Summary Background Since December, 2019, Wuhan, China, has experienced an outbreak of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Epidemiological and clinical characteristics of patients with COVID-19 have been reported but risk factors for mortality and a detailed clinical course of illness, including viral shedding, have not been well described. Methods In this retrospective, multicentre cohort study, we included all adult inpatients (≥18 years old) with laboratory-confirmed COVID-19 from Jinyintan Hospital and Wuhan Pulmonary Hospital (Wuhan, China) who had been discharged or had died by Jan 31, 2020. Demographic, clinical, treatment, and laboratory data, including serial samples for viral RNA detection, were extracted from electronic medical records and compared between survivors and non-survivors. We used univariable and multivariable logistic regression methods to explore the risk factors associated with in-hospital death. Findings 191 patients (135 from Jinyintan Hospital and 56 from Wuhan Pulmonary Hospital) were included in this study, of whom 137 were discharged and 54 died in hospital. 91 (48%) patients had a comorbidity, with hypertension being the most common (58 [30%] patients), followed by diabetes (36 [19%] patients) and coronary heart disease (15 [8%] patients). Multivariable regression showed increasing odds of in-hospital death associated with older age (odds ratio 1·10, 95% CI 1·03–1·17, per year increase; p=0·0043), higher Sequential Organ Failure Assessment (SOFA) score (5·65, 2·61–12·23; p Interpretation The potential risk factors of older age, high SOFA score, and d-dimer greater than 1 μg/mL could help clinicians to identify patients with poor prognosis at an early stage. Prolonged viral shedding provides the rationale for a strategy of isolation of infected patients and optimal antiviral interventions in the future. Funding Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences; National Science Grant for Distinguished Young Scholars; National Key Research and Development Program of China; The Beijing Science and Technology Project; and Major Projects of National Science and Technology on New Drug Creation and Development.

Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study

The coronavirus disease 2019 (COVID-19) pandemic has placed epidemic modeling at the forefront of worldwide public policy making. Nonetheless, modeling and forecasting the spread of COVID-19 remains a challenge. Here, we detail three regional-scale models for forecasting and assessing the course of the pandemic. This work demonstrates the utility of parsimonious models for early-time data and provides an accessible framework for generating policy-relevant insights into its course. We show how these models can be connected to each other and to time series data for a particular region. Capable of measuring and forecasting the impacts of social distancing, these models highlight the dangers of relaxing nonpharmaceutical public health interventions in the absence of a vaccine or antiviral therapies.

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The challenges of modeling and forecasting the spread of COVID-19.

(2001). Empirical Processes in M-Estimation. Journal of the American Statistical Association: Vol. 96, No. 454, pp. 779-780.

Empirical Processes in M-Estimation

A. Sinclair and M. Jerrum (1988) derived a bound on the mixing rate of time-reversible Markov chains in terms of their conductance. The authors generalize this result by not assuming time reversibility and using a weaker notion of conductance. They prove an isoperimetric inequality for subsets of a convex body. These results are combined to simplify an algorithm of M. Dyer et al. (1989) for approximating the volume of a convex body and to improve running-time bounds. >

The mixing rate of Markov chains, an isoperimetric inequality, and computing the volume

We study the problem of sampling from a distribution $p^*(x) \propto \exp\left(-U(x)\right)$, where the function $U$ is $L$-smooth everywhere and $m$-strongly convex outside a ball of radius $R$, but potentially nonconvex inside this ball. We study both overdamped and underdamped Langevin MCMC and establish upper bounds on the number of steps required to obtain a sample from a distribution that is within $\epsilon$ of $p^*$ in $1$-Wasserstein distance. For the first-order method (overdamped Langevin MCMC), the iteration complexity is $\tilde{\mathcal{O}}\left(e^{cLR^2}d/\epsilon^2\right)$, where $d$ is the dimension of the underlying space. For the second-order method (underdamped Langevin MCMC), the iteration complexity is $\tilde{\mathcal{O}}\left(e^{cLR^2}\sqrt{d}/\epsilon\right)$ for an explicit positive constant $c$. Surprisingly, the iteration complexity for both these algorithms is only polynomial in the dimension $d$ and the target accuracy $\epsilon$. It is exponential, however, in the problem parameter $LR^2$, which is a measure of non-log-concavity of the target distribution.

