From ECG signals to images: a transformation based approach for deep learning.
Ontology highlight
ABSTRACT:
SUBMITTER: Naz M
PROVIDER: S-EPMC7959637 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundIncreasing utilization of long-term outpatient ambulatory electrocardiographic (ECG) monitoring continues to drive the need for improved ECG interpretation algorithms.ObjectiveThe purpose of this study was to describe the BeatLogic® platform for ECG interpretation and to validate the platform using electrophysiologist-adjudicated real-world data and publicly available validation data.MethodsDeep learning models were trained to perform beat and rhythm detection/classification using ECGs collected with the Preventice BodyGuardian® Heart monitor. Training annotations were created by certified ECG technicians, and validation annotations were adjudicated by a team of board-certified electrophysiologists. Deep learning model classification results were used to generate contiguous annotation results, and performance was assessed in accordance with the EC57 standard.ResultsOn the real-world validation dataset, BeatLogic beat detection sensitivity and positive predictive value were 99.84% and 99.78%, respectively. Ventricular ectopic beat classification sensitivity and positive predictive value were 89.4% and 97.8%, respectively. Episode and duration F1 scores (range 0-100) exceeded 70 for all 14 rhythms (including noise) that were evaluated. F1 scores for 11 rhythms exceeded 80, 7 exceeded 90, and 5 including atrial fibrillation/flutter, ventricular tachycardia, ventricular bigeminy, ventricular trigeminy, and third-degree heart block exceeded 95.ConclusionThe BeatLogic platform represents the next stage of advancement for algorithmic ECG interpretation. This comprehensive platform performs beat detection, beat classification, and rhythm detection/classification with greatly improved performance over the current state of the art, with comparable or improved performance over previously published algorithms that can accomplish only 1 of these 3 tasks.
| S-EPMC9247885 | biostudies-literature
Project description:Preliminary diagnosis of fungal infections can rely on microscopic examination. However, in many cases, it does not allow unambiguous identification of the species due to their visual similarity. Therefore, it is usually necessary to use additional biochemical tests. That involves additional costs and extends the identification process up to 10 days. Such a delay in the implementation of targeted therapy may be grave in consequence as the mortality rate for immunosuppressed patients is high. In this paper, we apply a machine learning approach based on deep neural networks and bag-of-words to classify microscopic images of various fungi species. Our approach makes the last stage of biochemical identification redundant, shortening the identification process by 2-3 days, and reducing the cost of the diagnosis.
| S-EPMC7326179 | biostudies-literature
Project description:Deep learning has shown remarkable results for image analysis and is expected to aid individual treatment decisions in health care. Treatment recommendations are predictions with an inherently causal interpretation. To use deep learning for these applications in the setting of observational data, deep learning methods must be made compatible with the required causal assumptions. We present a scenario with real-world medical images (CT-scans of lung cancer) and simulated outcome data. Through the data simulation scheme, the images contain two distinct factors of variation that are associated with survival, but represent a collider (tumor size) and a prognostic factor (tumor heterogeneity), respectively. When a deep network would use all the information available in the image to predict survival, it would condition on the collider and thereby introduce bias in the estimation of the treatment effect. We show that when this collider can be quantified, unbiased individual prognosis predictions are attainable with deep learning. This is achieved by (1) setting a dual task for the network to predict both the outcome and the collider and (2) enforcing a form of linear independence of the activation distributions of the last layer. Our method provides an example of combining deep learning and structural causal models to achieve unbiased individual prognosis predictions. Extensions of machine learning methods for applications to causal questions are required to attain the long-standing goal of personalized medicine supported by artificial intelligence.
| S-EPMC6904461 | biostudies-literature
Project description:Topological features such as persistence diagrams and their functional approximations like persistence images (PIs) have been showing substantial promise for machine learning and computer vision applications. This is greatly attributed to the robustness topological representations provide against different types of physical nuisance variables seen in real-world data, such as view-point, illumination, and more. However, key bottlenecks to their large scale adoption are computational expenditure and difficulty incorporating them in a differentiable architecture. We take an important step in this paper to mitigate these bottlenecks by proposing a novel one-step approach to generate PIs directly from the input data. We design two separate convolutional neural network architectures, one designed to take in multi-variate time series signals as input and another that accepts multi-channel images as input. We call these networks Signal PI-Net and Image PI-Net respectively. To the best of our knowledge, we are the first to propose the use of deep learning for computing topological features directly from data. We explore the use of the proposed PI-Net architectures on two applications: human activity recognition using tri-axial accelerometer sensor data and image classification. We demonstrate the ease of fusion of PIs in supervised deep learning architectures and speed up of several orders of magnitude for extracting PIs from data. Our code is available at https://github.com/anirudhsom/PI-Net.
