On Approximating the pIC50 Value of COVID-19 Medicines In Silico with Artificial Neural Networks.

In the case of pandemics such as COVID-19, the rapid development of medicines addressing the symptoms is necessary to alleviate the pressure on the medical system. One of the key steps in medicine evaluation is the determination of pIC50 factor, which is a negative logarithmic expression of the half maximal inhibitory concentration (IC50). Determining this value can be a lengthy and complicated process. A tool allowing for a quick approximation of pIC50 based on the molecular makeup of medicine could be valuable. In this paper, the creation of the artificial intelligence (AI)-based model is performed using a publicly available dataset of molecules and their pIC50 values. The modeling algorithms used are artificial and convolutional neural networks (ANN and CNN). Three approaches are tested-modeling using just molecular properties (MP), encoded SMILES representation of the molecule, and the combination of both input types. Models are evaluated using the coefficient of determination (R2) and mean absolute percentage error (MAPE) in a five-fold cross-validation scheme to assure the validity of the results. The obtained models show that the highest quality regression (R2¯=0.99, σR2¯=0.001; MAPE¯=0.009%, σMAPE¯=0.009), by a large margin, is obtained when using a hybrid neural network trained with both MP and SMILES.

Applying Regressive Machine Learning Techniques in Determination of COVID-19 Vaccinated Patients' Influence on the Number of Confirmed and Deceased Patients

Vaccinations are one of the most important steps in combat against viral diseases such as COVID-19. Determining the influence of the number of vaccinated patients on the infected population represents a complex problem. For this reason, the aim of this research is to model the influence of the total number of vaccinated or fully vaccinated patients on the number of infected and deceased patients. Five separate modeling algorithms are used: Linear Regression (LR), Logistic Regression (LogR), Least Absolute Shrinkage and Selection Operator (LASSO), Multilayer Perceptron (MLP), and Support Vector Regression (SVR). Cross-correlation analysis is performed to determine the optimal lags in data to assist in obtaining better scores. The cross-validation of models is performed, and the models are evaluated using Mean Absolute Percentage Error (MAPE). The modeling is performed for four different countries: Germany, India, the United Kingdom (UK), and the United States of America (USA). Models with an error below 1% are found for all the modeled cases, with the best models being achieved either by LR or MLP methods. The obtained results indicate that the influence of vaccination rates on the number of confirmed and deceased patients exists and can be modeled using ML methods with relatively high precision.

Epidemiological Predictive Modeling of COVID-19 Infection: Development, Testing, and Implementation on the Population of the Benelux Union.

Since the outbreak of coronavirus disease-2019 (COVID-19), the whole world has taken interest in the mechanisms of its spread and development. Mathematical models have been valuable instruments for the study of the spread and control of infectious diseases. For that purpose, we propose a two-way approach in modeling COVID-19 spread: a susceptible, exposed, infected, recovered, deceased (SEIRD) model based on differential equations and a long short-term memory (LSTM) deep learning model. The SEIRD model is a compartmental epidemiological model with included components: susceptible, exposed, infected, recovered, deceased. In the case of the SEIRD model, official statistical data available online for countries of Belgium, Netherlands, and Luxembourg (Benelux) in the period of March 15 2020 to March 15 2021 were used. Based on them, we have calculated key parameters and forward them to the epidemiological model, which will predict the number of infected, deceased, and recovered people. Results show that the SEIRD model is able to accurately predict several peaks for all the three countries of interest, with very small root mean square error (RMSE), except for the mild cases (maximum RMSE was 240.79 ± 90.556), which can be explained by the fact that no official data were available for mild cases, but this number was derived from other statistics. On the other hand, LSTM represents a special kind of recurrent neural network structure that can comparatively learn long-term temporal dependencies. Results show that LSTM is capable of predicting several peaks based on the position of previous peaks with low values of RMSE. Higher values of RMSE are observed in the number of infected cases in Belgium (RMSE was 535.93) and Netherlands (RMSE was 434.28), and are expected because of thousands of people getting infected per day in those countries. In future studies, we will extend the models to include mobility information, variants of concern, as well as a medical intervention, etc. A prognostic model could help us predict epidemic peaks. In that way, we could react in a timely manner by introducing new or tightening existing measures before the health system is overloaded.

