Thijs Kooi

Hyeonsoo Lee, Junha Kim, Eunkyung Park et al.

Recently, deep learning models have shown the potential to predict breast cancer risk and enable targeted screening strategies, but current models do not consider the change in the breast over time. In this paper, we present a new method, PRIME+, for breast cancer risk prediction that leverages prior mammograms using a transformer decoder, outperforming a state-of-the-art risk prediction method that only uses mammograms from a single time point. We validate our approach on a dataset with 16,113 exams and further demonstrate that it effectively captures patterns of changes from prior mammograms, such as changes in breast density, resulting in improved short-term and long-term breast cancer risk prediction. Experimental results show that our model achieves a statistically significant improvement in performance over the state-of-the-art based model, with a C-index increase from 0.68 to 0.73 (p < 0.05) on held-out test sets.

Gunhee Nam, Taesoo Kim, Sanghyup Lee et al.

The accurate localization of inserted medical tubes and parts of human anatomy is a common problem when analyzing chest radiographs and something deep neural networks could potentially automate. However, many foreign objects like tubes and various anatomical structures are small in comparison to the entire chest X-ray, which leads to severely unbalanced data and makes training deep neural networks difficult. In this paper, we present a simple yet effective `Only-One-Object-Exists' (OOOE) assumption to improve the deep network's ability to localize small landmarks in chest radiographs. The OOOE enables us to recast the localization problem as a classification problem and we can replace commonly used continuous regression techniques with a multi-class discrete objective. We validate our approach using a large scale proprietary dataset of over 100K radiographs as well as publicly available RANZCR-CLiP Kaggle Challenge dataset and show that our method consistently outperforms commonly used regression-based detection models as well as commonly used pixel-wise classification methods. Additionally, we find that the method using the OOOE assumption generalizes to multiple detection problems in chest X-rays and the resulting model shows state-of-the-art performance on detecting various tube tips inserted to the patient as well as patient anatomy.

Tae Soo Kim, Geonwoon Jang, Sanghyup Lee et al.

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.

Sumin Seo, JaeWoong Shin, Jaewoo Kang et al.

Deep learning has shown great potential in assisting radiologists in reading chest X-ray (CXR) images, but its need for expensive annotations for improving performance prevents widespread clinical application. Visual language pre-training (VLP) can alleviate the burden and cost of annotation by leveraging routinely generated reports for radiographs, which exist in large quantities as well as in paired form (image-text pairs). Additionally, extensions to localization-aware VLPs are being proposed to address the needs for accurate localization of abnormalities for computer-aided diagnosis (CAD) in CXR. However, we find that the formulation proposed by locality-aware VLP literature actually leads to a loss in spatial relationships required for downstream localization tasks. Therefore, we propose Empowering Locality of VLP with Intra-modal Similarity, ELVIS, a VLP aware of intra-modal locality, to better preserve the locality within radiographs or reports, which enhances the ability to comprehend location references in text reports. Our locality-aware VLP method significantly outperforms state-of-the art baselines in multiple segmentation tasks and the MS-CXR phrase grounding task. Qualitatively, we show that ELVIS focuses well on regions of interest described in the report text compared to prior approaches, allowing for enhanced interpretability.

Thijs Kooi

The idea of using computers to read medical scans was introduced as early as 1966. However, limits to machine learning technology meant progress was slow initially. The Alexnet breakthrough in 2012 sparked new interest in the topic, which resulted in the release of 100s of medical AI solutions on the market. In spite of success for some diseases and modalities, many challenges remain. Research typically focuses on the development of specific applications or techniques, clinical evaluation, or meta analysis of clinical studies or techniques through surveys or challenges. However, limited attention has been given to the development process of improving real world performance. In this tutorial, we address the latter and discuss some techniques to conduct the development process in order to make this as efficient as possible.

Thijs Kooi, Nico Karssemeijer

We investigate the addition of symmetry and temporal context information to a deep Convolutional Neural Network (CNN) with the purpose of detecting malignant soft tissue lesions in mammography. We employ a simple linear mapping that takes the location of a mass candidate and maps it to either the contra-lateral or prior mammogram and Regions Of Interest (ROI) are extracted around each location. We subsequently explore two different architectures (1) a fusion model employing two datastreams were both ROIs are fed to the network during training and testing and (2) a stage-wise approach where a single ROI CNN is trained on the primary image and subsequently used as feature extractor for both primary and symmetrical or prior ROIs. A 'shallow' Gradient Boosted Tree (GBT) classifier is then trained on the concatenation of these features and used to classify the joint representation. Results shown a significant increase in performance using the first architecture and symmetry information, but only marginal gains in performance using temporal data and the other setting. We feel results are promising and can greatly be improved when more temporal data becomes available.

Geert Litjens, Thijs Kooi, Babak Ehteshami Bejnordi et al.

Deep learning algorithms, in particular convolutional networks, have rapidly become a methodology of choice for analyzing medical images. This paper reviews the major deep learning concepts pertinent to medical image analysis and summarizes over 300 contributions to the field, most of which appeared in the last year. We survey the use of deep learning for image classification, object detection, segmentation, registration, and other tasks and provide concise overviews of studies per application area. Open challenges and directions for future research are discussed.