10 results on '"Fung, Kenneth"'
Search Results
2. Fully Automated Myocardial Strain Estimation from CMR Tagged Images using a Deep Learning Framework in the UK Biobank
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Ferdian, Edward, Suinesiaputra, Avan, Fung, Kenneth, Aung, Nay, Lukaschuk, Elena, Barutcu, Ahmet, Maclean, Edd, Paiva, Jose, Piechnik, Stefan K., Neubauer, Stefan, Petersen, Steffen E, and Young, Alistair A.
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Electrical Engineering and Systems Science - Image and Video Processing ,Computer Science - Computer Vision and Pattern Recognition ,Physics - Medical Physics - Abstract
Purpose: To demonstrate the feasibility and performance of a fully automated deep learning framework to estimate myocardial strain from short-axis cardiac magnetic resonance tagged images. Methods and Materials: In this retrospective cross-sectional study, 4508 cases from the UK Biobank were split randomly into 3244 training and 812 validation cases, and 452 test cases. Ground truth myocardial landmarks were defined and tracked by manual initialization and correction of deformable image registration using previously validated software with five readers. The fully automatic framework consisted of 1) a convolutional neural network (CNN) for localization, and 2) a combination of a recurrent neural network (RNN) and a CNN to detect and track the myocardial landmarks through the image sequence for each slice. Radial and circumferential strain were then calculated from the motion of the landmarks and averaged on a slice basis. Results: Within the test set, myocardial end-systolic circumferential Green strain errors were -0.001 +/- 0.025, -0.001 +/- 0.021, and 0.004 +/- 0.035 in basal, mid, and apical slices respectively (mean +/- std. dev. of differences between predicted and manual strain). The framework reproduced significant reductions in circumferential strain in diabetics, hypertensives, and participants with previous heart attack. Typical processing time was ~260 frames (~13 slices) per second on an NVIDIA Tesla K40 with 12GB RAM, compared with 6-8 minutes per slice for the manual analysis. Conclusions: The fully automated RNNCNN framework for analysis of myocardial strain enabled unbiased strain evaluation in a high-throughput workflow, with similar ability to distinguish impairment due to diabetes, hypertension, and previous heart attack., Comment: accepted in Radiology Cardiothoracic Imaging
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- 2020
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3. Improving the generalizability of convolutional neural network-based segmentation on CMR images
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Chen, Chen, Bai, Wenjia, Davies, Rhodri H., Bhuva, Anish N., Manisty, Charlotte, Moon, James C., Aung, Nay, Lee, Aaron M., Sanghvi, Mihir M., Fung, Kenneth, Paiva, Jose Miguel, Petersen, Steffen E., Lukaschuk, Elena, Piechnik, Stefan K., Neubauer, Stefan, and Rueckert, Daniel
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Electrical Engineering and Systems Science - Image and Video Processing ,Computer Science - Computer Vision and Pattern Recognition - Abstract
Convolutional neural network (CNN) based segmentation methods provide an efficient and automated way for clinicians to assess the structure and function of the heart in cardiac MR images. While CNNs can generally perform the segmentation tasks with high accuracy when training and test images come from the same domain (e.g. same scanner or site), their performance often degrades dramatically on images from different scanners or clinical sites. We propose a simple yet effective way for improving the network generalization ability by carefully designing data normalization and augmentation strategies to accommodate common scenarios in multi-site, multi-scanner clinical imaging data sets. We demonstrate that a neural network trained on a single-site single-scanner dataset from the UK Biobank can be successfully applied to segmenting cardiac MR images across different sites and different scanners without substantial loss of accuracy. Specifically, the method was trained on a large set of 3,975 subjects from the UK Biobank. It was then directly tested on 600 different subjects from the UK Biobank for intra-domain testing and two other sets for cross-domain testing: the ACDC dataset (100 subjects, 1 site, 2 scanners) and the BSCMR-AS dataset (599 subjects, 6 sites, 9 scanners). The proposed method produces promising segmentation results on the UK Biobank test set which are comparable to previously reported values in the literature, while also performing well on cross-domain test sets, achieving a mean Dice metric of 0.90 for the left ventricle, 0.81 for the myocardium and 0.82 for the right ventricle on the ACDC dataset; and 0.89 for the left ventricle, 0.83 for the myocardium on the BSCMR-AS dataset. The proposed method offers a potential solution to improve CNN-based model generalizability for the cross-scanner and cross-site cardiac MR image segmentation task., Comment: 15 pages, 8 figures