Artificial intelligence approach towards assessment of condition of COVID-19 patients - Identification of predictive biomarkers associated with severity of clinical condition and disease progression.

BACKGROUND AND OBJECTIVES: Although ML has been studied for different epidemiological and clinical issues as well as for survival prediction of COVID-19, there is a noticeable shortage of literature dealing with ML usage in prediction of disease severity changes through the course of the disease. In that way, predicting disease progression from mild towards moderate, severe and critical condition, would help not only to respond in a timely manner to prevent lethal results, but also to minimize the number of patients in hospitals where this is not necessary. METHODS: We present a methodology for the classification of patients into 4 distinct categories of the clinical condition of COVID-19 disease. Classification of patients is based on the values of blood biomarkers that were assessed by Gradient boosting regressor and which were selected as biomarkers that have the greatest influence in the classification of patients with COVID-19. RESULTS: The results show that among several tested algorithms, XGBoost classifier achieved best results with an average accuracy of 94% and an average F1-score of 94.3%. We have also extracted 10 best features from blood analysis that are strongly associated with patient condition and based on those features we can predict the severity of the clinical condition. CONCLUSIONS: The main advantage of our system is that it is a decision tree-based algorithm which is easier to interpret, instead of the use of black box models, which are not appealing in medical practice.

Estimation of COVID-19 Epidemiology Curve of the United States Using Genetic Programming Algorithm.

Estimation of the epidemiology curve for the COVID-19 pandemic can be a very computationally challenging task. Thus far, there have been some implementations of artificial intelligence (AI) methods applied to develop epidemiology curve for a specific country. However, most applied AI methods generated models that are almost impossible to translate into a mathematical equation. In this paper, the AI method called genetic programming (GP) algorithm is utilized to develop a symbolic expression (mathematical equation) which can be used for the estimation of the epidemiology curve for the entire U.S. with high accuracy. The GP algorithm is utilized on the publicly available dataset that contains the number of confirmed, deceased and recovered patients for each U.S. state to obtain the symbolic expression for the estimation of the number of the aforementioned patient groups. The dataset consists of the latitude and longitude of the central location for each state and the number of patients in each of the goal groups for each day in the period of 22nd January 2020-3rd December 2020. The obtained symbolic expressions for each state are summed up to obtain symbolic expressions for estimation of each of the patient groups (confirmed, deceased and recovered). These symbolic expressions are combined to obtain the symbolic expression for the estimation of the epidemiology curve for the entire U.S. The obtained symbolic expressions for the estimation of the number of confirmed, deceased and recovered patients for each state achieved R2 score in the ranges 0.9406-0.9992, 0.9404-0.9998 and 0.9797-0.99955, respectively. These equations are summed up to formulate symbolic expressions for the estimation of the number of confirmed, deceased and recovered patients for the entire U.S. with achieved R2 score of 0.9992, 0.9997 and 0.9996, respectively. Using these symbolic expressions, the equation for the estimation of the epidemiology curve for the entire U.S. is formulated which achieved R2 score of 0.9933. Investigation showed that GP algorithm can produce symbolic expressions for the estimation of the number of confirmed, recovered and deceased patients as well as the epidemiology curve not only for the states but for the entire U.S. with very high accuracy.

Estimation of COVID-19 epidemic curves using genetic programming algorithm.

This paper investigates the possibility of the implementation of Genetic Programming (GP) algorithm on a publicly available COVID-19 data set, in order to obtain mathematical models which could be used for estimation of confirmed, deceased, and recovered cases and the estimation of epidemiology curve for specific countries, with a high number of cases, such as China, Italy, Spain, and USA and as well as on the global scale. The conducted investigation shows that the best mathematical models produced for estimating confirmed and deceased cases achieved R2 scores of 0.999, while the models developed for estimation of recovered cases achieved the R2 score of 0.998. The equations generated for confirmed, deceased, and recovered cases were combined in order to estimate the epidemiology curve of specific countries and on the global scale. The estimated epidemiology curve for each country obtained from these equations is almost identical to the real data contained within the data set.

