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Register a new userSelf-attention based BiLSTM-CNN classifier for the prediction of ischemic and non-ischemic cardiomyopathy
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Added by
Vishal Srivastava Dr
Publication date
2019
fields
Informatics Engineering
and research's language is
English
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Heart Failure is a major component of healthcare expenditure and a leading cause of mortality worldwide. Despite higher inter-rater variability, endomyocardial biopsy (EMB) is still regarded as the standard technique, used to identify the cause (e.g. ischemic or non-ischemic cardiomyopathy, coronary artery disease, myocardial infarction etc.) of unexplained heart failure. In this paper, we focus on identifying cardiomyopathy as ischemic or non-ischemic. For this, we propose and implement a new unified architecture comprising CNN (inception-V3 model) and bidirectional LSTM (BiLSTM) with self-attention mechanism to predict the ischemic or non-ischemic to classify cardiomyopathy using histopathological images. The proposed model is based on self-attention that implicitly focuses on the information outputted from the hidden layers of BiLSTM. Through our results we demonstrate that this framework carries a high learning capacity and is able to improve the classification performance.
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We developed a novel patient-specific computational model for the numerical simulation of ventricular electromechanics in patients with ischemic cardiomyopathy (ICM). This model reproduces the activity both in sinus rhythm (SR) and in ventricular tachycardia (VT). The presence of scars, grey zones and non-remodeled regions of the myocardium is accounted for by the introduction of a spatially heterogeneous coefficient in the 3D electromechanics model. This 3D electromechanics model is firstly coupled with a 2-element Windkessel afterload model to fit the pressure-volume (PV) loop of a patient-specific left ventricle (LV) with ICM in SR. Then, we employ the coupling with a 0D closed-loop circulation model to analyze a VT circuit over multiple heartbeats on the same LV. We highlight similarities and differences on the solutions obtained by the electrophysiology model and those of the electromechanics model, while considering different scenarios for the circulatory system. We observe that very different parametrizations of the circulation model induce the same hemodynamical considerations for the patient at hand. Specifically, we classify this VT as unstable. We conclude by stressing the importance of combining electrophysiological, mechanical and hemodynamical models to provide relevant clinical indicators in how arrhythmias evolve and can potentially lead to sudden cardiac death.
Ischemic stroke lesion segmentation from Computed Tomography Perfusion (CTP) images is important for accurate diagnosis of stroke in acute care units. However, it is challenged by low image contrast and resolution of the perfusion parameter maps, in addition to the complex appearance of the lesion. To deal with this problem, we propose a novel framework based on synthesized pseudo Diffusion-Weighted Imaging (DWI) from perfusion parameter maps to obtain better image quality for more accurate segmentation. Our framework consists of three components based on Convolutional Neural Networks (CNNs) and is trained end-to-end. First, a feature extractor is used to obtain both a low-level and high-level compact representation of the raw spatiotemporal Computed Tomography Angiography (CTA) images. Second, a pseudo DWI generator takes as input the concatenation of CTP perfusion parameter maps and our extracted features to obtain the synthesized pseudo DWI. To achieve better synthesis quality, we propose a hybrid loss function that pays more attention to lesion regions and encourages high-level contextual consistency. Finally, we segment the lesion region from the synthesized pseudo DWI, where the segmentation network is based on switchable normalization and channel calibration for better performance. Experimental results showed that our framework achieved the top performance on ISLES 2018 challenge and: 1) our method using synthesized pseudo DWI outperformed methods segmenting the lesion from perfusion parameter maps directly; 2) the feature extractor exploiting additional spatiotemporal CTA images led to better synthesized pseudo DWI quality and higher segmentation accuracy; and 3) the proposed loss functions and network structure improved the pseudo DWI synthesis and lesion segmentation performance.
Crowd flow prediction has been increasingly investigated in intelligent urban computing field as a fundamental component of urban management system. The most challenging part of predicting crowd flow is to measure the complicated spatial-temporal dependencies. A prevalent solution employed in current methods is to divide and conquer the spatial and temporal information by various architectures (e.g., CNN/GCN, LSTM). However, this strategy has two disadvantages: (1) the sophisticated dependencies are also divided and therefore partially isolated; (2) the spatial-temporal features are transformed into latent representations when passing through different architectures, making it hard to interpret the predicted crowd flow. To address these issues, we propose a Spatial-Temporal Self-Attention Network (STSAN) with an ST encoding gate that calculates the entire spatial-temporal representation with positional and time encodings and therefore avoids dividing the dependencies. Furthermore, we develop a Multi-aspect attention mechanism that applies scaled dot-product attention over spatial-temporal information and measures the attention weights that explicitly indicate the dependencies. Experimental results on traffic and mobile data demonstrate that the proposed method reduces inflow and outflow RMSE by 16% and 8% on the Taxi-NYC dataset compared to the SOTA baselines.
Despite its best performance in image denoising, the supervised deep denoising methods require paired noise-clean data, which are often unavailable. To address this challenge, Noise2Noise was designed based on the fact that paired noise-clean images can be replaced by paired noise-noise images that are easier to collect. However, in many scenarios the collection of paired noise-noise images is still impractical. To bypass labeled images, Noise2Void methods predict masked pixels from their surroundings with single noisy images only and give improved denoising results that still need improvements. An observation on classic denoising methods is that non-local mean (NLM) outcomes are typically superior to locally denoised results. In contrast, Noise2Void and its variants do not utilize self-similarities in an image as the NLM-based methods do. Here we propose Noise2Sim, an NLM-inspired self-learning method for image denoising. Specifically, Noise2Sim leverages the self-similarity of image pixels to train the denoising network, requiring single noisy images only. Our theoretical analysis shows that Noise2Sim tends to be equivalent to Noise2Noise under mild conditions. To efficiently manage the computational burden for globally searching similar pixels, we design a two-step procedure to provide data for Noise2Sim training. Extensive experiments demonstrate the superiority of Noise2Sim on common benchmark datasets.
Topological data analysis aims to extract topological quantities from data, which tend to focus on the broader global structure of the data rather than local information. The Mapper method, specifically, generalizes clustering methods to identify significant global mathematical structures, which are out of reach of many other approaches. We propose a classifier based on applying the Mapper algorithm to data projected onto a latent space. We obtain the latent space by using PCA or autoencoders. Notably, a classifier based on the Mapper method is immune to any gradient based attack, and improves robustness over traditional CNNs (convolutional neural networks). We report theoretical justification and some numerical experiments that confirm our claims.
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