PAN-cODE: COVID-19 forecasting using conditional latent ODEs.
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ABSTRACT:
SUBMITTER: Shi R
PROVIDER: S-EPMC9667190 | biostudies-literature | 2022 Nov
REPOSITORIES: biostudies-literature
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Project description:The recent outbreak of novel Coronavirus disease or COVID-19 is declared a pandemic by the World Health Organization (WHO). The availability of social media platforms has played a vital role in providing and obtaining information about any ongoing event. However, consuming a vast amount of online textual data to predict an event's trends can be troublesome. To our knowledge, no study analyzes the online news articles and the disease data about coronavirus disease. Therefore, we propose an LDA-based topic model, called PAN-LDA (Pandemic-Latent Dirichlet allocation), that incorporates the COVID-19 cases data and news articles into common LDA to obtain a new set of features. The generated features are introduced as additional features to Machine learning(ML) algorithms to improve the forecasting of time series data. Furthermore, we are employing collapsed Gibbs sampling (CGS) as the underlying technique for parameter inference. The results from experiments suggest that the obtained features from PAN-LDA generate more identifiable topics and empirically add value to the outcome.
| S-EPMC8505021 | biostudies-literature
Project description:After nearly two years since the first identification of SARS-CoV-2 virus, the surge in cases because of virus mutations is a cause of grave public health concern across the globe. As a result of this health crisis, predicting the transmission pattern of the virus is one of the most vital tasks for preparing and controlling the pandemic. In addition to mathematical models, machine learning tools, especially deep learning models have been developed for forecasting the trend of the number of patients affected by SARS-CoV-2 with great success. In this paper, three deep learning models, including CNN, LSTM, and the CNN-LSTM have been developed to predict the number of COVID-19 cases for Brazil, India and Russia. We also compare the performance of our models with the previously developed deep learning models and notice significant improvements in prediction performance. Although our models have been used only for forecasting cases in these three countries, the models can be easily applied to datasets of other countries. Among the models developed in this work, the LSTM model has the highest performance when forecasting and shows an improvement in the forecasting accuracy compared with some existing models. The research will enable accurate forecasting of the COVID-19 cases and support the global fight against the pandemic.
| S-EPMC8864960 | biostudies-literature
Project description:BackgroundThe novel coronavirus (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2, and within a few months, it has become a global pandemic. This forced many affected countries to take stringent measures such as complete lockdown, shutting down businesses and trade, as well as travel restrictions, which has had a tremendous economic impact. Therefore, having knowledge and foresight about how a country might be able to contain the spread of COVID-19 will be of paramount importance to the government, policy makers, business partners and entrepreneurs. To help social and administrative decision making, a model that will be able to forecast when a country might be able to contain the spread of COVID-19 is needed.ResultsThe results obtained using our long short-term memory (LSTM) network-based model are promising as we validate our prediction model using New Zealand's data since they have been able to contain the spread of COVID-19 and bring the daily new cases tally to zero. Our proposed forecasting model was able to correctly predict the dates within which New Zealand was able to contain the spread of COVID-19. Similarly, the proposed model has been used to forecast the dates when other countries would be able to contain the spread of COVID-19.ConclusionThe forecasted dates are only a prediction based on the existing situation. However, these forecasted dates can be used to guide actions and make informed decisions that will be practically beneficial in influencing the real future. The current forecasting trend shows that more stringent actions/restrictions need to be implemented for most of the countries as the forecasting model shows they will take over three months before they can possibly contain the spread of COVID-19.
| S-EPMC8190741 | biostudies-literature
Project description:Particle accelerators are complex systems that focus, guide, and accelerate intense charged particle beams to high energy. Beam diagnostics present a challenging problem due to limited non-destructive measurements, computationally demanding simulations, and inherent uncertainties in the system. We propose a two-step unsupervised deep learning framework named as Conditional Latent Autoregressive Recurrent Model (CLARM) for learning the spatiotemporal dynamics of charged particles in accelerators. CLARM consists of a Conditional Variational Autoencoder transforming six-dimensional phase space into a lower-dimensional latent distribution and a Long Short-Term Memory network capturing temporal dynamics in an autoregressive manner. The CLARM can generate projections at various accelerator modules by sampling and decoding the latent space representation. The model also forecasts future states (downstream locations) of charged particles from past states (upstream locations). The results demonstrate that the generative and forecasting ability of the proposed approach is promising when tested against a variety of evaluation metrics.
