Machine Learning, Deep Learning, and Mathematical Models to Analyze Forecasting and Epidemiology of COVID-19: A Systematic Literature Review

COVID-19 vaccination strategies in Africa: A scoping review of the use of mathematical models to inform policy

OBJECTIVE

Mathematical models are vital tools to understand transmission dynamics and assess the impact of interventions to mitigate COVID-19. However, historically, their use in Africa has been limited. In this scoping review, we assess how mathematical models were used to study COVID-19 vaccination to potentially inform pandemic planning and response in Africa.

METHODS

We searched six electronic databases: MEDLINE, Embase, Web of Science, Global Health, MathSciNet and Africa-Wide NiPAD, using keywords to identify articles focused on the use of mathematical modelling studies of COVID-19 vaccination in Africa that were published as of October 2022. We extracted the details on the country, author affiliation, characteristics of models, policy intent and heterogeneity factors. We assessed quality using 21-point scale criteria on model characteristics and content of the studies.

RESULTS

The literature search yielded 462 articles, of which 32 were included based on the eligibility criteria. Nineteen (59%) studies had a first author affiliated with an African country. Of the 32 included studies, 30 (94%) were compartmental models. By country, most studies were about or included South Africa (n = 12, 37%), followed by Morocco (n = 6, 19%) and Ethiopia (n = 5, 16%). Most studies (n = 19, 59%) assessed the impact of increasing vaccination coverage on COVID-19 burden. Half (n = 16, 50%) had policy intent: prioritising or selecting interventions, pandemic planning and response, vaccine distribution and optimisation strategies and understanding transmission dynamics of COVID-19. Fourteen studies (44%) were of medium quality and eight (25%) were of high quality.

CONCLUSIONS

While decision-makers could draw vital insights from the evidence generated from mathematical modelling to inform policy, we found that there was limited use of such models exploring vaccination impacts for COVID-19 in Africa. The disparity can be addressed by scaling up mathematical modelling training, increasing collaborative opportunities between modellers and policymakers, and increasing access to funding.

Prediction of tuberculosis clusters in the riverine municipalities of the Brazilian Amazon with machine learning

OBJECTIVE

Tuberculosis (TB) is the second most deadly infectious disease globally, posing a significant burden in Brazil and its Amazonian region. This study focused on the "riverine municipalities" and hypothesizes the presence of TB clusters in the area. We also aimed to train a machine learning model to differentiate municipalities classified as hot spots vs. non-hot spots using disease surveillance variables as predictors.

METHODS

Data regarding the incidence of TB from 2019 to 2022 in the riverine town was collected from the Brazilian Health Ministry Informatics Department. Moran's I was used to assess global spatial autocorrelation, while the Getis-Ord GI* method was employed to detect high and low-incidence clusters. A Random Forest machine-learning model was trained using surveillance variables related to TB cases to predict hot spots among non-hot spot municipalities.

RESULTS

Our analysis revealed distinct geographical clusters with high and low TB incidence following a west-to-east distribution pattern. The Random Forest Classification model utilizes six surveillance variables to predict hot vs. non-hot spots. The machine learning model achieved an Area Under the Receiver Operator Curve (AUC-ROC) of 0.81.

CONCLUSION

Municipalities with higher percentages of recurrent cases, deaths due to TB, antibiotic regimen changes, percentage of new cases, and cases with smoking history were the best predictors of hot spots. This prediction method can be leveraged to identify the municipalities at the highest risk of being hot spots for the disease, aiding policymakers with an evidenced-based tool to direct resource allocation for disease control in the riverine municipalities.

DeepDynaForecast: Phylogenetic-informed graph deep learning for epidemic transmission dynamic prediction

In the midst of an outbreak or sustained epidemic, reliable prediction of transmission risks and patterns of spread is critical to inform public health programs. Projections of transmission growth or decline among specific risk groups can aid in optimizing interventions, particularly when resources are limited. Phylogenetic trees have been widely used in the detection of transmission chains and high-risk populations. Moreover, tree topology and the incorporation of population parameters (phylodynamics) can be useful in reconstructing the evolutionary dynamics of an epidemic across space and time among individuals. We now demonstrate the utility of phylodynamic trees for transmission modeling and forecasting, developing a phylogeny-based deep learning system, referred to as DeepDynaForecast. Our approach leverages a primal-dual graph learning structure with shortcut multi-layer aggregation, which is suited for the early identification and prediction of transmission dynamics in emerging high-risk groups. We demonstrate the accuracy of DeepDynaForecast using simulated outbreak data and the utility of the learned model using empirical, large-scale data from the human immunodeficiency virus epidemic in Florida between 2012 and 2020. Our framework is available as open-source software (MIT license) at github.com/lab-smile/DeepDynaForcast.

