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General General

A memory optimization method combined with adaptive time-step method for cardiac cell simulation based on multi-GPU.

In Medical & biological engineering & computing ; h5-index 32.0

Cardiac electrophysiological simulation is a very complex computational process, which can be run on graphics processing unit (GPU) to save computational cost greatly. The use of adaptive time-step can further effectively speed up the simulation of heart cells. However, if the adaptive time-step method applies to GPU, it suffers synchronization problem on GPU, weakening the acceleration of adaptive time-step method. The previous work ran on a single GPU with the adaptive time-step to get only 1.5 times (× 1.5) faster than the fixed time-step. This study proposes a memory allocation method, which can effectively implement the adaptive time-step method on GPU. The proposed method mainly focuses on the stimulus point and potential memory arrangement in order to achieve optimal memory storage efficiency. All calculation is implemented on GPU. Large matrices such as potential are arranged in column order, and the cells on the left are stimulated. The Luo-Rudy passive (LR1) and dynamic (LRd) ventricular action potential models are used with adaptive time-step methods, such as the traditional hybrid method (THM) and Chen-Chen-Luo's (CCL) "quadratic adaptive algorithm" method. As LR1 is solved by the THM or CCL on a single GPU, the acceleration is × 34 and × 75 respectively compared with the fixed time-step. With 2 or 4 GPUs, the acceleration of the THM and CCL is × 34 or × 35 and × 73 or × 75, but it would decrease to × 5 or × 3 and × 20 or × 15 without optimization. In an LRd model, the acceleration reaches × 27 or × 85 as solved by the THM or CCL compared with the fixed time-step on multi-GPU with linear speed up increase versus the number of GPU. However, with the increase of GPUs number, the acceleration of the THM and CCL is continuously weakened before optimization. The mixed root mean square error (MRMSE) lower than 5% is applied to ensure the accuracy of simulation. The result shows that the proposed memory arrangement method can save computational cost a lot to speed up the heart simulation greatly. Graphical abstract Acceleration ratio compared with CPU with fixed time-step (dt = 0.001 ms).

Luo Ching-Hsing, Ye Haiyi, Chen Xingji

2020-Sep-21

Adaptive time-step method, Computer simulation, High performance computing, Memory optimization, Ventricular cell

General General

Discriminating electrocardiographic responses to His-bundle pacing using machine learning.

In Cardiovascular digital health journal

Background : His-bundle pacing (HBP) has emerged as an alternative to conventional ventricular pacing because of its ability to deliver physiological ventricular activation. Pacing at the His bundle produces different electrocardiographic (ECG) responses: selective His-bundle pacing (S-HBP), non-selective His bundle pacing (NS-HBP), and myocardium-only capture (MOC). These 3 capture types must be distinguished from each other, which can be challenging and time-consuming even for experts.

Objective : The purpose of this study was to use artificial intelligence (AI) in the form of supervised machine learning using a convolutional neural network (CNN) to automate HBP ECG interpretation.

Methods : We identified patients who had undergone HBP and extracted raw 12-lead ECG data during S-HBP, NS-HBP, and MOC. A CNN was trained, using 3-fold cross-validation, on 75% of the segmented QRS complexes labeled with their capture type. The remaining 25% was kept aside as a testing dataset.

Results : The CNN was trained with 1297 QRS complexes from 59 patients. Cohen kappa for the neural network's performance on the 17-patient testing set was 0.59 (95% confidence interval 0.30 to 0.88; P <.0001), with an overall accuracy of 75%. The CNN's accuracy in the 17-patient testing set was 67% for S-HBP, 71% for NS-HBP, and 84% for MOC.

Conclusion : We demonstrated proof of concept that a neural network can be trained to automate discrimination between HBP ECG responses. When a larger dataset is trained to higher accuracy, automated AI ECG analysis could facilitate HBP implantation and follow-up and prevent complications resulting from incorrect HBP ECG analysis.

