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Register a new userWeakly Supervised Thoracic Disease Localization via Disease Masks
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Hong-Gyu Jung
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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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. To solve this issue, we propose a spatial attention method using disease masks that describe the areas where diseases mainly occur. We then apply the spatial attention to find the precise disease area by highlighting the highest probability of disease occurrence. Meanwhile, the various sizes, rotations and noise in chest X-ray images make generating the disease masks challenging. To reduce the variation among images, we employ an alignment module to transform an input X-ray image into a generalized image. Through extensive experiments on the NIH-Chest X-ray dataset with eight kinds of diseases, we show that the proposed method results in superior localization performances compared to state-of-the-art methods.
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Analysis of histopathology slides is a critical step for many diagnoses, and in particular in oncology where it defines the gold standard. In the case of digital histopathological analysis, highly trained pathologists must review vast whole-slide-images of extreme digital resolution ($100,000^2$ pixels) across multiple zoom levels in order to locate abnormal regions of cells, or in some cases single cells, out of millions. The application of deep learning to this problem is hampered not only by small sample sizes, as typical datasets contain only a few hundred samples, but also by the generation of ground-truth localized annotations for training interpretable classification and segmentation models. We propose a method for disease localization in the context of weakly supervised learning, where only image-level labels are available during training. Even without pixel-level annotations, we are able to demonstrate performance comparable with models trained with strong annotations on the Camelyon-16 lymph node metastases detection challenge. We accomplish this through the use of pre-trained deep convolutional networks, feature embedding, as well as learning via top instances and negative evidence, a multiple instance learning technique from the field of semantic segmentation and object detection.
Locating diseases in chest X-ray images with few careful annotations saves large human effort. Recent works approached this task with innovative weakly-supervised algorithms such as multi-instance learning (MIL) and class activation maps (CAM), however, these methods often yield inaccurate or incomplete regions. One of the reasons is the neglection of the pathological implications hidden in the relationship across anatomical regions within each image and the relationship across images. In this paper, we argue that the cross-region and cross-image relationship, as contextual and compensating information, is vital to obtain more consistent and integral regions. To model the relationship, we propose the Graph Regularized Embedding Network (GREN), which leverages the intra-image and inter-image information to locate diseases on chest X-ray images. GREN uses a pre-trained U-Net to segment the lung lobes, and then models the intra-image relationship between the lung lobes using an intra-image graph to compare different regions. Meanwhile, the relationship between in-batch images is modeled by an inter-image graph to compare multiple images. This process mimics the training and decision-making process of a radiologist: comparing multiple regions and images for diagnosis. In order for the deep embedding layers of the neural network to retain structural information (important in the localization task), we use the Hash coding and Hamming distance to compute the graphs, which are used as regularizers to facilitate training. By means of this, our approach achieves the state-of-the-art result on NIH chest X-ray dataset for weakly-supervised disease localization. Our codes are accessible online.
Detecting clinically relevant objects in medical images is a challenge despite large datasets due to the lack of detailed labels. To address the label issue, we utilize the scene-level labels with a detection architecture that incorporates natural language information. We present a challenging new set of radiologist paired bounding box and natural language annotations on the publicly available MIMIC-CXR dataset especially focussed on pneumonia and pneumothorax. Along with the dataset, we present a joint vision language weakly supervised transformer layer-selected one-stage dual head detection architecture (LITERATI) alongside strong baseline comparisons with class activation mapping (CAM), gradient CAM, and relevant implementations on the NIH ChestXray-14 and MIMIC-CXR dataset. Borrowing from advances in vision language architectures, the LITERATI method demonstrates joint image and referring expression (objects localized in the image using natural language) input for detection that scales in a purely weakly supervised fashion. The architectural modifications address three obstacles -- implementing a supervised vision and language detection method in a weakly supervised fashion, incorporating clinical referring expression natural language information, and generating high fidelity detections with map probabilities. Nevertheless, the challenging clinical nature of the radiologist annotations including subtle references, multi-instance specifications, and relatively verbose underlying medical reports, ensures the vision language detection task at scale remains stimulating for future investigation.
Identifying and locating diseases in chest X-rays are very challenging, due to the low visual contrast between normal and abnormal regions, and distortions caused by other overlapping tissues. An interesting phenomenon is that there exist many similar structures in the left and right parts of the chest, such as ribs, lung fields and bronchial tubes. This kind of similarities can be used to identify diseases in chest X-rays, according to the experience of broad-certificated radiologists. Aimed at improving the performance of existing detection methods, we propose a deep end-to-end module to exploit the contralateral context information for enhancing feature representations of disease proposals. First of all, under the guidance of the spine line, the spatial transformer network is employed to extract local contralateral patches, which can provide valuable context information for disease proposals. Then, we build up a specific module, based on both additive and subtractive operations, to fuse the features of the disease proposal and the contralateral patch. Our method can be integrated into both fully and weakly supervised disease detection frameworks. It achieves 33.17 AP50 on a carefully annotated private chest X-ray dataset which contains 31,000 images. Experiments on the NIH chest X-ray dataset indicate that our method achieves state-of-the-art performance in weakly-supervised disease localization.
The recent emerged weakly supervised object localization (WSOL) methods can learn to localize an object in the image only using image-level labels. Previous works endeavor to perceive the interval objects from the small and sparse discriminative attention map, yet ignoring the co-occurrence confounder (e.g., bird and sky), which makes the model inspection (e.g., CAM) hard to distinguish between the object and context. In this paper, we make an early attempt to tackle this challenge via causal intervention (CI). Our proposed method, dubbed CI-CAM, explores the causalities among images, contexts, and categories to eliminate the biased co-occurrence in the class activation maps thus improving the accuracy of object localization. Extensive experiments on several benchmarks demonstrate the effectiveness of CI-CAM in learning the clear object boundaries from confounding contexts. Particularly, in CUB-200-2011 which severely suffers from the co-occurrence confounder, CI-CAM significantly outperforms the traditional CAM-based baseline (58.39% vs 52.4% in top-1 localization accuracy). While in more general scenarios such as ImageNet, CI-CAM can also perform on par with the state of the arts.
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