Thoracic Disease Identification and Localization with Limited Supervision

Accurate identification and localization of abnormalities from radiology images play an integral part in clinical diagnosis and treatment planning. Building a highly accurate prediction model for these tasks usually requires a large number of images manually annotated with labels and finding sites of abnormalities. In reality, however, such annotated data are expensive to acquire, especially the ones with location annotations. We need methods that can work well with only a small amount of location annotations. To address this challenge, we present a unified approach that simultaneously performs disease identification and localization through the same underlying model for all images. We demonstrate that our approach can effectively leverage both class information as well as limited location annotation, and significantly outperforms the comparative reference baseline in both classification and localization tasks.Comment: Conference on Computer Vision and Pattern Recognition 2018 (CVPR 2018). V1: CVPR submission; V2: +supplementary; V3: CVPR camera-ready; V4: correction, update reference baseline results according to their latest post; V5: minor correction; V6: Identification results using NIH data splits and various image model

Did You Get What You Paid For? Rethinking Annotation Cost of Deep Learning Based Computer Aided Detection in Chest Radiographs

As deep networks require large amounts of accurately labeled training data, a strategy to collect sufficiently large and accurate annotations is as important as innovations in recognition methods. This is especially true for building Computer Aided Detection (CAD) systems for chest X-rays where domain expertise of radiologists is required to annotate the presence and location of abnormalities on X-ray images. However, there lacks concrete evidence that provides guidance on how much resource to allocate for data annotation such that the resulting CAD system reaches desired performance. Without this knowledge, practitioners often fall back to the strategy of collecting as much detail as possible on as much data as possible which is cost inefficient. In this work, we investigate how the cost of data annotation ultimately impacts the CAD model performance on classification and segmentation of chest abnormalities in frontal-view X-ray images. We define the cost of annotation with respect to the following three dimensions: quantity, quality and granularity of labels. Throughout this study, we isolate the impact of each dimension on the resulting CAD model performance on detecting 10 chest abnormalities in X-rays. On a large scale training data with over 120K X-ray images with gold-standard annotations, we find that cost-efficient annotations provide great value when collected in large amounts and lead to competitive performance when compared to models trained with only gold-standard annotations. We also find that combining large amounts of cost efficient annotations with only small amounts of expensive labels leads to competitive CAD models at a much lower cost.Comment: MICCAI 2022, Contains Supplemental Materia

Self-Guided Multiple Instance Learning for Weakly Supervised Disease Classification and Localization in Chest Radiographs

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 forming strictly binary from the predictions as done in previous loss formulations, we create targets in a more customized manner, which allows the loss to account for possible misclassification. We show that the supervision provided within the proposed learning scheme leads to better performance and more precise predictions on prevalent datasets for multiple-instance learning as well as on the NIH~ChestX-Ray14 benchmark for disease recognition than previously used losses

Detailed Annotations of Chest X-Rays via CT Projection for Report Understanding

In clinical radiology reports, doctors capture important information about the patient's health status. They convey their observations from raw medical imaging data about the inner structures of a patient. As such, formulating reports requires medical experts to possess wide-ranging knowledge about anatomical regions with their normal, healthy appearance as well as the ability to recognize abnormalities. This explicit grasp on both the patient's anatomy and their appearance is missing in current medical image-processing systems as annotations are especially difficult to gather. This renders the models to be narrow experts e.g. for identifying specific diseases. In this work, we recover this missing link by adding human anatomy into the mix and enable the association of content in medical reports to their occurrence in associated imagery (medical phrase grounding). To exploit anatomical structures in this scenario, we present a sophisticated automatic pipeline to gather and integrate human bodily structures from computed tomography datasets, which we incorporate in our PAXRay: A Projected dataset for the segmentation of Anatomical structures in X-Ray data. Our evaluation shows that methods that take advantage of anatomical information benefit heavily in visually grounding radiologists' findings, as our anatomical segmentations allow for up to absolute 50% better grounding results on the OpenI dataset as compared to commonly used region proposals. The PAXRay dataset is available at https://constantinseibold.github.io/paxray/.Comment: 33rd British Machine Vision Conference (BMVC 2022

Self-Guided Multiple Instance Learning for Weakly Supervised Thoracic DiseaseClassification and Localizationin Chest Radiographs

Due to the high complexity of medical images and the scarcity of trained personnel, most large-scale radiological datasets are lacking fine-grained annotations and are often only described on image-level. These shortcomings hinder 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 in a multiple-instance learning setting. To that end, we introduce a novel loss function for training convolutional neural networks increasing the localization confidence and assisting the overall disease identification. The loss leverages both image-and patch-level predictions to generate auxiliary supervision and enables specific training at patch-level. Rather than forming strictly binary from the predictions as done in previous loss formulations, we create targets in a more customized manner. This way, the loss accounts for possible misclassification of less certain instances. We show that the supervision provided within the proposed learning scheme leads to better performance and more precise predictions on prevalent datasets for multiple-instance learning as well as on the NIH ChestX-Ray14 benchmark for disease recognition than previously used losses

Rethinking annotation granularity for overcoming deep shortcut learning: A retrospective study on chest radiographs

Deep learning has demonstrated radiograph screening performances that are comparable or superior to radiologists. However, recent studies show that deep models for thoracic disease classification usually show degraded performance when applied to external data. Such phenomena can be categorized into shortcut learning, where the deep models learn unintended decision rules that can fit the identically distributed training and test set but fail to generalize to other distributions. A natural way to alleviate this defect is explicitly indicating the lesions and focusing the model on learning the intended features. In this paper, we conduct extensive retrospective experiments to compare a popular thoracic disease classification model, CheXNet, and a thoracic lesion detection model, CheXDet. We first showed that the two models achieved similar image-level classification performance on the internal test set with no significant differences under many scenarios. Meanwhile, we found incorporating external training data even led to performance degradation for CheXNet. Then, we compared the models' internal performance on the lesion localization task and showed that CheXDet achieved significantly better performance than CheXNet even when given 80% less training data. By further visualizing the models' decision-making regions, we revealed that CheXNet learned patterns other than the target lesions, demonstrating its shortcut learning defect. Moreover, CheXDet achieved significantly better external performance than CheXNet on both the image-level classification task and the lesion localization task. Our findings suggest improving annotation granularity for training deep learning systems as a promising way to elevate future deep learning-based diagnosis systems for clinical usage.Comment: 22 pages of main text, 18 pages of supplementary table