scholarly journals Towards computer-aided severity assessment via deep neural networks for geographic and opacity extent scoring of SARS-CoV-2 chest X-rays

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
A. Wong ◽  
Z. Q. Lin ◽  
L. Wang ◽  
A. G. Chung ◽  
B. Shen ◽  
...  
Keyword(s):  
Neural Networks ◽  
Monte Carlo ◽  
Lung Disease ◽  
Disease Severity ◽  
Deep Neural Networks ◽  
Cross Validation ◽  
X Rays ◽  
Computer Aided ◽  
Monte Carlo Cross Validation ◽  
Validation Experiments

AbstractA critical step in effective care and treatment planning for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause for the coronavirus disease 2019 (COVID-19) pandemic, is the assessment of the severity of disease progression. Chest x-rays (CXRs) are often used to assess SARS-CoV-2 severity, with two important assessment metrics being extent of lung involvement and degree of opacity. In this proof-of-concept study, we assess the feasibility of computer-aided scoring of CXRs of SARS-CoV-2 lung disease severity using a deep learning system. Data consisted of 396 CXRs from SARS-CoV-2 positive patient cases. Geographic extent and opacity extent were scored by two board-certified expert chest radiologists (with 20+ years of experience) and a 2nd-year radiology resident. The deep neural networks used in this study, which we name COVID-Net S, are based on a COVID-Net network architecture. 100 versions of the network were independently learned (50 to perform geographic extent scoring and 50 to perform opacity extent scoring) using random subsets of CXRs from the study, and we evaluated the networks using stratified Monte Carlo cross-validation experiments. The COVID-Net S deep neural networks yielded R$$^2$$ 2 of $$0.664 \pm 0.032$$ 0.664 ± 0.032 and $$0.635 \pm 0.044$$ 0.635 ± 0.044 between predicted scores and radiologist scores for geographic extent and opacity extent, respectively, in stratified Monte Carlo cross-validation experiments. The best performing COVID-Net S networks achieved R$$^2$$ 2 of 0.739 and 0.741 between predicted scores and radiologist scores for geographic extent and opacity extent, respectively. The results are promising and suggest that the use of deep neural networks on CXRs could be an effective tool for computer-aided assessment of SARS-CoV-2 lung disease severity, although additional studies are needed before adoption for routine clinical use.

scholarly journals Forecasting Reservoir Water Levels Using Deep Neural Networks: A Case Study of Angat Dam in the Philippines

Water ◽  
2021 ◽  
Vol 14 (1) ◽  
pp. 34
Author(s):  
Sebastian C. Ibañez ◽  
Carlo Vincienzo G. Dajac ◽  
Marissa P. Liponhay ◽  
Erika Fille T. Legara ◽  
Jon Michael H. Esteban ◽  
...  
Keyword(s):  
Neural Networks ◽  
Time Series ◽  
Deep Neural Networks ◽  
Cross Validation ◽  
The Philippines ◽  
Water Levels ◽  
Short Term ◽  
Exogenous Variables ◽  
Reservoir Water ◽  
Forecasting Performance

Forecasting reservoir water levels is essential in water supply management, impacting both operations and intervention strategies. This paper examines the short-term and long-term forecasting performance of several statistical and machine learning-based methods for predicting the water levels of the Angat Dam in the Philippines. A total of six forecasting methods are compared: naïve/persistence; seasonal mean; autoregressive integrated moving average (ARIMA); gradient boosting machines (GBM); and two deep neural networks (DNN) using a long short-term memory-based (LSTM) encoder-decoder architecture: a univariate model (DNN-U) and a multivariate model (DNN-M). Daily historical water levels from 2001 to 2021 are used in predicting future water levels. In addition, we include meteorological data (rainfall and the Oceanic Niño Index) and irrigation data as exogenous variables. To evaluate the forecast accuracy of our methods, we use a time series cross-validation approach to establish a more robust estimate of the error statistics. Our results show that our DNN-U model has the best accuracy in the 1-day-ahead scenario with a mean absolute error (MAE) and root mean square error (RMSE) of 0.2 m. In the 30-day-, 90-day-, and 180-day-ahead scenarios, the DNN-M shows the best performance with MAE (RMSE) scores of 2.9 (3.3), 5.1 (6.0), and 6.7 (8.1) meters, respectively. Additionally, we demonstrate that further improvements in performance are possible by scanning over all possible combinations of the exogenous variables and only using a subset of them as features. In summary, we provide a comprehensive framework for evaluating water level forecasting by defining a baseline accuracy, analyzing performance across multiple prediction horizons, using time series cross-validation to assess accuracy and uncertainty, and examining the effects of exogenous variables on forecasting performance. In the process, our work addresses several notable gaps in the methodologies of previous works.