| S-EPMC7521829 | biostudies-literature
Project description:BackgroundQuantification of myocardium scarring in late gadolinium enhanced (LGE) cardiac magnetic resonance imaging can be challenging due to low scar-to-background contrast and low image quality. To resolve ambiguous LGE regions, experienced readers often use conventional cine sequences to accurately identify the myocardium borders.PurposeTo develop a deep learning model for combining LGE and cine images to improve the robustness and accuracy of LGE scar quantification.Study typeRetrospective.PopulationA total of 191 hypertrophic cardiomyopathy patients: 1) 162 patients from two sites randomly split into training (50%; 81 patients), validation (25%, 40 patients), and testing (25%; 41 patients); and 2) an external testing dataset (29 patients) from a third site.Field strength/sequence1.5T, inversion-recovery segmented gradient-echo LGE and balanced steady-state free-precession cine sequences ASSESSMENT: Two convolutional neural networks (CNN) were trained for myocardium and scar segmentation, one with and one without LGE-Cine fusion. For CNN with fusion, the input was two aligned LGE and cine images at matched cardiac phase and anatomical location. For CNN without fusion, only LGE images were used as input. Manual segmentation of the datasets was used as reference standard.Statistical testsManual and CNN-based quantifications of LGE scar burden and of myocardial volume were assessed using Pearson linear correlation coefficients (r) and Bland-Altman analysis.ResultsBoth CNN models showed strong agreement with manual quantification of LGE scar burden and myocardium volume. CNN with LGE-Cine fusion was more robust than CNN without LGE-Cine fusion, allowing for successful segmentation of significantly more slices (603 [95%] vs. 562 (89%) of 635 slices; P < 0.001). Also, CNN with LGE-Cine fusion showed better agreement with manual quantification of LGE scar burden than CNN without LGE-Cine fusion (%ScarLGE-cine = 0.82 × %Scarmanual , r = 0.84 vs. %ScarLGE = 0.47 × %Scarmanual , r = 0.81) and myocardium volume (VolumeLGE-cine = 1.03 × Volumemanual , r = 0.96 vs. VolumeLGE = 0.91 × Volumemanual , r = 0.91).Data conclusionCNN based LGE-Cine fusion can improve the robustness and accuracy of automated scar quantification.Level of evidence3 TECHNICAL EFFICACY: 1.
| S-EPMC8359184 | biostudies-literature
Project description:This study proposes a simple convolutional neural network (CNN)-based model for vehicle classification in low resolution surveillance images collected by a standard security camera installed distant from a traffic scene. In order to evaluate its effectiveness, the proposed model is tested on a new dataset containing tiny (100 × 100 pixels) and low resolution (96 dpi) vehicle images. The proposed model is then compared with well-known VGG16-based CNN models in terms of accuracy and complexity. Results indicate that although the well-known models provide higher accuracy, the proposed method offers an acceptable accuracy (92.9%) as well as a simple and lightweight solution for vehicle classification in low quality images. Thus, it is believed that this study might provide useful perception and understanding for further research on the use of standard low-cost cameras to enhance the ability of the intelligent systems such as intelligent transportation system applications.
| S-EPMC9268885 | biostudies-literature
Project description:The detailed anatomical information of the brain provided by 3D magnetic resonance imaging (MRI) enables various neuroscience research. However, due to the long scan time for 3D MR images, 2D images are mainly obtained in clinical environments. The purpose of this study is to generate 3D images from a sparsely sampled 2D images using an inpainting deep neural network that has a U-net-like structure and DenseNet sub-blocks. To train the network, not only fidelity loss but also perceptual loss based on the VGG network were considered. Various methods were used to assess the overall similarity between the inpainted and original 3D data. In addition, morphological analyzes were performed to investigate whether the inpainted data produced local features similar to the original 3D data. The diagnostic ability using the inpainted data was also evaluated by investigating the pattern of morphological changes in disease groups. Brain anatomy details were efficiently recovered by the proposed neural network. In voxel-based analysis to assess gray matter volume and cortical thickness, differences between the inpainted data and the original 3D data were observed only in small clusters. The proposed method will be useful for utilizing advanced neuroimaging techniques with 2D MRI data.
