning presented on Car Dataset. In addition, the generated labels are included in the comparison, and the solution turned into Unsupervised Learning. This paper investigates multiple setups for car localization in the images with other approaches rather than Supervised Learning. To predict localization labels, Class Activation Mapping (CAM) is implemented and from the results, the bounding boxes are extracted by using morphological edge detection. …
The Hong Kong University of Science and Technology（香港科技大学）；HKUST Shenzhen Research Institute（香港科技大学深圳研究院）
Developing an AI-assisted gland segmentation method from histology images is critical for automatic cancer diagnosis and prognosis; however, the high cost of pixel-level annotations hinders its applications to broader diseases. Existing weakly-supervised semantic segmentation methods in computer vision achieve degenerative results for gland segmentation, since the characteristics and problems of glandular datasets are different from general object datasets. We observe that, unlike natural images, the key problem with histology images is the confusion of classes owning to morphological homogene…
TU Munich（慕尼黑工业大学）；Universitat Pompeu Fabra（庞培法布拉大学）；Klinikum rechts der Isar（伊萨尔河右岸医院）；Ludwig Maximilian University（路德维希-马克西米利安大学）；CNRS（法国国家科学研究中心）；Ecole Centrale Nantes（南特中央理工学院）；Johns Hopkins University（约翰斯·霍普金斯大学）
In this paper, we target the problem of fracture classification from clinical X-Ray images towards an automated Computer Aided Diagnosis (CAD) system. Although primarily dealing with an image classification problem, we argue that localizing the fracture in the image is crucial to make good class predictions. Therefore, we propose and thoroughly analyze several schemes for simultaneous fracture localization and classification. We show that using an auxiliary localization task, in general, improves the classification performance. Moreover, it is possible to avoid the need for additional localiza…
Accurate abnormality localization in chest X-rays (CXR) can benefit the clinical diagnosis of various thoracic diseases. However, the lesion-level annotation can only be performed by experienced radiologists, and it is tedious and time-consuming, thus difficult to acquire. Such a situation results in a difficulty to develop a fully-supervised abnormality localization system for CXR. In this regard, we propose to train the CXR abnormality localization framework via a weakly semi-supervised strategy, termed Point Beyond Class (PBC), which utilizes a small number of fully annotated CXRs with lesi…
One of the biggest challenges for applying machine learning to histopathology is weak supervision: whole-slide images have billions of pixels yet often only one global label. The state of the art therefore relies on strongly-supervised model training using additional local annotations from domain experts. However, in the absence of detailed annotations, most weakly-supervised approaches depend on a frozen feature extractor pre-trained on ImageNet. We identify this as a key weakness and propose to train an in-domain feature extractor on histology images using MoCo v2, a recent self-supervised l…
École de technologie supérieure（高等技术学院）；Goodman Cancer Research Centre（古德曼癌症研究中心）；McGill University（麦吉尔大学）
Weakly-supervised learning (WSL) has recently triggered substantial interest as it mitigates the lack of pixel-wise annotations. Given global image labels, WSL methods yield pixel-level predictions (segmentations), which enable to interpret class predictions. Despite their recent success, mostly with natural images, such methods can face important challenges when the foreground and background regions have similar visual cues, yielding high false-positive rates in segmentations, as is the case in challenging histology images. WSL training is commonly driven by standard classification losses, wh…
PixelCAM: Pixel Class Activation Mapping for Histology Image Classification and ROI Localization
LIVIA, Dept. of Systems Engineering, ETS Montreal, Canada（LIVIA系统工程系，蒙特利尔大学ETS分校，加拿大）；Goodman Cancer Research Centre, Dept. of Oncology, McGill University, Montreal, Canada（Goodman癌症研究中心，麦吉尔大学肿瘤学系，加拿大）
Temporally localizing activities within untrimmed videos has been extensively studied in recent years. Despite recent advances, existing methods for weakly-supervised temporal activity localization struggle to recognize when an activity is not occurring. To address this issue, we propose a novel method named A2CL-PT. Two triplets of the feature space are considered in our approach: one triplet is used to learn discriminative features for each activity class, and the other one is used to distinguish the features where no activity occurs (i.e. background features) from activity-related features …
Prostate cancer is one of the main diseases affecting men worldwide. The Gleason scoring system is the primary diagnostic tool for prostate cancer. This is obtained via the visual analysis of cancerous patterns in prostate biopsies performed by expert pathologists, and the aggregation of the main Gleason grades in a combined score. Computer-aided diagnosis systems allow to reduce the workload of pathologists and increase the objectivity. Recently, efforts have been made in the literature to develop algorithms aiming the direct estimation of the global Gleason score at biopsy/core level with gl…
