A key issue for all observational causal inference is that it relies on an unverifiable assumption - that observed characteristics are sufficient to proxy for treatment confounding. In this paper we argue that in medical cases these conditions are more likely to be met in cases where standardized treatment guidelines do not yet exist. One example of such a situation is the emergence of a novel disease. We study the case of early COVID-19 in New York City hospitals and show that observational analysis of two important thereapeutics, anti-coagulation and steroid therapy, gives results that agree with later guidelines issued via combinations of randomized trials and other evidence. We also argue that observational causal inference cannot be applied mechanically and requires domain expertise by the analyst by showing a cautionary tale of a treatment that appears extremely promising in the data, but the result is due to a quirk of hospital policy.
In this paper we develop statistical methods for causal inference in epidemics. Our focus is in estimating the effect of social mobility on deaths in the Covid-19 pandemic. We propose a marginal structural model motivated by a modified version of a basic epidemic model. We estimate the counterfactual time series of deaths under interventions on mobility. We conduct several types of sensitivity analyses. We find that the data support the idea that reduced mobility causes reduced deaths, but the conclusion comes with caveats. There is evidence of sensitivity to model misspecification and unmeasu…
We point out an instantiation of Simpson's paradox in Covid-19 case fatality rates (CFRs): comparing a large-scale study from China (17 Feb) with early reports from Italy (9 Mar), we find that CFRs are lower in Italy for every age group, but higher overall. This phenomenon is explained by a stark difference in case demographic between the two countries. Using this as a motivating example, we introduce basic concepts from mediation analysis and show how these can be used to quantify different direct and indirect effects when assuming a coarse-grained causal graph involving country, age, and cas…
University of Virginia（弗吉尼亚大学）；Global Infectious Disease Institute, University of Virginia（弗吉尼亚大学全球传染病研究所）
To mitigate the spread of COVID-19 pandemic, decision-makers and public authorities have announced various non-pharmaceutical policies. Analyzing the causal impact of these policies in reducing the spread of COVID-19 is important for future policy-making. The main challenge here is the existence of unobserved confounders (e.g., vigilance of residents). Besides, as the confounders may be time-varying during COVID-19 (e.g., vigilance of residents changes in the course of the pandemic), it is even more difficult to capture them. In this paper, we study the problem of assessing the causal effects …
Auburn University（奥本大学）；DESY（德国电子同步加速器研究所）；Humboldt-Universität zu Berlin（柏林洪堡大学）；BASIS Independent Silicon Valley（贝赛思独立学校硅谷校区）；Stanford Online High School（斯坦福在线高中）；NTNU（挪威科技大学）；SimulaMet（SimulaMet研究所）
The analysis of causation is a challenging task that can be approached in various ways. With the increasing use of machine learning based models in computational socioeconomics, explaining these models while taking causal connections into account is a necessity. In this work, we advocate the use of an explanatory framework from cooperative game theory augmented with $do$ calculus, namely causal Shapley values. Using causal Shapley values, we analyze socioeconomic disparities that have a causal link to the spread of COVID-19 in the USA. We study several phases of the disease spread to show how …
Econometric vs. Causal Structure-Learning for Time-Series Policy Decisions: Evidence from the UK COVID-19 Policies
Bayesian Artificial Intelligence research lab, MInDS research group（贝叶斯人工智能研究实验室，MInDS研究小组）；School of Electronic Engineering and Computer Science, Queen Mary University of London（电子工程与计算机科学学院，伦敦女王玛丽大学）
The COVID-19 pandemic has highlighted delayed reporting as a significant impediment to effective disease surveillance and decision-making. In the absence of timely data, statistical models which account for delays can be adopted to nowcast and forecast cases or deaths. We discuss the four key sources of systematic and random variability in available data for COVID-19 and other diseases, and critically evaluate current state-of-the-art methods with respect to appropriately separating and capturing this variability. We present a general spatio-temporal hierarchical framework for correcting delay…
In this work, we study the causal relations among German regions in terms of the spread of Covid-19 since the beginning of the pandemic, taking into account the restriction policies that were applied by the different federal states. We propose and prove a new theorem for a causal feature selection method for time series data, robust to latent confounders, which we subsequently apply on Covid-19 case numbers. We present findings about the spread of the virus in Germany and the causal impact of restriction measures, discussing the role of various policies in containing the spread. Since our resu…
A spatial analysis of COVID-19 reported cases in the Gauteng province, South Africa: Identifying wards to be targeted early in future infectious diseases outbreak
The emergence of Covid-19 requires new effective tools for epidemiological surveillance. Spatio-temporal disease mapping models, which allow dealing with highly disaggregated spatial and temporal units of analysis, are a priority in this sense. Spatio-temporal models provide a geographically detailed and temporally updated overview of the current state of the pandemics, making public health interventions to be more effective. Moreover, the use of spatio-temporal disease mapping models in the new Covid-19 epidemic context, facilitates estimating newly demanded epidemiological indicators, such a…
As the COVID-19 ravaging through the globe, accurate forecasts of the disease spread is crucial for situational awareness, resource allocation, and public health decision-making. Alternative to the traditional disease surveillance data collected by the United States (US) Centers for Disease Control and Prevention (CDC), big data from Internet such as online search volumes has been previously shown to contain valuable information for tracking infectious disease dynamics. In this study, we evaluate the feasibility of using Internet search volume of relevant queries to track and predict COVID-19 …