Artificial intelligence-driven prediction of COVID-19-related hospitalization and death: a systematic review

Aim

To perform a systematic review on the use of Artificial Intelligence (AI) techniques for predicting COVID-19 hospitalization and mortality using primary and secondary data sources.

Study eligibility criteria

Cohort, clinical trials, meta-analyses, and observational studies investigating COVID-19 hospitalization or mortality using artificial intelligence techniques were eligible. Articles without a full text available in the English language were excluded.

Data sources

Articles recorded in Ovid MEDLINE from 01/01/2019 to 22/08/2022 were screened.

Data extraction

We extracted information on data sources, AI models, and epidemiological aspects of retrieved studies.

Bias assessment

A bias assessment of AI models was done using PROBAST.

Participants

Patients tested positive for COVID-19.

Results

We included 39 studies related to AI-based prediction of hospitalization and death related to COVID-19. The articles were published in the period 2019-2022, and mostly used Random Forest as the model with the best performance. AI models were trained using cohorts of individuals sampled from populations of European and non-European countries, mostly with cohort sample size <5,000. Data collection generally included information on demographics, clinical records, laboratory results, and pharmacological treatments (i.e., high-dimensional datasets). In most studies, the models were internally validated with cross-validation, but the majority of studies lacked external validation and calibration. Covariates were not prioritized using ensemble approaches in most of the studies, however, models still showed moderately good performances with Area under the Receiver operating characteristic Curve (AUC) values >0.7. According to the assessment with PROBAST, all models had a high risk of bias and/or concern regarding applicability.

Conclusions

A broad range of AI techniques have been used to predict COVID-19 hospitalization and mortality. The studies reported good prediction performance of AI models, however, high risk of bias and/or concern regarding applicability were detected.

Applying machine learning techniques to predict the risk of lung metastases from rectal cancer: a real-world retrospective study

Background

Metastasis in the lungs is common in patients with rectal cancer, and it can have severe consequences on their survival and quality of life. Therefore, it is essential to identify patients who may be at risk of developing lung metastasis from rectal cancer.

Methods

In this study, we utilized eight machine-learning methods to create a model for predicting the risk of lung metastasis in patients with rectal cancer. Our cohort consisted of 27,180 rectal cancer patients selected from the Surveillance, Epidemiology and End Results (SEER) database between 2010 and 2017 for model development. Additionally, we validated our models using 1118 rectal cancer patients from a Chinese hospital to evaluate model performance and generalizability. We assessed our models' performance using various metrics, including the area under the curve (AUC), the area under the precision-recall curve (AUPR), the Matthews Correlation Coefficient (MCC), decision curve analysis (DCA), and calibration curves. Finally, we applied the best model to develop a web-based calculator for predicting the risk of lung metastasis in patients with rectal cancer.

Result

Our study employed tenfold cross-validation to assess the performance of eight machine-learning models for predicting the risk of lung metastasis in patients with rectal cancer. The AUC values ranged from 0.73 to 0.96 in the training set, with the extreme gradient boosting (XGB) model achieving the highest AUC value of 0.96. Moreover, the XGB model obtained the best AUPR and MCC in the training set, reaching 0.98 and 0.88, respectively. We found that the XGB model demonstrated the best predictive power, achieving an AUC of 0.87, an AUPR of 0.60, an accuracy of 0.92, and a sensitivity of 0.93 in the internal test set. Furthermore, the XGB model was evaluated in the external test set and achieved an AUC of 0.91, an AUPR of 0.63, an accuracy of 0.93, a sensitivity of 0.92, and a specificity of 0.93. The XGB model obtained the highest MCC in the internal test set and external validation set, with 0.61 and 0.68, respectively. Based on the DCA and calibration curve analysis, the XGB model had better clinical decision-making ability and predictive power than the other seven models. Lastly, we developed an online web calculator using the XGB model to assist doctors in making informed decisions and to facilitate the model's wider adoption (https://share.streamlit.io/woshiwz/rectal_cancer/main/lung.py).

Conclusion

In this study, we developed an XGB model based on clinicopathological information to predict the risk of lung metastasis in patients with rectal cancer, which may help physicians make clinical decisions.