IBM Zurich Research Lab（IBM苏黎世研究实验室）；EPFL（洛桑联邦理工学院）；APHP. Centre（巴黎公立医院中心）；Cochin hospital（科钦医院）；Université de Paris（巴黎大学）；ETH Zurich（苏黎世联邦理工学院）；Uppsala University（乌普萨拉大学）
Segmenting histology images into diagnostically relevant regions is imperative to support timely and reliable decisions by pathologists. To this end, computer-aided techniques have been proposed to delineate relevant regions in scanned histology slides. However, the techniques necessitate task-specific large datasets of annotated pixels, which is tedious, time-consuming, expensive, and infeasible to acquire for many histology tasks. Thus, weakly-supervised semantic segmentation techniques are proposed to utilize weak supervision that is cheaper and quicker to acquire. In this paper, we propose…
ÉTS Montreal（蒙特利尔高等技术学院）；Goodman Cancer Research Centre（古德曼癌症研究中心）；McGill University（麦吉尔大学）
Using only global image-class labels, weakly-supervised learning methods, such as class activation mapping, allow training CNNs to jointly classify an image, and locate regions of interest associated with the predicted class. However, without any guidance at the pixel level, such methods may yield inaccurate regions. This problem is known to be more challenging with histology images than with natural ones, since objects are less salient, structures have more variations, and foreground and background regions have stronger similarities. Therefore, computer vision methods for visual interpretatio…
Histopathological image segmentation is a challenging and important topic in medical imaging with tremendous potential impact in clinical practice. State of the art methods rely on hand-crafted annotations which hinder clinical translation since histology suffers from significant variations between cancer phenotypes. In this paper, we propose a weakly supervised framework for whole slide imaging segmentation that relies on standard clinical annotations, available in most medical systems. In particular, we exploit a multiple instance learning scheme for training models. The proposed framework h…
Queen Mary University of London（伦敦玛丽女王大学）；University of Leicester（莱斯特大学）
The detection of nuclei and cells in histology images is of great value in both clinical practice and pathological studies. However, multiple reasons such as morphological variations of nuclei or cells make it a challenging task where conventional object detection methods cannot obtain satisfactory performance in many cases. A detection task consists of two sub-tasks, classification and localization. Under the condition of dense object detection, classification is a key to boost the detection performance. Considering this, we propose similarity based region proposal networks (SRPN) for nuclei …
The success of supervised deep learning models in medical image segmentation relies on detailed annotations. However, labor-intensive manual labeling is costly and inefficient, especially in dense object segmentation. To this end, we propose a self-supervised learning based approach with a Prior Self-activation Module (PSM) that generates self-activation maps from the input images to avoid labeling costs and further produce pseudo masks for the downstream task. To be specific, we firstly train a neural network using self-supervised learning and utilize the gradient information in the shallow l…
Brigham and Women’s Hospital（布莱根妇女医院）；Harvard Medical School（哈佛医学院）；Dana-Farber Cancer Institute（丹娜-法伯癌症研究所）；Broad Institute of Harvard and MIT（哈佛-麻省理工学院博德研究所）
Cancer prognostication is a challenging task in computational pathology that requires context-aware representations of histology features to adequately infer patient survival. Despite the advancements made in weakly-supervised deep learning, many approaches are not context-aware and are unable to model important morphological feature interactions between cell identities and tissue types that are prognostic for patient survival. In this work, we present Patch-GCN, a context-aware, spatially-resolved patch-based graph convolutional network that hierarchically aggregates instance-level histology …
Brigham and Women’s Hospital（布莱根妇女医院）；Harvard Medical School（哈佛医学院）；Broad Institute of Harvard and MIT（哈佛-麻省理工学院博德研究所）；Dana-Farber Cancer Institute（丹娜-法伯癌症研究所）；Harvard University（哈佛大学）
The rapidly emerging field of deep learning-based computational pathology has demonstrated promise in developing objective prognostic models from histology whole slide images. However, most prognostic models are either based on histology or genomics alone and do not address how histology and genomics can be integrated to develop joint image-omic prognostic models. Additionally identifying explainable morphological and molecular descriptors from these models that govern such prognosis is of interest. We used multimodal deep learning to integrate gigapixel whole slide pathology images, RNA-seq a…
HIDSS4Health - Helmholtz Information and Data Science School for Health（HIDSS4Health——亥姆霍兹健康信息与数据科学学院）；Karlsruhe Institute of Technology（卡尔斯鲁厄理工学院）；German Cancer Research Center Heidelberg（海德堡德国癌症研究中心）