Since December 2019, the world has been witnessing the gigantic effect of an unprecedented global pandemic called Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) - COVID-19. So far, 38,619,674 confirmed cases and 1,093,522 confirmed deaths due to COVID-19 have been reported. In the United States (US), the cases and deaths are recorded as 7,833,851 and 215,199. Several timely researches have discussed the local and global effects of the confounding factors on COVID-19 casualties in the US. However, most of these studies considered little about the time varying associations between an…
In mid of March 2020, Coronaviruses such as COVID-19 is declared as an international epidemic. More than 125000 confirmed cases and 4,607 death cases have been recorded around more than 118 countries. Unfortunately, a coronavirus vaccine is expected to take at least 18 months if it works at all. Moreover, COVID -19 epidemics can mutate into a more aggressive form. Day level information about the COVID -19 spread is crucial to measure the behavior of this new virus globally. Therefore, this study presents a comparison of day level forecasting models on COVID-19 affected cases using time series …
A reasonable prediction of infectious diseases transmission process under different disease control strategies is an important reference point for policy makers. Here we established a dynamic transmission model via Python and realized comprehensive regulation of disease control measures. We classified government interventions into three categories and introduced three parameters as descriptions for the key points in disease control, these being intraregional growth rate, interregional communication rate, and detection rate of infectors. Our simulation predicts the infection by COVID-19 in the …
College of Computing, Georgia Institute of Technology（佐治亚理工学院计算学院）；Department of Computer Science, Virginia Tech（弗吉尼亚理工大学计算机系）；Department of Computer Science, University of Iowa（爱荷华大学计算机系）
Forecasting influenza in a timely manner aids health organizations and policymakers in adequate preparation and decision making. However, effective influenza forecasting still remains a challenge despite increasing research interest. It is even more challenging amidst the COVID pandemic, when the influenza-like illness (ILI) counts are affected by various factors such as symptomatic similarities with COVID-19 and shift in healthcare seeking patterns of the general population. Under the current pandemic, historical influenza models carry valuable expertise about the disease dynamics but face di…
We provide a methodology by which an epidemiologist may arrive at an optimal design for a survey whose goal is to estimate the disease burden in a population. For serosurveys with a given budget of $C$ rupees, a specified set of tests with costs, sensitivities, and specificities, we show the existence of optimal designs in four different contexts, including the well known c-optimal design. Usefulness of the results are illustrated via numerical examples. Our results are applicable to a wide range of epidemiological surveys under the assumptions that the estimate's Fisher-information matrix sat…
At a national-level, we sought to investigate the effect of public masking mandates on COVID-19 in Fall 2020. Specifically, we aimed to evaluate how the relative growth of COVID-19 cases and deaths would have differed if all states had issued a mandate to mask in public by September 1, 2020 versus if all states had delayed issuing such a mandate. To do so, we applied the Causal Roadmap, a formal framework for causal and statistical inference. The outcome was defined as the state-specific relative increase in cumulative cases and in cumulative deaths {21, 30, 45, 60}-days after September 1. Des…
Mathematical models of infectious diseases exhibit robust dynamics such as stable endemic or a disease-free equilibrium, or convergence of the solutions to periodic epidemic waves. The present work shows that the accuracy of such dynamics can be significantly improved by incorporating both local and global dynamics of the infection in disease models. To demonstrate improved accuracies, we extended a standard Susceptible-Infected-Recovered (SIR) model by incorporating global dynamics of the COVID-19 pandemic. The extended SIR model assumes three possibilities for the susceptible individuals tra…
COVID-19 is an acute respiratory disease that has been classified as a pandemic by the World Health Organization. Characterization of this disease is still in its early stages. However, it is known to have high mortality rates, particularly among individuals with preexisting medical conditions. Creating models to identify individuals who are at the greatest risk for severe complications due to COVID-19 will be useful for outreach campaigns to help mitigate the disease's worst effects. While information specific to COVID-19 is limited, a model using complications due to other upper respiratory …
The coronavirus disease 2019 (COVID-19) has quickly grown from a regional outbreak in Wuhan, China to a global pandemic. Early estimates of the epidemic growth and incubation period of COVID-19 may have been biased due to sample selection. Using detailed case reports from 14 locations in and outside mainland China, we obtained 378 Wuhan-exported cases who left Wuhan before an abrupt travel quarantine. We developed a generative model we call BETS for four key epidemiological events---Beginning of exposure, End of exposure, time of Transmission, and time of Symptom onset (BETS)---and derived exp…
The outbreaks of Coronavirus Disease 2019 (COVID-19) have impacted the world significantly. Modeling the trend of infection and real-time forecasting of cases can help decision making and control of the disease spread. However, data-driven methods such as recurrent neural networks (RNN) can perform poorly due to limited daily samples in time. In this work, we develop an integrated spatiotemporal model based on the epidemic differential equations (SIR) and RNN. The former after simplification and discretization is a compact model of temporal infection trend of a region while the latter models t…