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- 2019
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4. Unsupervised shape and motion analysis of 3822 cardiac 4D MRIs of UK Biobank
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Zheng, Qiao, Delingette, Hervé, Fung, Kenneth, Petersen, Steffen E., and Ayache, Nicholas
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Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Artificial Intelligence ,Computer Science - Machine Learning - Abstract
We perform unsupervised analysis of image-derived shape and motion features extracted from 3822 cardiac 4D MRIs of the UK Biobank. First, with a feature extraction method previously published based on deep learning models, we extract from each case 9 feature values characterizing both the cardiac shape and motion. Second, a feature selection is performed to remove highly correlated feature pairs. Third, clustering is carried out using a Gaussian mixture model on the selected features. After analysis, we identify two small clusters which probably correspond to two pathological categories. Further confirmation using a trained classification model and dimensionality reduction tools is carried out to support this discovery. Moreover, we examine the differences between the other large clusters and compare our measures with the ground-truth.
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- 2019
5. Automated Quality Control in Image Segmentation: Application to the UK Biobank Cardiac MR Imaging Study
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Robinson, Robert, Valindria, Vanya V., Bai, Wenjia, Oktay, Ozan, Kainz, Bernhard, Suzuki, Hideaki, Sanghvi, Mihir M., Aung, Nay, Paiva, Jos$é$ Miguel, Zemrak, Filip, Fung, Kenneth, Lukaschuk, Elena, Lee, Aaron M., Carapella, Valentina, Kim, Young Jin, Piechnik, Stefan K., Neubauer, Stefan, Petersen, Steffen E., Page, Chris, Matthews, Paul M., Rueckert, Daniel, and Glocker, Ben
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Computer Science - Computer Vision and Pattern Recognition - Abstract
Background: The trend towards large-scale studies including population imaging poses new challenges in terms of quality control (QC). This is a particular issue when automatic processing tools, e.g. image segmentation methods, are employed to derive quantitative measures or biomarkers for later analyses. Manual inspection and visual QC of each segmentation isn't feasible at large scale. However, it's important to be able to automatically detect when a segmentation method fails so as to avoid inclusion of wrong measurements into subsequent analyses which could lead to incorrect conclusions. Methods: To overcome this challenge, we explore an approach for predicting segmentation quality based on Reverse Classification Accuracy, which enables us to discriminate between successful and failed segmentations on a per-cases basis. We validate this approach on a new, large-scale manually-annotated set of 4,800 cardiac magnetic resonance scans. We then apply our method to a large cohort of 7,250 cardiac MRI on which we have performed manual QC. Results: We report results used for predicting segmentation quality metrics including Dice Similarity Coefficient (DSC) and surface-distance measures. As initial validation, we present data for 400 scans demonstrating 99% accuracy for classifying low and high quality segmentations using predicted DSC scores. As further validation we show high correlation between real and predicted scores and 95% classification accuracy on 4,800 scans for which manual segmentations were available. We mimic real-world application of the method on 7,250 cardiac MRI where we show good agreement between predicted quality metrics and manual visual QC scores. Conclusions: We show that RCA has the potential for accurate and fully automatic segmentation QC on a per-case basis in the context of large-scale population imaging as in the UK Biobank Imaging Study., Comment: 14 pages, 7 figures, Journal of Cardiovascular Magnetic Resonance
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- 2019
6. Real-time Prediction of Segmentation Quality
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Robinson, Robert, Oktay, Ozan, Bai, Wenjia, Valindria, Vanya, Sanghvi, Mihir, Aung, Nay, Paiva, José, Zemrak, Filip, Fung, Kenneth, Lukaschuk, Elena, Lee, Aaron, Carapella, Valentina, Kim, Young Jin, Kainz, Bernhard, Piechnik, Stefan, Neubauer, Stefan, Petersen, Steffen, Page, Chris, Rueckert, Daniel, and Glocker, Ben
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Computer Science - Computer Vision and Pattern Recognition - Abstract