The lack of fine-grained annotations hinders the deployment of automated diagnosis systems, which require human-interpretable justification for their decision process. In this paper, we address the problem of weakly supervised identification and localization of abnormalities in chest radiographs. To that end, we introduce a novel loss function for training convolutional neural networks increasing the \emph{localization confidence} and assisting the overall \emph{disease identification}. The loss leverages both image- and patch-level predictions to generate auxiliary supervision. Rather than fo…
High-Resolution Spatial Transcriptomics from Histology Images using HisToSGE
School of Information Science and Engineering, Yunnan University（云南大学信息科学与工程学院）；College of Nursing Health Sciences, Yunnan Open University（云南开放大学护理与健康科学学院）
Brigham and Women’s Hospital（布里格姆妇女医院）；Harvard Medical School（哈佛医学院）；Broad Institute of Harvard and MIT（哈佛-麻省理工学院布罗德研究所）；Department of Pathology（病理系）；Northwell Health（诺斯韦尔健康）；Department of Biomedical Informatics（生物医学信息学系）；Dana-Farber Cancer Institute（达纳-法伯癌症研究所）；Cancer Program（癌症项目）；Cancer Data Science（癌症数据科学）
Deep Learning-based computational pathology algorithms have demonstrated profound ability to excel in a wide array of tasks that range from characterization of well known morphological phenotypes to predicting non-human-identifiable features from histology such as molecular alterations. However, the development of robust, adaptable, and accurate deep learning-based models often rely on the collection and time-costly curation large high-quality annotated training data that should ideally come from diverse sources and patient populations to cater for the heterogeneity that exists in such dataset…
Temporal action localization is an important step towards video understanding. Most current action localization methods depend on untrimmed videos with full temporal annotations of action instances. However, it is expensive and time-consuming to annotate both action labels and temporal boundaries of videos. To this end, we propose a weakly supervised temporal action localization method that only requires video-level action instances as supervision during training. We propose a classification module to generate action labels for each segment in the video, and a deep metric learning module to le…
Obtaining accurate pixel-level localization from class labels is a crucial process in weakly supervised semantic segmentation and object localization. Attribution maps from a trained classifier are widely used to provide pixel-level localization, but their focus tends to be restricted to a small discriminative region of the target object. An AdvCAM is an attribution map of an image that is manipulated to increase the classification score produced by a classifier before the final softmax or sigmoid layer. This manipulation is realized in an anti-adversarial manner, so that the original image is…
The effective localization of mitosis is a critical precursory task for deciding tumor prognosis and grade. Automated mitosis detection through deep learning-oriented image analysis often fails on unseen patient data due to inherent domain biases. This paper proposes a domain homogenizer for mitosis detection that attempts to alleviate domain differences in histology images via adversarial reconstruction of input images. The proposed homogenizer is based on a U-Net architecture and can effectively reduce domain differences commonly seen with histology imaging data. We demonstrate our domain ho…
We propose `Hide-and-Seek', a weakly-supervised framework that aims to improve object localization in images and action localization in videos. Most existing weakly-supervised methods localize only the most discriminative parts of an object rather than all relevant parts, which leads to suboptimal performance. Our key idea is to hide patches in a training image randomly, forcing the network to seek other relevant parts when the most discriminative part is hidden. Our approach only needs to modify the input image and can work with any network designed for object localization. During testing, we…
Nanjing University（南京大学）；University of Wisconsin-Madison（威斯康星大学麦迪逊分校）
Modern deep learning models require large amounts of accurately annotated data, which is often difficult to satisfy. Hence, weakly supervised tasks, including weakly supervised object localization~(WSOL) and detection~(WSOD), have recently received attention in the computer vision community. In this paper, we motivate and propose the weakly supervised foreground learning (WSFL) task by showing that both WSOL and WSOD can be greatly improved if groundtruth foreground masks are available. More importantly, we propose a complete WSFL pipeline with low computational cost, which generates pseudo bo…
Recent advances of deep learning have achieved remarkable performances in various challenging computer vision tasks. Especially in object localization, deep convolutional neural networks outperform traditional approaches based on extraction of data/task-driven features instead of hand-crafted features. Although location information of region-of-interests (ROIs) gives good prior for object localization, it requires heavy annotation efforts from human resources. Thus a weakly supervised framework for object localization is introduced. The term "weakly" means that this framework only uses image-l…