| S-EPMC7814079 | biostudies-literature
Project description:Drill core lithology is an important indicator reflecting the geological conditions of the drilling area. Traditional lithology identification usually relies on manual visual inspection, which is time-consuming and professionally demanding. In recent years, the rapid development of convolutional neural networks has provided an innovative way for the automatic prediction of drill core images. In this work, a core dataset containing a total of 10 common lithology categories in underground engineering was constructed. ResNeSt-50 we adopted uses a strategy of combining channel-wise attention and multi-path network to achieve cross-channel feature correlations, which significantly improves the model accuracy without high model complexity. Transfer learning was used to initialize the model parameters, to extract the feature of core images more efficiently. The model achieved superior performance on testing images compared with other discussed CNN models, the average value of its Precision, Recall, F1-score for each category of lithology is 99.62%, 99.62%, and 99.59%, respectively, and the prediction accuracy is 99.60%. The test results show that the proposed method is optimal and effective for automatic lithology classification of borehole cores.
| S-EPMC9249224 | biostudies-literature
Project description:PurposeTo develop a deep learning algorithm for the automatic assessment of the extent of systemic sclerosis (SSc)-related interstitial lung disease (ILD) on chest CT images.Materials and methodsThis retrospective study included 208 patients with SSc (median age, 57 years; 167 women) evaluated between January 2009 and October 2017. A multicomponent deep neural network (AtlasNet) was trained on 6888 fully annotated CT images (80% for training and 20% for validation) from 17 patients with no, mild, or severe lung disease. The model was tested on a dataset of 400 images from another 20 patients, independently partially annotated by three radiologist readers. The ILD contours from the three readers and the deep learning neural network were compared by using the Dice similarity coefficient (DSC). The correlation between disease extent obtained from the deep learning algorithm and that obtained by using pulmonary function tests (PFTs) was then evaluated in the remaining 171 patients and in an external validation dataset of 31 patients based on the analysis of all slices of the chest CT scan. The Spearman rank correlation coefficient (ρ) was calculated to evaluate the correlation between disease extent and PFT results.ResultsThe median DSCs between the readers and the deep learning ILD contours ranged from 0.74 to 0.75, whereas the median DSCs between contours from radiologists ranged from 0.68 to 0.71. The disease extent obtained from the algorithm, by analyzing the whole CT scan, correlated with the diffusion lung capacity for carbon monoxide, total lung capacity, and forced vital capacity (ρ = -0.76, -0.70, and -0.62, respectively; P < .001 for all) in the dataset for the correlation with PFT results. The disease extents correlated with diffusion lung capacity for carbon monoxide, total lung capacity, and forced vital capacity were ρ = -0.65, -0.70, and -0.57, respectively, in the external validation dataset (P < .001 for all).ConclusionThe developed algorithm performed similarly to radiologists for disease-extent contouring, which correlated with pulmonary function to assess CT images from patients with SSc-related ILD.Supplemental material is available for this article.© RSNA, 2020.
| S-EPMC8082359 | biostudies-literature
Project description:Pulmonary fissure detection in computed tomography (CT) is a critical component for automatic lobar segmentation. The majority of fissure detection methods use feature descriptors that are hand-crafted, low-level, and have local spatial extent. The design of such feature detectors is typically targeted toward normal fissure anatomy, yielding low sensitivity to weak, and abnormal fissures that are common in clinical data sets. Furthermore, local features commonly suffer from low specificity, as the complex textures in the lung can be indistinguishable from the fissure when the global context is not considered. We propose a supervised discriminative learning framework for simultaneous feature extraction and classification. The proposed framework, called FissureNet, is a coarse-to-fine cascade of two convolutional neural networks. The coarse-to-fine strategy alleviates the challenges associated with training a network to segment a thin structure that represents a small fraction of the image voxels. FissureNet was evaluated on a cohort of 3706 subjects with inspiration and expiration 3DCT scans from the COPDGene clinical trial and a cohort of 20 subjects with 4DCT scans from a lung cancer clinical trial. On both data sets, FissureNet showed superior performance compared with a deep learning approach using the U-Net architecture and a Hessian-based fissure detection method in terms of area under the precision-recall curve (PR-AUC). The overall PR-AUC for FissureNet, U-Net, and Hessian on the COPDGene (lung cancer) data set was 0.980 (0.966), 0.963 (0.937), and 0.158 (0.182), respectively. On a subset of 30 COPDGene scans, FissureNet was compared with a recently proposed advanced fissure detection method called derivative of sticks (DoS) and showed superior performance with a PR-AUC of 0.991 compared with 0.668 for DoS.
| S-EPMC6318012 | biostudies-literature