Author
Veronika Cheplygina
Other affiliations: Erasmus University Rotterdam, Delft University of Technology, Max Planck Society ...read more
Bio: Veronika Cheplygina is an academic researcher from Eindhoven University of Technology. The author has contributed to research in topics: Computer science & Supervised learning. The author has an hindex of 18, co-authored 68 publications receiving 1314 citations. Previous affiliations of Veronika Cheplygina include Erasmus University Rotterdam & Delft University of Technology.
Papers
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TL;DR: In this article, a survey of semi-supervised, multiple instance and transfer learning in medical image segmentation is presented, and connections between these learning scenarios, and opportunities for future research are discussed.
531 citations
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TL;DR: A comprehensive survey of the characteristics which define and differentiate the types of MIL problems is provided, providing insight on how the problem characteristics affect MIL algorithms, recommendations for future benchmarking and promising avenues for research.
486 citations
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TL;DR: A general bag dissimilarities framework for multiple instance learning is explored and several alternatives to define a dissimilarity between bags are shown and discussed, which definitions are more suitable for particular MIL problems.
115 citations
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TL;DR: In this article , the authors review roadblocks to developing and assessing methods in computer analysis of medical images and provide recommendations on how to further address these problems in the future, and also discuss on-going efforts to counteract these problems.
Abstract: Research in computer analysis of medical images bears many promises to improve patients' health. However, a number of systematic challenges are slowing down the progress of the field, from limitations of the data, such as biases, to research incentives, such as optimizing for publication. In this paper we review roadblocks to developing and assessing methods. Building our analysis on evidence from the literature and data challenges, we show that at every step, potential biases can creep in. On a positive note, we also discuss on-going efforts to counteract these problems. Finally we provide recommendations on how to further address these problems in the future.
114 citations
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TL;DR: A technique to automatically estimate circular cross-sections of the vessels in CT scans by using the Hough transform and a parametric snake model to estimate the local probability density functions of the image intensity inside and outside the vessels.
Abstract: In this work we propose a technique to automatically estimate circular cross-sections of the vessels in CT scans. First, a circular contour is extracted for each slice of the CT by using the Hough transform. Afterward, the locations of the circles are optimized by means of a parametric snake model, and those circles which best fit the contours of the vessels are selected by applying a robust quality criterion. Finally, this collection of circles is used to estimate the local probability density functions of the image intensity inside and outside the vessels. We present a large variety of experiments on CT scans which show the reliability of the proposed method.
77 citations
Cited by
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TL;DR: Machine learning addresses many of the same research questions as the fields of statistics, data mining, and psychology, but with differences of emphasis.
Abstract: Machine Learning is the study of methods for programming computers to learn. Computers are applied to a wide range of tasks, and for most of these it is relatively easy for programmers to design and implement the necessary software. However, there are many tasks for which this is difficult or impossible. These can be divided into four general categories. First, there are problems for which there exist no human experts. For example, in modern automated manufacturing facilities, there is a need to predict machine failures before they occur by analyzing sensor readings. Because the machines are new, there are no human experts who can be interviewed by a programmer to provide the knowledge necessary to build a computer system. A machine learning system can study recorded data and subsequent machine failures and learn prediction rules. Second, there are problems where human experts exist, but where they are unable to explain their expertise. This is the case in many perceptual tasks, such as speech recognition, hand-writing recognition, and natural language understanding. Virtually all humans exhibit expert-level abilities on these tasks, but none of them can describe the detailed steps that they follow as they perform them. Fortunately, humans can provide machines with examples of the inputs and correct outputs for these tasks, so machine learning algorithms can learn to map the inputs to the outputs. Third, there are problems where phenomena are changing rapidly. In finance, for example, people would like to predict the future behavior of the stock market, of consumer purchases, or of exchange rates. These behaviors change frequently, so that even if a programmer could construct a good predictive computer program, it would need to be rewritten frequently. A learning program can relieve the programmer of this burden by constantly modifying and tuning a set of learned prediction rules. Fourth, there are applications that need to be customized for each computer user separately. Consider, for example, a program to filter unwanted electronic mail messages. Different users will need different filters. It is unreasonable to expect each user to program his or her own rules, and it is infeasible to provide every user with a software engineer to keep the rules up-to-date. A machine learning system can learn which mail messages the user rejects and maintain the filtering rules automatically. Machine learning addresses many of the same research questions as the fields of statistics, data mining, and psychology, but with differences of emphasis. Statistics focuses on understanding the phenomena that have generated the data, often with the goal of testing different hypotheses about those phenomena. Data mining seeks to find patterns in the data that are understandable by people. Psychological studies of human learning aspire to understand the mechanisms underlying the various learning behaviors exhibited by people (concept learning, skill acquisition, strategy change, etc.).
13,246 citations
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TL;DR: Li et al. as discussed by the authors proposed a COVID-19 Lung Infection Segmentation Deep Network ( Inf-Net) to automatically identify infected regions from chest CT slices, where a parallel partial decoder is used to aggregate the high-level features and generate a global map.
Abstract: Coronavirus Disease 2019 (COVID-19) spread globally in early 2020, causing the world to face an existential health crisis. Automated detection of lung infections from computed tomography (CT) images offers a great potential to augment the traditional healthcare strategy for tackling COVID-19. However, segmenting infected regions from CT slices faces several challenges, including high variation in infection characteristics, and low intensity contrast between infections and normal tissues. Further, collecting a large amount of data is impractical within a short time period, inhibiting the training of a deep model. To address these challenges, a novel COVID-19 Lung Infection Segmentation Deep Network ( Inf-Net ) is proposed to automatically identify infected regions from chest CT slices. In our Inf-Net , a parallel partial decoder is used to aggregate the high-level features and generate a global map. Then, the implicit reverse attention and explicit edge-attention are utilized to model the boundaries and enhance the representations. Moreover, to alleviate the shortage of labeled data, we present a semi-supervised segmentation framework based on a randomly selected propagation strategy, which only requires a few labeled images and leverages primarily unlabeled data. Our semi-supervised framework can improve the learning ability and achieve a higher performance. Extensive experiments on our COVID-SemiSeg and real CT volumes demonstrate that the proposed Inf-Net outperforms most cutting-edge segmentation models and advances the state-of-the-art performance.
633 citations
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TL;DR: In this article, a survey of semi-supervised, multiple instance and transfer learning in medical image segmentation is presented, and connections between these learning scenarios, and opportunities for future research are discussed.
531 citations
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TL;DR: The general principles of DL and convolutional neural networks are introduced, five major areas of application of DL in medical imaging and radiation therapy are surveyed, common themes are identified, methods for dataset expansion are discussed, and lessons learned, remaining challenges, and future directions are summarized.
Abstract: The goals of this review paper on deep learning (DL) in medical imaging and radiation therapy are to (a) summarize what has been achieved to date; (b) identify common and unique challenges, and strategies that researchers have taken to address these challenges; and (c) identify some of the promising avenues for the future both in terms of applications as well as technical innovations. We introduce the general principles of DL and convolutional neural networks, survey five major areas of application of DL in medical imaging and radiation therapy, identify common themes, discuss methods for dataset expansion, and conclude by summarizing lessons learned, remaining challenges, and future directions.
525 citations