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Vector Auto-Regressive Deep Neural Network: A Data-Driven Deep Learning-Based Directed Functional Connectivity Estimation Toolbox.

ABSTRACT: An important goal in neuroscience is to elucidate the causal relationships between the brain's different regions. This can help reveal the brain's functional circuitry and diagnose lesions. Currently there are a lack of approaches to functional connectome estimation that leverage the state-of-the-art in deep learning architectures and training methodologies. Therefore, we propose a new framework based on a vector auto-regressive deep neural network (VARDNN) architecture. Our approach consists of a set of nodes, each with a deep neural network structure. These nodes can be mapped to any spatial sub-division based on the data to be analyzed, such as anatomical brain regions from which representative neural signals can be obtained. VARDNN learns to reproduce experimental time series data using modern deep learning training techniques. Based on this, we developed two novel directed functional connectivity (dFC) measures, namely VARDNN-DI and VARDNN-GC. We evaluated our measures against a number of existing functional connectome estimation measures, such as partial correlation and multivariate Granger causality combined with large dimensionality counter-measure techniques. Our measures outperformed them across various types of ground truth data, especially as the number of nodes increased. We applied VARDNN to fMRI data to compare the dFC between 41 healthy control vs. 32 Alzheimer's disease subjects. Our VARDNN-DI measure detected lesioned regions consistent with previous studies and separated the two groups well in a subject-wise evaluation framework. Summarily, the VARDNN framework has powerful capabilities for whole brain dFC estimation. We have implemented VARDNN as an open-source toolbox that can be freely downloaded for researchers who wish to carry out functional connectome analysis on their own data.

SUBMITTER: Okuno T

PROVIDER: S-EPMC8651499 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Most countries are reopening or considering lifting the stringent prevention policies such as lockdowns, consequently, daily coronavirus disease (COVID-19) cases (confirmed, recovered and deaths) are increasing significantly. As of July 25th, there are 16.5 million global cumulative confirmed cases, 9.4 million cumulative recovered cases and 0.65 million deaths. There is a tremendous necessity of supervising and estimating future COVID-19 cases to control the spread and help countries prepare their healthcare systems. In this study, time-series models - Auto-Regressive Integrated Moving Average (ARIMA) and Seasonal Auto-Regressive Integrated Moving Average (SARIMA) are used to forecast the epidemiological trends of the COVID-19 pandemic for top-16 countries where 70%-80% of global cumulative cases are located. Initial combinations of the model parameters were selected using the auto-ARIMA model followed by finding the optimized model parameters based on the best fit between the predictions and test data. Analytical tools Auto-Correlation function (ACF), Partial Auto-Correlation Function (PACF), Akaike Information Criterion (AIC) and Bayesian Information Criterion (BIC) were used to assess the reliability of the models. Evaluation metrics Mean Absolute Error (MAE), Mean Square Error (MSE), Root Mean Square Error (RMSE) and Mean Absolute Percent Error (MAPE) were used as criteria for selecting the best model. A case study was presented where the statistical methodology was discussed in detail for model selection and the procedure for forecasting the COVID-19 cases of the USA. Best model parameters of ARIMA and SARIMA for each country are selected manually and the optimized parameters are then used to forecast the COVID-19 cases. Forecasted trends for confirmed and recovered cases showed an exponential rise for countries such as the United States, Brazil, South Africa, Colombia, Bangladesh, India, Mexico and Pakistan. Similarly, trends for cumulative deaths showed an exponential rise for countries Brazil, South Africa, Chile, Colombia, Bangladesh, India, Mexico, Iran, Peru, and Russia. SARIMA model predictions are more realistic than that of the ARIMA model predictions confirming the existence of seasonality in COVID-19 data. The results of this study not only shed light on the future trends of the COVID-19 outbreak in top-16 countries but also guide these countries to prepare their health care policies for the ongoing pandemic. The data used in this work is obtained from publicly available John Hopkins University's COVID-19 database.

Dataset Information

Vector Auto-Regressive Deep Neural Network: A Data-Driven Deep Learning-Based Directed Functional Connectivity Estimation Toolbox.

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