The needs of mitigating COVID-19 epidemic prompt policymakers to make public health-related decision under the guidelines of science.Tremendous unstructured COVID-19 publications make it challenging for policymakers t...The needs of mitigating COVID-19 epidemic prompt policymakers to make public health-related decision under the guidelines of science.Tremendous unstructured COVID-19 publications make it challenging for policymakers to obtain relevant evidence.Knowledge graphs(KGs)can formalize unstructured knowledge into structured form and have been used in supporting decision-making recently.Here,we introduce a novel framework that can ex-tract the COVID-19 public health evidence knowledge graph(CPHE-KG)from papers relating to a modelling study.We screen out a corpus of 3096 COVID-19 modelling study papers by performing a literature assessment process.We define a novel annotation schema to construct the COVID-19 modelling study-related IE dataset(CPHIE).We also propose a novel multi-tasks document-level information extraction model SS-DYGIE++based on the dataset.Leveraging the model on the new corpus,we construct CPHE-KG containing 60,967 entities and 51,140 rela-tions.Finally,we seek to apply our KG to support evidence querying and evidence mapping visualization.Our SS-DYGIE++(SpanBERT)model has achieved a F1 score of 0.77 and 0.55 respectively in document-level entity recognition and coreference resolution tasks.It has also shown high performance in the relation identification task.With evidence querying,our KG can present the dynamic transmissions of COVID-19 pandemic in different countries and regions.The evidence mapping of our KG can show the impacts of variable non-pharmacological interventions to COVID-19 pandemic.Analysis demonstrates the quality of our KG and shows that it has the potential to support COVID-19 policy making in public health.展开更多
Introduction:Multivariate time series prediction of infectious diseases is significant to public health,and the deep learning method has attracted increasing attention in this research field.Material and methods:An ad...Introduction:Multivariate time series prediction of infectious diseases is significant to public health,and the deep learning method has attracted increasing attention in this research field.Material and methods:An adaptively temporal graph convolution(ATGCN)model,which leams the contact patterns of multiple age groups in a graph-based approach,was proposed for COVID-19 and influenza prediction.We compared ATGCN with autoregressive models,deep sequence learning models,and experience-based ATGCN models in short-term and long-term prediction tasks.Results:Results showed that the ATGCN model performed better than the autoregressive models and the deep sequence learning models on two datasets in both short-term(12.5%and 10%improvements on RMSE)and longterm(12.4%and 5%improvements on RMSE)prediction tasks.And the RMSE of ATGCN predictions fluctuated least in different age groups of COVID-19(0.029±0.003)and influenza(0.059±0.008).Compared with the Ones-ATGCN model or the Pre-ATGCN model,the ATGCN model was more robust in performance,with RMSE of 0.0293 and 0.06 on two datasets when horizon is one.Discussion:Our research indicates a broad application prospect of deep learning in the field of infectious disease prediction.Transmission characteristics and domain knowledge of infectious diseases should be further applied to the design of deep learning models and feature selection.Conclusion:The ATGCN model addressed the multivariate time series forecasting in a graph-based deep learning approach and achieved robust prediction on the confirmed cases of multiple age groups,indicating its great potentials for exploring the implicit interactions of multivariate variables.展开更多
基金This work was supported in part by the National Natural Science Foundation of China(Grants No.72025404 and No.71621002)Bei-jing Natural Science Foundation(L192012)Beijing Nova Program(Z201100006820085).
文摘The needs of mitigating COVID-19 epidemic prompt policymakers to make public health-related decision under the guidelines of science.Tremendous unstructured COVID-19 publications make it challenging for policymakers to obtain relevant evidence.Knowledge graphs(KGs)can formalize unstructured knowledge into structured form and have been used in supporting decision-making recently.Here,we introduce a novel framework that can ex-tract the COVID-19 public health evidence knowledge graph(CPHE-KG)from papers relating to a modelling study.We screen out a corpus of 3096 COVID-19 modelling study papers by performing a literature assessment process.We define a novel annotation schema to construct the COVID-19 modelling study-related IE dataset(CPHIE).We also propose a novel multi-tasks document-level information extraction model SS-DYGIE++based on the dataset.Leveraging the model on the new corpus,we construct CPHE-KG containing 60,967 entities and 51,140 rela-tions.Finally,we seek to apply our KG to support evidence querying and evidence mapping visualization.Our SS-DYGIE++(SpanBERT)model has achieved a F1 score of 0.77 and 0.55 respectively in document-level entity recognition and coreference resolution tasks.It has also shown high performance in the relation identification task.With evidence querying,our KG can present the dynamic transmissions of COVID-19 pandemic in different countries and regions.The evidence mapping of our KG can show the impacts of variable non-pharmacological interventions to COVID-19 pandemic.Analysis demonstrates the quality of our KG and shows that it has the potential to support COVID-19 policy making in public health.
基金This work was supported in part by grants from the National Natural Science Foundation of China(Grants No.72025404 and 71621002)Beijing Natural Science Foundation(Grant No.LI92012)Beijing Nova Program(Grant No.Z201100006820085).
文摘Introduction:Multivariate time series prediction of infectious diseases is significant to public health,and the deep learning method has attracted increasing attention in this research field.Material and methods:An adaptively temporal graph convolution(ATGCN)model,which leams the contact patterns of multiple age groups in a graph-based approach,was proposed for COVID-19 and influenza prediction.We compared ATGCN with autoregressive models,deep sequence learning models,and experience-based ATGCN models in short-term and long-term prediction tasks.Results:Results showed that the ATGCN model performed better than the autoregressive models and the deep sequence learning models on two datasets in both short-term(12.5%and 10%improvements on RMSE)and longterm(12.4%and 5%improvements on RMSE)prediction tasks.And the RMSE of ATGCN predictions fluctuated least in different age groups of COVID-19(0.029±0.003)and influenza(0.059±0.008).Compared with the Ones-ATGCN model or the Pre-ATGCN model,the ATGCN model was more robust in performance,with RMSE of 0.0293 and 0.06 on two datasets when horizon is one.Discussion:Our research indicates a broad application prospect of deep learning in the field of infectious disease prediction.Transmission characteristics and domain knowledge of infectious diseases should be further applied to the design of deep learning models and feature selection.Conclusion:The ATGCN model addressed the multivariate time series forecasting in a graph-based deep learning approach and achieved robust prediction on the confirmed cases of multiple age groups,indicating its great potentials for exploring the implicit interactions of multivariate variables.
