Pandemic velocity: Forecasting COVID-19 in the US with a machine learning & Bayesian time series compartmental model.
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ABSTRACT:
SUBMITTER: Watson GL
PROVIDER: S-EPMC8031749 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:ImportanceForecasting the volume of hospital discharges has important implications for resource allocation and represents an opportunity to improve patient safety at periods of elevated risk.ObjectiveTo determine the performance of a new time-series machine learning method for forecasting hospital discharge volume compared with simpler methods.DesignA retrospective cohort study of daily hospital discharge volumes at 2 large, New England academic medical centers between January 1, 2005, and December 31, 2014 (hospital 1), or January 1, 2005, and December 31, 2010 (hospital 2), comparing time-series forecasting methods for prediction was performed. Data analysis was conducted from February 28, 2017, to August 30, 2018. Group-level data for all discharges from inpatient units were included. In addition to conventional methods, a technique originally developed for allocating data center resources, and comparison strategies for incorporating prior data and frequency of model updates, was conducted to identify the model application that optimized forecast accuracy.Main outcomes and measuresModel calibration as measured by R2 and, secondarily, number of days with errors greater than 1 SD of daily volume.ResultsDuring the forecasted year, hospital 1 had 54?411 discharges (daily mean, 149) and hospital 2 had 47?456 discharges (daily mean, 130). The machine learning method was well calibrated at both sites (R2, 0.843 and 0.726, respectively) and made errors greater than 1 SD of daily volume on only 13 and 22 days, respectively, of the forecast year at the 2 sites. Last-value-carried-forward models performed somewhat less well (calibration R2, 0.781 and 0.596, respectively) with 13 and 46 errors of 1 SD or greater, respectively. More frequent retraining and training sets of longer than 1 year had minimal effects on the machine learning method's performance.Conclusions and relevanceVolume of hospital discharges can perhaps be reliably forecasted using simple carry-forward models as well as methods drawn from machine learning. The benefit of the latter does not appear to be dependent on extensive training data and may enable forecasts up to 1 year in advance with superior absolute accuracy to carry-forward models.
| S-EPMC6324591 | biostudies-literature
Project description:Coronavirus disease (COVID-19) is an inflammation disease from a new virus. The disease causes respiratory ailment (like influenza) with manifestations, for example, cold, cough and fever, and in progressively serious cases, the problem in breathing. COVID-2019 has been perceived as a worldwide pandemic and a few examinations are being led utilizing different numerical models to anticipate the likely advancement of this pestilence. These numerical models dependent on different factors and investigations are dependent upon potential inclination. Here, we presented a model that could be useful to predict the spread of COVID-2019. We have performed linear regression, Multilayer perceptron and Vector autoregression method for desire on the COVID-19 Kaggle data to anticipate the epidemiological example of the ailment and pace of COVID-2019 cases in India. Anticipated the potential patterns of COVID-19 effects in India dependent on data gathered from Kaggle. With the common data about confirmed, death and recovered cases across India for over the time length helps in anticipating and estimating the not so distant future. For extra assessment or future perspective, case definition and data combination must be kept up persistently.
| S-EPMC7261047 | biostudies-literature
Project description:The application of machine learning (ML) for use in generating insights and making predictions on new records continues to expand within the medical community. Despite this progress to date, the application of time series analysis has remained underexplored due to complexity of the underlying techniques. In this study, we have deployed a novel ML, called automated time series (AutoTS) machine learning, to automate data processing and the application of a multitude of models to assess which best forecasts future values. This rapid experimentation allows for and enables the selection of the most accurate model in order to perform time series predictions. By using the nation-wide ICD-10 (International Classification of Diseases, Tenth Revision) dataset of hospitalized patients of Romania, we have generated time series datasets over the period of 2008-2018 and performed highly accurate AutoTS predictions for the ten deadliest diseases. Forecast results for the years 2019 and 2020 were generated on a NUTS 2 (Nomenclature of Territorial Units for Statistics) regional level. This is the first study to our knowledge to perform time series forecasting of multiple diseases at a regional level using automated time series machine learning on a national ICD-10 dataset. The deployment of AutoTS technology can help decision makers in implementing targeted national health policies more efficiently.