Recent advances in deep learning based image segmentation methods have enabled real-time performance with human-level accuracy. However, occasionally even the best method fails due to low image quality, artifacts or unexpected behaviour of black box algorithms. Being able to predict segmentation quality in the absence of ground truth is of paramount importance in clinical practice, but also in large-scale studies to avoid the inclusion of invalid data in subsequent analysis. In this work, we propose two approaches of real-time automated quality control for cardiovascular MR segmentations using deep learning. First, we train a neural network on 12,880 samples to predict Dice Similarity Coefficients (DSC) on a per-case basis. We report a mean average error (MAE) of 0.03 on 1,610 test samples and 97% binary classification accuracy for separating low and high quality segmentations. Secondly, in the scenario where no manually annotated data is available, we train a network to predict DSC scores from estimated quality obtained via a reverse testing strategy. We report an MAE=0.14 and 91% binary classification accuracy for this case. Predictions are obtained in real-time which, when combined with real-time segmentation methods, enables instant feedback on whether an acquired scan is analysable while the patient is still in the scanner. This further enables new applications of optimising image acquisition towards best possible analysis results., Comment: Accepted at MICCAI 2018
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- 2018
7. Automated cardiovascular magnetic resonance image analysis with fully convolutional networks
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Bai, Wenjia, Sinclair, Matthew, Tarroni, Giacomo, Oktay, Ozan, Rajchl, Martin, Vaillant, Ghislain, Lee, Aaron M., Aung, Nay, Lukaschuk, Elena, Sanghvi, Mihir M., Zemrak, Filip, Fung, Kenneth, Paiva, Jose Miguel, Carapella, Valentina, Kim, Young Jin, Suzuki, Hideaki, Kainz, Bernhard, Matthews, Paul M., Petersen, Steffen E., Piechnik, Stefan K., Neubauer, Stefan, Glocker, Ben, and Rueckert, Daniel
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Computer Science - Computer Vision and Pattern Recognition - Abstract
Cardiovascular magnetic resonance (CMR) imaging is a standard imaging modality for assessing cardiovascular diseases (CVDs), the leading cause of death globally. CMR enables accurate quantification of the cardiac chamber volume, ejection fraction and myocardial mass, providing information for diagnosis and monitoring of CVDs. However, for years, clinicians have been relying on manual approaches for CMR image analysis, which is time consuming and prone to subjective errors. It is a major clinical challenge to automatically derive quantitative and clinically relevant information from CMR images. Deep neural networks have shown a great potential in image pattern recognition and segmentation for a variety of tasks. Here we demonstrate an automated analysis method for CMR images, which is based on a fully convolutional network (FCN). The network is trained and evaluated on a large-scale dataset from the UK Biobank, consisting of 4,875 subjects with 93,500 pixelwise annotated images. The performance of the method has been evaluated using a number of technical metrics, including the Dice metric, mean contour distance and Hausdorff distance, as well as clinically relevant measures, including left ventricle (LV) end-diastolic volume (LVEDV) and end-systolic volume (LVESV), LV mass (LVM); right ventricle (RV) end-diastolic volume (RVEDV) and end-systolic volume (RVESV). By combining FCN with a large-scale annotated dataset, the proposed automated method achieves a high performance on par with human experts in segmenting the LV and RV on short-axis CMR images and the left atrium (LA) and right atrium (RA) on long-axis CMR images., Comment: Accepted for publication by Journal of Cardiovascular Magnetic Resonance
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- 2017
8. The optimisation of low-acceleration interstellar relativistic rocket trajectories using genetic algorithms
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Fung, Kenneth K H, Lewis, Geraint F, and Wu, Xiaofeng
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Physics - Space Physics ,Astrophysics - Astrophysics of Galaxies ,Astrophysics - Instrumentation and Methods for Astrophysics - Abstract