Arnold Ahran D, Howard James P, Gopi Aiswarya A, Chan Cheng Pou, Ali Nadine, Keene Daniel, Shun-Shin Matthew J, Ahmad Yousif, Wright Ian J, Ng Fu Siong, Linton Nick W F, Kanagaratnam Prapa, Peters Nicholas S, Rueckert Daniel, Francis Darrel P, Whinnett Zachary I

Artificial intelligence, Conduction system pacing, Electrocardiography, His-bundle pacing, Machine learning, Neural networks, Pacemakers

General General

Prediction of conversion to Alzheimer's disease using deep survival analysis of MRI images.

In Brain communications

The prediction of the conversion of healthy individuals and those with mild cognitive impairment to the status of active Alzheimer's disease is a challenging task. Recently, a survival analysis based upon deep learning was developed to enable predictions regarding the timing of an event in a dataset containing censored data. Here, we investigated whether a deep survival analysis could similarly predict the conversion to Alzheimer's disease. We selected individuals with mild cognitive impairment and cognitively normal subjects and used the grey matter volumes of brain regions in these subjects as predictive features. We then compared the prediction performances of the traditional standard Cox proportional-hazard model, the DeepHit model and our deep survival model based on a Weibull distribution. Our model achieved a maximum concordance index of 0.835, which was higher than that yielded by the Cox model and comparable to that of the DeepHit model. To our best knowledge, this is the first report to describe the application of a deep survival model to brain magnetic resonance imaging data. Our results demonstrate that this type of analysis could successfully predict the time of an individual's conversion to Alzheimer's disease.

Nakagawa Tomonori, Ishida Manabu, Naito Junpei, Nagai Atsushi, Yamaguchi Shuhei, Onoda Keiichi

2020

Alzheimer’s disease, deep survival analysis, mild cognitive impairment, prediction of conversion

General General

COVID-19 detection in CT images with deep learning: A voting-based scheme and cross-datasets analysis.

In Informatics in medicine unlocked

Early detection and diagnosis are critical factors to control the COVID-19 spreading. A number of deep learning-based methodologies have been recently proposed for COVID-19 screening in CT scans as a tool to automate and help with the diagnosis. These approaches, however, suffer from at least one of the following problems: (i) they treat each CT scan slice independently and (ii) the methods are trained and tested with sets of images from the same dataset. Treating the slices independently means that the same patient may appear in the training and test sets at the same time which may produce misleading results. It also raises the question of whether the scans from the same patient should be evaluated as a group or not. Moreover, using a single dataset raises concerns about the generalization of the methods. Different datasets tend to present images of varying quality which may come from different types of CT machines reflecting the conditions of the countries and cities from where they come from. In order to address these two problems, in this work, we propose an Efficient Deep Learning Technique for the screening of COVID-19 with a voting-based approach. In this approach, the images from a given patient are classified as group in a voting system. The approach is tested in the two biggest datasets of COVID-19 CT analysis with a patient-based split. A cross dataset study is also presented to assess the robustness of the models in a more realistic scenario in which data comes from different distributions. The cross-dataset analysis has shown that the generalization power of deep learning models is far from acceptable for the task since accuracy drops from 87.68% to 56.16% on the best evaluation scenario. These results highlighted that the methods that aim at COVID-19 detection in CT-images have to improve significantly to be considered as a clinical option and larger and more diverse datasets are needed to evaluate the methods in a realistic scenario.

Silva Pedro, Luz Eduardo, Silva Guilherme, Moreira Gladston, Silva Rodrigo, Lucio Diego, Menotti David

2020

COVID-19, Chest radiography, Deep learning, EfficientNet, Pneumonia

Radiology Radiology

Temporal changes of COVID-19 pneumonia by mass evaluation using CT: a retrospective multi-center study.

In Annals of translational medicine

Background : Coronavirus disease 2019 (COVID-19) has widely spread worldwide and caused a pandemic. Chest CT has been found to play an important role in the diagnosis and management of COVID-19. However, quantitatively assessing temporal changes of COVID-19 pneumonia over time using CT has still not been fully elucidated. The purpose of this study was to perform a longitudinal study to quantitatively assess temporal changes of COVID-19 pneumonia.