Ludwig Maximilian Universität（路德维希-马克西米利安大学）；Helmholtz Zentrum München – German Research Center for Environmental Health（亥姆霍兹慕尼黑中心——德国环境健康研究中心）
During 2020, the infection rate of COVID-19 has been investigated by many scholars from different research fields. In this context, reliable and interpretable forecasts of disease incidents are a vital tool for policymakers to manage healthcare resources. Several experts have called for the necessity to account for human mobility to explain the spread of COVID-19. Existing approaches are often applying standard models of the respective research field. This habit, however, often comes along with certain restrictions. For instance, most statistical or epidemiological models cannot directly incor…
Knowing the true effect size of clinical interventions in randomised clinical trials is key to informing the public health policies. Vaccine efficacy is defined in terms of the relative risk or the ratio of two disease risks. However, only approximate methods are available for estimating the variance of the relative risk. In this article, we show using a probabilistic model that uncertainty in the efficacy rate could be underestimated when the disease risk is low. Factoring in the baseline rate of the disease, we estimate broader confidence intervals for the efficacy rates of the vaccines rece…
With COVID-19 affecting every country globally and changing everyday life, the ability to forecast the spread of the disease is more important than any previous epidemic. The conventional methods of disease-spread modeling, compartmental models, are based on the assumption of spatiotemporal homogeneity of the spread of the virus, which may cause forecasting to underperform, especially at high spatial resolutions. In this paper we approach the forecasting task with an alternative technique - spatiotemporal machine learning. We present COVID-LSTM, a data-driven model based on a Long Short-term M…
The ongoing COVID-19 pandemic has brought science to the fore of the public discourse and considering the complexity of the issues involved, with it also the challenge of effective and informative science communication. A particularly contentious topic, in that it is both highly emotional in and of itself, as well as in that it sits at the nexus of the decision-making process regarding the handling of the pandemic, which has effected lockdowns, social behaviour measures, business closures, and others, concerns the recording and the reporting of the disease mortality. To clarify a point which h…
Currently, novel coronavirus disease 2019 (COVID-19) is a big threat to global health. The rapid spread of the virus has created pandemic, and countries all over the world are struggling with a surge in COVID-19 infected cases. There are no drugs or other therapeutics approved by the US Food and Drug Administration to prevent or treat COVID-19: information on the disease is very limited and scattered even if it exists. This motivates the use of data integration, combining data from diverse sources and eliciting useful information with a unified view of them. In this paper, we propose a Bayesia…
As COVID-19 pandemic progresses, severe flu seasons may happen alongside an increase in cases in cases and death of COVID-19, causing severe burdens on health care resources and public safety. A consequence of a twindemic may be a mixture of two different infections in the same person at the same time, "flurona". Admist the raising trend of "flurona", forecasting both influenza outbreaks and COVID-19 waves in a timely manner is more urgent than ever, as accurate joint real-time tracking of the twindemic aids health organizations and policymakers in adequate preparation and decision making. Und…
Start from the End: A Framework for Computational Policy Exploration to Inform Effective and Geospatially Consistent Interventions applied to COVID-19 in St. Louis
The ongoing pandemic of Coronavirus disease (COVID-19) emerged in Wuhan, China in the end of 2019. It has already affected more than 300,000 people, with the number of deaths nearing 13000 across the world. As it has been posing a huge threat to global public health, it is of utmost importance to identify the rate at which the disease is spreading. In this study, we propose a time series model to analyze the trend pattern of the incidence of COVID-19 outbreak. We also incorporate information on total or partial lockdown, wherever available, into the model. The model is concise in structure, an…
As of December 2020, the COVID-19 pandemic has infected over 75 million people, making it the deadliest pandemic in modern history. This study develops a novel compartmental epidemiological model specific to the SARS-CoV-2 virus and analyzes the effect of common preventative measures such as testing, quarantine, social distancing, and vaccination. By accounting for the most prevalent interventions that have been enacted to minimize the spread of the virus, the model establishes a paramount foundation for future mathematical modeling of COVID-19 and other modern pandemics. Specifically, the mod…
Recently, Phillippe Lemoine posted a critique of our paper "Causal Impact of Masks, Policies, Behavior on Early Covid-19 Pandemic in the U.S." [arXiv:2005.14168] at his post titled "Lockdowns, econometrics and the art of putting lipstick on a pig." Although Lemoine's critique appears ideologically driven and overly emotional, some of his points are worth addressing. In particular, the sensitivity of our estimation results for (i) including "masks in public spaces" and (ii) updating the data seems important critiques and, therefore, we decided to analyze the updated data ourselves. This note su…
Governments around the world have implemented preventive measures against the spread of the coronavirus disease (COVID-19). In this study, we consider a multivariate discrete-time Markov model to analyze the propagation of COVID-19 across 33 provincial regions in China. This approach enables us to evaluate the effect of mobility restriction policies on the spread of the disease. We use data on daily human mobility across regions and apply the Bayesian framework to estimate the proposed model. The results show that the spread of the disease in China was predominately driven by community transmi…
