Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userLongitudinal Pooling & Consistency Regularization to Model Disease Progression from MRIs
139
0
0.0
(
0
)
Ask ChatGPT about the research
No Arabic abstract
Many neurological diseases are characterized by gradual deterioration of brain structure and function. Large longitudinal MRI datasets have revealed such deterioration, in part, by applying machine and deep learning to predict diagnosis. A popular approach is to apply Convolutional Neural Networks (CNN) to extract informative features from each visit of the longitudinal MRI and then use those features to classify each visit via Recurrent Neural Networks (RNNs). Such modeling neglects the progressive nature of the disease, which may result in clinically implausible classifications across visits. To avoid this issue, we propose to combine features across visits by coupling feature extraction with a novel longitudinal pooling layer and enforce consistency of the classification across visits in line with disease progression. We evaluate the proposed method on the longitudinal structural MRIs from three neuroimaging datasets: Alzheimers Disease Neuroimaging Initiative (ADNI, N=404), a dataset composed of 274 normal controls and 329 patients with Alcohol Use Disorder (AUD), and 255 youths from the National Consortium on Alcohol and NeuroDevelopment in Adolescence (NCANDA). In all three experiments our method is superior to other widely used approaches for longitudinal classification thus making a unique contribution towards more accurate tracking of the impact of conditions on the brain. The code is available at https://github.com/ouyangjiahong/longitudinal-pooling.
rate research
Read More
Longitudinal imaging is capable of capturing the static ana-to-mi-cal structures and the dynamic changes of the morphology resulting from aging or disease progression. Self-supervised learning allows to learn new representation from available large unlabelled data without any expert knowledge. We propose a deep learning self-supervised approach to model disease progression from longitudinal retinal optical coherence tomography (OCT). Our self-supervised model takes benefit from a generic time-related task, by learning to estimate the time interval between pairs of scans acquired from the same patient. This task is (i) easy to implement, (ii) allows to use irregularly sampled data, (iii) is tolerant to poor registration, and (iv) does not rely on additional annotations. This novel method learns a representation that focuses on progression specific information only, which can be transferred to other types of longitudinal problems. We transfer the learnt representation to a clinically highly relevant task of predicting the onset of an advanced stage of age-related macular degeneration within a given time interval based on a single OCT scan. The boost in prediction accuracy, in comparison to a network learned from scratch or transferred from traditional tasks, demonstrates that our pretrained self-supervised representation learns a clinically meaningful information.
Chest computed tomography (CT) has played an essential diagnostic role in assessing patients with COVID-19 by showing disease-specific image features such as ground-glass opacity and consolidation. Image segmentation methods have proven to help quantify the disease burden and even help predict the outcome. The availability of longitudinal CT series may also result in an efficient and effective method to reliably assess the progression of COVID-19, monitor the healing process and the response to different therapeutic strategies. In this paper, we propose a new framework to identify infection at a voxel level (identification of healthy lung, consolidation, and ground-glass opacity) and visualize the progression of COVID-19 using sequential low-dose non-contrast CT scans. In particular, we devise a longitudinal segmentation network that utilizes the reference scan information to improve the performance of disease identification. Experimental results on a clinical longitudinal dataset collected in our institution show the effectiveness of the proposed method compared to the static deep neural networks for disease quantification.
Analyzing disease progression patterns can provide useful insights into the disease processes of many chronic conditions. These analyses may help inform recruitment for prevention trials or the development and personalization of treatments for those affected. We learn disease progression patterns using Hidden Markov Models (HMM) and distill them into distinct trajectories using visualization methods. We apply it to the domain of Type 1 Diabetes (T1D) using large longitudinal observational data from the T1DI study group. Our method discovers distinct disease progression trajectories that corroborate with recently published findings. In this paper, we describe the iterative process of developing the model. These methods may also be applied to other chronic conditions that evolve over time.
There are various inverse problems -- including reconstruction problems arising in medical imaging -- where one is often aware of the forward operator that maps variables of interest to the observations. It is therefore natural to ask whether such knowledge of the forward operator can be exploited in deep learning approaches increasingly used to solve inverse problems. In this paper, we provide one such way via an analysis of the generalisation error of deep learning methods applicable to inverse problems. In particular, by building on the algorithmic robustness framework, we offer a generalisation error bound that encapsulates key ingredients associated with the learning problem such as the complexity of the data space, the size of the training set, the Jacobian of the deep neural network and the Jacobian of the composition of the forward operator with the neural network. We then propose a plug-and-play regulariser that leverages the knowledge of the forward map to improve the generalization of the network. We likewise also propose a new method allowing us to tightly upper bound the Lipschitz constants of the relevant functions that is much more computational efficient than existing ones. We demonstrate the efficacy of our model-aware regularised deep learning algorithms against other state-of-the-art approaches on inverse problems involving various sub-sampling operators such as those used in classical compressed sensing setup and accelerated Magnetic Resonance Imaging (MRI).
Light field (LF) images acquired by hand-held devices usually suffer from low spatial resolution as the limited detector resolution has to be shared with the angular dimension. LF spatial super-resolution (SR) thus becomes an indispensable part of the LF camera processing pipeline. The high-dimensionality characteristic and complex geometrical structure of LF images make the problem more challenging than traditional single-image SR. The performance of existing methods is still limited as they fail to thoroughly explore the coherence among LF sub-aperture images (SAIs) and are insufficient in accurately preserving the scenes parallax structure. To tackle this challenge, we propose a novel learning-based LF spatial SR framework. Specifically, each SAI of an LF image is first coarsely and individually super-resolved by exploring the complementary information among SAIs with selective combinatorial geometry embedding. To achieve efficient and effective selection of the complementary information, we propose two novel sub-modules conducted hierarchically: the patch selector provides an option of retrieving similar image patches based on offline disparity estimation to handle large-disparity correlations; and the SAI selector adaptively and flexibly selects the most informative SAIs to improve the embedding efficiency. To preserve the parallax structure among the reconstructed SAIs, we subsequently append a consistency regularization network trained over a structure-aware loss function to refine the parallax relationships over the coarse estimation. In addition, we extend the proposed method to irregular LF data. To the best of our knowledge, this is the first learning-based SR method for irregular LF data. Experimental results over both synthetic and real-world LF datasets demonstrate the significant advantage of our approach over state-of-the-art methods.
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