Methods : This retrospective and multi-center study included patients with laboratory-confirmed COVID-19 infection from 16 hospitals between January 19 and March 27, 2020. Mass was used as an approach to quantitatively measure dynamic changes of pulmonary involvement in patients with COVID-19. Artificial intelligence (AI) was employed as image segmentation and analysis tool for calculating the mass of pulmonary involvement.

Results : A total of 581 confirmed patients with 1,309 chest CT examinations were included in this study. The median age was 46 years (IQR, 35-55; range, 4-87 years), and 311 (53.5%) patients were male. The mass of pulmonary involvement peaked on day 10 after the onset of initial symptoms. Furthermore, the mass of pulmonary involvement of older patients (>45 years) was significantly severer (P<0.001) and peaked later (day 11 vs. day 8) than that of younger patients (≤45 years). In addition, there were no significant differences in the peak time (day 10 vs. day 10) and median mass (P=0.679) of pulmonary involvement between male and female.

Conclusions : Pulmonary involvement peaked on day 10 after the onset of initial symptoms in patients with COVID-19. Further, pulmonary involvement of older patients was severer and peaked later than that of younger patients. These findings suggest that AI-based quantitative mass evaluation of COVID-19 pneumonia hold great potential for monitoring the disease progression.

Wang Chao, Huang Peiyu, Wang Lihua, Shen Zhujing, Lin Bin, Wang Qiyuan, Zhao Tongtong, Zheng Hanpeng, Ji Wenbin, Gao Yuantong, Xia Junli, Cheng Jianmin, Ma Jianbing, Liu Jun, Liu Yongqiang, Su Miaoguang, Ruan Guixiang, Shu Jiner, Ren Dawei, Zhao Zhenhua, Yao Weigen, Yang Yunjun, Liu Bo, Zhang Minming

2020-Aug

Coronavirus disease 2019 (COVID-19), artificial intelligence (AI), chest CT, temporal changes

Radiology Radiology

A CT-derived deep neural network predicts for programmed death ligand-1 expression status in advanced lung adenocarcinomas.

In Annals of translational medicine

Background : Programmed death ligand-1 (PD-L1) expression remains a crucial predictor in selecting patients for immunotherapy. The current study aimed to non-invasively predict PD-L1 expression based on chest computed tomography (CT) images in advanced lung adenocarcinomas (LUAD), thus help select optimal patients who can potentially benefit from immunotherapy.

Methods : A total of 127 patients with stage III and IV LUAD were enrolled into this study. Pretreatment enhanced thin-section CT images were available for all patients and were analyzed in terms of both morphologic characteristics by radiologists and deep learning (DL), so to further determine the association between CT features and PD-L1 expression status. Univariate analysis and multivariate logical regression analysis were applied to evaluate significant variables. For DL, the 3D DenseNet model was built and validated. The study cohort were grouped by PD-L1 Tumor Proportion Scores (TPS) cutoff value of 1% (positive/negative expression) and 50% respectively.

Results : Among 127 LUAD patients, 46 (36.2%) patients were PD-L1-positive and 38 (29.9%) patients expressed PD-L1-TPS ≥50%. For morphologic characteristics, univariate and multivariate analysis revealed that only lung metastasis was significantly associated with PD-L1 expression status despite of different PD-L1 TPS cutoff values, and its Area under the receiver operating characteristic curve (AUC) for predicting PD-L1 expression were less than 0.700. On the other hand, the predictive value of DL-3D DenseNet model was higher than that of the morphologic characteristics, with AUC more than 0.750.

Conclusions : The traditional morphologic CT characteristics analyzed by radiologists show limited prediction efficacy for PD-L1 expression. By contrast, CT-derived deep neural network improves the prediction efficacy, it may serve as an important alternative marker for clinical PD-L1 detection.

Zhu Ying, Liu Yang-Li, Feng Yu, Yang Xiao-Yu, Zhang Jing, Chang Dan-Dan, Wu Xi, Tian Xi, Tang Ke-Jing, Xie Can-Mao, Guo Yu-Biao, Feng Shi-Ting, Ke Zun-Fu

2020-Aug

Programmed death ligand-1 (PD-L1), X-ray computed tomography (X-ray CT), deep learning (DL), lung cancer, neural networks