| S-EPMC7400312 | biostudies-literature
Project description:Wastewater-based epidemiology (WBE) has gained increasing attention as a complementary tool to conventional surveillance methods with potential for significant resource and labour savings when used for public health monitoring. Using WBE datasets to train machine learning algorithms and develop predictive models may also facilitate early warnings for the spread of outbreaks. The challenges associated with using machine learning for the analysis of WBE datasets and timeseries forecasting of COVID-19 were explored by running Random Forest (RF) algorithms on WBE datasets across 108 sites in five regions: Scotland, Catalonia, Ohio, the Netherlands, and Switzerland. This method uses measurements of SARS-CoV-2 RNA fragment concentration in samples taken at the inlets of wastewater treatment plants, providing insight into the prevalence of infection in upstream wastewater catchment populations. RF's forecasting performance at each site was quantitatively evaluated by determining mean absolute percentage error (MAPE) values, which was used to highlight challenges affecting future implementations of RF for WBE forecasting efforts. Performance was generally poor using WBE datasets from Catalonia, Scotland, and Ohio with 'reasonable' or better forecasts constituting 0 %, 5 %, and 0 % of these regions' forecasts, respectively. RF's performance was much stronger with WBE data from the Netherlands and Switzerland, which provided 55 % and 45 % 'reasonable' or better forecasts respectively. Sampling frequency and training set size were identified as key factors contributing to accuracy, while inclusion of too many unnecessary variables (or e.g., flow data) was identified as a contributing factor to poor performance. The contribution of catchment population on forecast accuracy was more ambiguous. This study determined that the factors governing RF's forecast performance are complicated and interrelated, which presents challenges for further work in this space. A sufficiently accurate further iteration of the tool discussed within this study would provide significant but varying value for public health departments for monitoring future, or ongoing outbreaks, assisting the implementation of on-time health response measures.
| S-EPMC9597519 | biostudies-literature
Project description:This paper follows an integrated approach of Internet of Things based sensing and machine learning for crop growth prediction in agriculture. A Dynamic Bayesian Network (DBN) relates crop growth associated measurement data to environmental control data via hidden states. The measurement data, having (non-linear) sigmoid-type dynamics, are instances of the two classes observed and missing, respectively. Considering that the time series of the logistic sigmoid function is the solution to a reciprocal linear dynamic model, the exact expectation-maximization algorithm can be applied to infer the hidden states and to learn the parameters of the model. At iterative convergence, the parameter estimates are then used to derive a predictor of the measurement data several days ahead. To evaluate the performance of the proposed DBN, we followed three cultivation cycles of micro-tomatoes (MicroTom) in a mini-greenhouse. The environmental parameters were temperature, converted into Growing Degree Days (GDD), and the solar irradiance, both at a daily granularity. The measurement data were Leaf Area Index (LAI) and Evapotranspiration (ET). Although measurement data were only available scarcely, it turned out that high quality measurement data predictions were possible up to three weeks ahead.
| S-EPMC7309099 | biostudies-literature
Project description:The pandemic of novel coronavirus disease 2019 (Covid-19) has left the world to a standstill by creating a calamitous situation. To mitigate this devastating effect the inception of artificial intelligence into medical health care is mandatory. This study aims to present the educational perspective of Covid-19 and forecast the number of confirmed and death cases in the USA, India, and Brazil along with the discussion of endothelial dysfunction in epithelial cells and Angiotensin-Converting Enzyme 2 receptor (ACE2) with the Covid-19. Three different deep learning based experimental setups have been framed to forecast Covid-19. Models are (i) Bi-directional Long Short Term Memory (LSTM) (ii) Convolutional LSTM (iii) Proposed ensemble of Convolutional and Bi-directional LSTM network are known as CoBiD-Net ensemble. The educational perspective of Covid-19 has been given along with an architectural discussion of multi-organ failure due to intrusion of Covid-19 with the cell receptors of the human body. Different classification metrics have been calculated using all three models. Proposed CoBiD-Net ensemble model outperforms the other two models with respect to accuracy and mean absolute percentage error (MAPE). Using CoBiD-Net ensemble, accuracy for Covid-19 cases ranges from 98.10 to 99.13% with MAPE ranges from 0.87 to 1.90. This study will help the countries to know the severity of Covid-19 concerning education in the future along with forecasting of Covid-19 cases and human body interaction with the Covid-19 to make it the self-replicating phenomena. Supplementary Information The online version contains supplementary material available at 10.1007/s41324-021-00408-3.
| S-EPMC8196282 | biostudies-literature
Project description:The epidemiology of neglected tropical diseases (NTD) is persistently underprioritized, despite NTD being widespread among the poorest populations and in the least developed countries on earth. This situation necessitates thorough and efficient public health intervention. Romania is at the brink of becoming a developed country. However, this South-Eastern European country appears to be a region that is susceptible to an underestimated burden of parasitic diseases despite recent public health reforms. Moreover, there is an evident lack of new epidemiologic data on NTD after Romania's accession to the European Union (EU) in 2007. Using the national ICD-10 dataset for hospitalized patients in Romania, we generated time series datasets for 2008-2018. The objective was to gain deep understanding of the epidemiological distribution of three selected and highly endemic parasitic diseases, namely, ascariasis, enterobiasis and cystic echinococcosis (CE), during this period and forecast their courses for the ensuing two years. Through descriptive and inferential analysis, we observed a decline in case numbers for all three NTD. Several distributional particularities at regional level emerged. Furthermore, we performed predictions using a novel automated time series (AutoTS) machine learning tool and could interestingly show a stable course for these parasitic NTD. Such predictions can help public health officials and medical organizations to implement targeted disease prevention and control. To our knowledge, this is the first study involving a retrospective analysis of ascariasis, enterobiasis and CE on a nationwide scale in Romania. It is also the first to use AutoTS technology for parasitic NTD.
