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Register a new userExploring large scale public medical image datasets
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Luke Oakden-Rayner
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Rationale and Objectives: Medical artificial intelligence systems are dependent on well characterised large scale datasets. Recently released public datasets have been of great interest to the field, but pose specific challenges due to the disconnect they cause between data generation and data usage, potentially limiting the utility of these datasets. Materials and Methods: We visually explore two large public datasets, to determine how accurate the provided labels are and whether other subtle problems exist. The ChestXray14 dataset contains 112,120 frontal chest films, and the MURA dataset contains 40,561 upper limb radiographs. A subset of around 700 images from both datasets was reviewed by a board-certified radiologist, and the quality of the original labels was determined. Results: The ChestXray14 labels did not accurately reflect the visual content of the images, with positive predictive values mostly between 10% and 30% lower than the values presented in the original documentation. There were other significant problems, with examples of hidden stratification and label disambiguation failure. The MURA labels were more accurate, but the original normal/abnormal labels were inaccurate for the subset of cases with degenerative joint disease, with a sensitivity of 60% and a specificity of 82%. Conclusion: Visual inspection of images is a necessary component of understanding large image datasets. We recommend that teams producing public datasets should perform this important quality control procedure and include a thorough description of their findings, along with an explanation of the data generating procedures and labelling rules, in the documentation for their datasets.
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The astounding success made by artificial intelligence (AI) in healthcare and other fields proves that AI can achieve human-like performance. However, success always comes with challenges. Deep learning algorithms are data-dependent and require large datasets for training. The lack of data in the medical imaging field creates a bottleneck for the application of deep learning to medical image analysis. Medical image acquisition, annotation, and analysis are costly, and their usage is constrained by ethical restrictions. They also require many resources, such as human expertise and funding. That makes it difficult for non-medical researchers to have access to useful and large medical data. Thus, as comprehensive as possible, this paper provides a collection of medical image datasets with their associated challenges for deep learning research. We have collected information of around three hundred datasets and challenges mainly reported between 2013 and 2020 and categorized them into four categories: head & neck, chest & abdomen, pathology & blood, and ``others. Our paper has three purposes: 1) to provide a most up to date and complete list that can be used as a universal reference to easily find the datasets for clinical image analysis, 2) to guide researchers on the methodology to test and evaluate their methods performance and robustness on relevant datasets, 3) to provide a ``route to relevant algorithms for the relevant medical topics, and challenge leaderboards.
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Medical images are increasingly used as input to deep neural networks to produce quantitative values that aid researchers and clinicians. However, standard deep neural networks do not provide a reliable measure of uncertainty in those quantitative values. Recent work has shown that using dropout during training and testing can provide estimates of uncertainty. In this work, we investigate using dropout to estimate epistemic and aleatoric uncertainty in a CT-to-MR image translation task. We show that both types of uncertainty are captured, as defined, providing confidence in the output uncertainty estimates.
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