| S-EPMC11300895 | biostudies-literature
Project description:ObjectivesForecasting epidemics like COVID-19 is of crucial importance, it will not only help the governments but also, the medical practitioners to know the future trajectory of the spread, which might help them with the best possible treatments, precautionary measures and protections. In this study, the popular autoregressive integrated moving average (ARIMA) will be used to forecast the cumulative number of confirmed, recovered cases, and the number of deaths in Pakistan from COVID-19 spanning June 25, 2020 to July 04, 2020 (10 days ahead forecast).MethodsTo meet the desire objectives, data for this study have been taken from the Ministry of National Health Service of Pakistan's website from February 27, 2020 to June 24, 2020. Two different ARIMA models will be used to obtain the next 10 days ahead point and 95% interval forecast of the cumulative confirmed cases, recovered cases, and deaths. Statistical software, RStudio, with "forecast", "ggplot2", "tseries", and "seasonal" packages have been used for data analysis.ResultsThe forecasted cumulative confirmed cases, recovered, and the number of deaths up to July 04, 2020 are 231239 with a 95% prediction interval of (219648, 242832), 111616 with a prediction interval of (101063, 122168), and 5043 with a 95% prediction interval of (4791, 5295) respectively. Statistical measures i.e. root mean square error (RMSE) and mean absolute error (MAE) are used for model accuracy. It is evident from the analysis results that the ARIMA and seasonal ARIMA model is better than the other time series models in terms of forecasting accuracy and hence recommended to be used for forecasting epidemics like COVID-19.ConclusionIt is concluded from this study that the forecasting accuracy of ARIMA models in terms of RMSE, and MAE are better than the other time series models, and therefore could be considered a good forecasting tool in forecasting the spread, recoveries, and deaths from the current outbreak of COVID-19. Besides, this study can also help the decision-makers in developing short-term strategies with regards to the current number of disease occurrences until an appropriate medication is developed.
| S-EPMC7703963 | biostudies-literature
Project description:BackgroundFor each of the COVID-19 pandemic waves, hospitals have had to plan for deploying surge capacity and resources to manage large but transient increases in COVID-19 admissions. While a lot of effort has gone into predicting regional trends in COVID-19 cases and hospitalizations, there are far fewer successful tools for creating accurate hospital-level forecasts.MethodsLarge-scale, anonymized mobile phone data has been shown to correlate with regional case counts during the first two waves of the pandemic (spring 2020, and fall/winter 2021). Building off this success, we developed a multi-step, recursive forecasting model to predict individual hospital admissions; this model incorporates the following data: (i) hospital-level COVID-19 admissions, (ii) statewide test positivity data, and (iii) aggregate measures of large-scale human mobility, contact patterns, and commuting volume.ResultsIncorporating large-scale, aggregate mobility data as exogenous variables in prediction models allows us to make hospital-specific COVID-19 admission forecasts 21 days ahead. We show this through highly accurate predictions of hospital admissions for five hospitals in Massachusetts during the first year of the COVID-19 pandemic.ConclusionsThe high predictive capability of the model was achieved by combining anonymized, aggregated mobile device data about users' contact patterns, commuting volume, and mobility range with COVID hospitalizations and test-positivity data. Mobility-informed forecasting models can increase the lead-time of accurate predictions for individual hospitals, giving managers valuable time to strategize how best to allocate resources to manage forthcoming surges.