Automatic Evaluation of the Lung Condition of COVID-19 Patients Using X-ray Images and Convolutional Neural Networks.

COVID-19 represents one of the greatest challenges in modern history. Its impact is most noticeable in the health care system, mostly due to the accelerated and increased influx of patients with a more severe clinical picture. These facts are increasing the pressure on health systems. For this reason, the aim is to automate the process of diagnosis and treatment. The research presented in this article conducted an examination of the possibility of classifying the clinical picture of a patient using X-ray images and convolutional neural networks. The research was conducted on the dataset of 185 images that consists of four classes. Due to a lower amount of images, a data augmentation procedure was performed. In order to define the CNN architecture with highest classification performances, multiple CNNs were designed. Results show that the best classification performances can be achieved if ResNet152 is used. This CNN has achieved AUCmacro¯ and AUCmicro¯ up to 0.94, suggesting the possibility of applying CNN to the classification of the clinical picture of COVID-19 patients using an X-ray image of the lungs. When higher layers are frozen during the training procedure, higher AUCmacro¯ and AUCmicro¯ values are achieved. If ResNet152 is utilized, AUCmacro¯ and AUCmicro¯ values up to 0.96 are achieved if all layers except the last 12 are frozen during the training procedure.

Impact of COVID-19 on Forecasting Stock Prices: An Integration of Stationary Wavelet Transform and Bidirectional Long Short-Term Memory

COVID-19 is an infectious disease that mostly affects the respiratory system. At the time of this research being performed, there were more than 1.4 million cases of COVID-19, and one of the biggest anxieties is not just our health, but our livelihoods, too. In this research, authors investigate the impact of COVID-19 on the global economy, more specifically, the impact of COVID-19 on the financial movement of Crude Oil price and three US stock indexes: DJI, S&P 500, and NASDAQ Composite. The proposed system for predicting commodity and stock prices integrates the stationary wavelet transform (SWT) and bidirectional long short-term memory (BDLSTM) networks. Firstly, SWT is used to decompose the data into approximation and detail coefficients. After decomposition, data of Crude Oil price and stock market indexes along with COVID-19 confirmed cases were used as input variables for future price movement forecasting. As a result, the proposed system BDLSTM + WT-ADA achieved satisfactory results in terms of five-day Crude Oil price forecast.

Modeling the Spread of COVID-19 Infection Using a Multilayer Perceptron.

Coronavirus (COVID-19) is a highly infectious disease that has captured the attention of the worldwide public. Modeling of such diseases can be extremely important in the prediction of their impact. While classic, statistical, modeling can provide satisfactory models, it can also fail to comprehend the intricacies contained within the data. In this paper, authors use a publicly available dataset, containing information on infected, recovered, and deceased patients in 406 locations over 51 days (22nd January 2020 to 12th March 2020). This dataset, intended to be a time-series dataset, is transformed into a regression dataset and used in training a multilayer perceptron (MLP) artificial neural network (ANN). The aim of training is to achieve a worldwide model of the maximal number of patients across all locations in each time unit. Hyperparameters of the MLP are varied using a grid search algorithm, with a total of 5376 hyperparameter combinations. Using those combinations, a total of 48384 ANNs are trained (16128 for each patient group-deceased, recovered, and infected), and each model is evaluated using the coefficient of determination (R2). Cross-validation is performed using K-fold algorithm with 5-folds. Best models achieved consists of 4 hidden layers with 4 neurons in each of those layers, and use a ReLU activation function, with R2 scores of 0.98599 for confirmed, 0.99429 for deceased, and 0.97941 for recovered patient models. When cross-validation is performed, these scores drop to 0.94 for confirmed, 0.781 for recovered, and 0.986 for deceased patient models, showing high robustness of the deceased patient model, good robustness for confirmed, and low robustness for recovered patient model.