| S-EPMC8584970 | biostudies-literature
Project description:BackgroundCOVID-19 poses a severe threat to global human health, especially the USA, Brazil, and India cases continue to increase dynamically, which has a far-reaching impact on people's health, social activities, and the local economic situation.MethodsThe study proposed the ARIMA, SARIMA and Prophet models to predict daily new cases and cumulative confirmed cases in the USA, Brazil and India over the next 30 days based on the COVID-19 new confirmed cases and cumulative confirmed cases data set(May 1, 2020, and November 30, 2021) published by the official WHO, Three models were implemented in the R 4.1.1 software with forecast and prophet package. The performance of different models was evaluated by using root mean square error (RMSE), mean absolute error (MAE) and mean absolute percentage error (MAPE).ResultsThrough the fitting and prediction of daily new case data, we reveal that the Prophet model has more advantages in the prediction of the COVID-19 of the USA, which could compose data components and capture periodic characteristics when the data changes significantly, while SARIMA is more likely to appear over-fitting in the USA. And the SARIMA model captured a seven-day period hidden in daily COVID-19 new cases from 3 countries. While in the prediction of new cumulative cases, the ARIMA model has a better ability to fit and predict the data with a positive growth trend in different countries(Brazil and India).ConclusionsThis study can shed light on understanding the outbreak trends and give an insight into the epidemiological control of these regions. Further, the prediction of the Prophet model showed sufficient accuracy in the daily COVID-19 new cases of the USA. The ARIMA model is suitable for predicting Brazil and India, which can help take precautions and policy formulation for this epidemic in other countries.
| S-EPMC9131989 | biostudies-literature
Project description:Background and aimsHarmful alcohol use places a significant burden on health services. Sophisticated nowcasting and forecasting methods could support service planning, but their use in public health has been limited. We aimed to use a novel analysis framework, combined with routine public health data, to improve now- and forecasting of alcohol-related harms.DesignWe used Bayesian structural time-series models to forecast alcohol-related hospital admissions for 2020/21 (from 2015 to 2016).SettingEngland.ParticipantsWe developed separate models for each English lower-tier local authority.MeasurementsOur primary outcome was alcohol-related hospital admissions. Model covariates were population size and age-structure.FindingsNowcasting validation indicated adequate accuracy, with 5-year nowcasts underestimating admissions by 2.2% nationally and 3.3% locally, on average. Forecasts indicated a 3.3% increase in national admissions in 2020/21, corresponding to a 0.2% reduction in the crude rate of new admissions, due to population size changes. Locally, the largest increases were forecast in urban, industrial and coastal areas and the largest decreases in university towns and ethnically diverse areas.ConclusionsIn 2020/21, alcohol-related hospital admissions are expected to increase in urban and coastal areas and decrease in areas associated with inward migration of younger people, including university towns and areas with greater ethnic diversity. Bayesian structural time-series models enable investigation of the future impacts of alcohol-related harms in population subgroups and could improve service planning and the evaluation of natural experiments on the impact of interventions to reduce the societal impacts of alcohol.
| S-EPMC6563459 | biostudies-literature
Project description:Recently, there has been much attention in the use of machine learning methods, particularly deep learning for stock price prediction. A major limitation of conventional deep learning is uncertainty quantification in predictions which affect investor confidence. Bayesian neural networks feature Bayesian inference for providing inference (training) of model parameters that provides a rigorous methodology for uncertainty quantification in predictions. Markov Chain Monte Carlo (MCMC) sampling methods have been prominent in implementing inference of Bayesian neural networks; however certain limitations existed due to a large number of parameters and the need for better computational resources. Recently, there has been much progress in the area of Bayesian neural networks given the use of Langevin gradients with parallel tempering MCMC that can be implemented in a parallel computing environment. The COVID-19 pandemic had a drastic impact in the world economy and stock markets given different levels of lockdowns due to rise and fall of daily infections. It is important to investigate the performance of related forecasting models during the COVID-19 pandemic given the volatility in stock markets. In this paper, we use novel Bayesian neural networks for multi-step-ahead stock price forecasting before and during COVID-19. We also investigate if the pre-COVID-19 datasets are useful of modelling stock price forecasting during COVID-19. Our results indicate due to high volatility in the stock-price during COVID-19, it is more challenging to provide forecasting. However, we found that Bayesian neural networks could provide reasonable predictions with uncertainty quantification despite high market volatility during the first peak of the COVID-19 pandemic.
| S-EPMC8248663 | biostudies-literature