Sharp Convergence Rates for Langevin Dynamics in the Nonconvex Setting.

We consider the problem of sampling from a strongly log-concave density in $\mathbb{R}^d$, and prove a non-asymptotic upper bound on the mixing time of the Metropolis-adjusted Langevin algorithm (MALA). The method draws samples by simulating a Markov chain obtained from the discretization of an appropriate Langevin diffusion, combined with an accept-reject step. Relative to known guarantees for the unadjusted Langevin algorithm (ULA), our bounds show that the use of an accept-reject step in MALA leads to an exponentially improved dependence on the error-tolerance. Concretely, in order to obtain samples with TV error at most $\delta$ for a density with condition number $\kappa$, we show that MALA requires $\mathcal{O} \big(\kappa d \log(1/\delta) \big)$ steps, as compared to the $\mathcal{O} \big(\kappa^2 d/\delta^2 \big)$ steps established in past work on ULA. We also demonstrate the gains of MALA over ULA for weakly log-concave densities. Furthermore, we derive mixing time bounds for the Metropolized random walk (MRW) and obtain $\mathcal{O}(\kappa)$ mixing time slower than MALA. We provide numerical examples that support our theoretical findings, and demonstrate the benefits of Metropolis-Hastings adjustment for Langevin-type sampling algorithms.

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Log-concave sampling: Metropolis-Hastings algorithms are fast

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Log-concave sampling: Metropolis-Hastings algorithms are fast!

Hamiltonian Monte Carlo (HMC) is a state-of-the-art Markov chain Monte Carlo sampling algorithm for drawing samples from smooth probability densities over continuous spaces. We study the variant most widely used in practice, Metropolized HMC with the Stormer-Verlet or leapfrog integrator, and make two primary contributions. First, we provide a non-asymptotic upper bound on the mixing time of the Metropolized HMC with explicit choices of step-size and number of leapfrog steps. This bound gives a precise quantification of the faster convergence of Metropolized HMC relative to simpler MCMC algorithms such as the Metropolized random walk, or Metropolized Langevin algorithm. Second, we provide a general framework for sharpening mixing time bounds of Markov chains initialized at a substantial distance from the target distribution over continuous spaces. We apply this sharpening device to the Metropolized random walk and Langevin algorithms, thereby obtaining improved mixing time bounds from a non-warm initial distribution.

Fast mixing of Metropolized Hamiltonian Monte Carlo: Benefits of multi-step gradients

As the COVID-19 outbreak evolves, accurate forecasting continues to play an extremely important role in informing policy decisions. In this article we present our continuous curation of a large data repository containing COVID-19 information from a range of sources. We use this data to develop predictions and corresponding prediction intervals for the short-term trajectory of COVID-19 cumulative death counts at the county level in the United States up to 2 weeks ahead. Using data from January 23 to June 20, 2020, we develop and combine multiple forecasts using ensembling techniques, resulting in an ensemble we refer to as combined linear and exponential predictors (CLEP). Our individual predictors include county-specific exponential and linear predictors, a shared exponential predictor that pools data together across counties, an expanded shared exponential predictor that uses data from neighboring counties, and a demographics-based shared exponential predictor. We use prediction errors from the past 5 days to assess the uncertainty of our death predictions, resulting in generally applicable prediction intervals, maximum (absolute) error prediction intervals (MEPI). MEPI achieves a coverage rate of more than 94% when averaged across counties for predicting cumulative recorded death counts 2 weeks in the future. Our forecasts are currently being used by the nonprofit organization Response4Life to determine the medical supply need for individual hospitals and have directly contributed to the distribution of medical supplies across the country. We hope that our forecasts and data repository at https://covidseverity.com can help guide necessary county-specific decision making and help counties prepare for their continued fight against COVID-19.

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Raaz Dwivedi

Papers

Log-concave sampling: Metropolis-Hastings algorithms are fast

Log-concave sampling: Metropolis-Hastings algorithms are fast!

Fast mixing of Metropolized Hamiltonian Monte Carlo: Benefits of multi-step gradients

Curating a COVID-19 Data Repository and Forecasting County-Level Death Counts in the United States

Log-concave sampling: Metropolis-Hastings algorithms are fast