Promptable cancer segmentation using minimal expert-curated data
Department of Medical Physics and Biomedical Engineering, University College London（医学物理与生物医学工程系，伦敦大学学院）；UCL Hawkes Institute, University College London（UCL Hawkes研究所，伦敦大学学院）；Division of Surgery and Interventional Science, University College London（外科与介入科学系，伦敦大学学院）；Department of Radiology（放射科；泌尿科，斯坦福大学）；and Department of Urology, Stanford University
Yonsei University（延世大学）；University of Tuebingen（图宾根大学）
Weakly-supervised object localization (WSOL) has gained popularity over the last years for its promise to train localization models with only image-level labels. Since the seminal WSOL work of class activation mapping (CAM), the field has focused on how to expand the attention regions to cover objects more broadly and localize them better. However, these strategies rely on full localization supervision to validate hyperparameters and for model selection, which is in principle prohibited under the WSOL setup. In this paper, we argue that WSOL task is ill-posed with only image-level labels, and …
Weakly-supervised object localization methods tend to fail for object classes that consistently co-occur with the same background elements, e.g. trains on tracks. We propose a method to overcome these failures by adding a very small amount of model-specific additional annotation. The main idea is to cluster a deep network's mid-level representations and assign object or distractor labels to each cluster. Experiments show substantially improved localization results on the challenging ILSVC2014 dataset for bounding box detection and the PASCAL VOC2012 dataset for semantic segmentation.
National Key Laboratory for Novel Software Technology（新型软件技术国家重点实验室）；Nanjing University（南京大学）
Weakly supervised object localization (WSOL) aims to localize objects with only image-level labels. Previous methods often try to utilize feature maps and classification weights to localize objects using image level annotations indirectly. In this paper, we demonstrate that weakly supervised object localization should be divided into two parts: class-agnostic object localization and object classification. For class-agnostic object localization, we should use class-agnostic methods to generate noisy pseudo annotations and then perform bounding box regression on them without class labels. We pro…
We propose an improved technique for weakly-supervised object localization. Conventional methods have a limitation that they focus only on most discriminative parts of the target objects. The recent study addressed this issue and resolved this limitation by augmenting the training data for less discriminative parts. To this end, we employ an effective data augmentation for improving the accuracy of the object localization. In addition, we introduce improved learning techniques by optimizing Convolutional Neural Networks (CNN) based on the state-of-the-art model. Based on extensive experiments,…
Seoul National University（首尔国立大学）；LG AI Research（LG人工智能研究院）
Weakly supervised object localization aims to find a target object region in a given image with only weak supervision, such as image-level labels. Most existing methods use a class activation map (CAM) to generate a localization map; however, a CAM identifies only the most discriminative parts of a target object rather than the entire object region. In this work, we find the gap between classification and localization in terms of the misalignment of the directions between an input feature and a class-specific weight. We demonstrate that the misalignment suppresses the activation of CAM in area…
Institute of Medical Technology Peking University（北京大学医学技术研究院）；Bytedance AI Lab（字节跳动人工智能实验室）；Department of Biomedical Engineering Peking University（北京大学生物医学工程系）；University of Western Ontario（西安大略大学）；Institute of Biomedical Engineering Peking University Shenzhen Graduate School（北京大学深圳研究生院生物医学工程研究所）
Weakly supervised object localization (WSOL) focuses on localizing objects only with the supervision of image-level classification masks. Most previous WSOL methods follow the classification activation map (CAM) that localizes objects based on the classification structure with the multi-instance learning (MIL) mechanism. However, the MIL mechanism makes CAM only activate discriminative object parts rather than the whole object, weakening its performance for localizing objects. To avoid this problem, this work provides a novel perspective that models WSOL as a domain adaption (DA) task, where t…
The Hong Kong University of Science and Technology（香港科技大学）
Despite deep convolutional neural networks boost the performance of image classification and segmentation in digital pathology analysis, they are usually weak in interpretability for clinical applications or require heavy annotations to achieve object localization. To overcome this problem, we propose a weakly supervised learning-based approach that can effectively learn to localize the discriminative evidence for a diagnostic label from weakly labeled training data. Experimental results show that our proposed method can reliably pinpoint the location of cancerous evidence supporting the decis…