Worshiping Computers

2019 ◽  
pp. 85-110
Author(s):  
Gary Smith ◽  
Jay Cordes
Keyword(s):  
Neural Networks ◽  
Monte Carlo ◽  
Monte Carlo Simulations ◽  
Common Sense ◽  
Deep Neural Networks ◽  
Computer Software ◽  
Square Roots ◽  
The World ◽  
The Way

Computer software, particularly deep neural networks and Monte Carlo simulations, are extremely useful for the specific tasks that they have been designed to do, and they will get even better, much better. However, we should not assume that computers are smarter than us just because they can tell us the first 2000 digits of pi or show us a street map of every city in the world. One of the paradoxical things about computers is that they can excel at things that humans consider difficult (like calculating square roots) while failing at things that humans consider easy (like recognizing stop signs). They can’t pass simple tests like the Winograd Schema Challenge because they do not understand the world the way humans do. They have neither common sense nor wisdom. They are our tools, not our masters.

scholarly journals Revealing pathway cross-talk related to diabetes mellitus by Monte Carlo Cross-Validation analysis

2017 ◽  
Vol 12 (1) ◽  
pp. 473-480
Author(s):  
Han-Qing Cai ◽  
Shi-Hong Lv ◽  
Chun-Jing Shi
Keyword(s):  
Diabetes Mellitus ◽  
Monte Carlo ◽  
Cross Talk ◽  
Cross Validation ◽  
Area Under The Curve ◽  
Pathway Crosstalk ◽  
High Area ◽  
Pathways Analysis ◽  
Auc Value ◽  
Monte Carlo Cross Validation

AbstractObjectiveTo explore potential functional biomarkers in diabetes mellitus (DM) by utilizing gene pathway cross-talk.MethodsFirstly, potential disrupted pathways that were enriched by differentially expressed genes (DEGs) were identified based on biological pathways downloaded from the Ingenuity Pathways Analysis (IPA) database. In addition, we quantified the pathway crosstalk for each pair of pathways based on Discriminating Score (DS). Random forest (RF) classification was then employed to find the top 10 pairs of pathways with a high area under the curve (AUC) value between DM samples versus normal samples based on 10-fold cross-validation. Finally, a Monte Carlo Cross-Validation was applied to demonstrate the identified pairs of pathways by a mutual information analysis.ResultsA total of 247 DEGs in normal and disease samples were identified. Based on the F-test, 50 disrupted pathways were obtained with false discovery rate (FDR) < 0.01. Simultaneously, after calculating the DS, the top 10 pairs of pathways were selected based on a higher AUC value as measured by RF classification. From the Monte Carlo Cross-Validation, we considered the top 10 pairs of pathways with higher AUC values ranked for all 50 bootstraps as the most frequently detected ones.ConclusionThe pairs of pathways identified in our study might be key regulators in DM.

scholarly journals A Deep Convolutional Neural Network Based Lung Disorder Diagnosis

2019 ◽  
pp. 102-112
Author(s):  
J. Juditha Mercina ◽  
J. Madhumathi ◽  
V. Priyanga ◽  
M. Deva Priya
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Lung Disease ◽  
Lung Diseases ◽  
Intelligent System ◽  
Lung Disorder ◽  
X Ray ◽  
Cad System ◽  
Computer Aided ◽  
Aided Diagnosis

Lungs play an important role in human respiratory system. There are diseases that affect the functioning of lungs. To analyse lung diseases in the chest region using X-ray based Computer-Aided Diagnosis (CAD) system, it is necessary to determine the lung regions subject to analysis. In this paper, an intelligent system is proposed for lung disease detection. In this paper, Interstitial Lung Disease (ILD) patterns are classified using Convolutional Neural Networks (CNN). The proposed system involves five convolutional layers and three dense layers. The performance of the classification demonstrates the potential of CNN in analysing lung patterns.

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