A vast wealth of literature exists on the topic of rocket trajectory optimisation, particularly in the area of interplanetary trajectories due to its relevance today. Studies on optimising interstellar and intergalactic trajectories are usually performed in flat spacetime using an analytical approach, with very little focus on optimising interstellar trajectories in a general relativistic framework. This paper examines the use of low-acceleration rockets to reach galactic destinations in the least possible time, with a genetic algorithm being employed for the optimisation process. The fuel required for each journey was calculated for various types of propulsion systems to determine the viability of low-acceleration rockets to colonise the Milky Way. The results showed that to limit the amount of fuel carried on board, an antimatter propulsion system would likely be the minimum technological requirement to reach star systems tens of thousands of light years away. However, using a low-acceleration rocket would require several hundreds of thousands of years to reach these star systems, with minimal time dilation effects since maximum velocities only reached about 0.2c. Such transit times are clearly impractical, and thus, any kind of colonisation using low acceleration rockets would be difficult. High accelerations, on the order of 1g, are likely required to complete interstellar journeys within a reasonable time frame, though they may require prohibitively large amounts of fuel. So for now, it appears that humanity's ultimate goal of a galactic empire may only be possible at significantly higher accelerations, though the propulsion technology requirement for a journey that uses realistic amounts of fuel remains to be determined., Comment: 32 pages, 16 figures, Accepted for publication in Acta Astronautica
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- 2017
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9. A computational approach to the twin paradox in curved spacetime
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Fung, Kenneth K. H., Clark, Hamish A., Lewis, Geraint F., and Wu, Xiaofeng
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General Relativity and Quantum Cosmology - Abstract
Despite being a major component in the teaching of special relativity, the twin `paradox' is generally not examined in courses on general relativity. Due to the complexity of analytical solutions to the problem, the paradox is often neglected entirely, and students are left with an incomplete understanding of the relativistic behaviour of time. This article outlines a project, undertaken by undergraduate physics students at the University of Sydney, in which a novel computational method was derived in order to predict the time experienced by a twin following a number of paths between two given spacetime coordinates. By utilising this method, it is possible to make clear to students that following a geodesic in curved spacetime does not always result in the greatest experienced proper time., Comment: 14 pages, 5 figues, Accepted for publication in EJP
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- 2016
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10. An Integrative Approach to Cultural Competence in the Psychiatric Curriculum
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Fung, Kenneth, Andermann, Lisa, Zaretsky, Ari, and Lo, Hung-Tat
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Objective: As it is increasingly recognized that cultural competence is an essential quality for any practicing psychiatrist, postgraduate psychiatry training programs need to incorporate cultural competence training into their curricula. This article documents the unique approach to resident cultural competence training being developed in the Department of Psychiatry at the University of Toronto, which has the largest residency training program in North America and is situated in an ethnically diverse city and country. Methods: The authors conducted a systematic review of cultural competence by searching databases including PubMed, PsycINFO, PsycArticles, CINAHL, Social Science Abstracts, and Sociological Abstracts; by searching government and professional association publications; and through on-site visits to local crosscultural training programs. Based on the results of the review, a resident survey, and a staff retreat, the authors developed a deliberate "integrative" approach with a mindful, balanced emphasis on both generic and specific cultural competencies. Results: Learning objectives were derived from integrating the seven core competencies of a physician as defined by the Canadian Medical Education Directions for Specialists (CanMEDS) roles framework with the tripartite model of attitudes, knowledge, and skills. The learning objectives and teaching program were further integrated across different psychiatric subspecialties and across the successive years of residency. Another unique strategy used to foster curricular and institutional change was the program's emphasis on evaluation, making use of insights from modern educational theories such as formative feedback and blueprinting. Course evaluations of the core curriculum from the first group of residents were positive. Conclusion: The authors propose that these changes to the curriculum may lead to enhanced cultural competence and clinical effectiveness in health care.
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- 2008
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