Weakly-supervised temporal action localization aims to learn detecting temporal intervals of action classes with only video-level labels. To this end, it is crucial to separate frames of action classes from the background frames (i.e., frames not belonging to any action classes). In this paper, we present a new perspective on background frames where they are modeled as out-of-distribution samples regarding their inconsistency. Then, background frames can be detected by estimating the probability of each frame being out-of-distribution, known as uncertainty, but it is infeasible to directly lea…
Localization of chest pathologies in chest X-ray images is a challenging task because of their varying sizes and appearances. We propose a novel weakly supervised method to localize chest pathologies using class aware deep multiscale feature learning. Our method leverages intermediate feature maps from CNN layers at different stages of a deep network during the training of a classification model using image level annotations of pathologies. During the training phase, a set of \emph{layer relevance weights} are learned for each pathology class and the CNN is optimized to perform pathology class…
École de technologie supérieure, Université du Québec（魁北克大学高等技术学院）；Rosalind and Morris Goodman Cancer Research Centre（罗莎琳德与莫里斯·古德曼癌症研究中心）；McGill University（麦吉尔大学）
Pointwise localization allows more precise localization and accurate interpretability, compared to bounding box, in applications where objects are highly unstructured such as in medical domain. In this work, we focus on weakly supervised localization (WSL) where a model is trained to classify an image and localize regions of interest at pixel-level using only global image annotation. Typical convolutional attentions maps are prune to high false positive regions. To alleviate this issue, we propose a new deep learning method for WSL, composed of a localizer and a classifier, where the localizer…
Shanghai Jiao Tong University（上海交通大学）；Shanghai Frontier Science Research Center for Gravitational Wave Detection（上海引力波探测前沿科学研究中心）
Pseudo-supervised learning methods have been shown to be effective for weakly supervised object localization tasks. However, the effectiveness depends on the powerful regularization ability of deep neural networks. Based on the assumption that the localization network should have similar location predictions on different versions of the same image, we propose a two-stage approach to learn more consistent localization. In the first stage, we propose a mask-based pseudo label generator algorithm, and use the pseudo-supervised learning method to initialize an object localization network. In the s…
University of California, Santa Barbara（加州大学圣巴巴拉分校）；Army Research Laboratory（陆军研究实验室）
Object localization is an important computer vision problem with a variety of applications. The lack of large scale object-level annotations and the relative abundance of image-level labels makes a compelling case for weak supervision in the object localization task. Deep Convolutional Neural Networks are a class of state-of-the-art methods for the related problem of object recognition. In this paper, we describe a novel object localization algorithm which uses classification networks trained on only image labels. This weakly supervised method leverages local spatial and semantic patterns capt…
We aim to localize objects in images using image-level supervision only. Previous approaches to this problem mainly focus on discriminative object regions and often fail to locate precise object boundaries. We address this problem by introducing two types of context-aware guidance models, additive and contrastive models, that leverage their surrounding context regions to improve localization. The additive model encourages the predicted object region to be supported by its surrounding context region. The contrastive model encourages the predicted object region to be outstanding from its surroun…
We present a method for weakly-supervised action localization based on graph convolutions. In order to find and classify video time segments that correspond to relevant action classes, a system must be able to both identify discriminative time segments in each video, and identify the full extent of each action. Achieving this with weak video level labels requires the system to use similarity and dissimilarity between moments across videos in the training data to understand both how an action appears, as well as the sub-actions that comprise the action's full extent. However, current methods do…
In medical imaging, Class-Activation Map (CAM) serves as the main explainability tool by pointing to the region of interest. Since the localization accuracy from CAM is constrained by the resolution of the model's feature map, one may expect that segmentation models, which generally have large feature maps, would produce more accurate CAMs. However, we have found that this is not the case due to task mismatch. While segmentation models are developed for datasets with pixel-level annotation, only image-level annotation is available in most medical imaging datasets. Our experiments suggest that …