| S-EPMC9927044 | biostudies-literature
Project description:The novel Coronavirus disease (COVID-19) was first identified in Wuhan, China in December 2019 but later spread to other parts of the world. The disease as at the point of writing this paper has been declared a pandemic by the World Health Organization (WHO). The application of mathematical models, artificial intelligence, big data, and similar methodologies are potential tools to predict the extent of the spread and effectiveness of containment strategies to stem the transmission of this disease. In societies with constrained data infrastructures, modeling and forecasting COVID-19 becomes an extremely difficult endeavor. Nonetheless, we propose an online forecasting mechanism that streams data from the Nigeria Center for Disease Control to update the parameters of an ensemble model which in turn provides updated COVID-19 forecasts every 24 hours. The ensemble combines an Auto-Regressive Integrated Moving Average model (ARIMA), Prophet - an additive regression model developed by Facebook, and a Holt-Winters Exponential Smoothing model combined with Generalized Autoregressive Conditional Heteroscedasticity (GARCH). The outcomes of these efforts are expected to provide academic thrust in guiding the policymakers in the deployment of containment strategies and/or assessment of containment interventions in stemming the spread of the disease in Nigeria
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Project description:The novel Coronavirus disease (COVID-19) was first identified in Wuhan, China in December 2019 but later spread to other parts of the world. The disease as at the point of writing this paper has been declared a pandemic by the World Health Organization (WHO). The application of mathematical models, artificial intelligence, big data, and similar methodologies are potential tools to predict the extent of the spread and effectiveness of containment strategies to stem the transmission of this disease. In societies with constrained data infrastructures, modeling and forecasting COVID-19 becomes an extremely difficult endeavor. Nonetheless, we propose an online forecasting mechanism that streams data from the Nigeria Center for Disease Control to update the parameters of an ensemble model which in turn provides updated COVID-19 forecasts every 24 hours. The ensemble combines an Auto-Regressive Integrated Moving Average model (ARIMA), Prophet - an additive regression model developed by Facebook, and a Holt-Winters Exponential Smoothing model combined with Generalized Autoregressive Conditional Heteroscedasticity (GARCH). The outcomes of these efforts are expected to provide academic thrust in guiding the policymakers in the deployment of containment strategies and/or assessment of containment interventions in stemming the spread of the disease in Nigeria.
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Project description:Accurate forecasting of hospital bed demand is crucial during infectious disease epidemics to avoid overwhelming healthcare facilities. To address this, we developed an intuitive online tool for individual hospitals to forecast COVID-19 bed demand. The tool utilizes local data, including incidence, vaccination, and bed occupancy data, at customizable geographical resolutions. Users can specify their hospital's catchment area and adjust the initial number of COVID-19 occupied beds. We assessed the model's performance by forecasting ICU bed occupancy for several university hospitals and regions in Germany. The model achieves optimal results when the selected catchment area aligns with the hospital's local catchment. While expanding the catchment area reduces accuracy, it improves precision. However, forecasting performance diminishes during epidemic turning points. Incorporating variants of concern slightly decreases precision around turning points but does not significantly impact overall bed occupancy results. Our study highlights the significance of using local data for epidemic forecasts. Forecasts based on the hospital's specific catchment area outperform those relying on national or state-level data, striking a better balance between accuracy and precision. These hospital-specific bed demand forecasts offer valuable insights for hospital planning, such as adjusting elective surgeries to create additional bed capacity promptly.
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Project description:As the number of global coronavirus disease (COVID-19) cases increases, the number of imported cases is gradually rising. Furthermore, there is no reduction in domestic outbreaks. To assess the risks from imported COVID-19 cases in South Korea, we suggest using the daily risk score. Confirmed COVID-19 cases reported by John Hopkins University Center, roaming data collected from Korea Telecom, and the Oxford COVID-19 Government Response Tracker index were included in calculating the risk score. The risk score was highly correlated with imported COVID-19 cases after 12 days. To forecast daily imported COVID-19 cases after 12 days in South Korea, we developed prediction models using simple linear regression and autoregressive integrated moving average, including exogenous variables (ARIMAX). In the validation set, the root mean squared error of the linear regression model using the risk score was 6.2, which was lower than that of the autoregressive integrated moving average (ARIMA; 22.3) without the risk score as a reference. Correlation coefficient of ARIMAX using the risk score (0.925) was higher than that of ARIMA (0.899). A possible reason for this time lag of 12 days between imported cases and the risk score could be the delay that occurs before the effect of government policies such as closure of airports or lockdown of cities. Roaming data could help warn roaming users regarding their COVID-19 risk status and inform the national health agency of possible high-risk areas for domestic outbreaks.
| S-EPMC7641397 | biostudies-literature