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Register a new userEfficient video indexing for monitoring disease activity and progression in the upper gastrointestinal tract
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Added by
Sharib Ali Dr.
Publication date
2019
fields
Informatics Engineering
and research's language is
English
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Endoscopy is a routine imaging technique used for both diagnosis and minimally invasive surgical treatment. While the endoscopy video contains a wealth of information, tools to capture this information for the purpose of clinical reporting are rather poor. In date, endoscopists do not have any access to tools that enable them to browse the video data in an efficient and user friendly manner. Fast and reliable video retrieval methods could for example, allow them to review data from previous exams and therefore improve their ability to monitor disease progression. Deep learning provides new avenues of compressing and indexing video in an extremely efficient manner. In this study, we propose to use an autoencoder for efficient video compression and fast retrieval of video images. To boost the accuracy of video image retrieval and to address data variability like multi-modality and view-point changes, we propose the integration of a Siamese network. We demonstrate that our approach is competitive in retrieving images from 3 large scale videos of 3 different patients obtained against the query samples of their previous diagnosis. Quantitative validation shows that the combined approach yield an overall improvement of 5% and 8% over classical and variational autoencoders, respectively.
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Alzheimers disease (AD) is known as one of the major causes of dementia and is characterized by slow progression over several years, with no treatments or available medicines. In this regard, there have been efforts to identify the risk of developing AD in its earliest time. While many of the previous works considered cross-sectional analysis, more recent studies have focused on the diagnosis and prognosis of AD with longitudinal or time series data in a way of disease progression modeling (DPM). Under the same problem settings, in this work, we propose a novel computational framework that can predict the phenotypic measurements of MRI biomarkers and trajectories of clinical status along with cognitive scores at multiple future time points. However, in handling time series data, it generally faces with many unexpected missing observations. In regard to such an unfavorable situation, we define a secondary problem of estimating those missing values and tackle it in a systematic way by taking account of temporal and multivariate relations inherent in time series data. Concretely, we propose a deep recurrent network that jointly tackles the four problems of (i) missing value imputation, (ii) phenotypic measurements forecasting, (iii) trajectory estimation of the cognitive score, and (iv) clinical status prediction of a subject based on his/her longitudinal imaging biomarkers. Notably, the learnable model parameters of our network are trained in an end-to-end manner with our circumspectly defined loss function. In our experiments over TADPOLE challenge cohort, we measured performance for various metrics and compared our method to competing methods in the literature. Exhaustive analyses and ablation studies were also conducted to better confirm the effectiveness of our method.
In this paper, we explore the spatial redundancy in video recognition with the aim to improve the computational efficiency. It is observed that the most informative region in each frame of a video is usually a small image patch, which shifts smoothly across frames. Therefore, we model the patch localization problem as a sequential decision task, and propose a reinforcement learning based approach for efficient spatially adaptive video recognition (AdaFocus). In specific, a light-weighted ConvNet is first adopted to quickly process the full video sequence, whose features are used by a recurrent policy network to localize the most task-relevant regions. Then the selected patches are inferred by a high-capacity network for the final prediction. During offline inference, once the informative patch sequence has been generated, the bulk of computation can be done in parallel, and is efficient on modern GPU devices. In addition, we demonstrate that the proposed method can be easily extended by further considering the temporal redundancy, e.g., dynamically skipping less valuable frames. Extensive experiments on five benchmark datasets, i.e., ActivityNet, FCVID, Mini-Kinetics, Something-Something V1&V2, demonstrate that our method is significantly more efficient than the competitive baselines. Code is available at https://github.com/blackfeather-wang/AdaFocus.
Over the past few decades, in silico modeling of organ systems has significantly furthered our understanding of their physiology and biomechanical function. In this work, we present a detailed numerical model of the upper gastrointestinal (GI) tract that not only accounts for the fiber architecture of the muscle walls, but also the multiphasic components they help transport during normal digestive function. Construction details for 3D models of representative stomach geometry are presented along with a simple strategy for assigning circular and longitudinal muscle fiber orientations for each layer. Based on our previous work that created a fully resolved model of esophageal peristalsis, we extend the same principles to simulate gastric peristalsis by systematically activating muscle fibers embedded in the stomach. Following this, for the first time, we simulate gravity driven bolus emptying into the stomach due to density differences between ingested contents and fluid contents of the stomach. This detailed computational model of the upper gastrointestinal tract provides a foundation on which future models can be based that seek to investigate the biomechanics of acid reflux and probe various strategies for gastric bypass surgeries to address the growing problem of adult obesity.
Video transmission applications (e.g., conferencing) are gaining momentum, especially in times of global health pandemic. Video signals are transmitted over lossy channels, resulting in low-quality received signals. To restore videos on recipient edge devices in real-time, we introduce an efficient video restoration network, EVRNet. EVRNet efficiently allocates parameters inside the network using alignment, differential, and fusion modules. With extensive experiments on video restoration tasks (deblocking, denoising, and super-resolution), we demonstrate that EVRNet delivers competitive performance to existing methods with significantly fewer parameters and MACs. For example, EVRNet has 260 times fewer parameters and 958 times fewer MACs than enhanced deformable convolution-based video restoration network (EDVR) for 4 times video super-resolution while its SSIM score is 0.018 less than EDVR. We also evaluated the performance of EVRNet under multiple distortions on unseen dataset to demonstrate its ability in modeling variable-length sequences under both camera and object motion.
Ability to quantify and predict progression of a disease is fundamental for selecting an appropriate treatment. Many clinical metrics cannot be acquired frequently either because of their cost (e.g. MRI, gait analysis) or because they are inconvenient or harmful to a patient (e.g. biopsy, x-ray). In such scenarios, in order to estimate individual trajectories of disease progression, it is advantageous to leverage similarities between patients, i.e. the covariance of trajectories, and find a latent representation of progression. Most of existing methods for estimating trajectories do not account for events in-between observations, what dramatically decreases their adequacy for clinical practice. In this study, we develop a machine learning framework named Coordinatewise-Soft-Impute (CSI) for analyzing disease progression from sparse observations in the presence of confounding events. CSI is guaranteed to converge to the global minimum of the corresponding optimization problem. Experimental results also demonstrates the effectiveness of CSI using both simulated and real dataset.
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