Journal of Data Science

Time-to-event data analysis without a well-defined time origin commonly occurs in observational studies that retrospectively collect survival endpoints. For instance, after enrolling participants who have or have not received a specific treatment, an event status can be observed for all participants; however, the start date of treatment is only observable for the treatment group. The corresponding time origin does not exist for the control group, resulting in missing survival time data. Complete-case analysis is often considered the standard approach, but it disregards information from all participants in the control group and does not allow us to compare their survival distributions. To address this challenge, we propose a novel semiparametric proportional hazards model by regarding these missing time origins as nuisance parameters. We approximate the risk sets as cumulative normal distributions to deal with these nuisance parameters and develop estimation and inference procedures for our proposed estimator. We study the asymptotic properties of this model and conduct the simulation studies to validate its finite sample property. Analysis of data from a recent SARS-CoV-2 seroprevaluence study illustrates the applicability of our methods. The proposed methods are implemented in the R package coxphm.

Millions of people travel from Wuhan to other cities from Jan. 1st 2020 to Jan 23rd 2020. Taking advantage of the masked software development kit data from Aurora Mobile Ltd and open epidemic data released by health authorities, we analyze the relationship between number of confirmed COVID-19 cases in a region and the people who traveled from Wuhan to this region in this period. Further, we identify high risk carriers of COVID-19 to improve the control of COVID-19. The key findings are three-folds: (1) in each region the number of high-risk carriers is highly positively correlated with the severity of illness; (2) history of visit to the 62 designated hospitals is the foremost index of risk; (3) the second most important index is the travelers’ duration of stay in Wuhan. Based on our analysis, we estimate that, as of February 4, 2020, (a) among the 8.5 million people held up in Wuhan, there are 425 thousand high risk carriers; and (b) among all the 3.5 million migrant workers held up in Hubei, there are 175 thousand high risk carriers. The disease control authorities should closely minotor these groups.

Proteins play a key role in facilitating the infectiousness of the 2019 novel coronavirus. A specific spike protein enables this virus to bind to human cells, and a thorough understanding of its 3-dimensional structure is therefore critical for developing effective therapeutic interventions. However, its structure may continue to evolve over time as a result of mutations. In this paper, we use a data science perspective to study the potential structural impacts due to ongoing mutations in its amino acid sequence. To do so, we identify a key segment of the protein and apply a sequential Monte Carlo sampling method to detect possible changes to the space of lowenergy conformations for different amino acid sequences. Such computational approaches can further our understanding of this protein structure and complement laboratory efforts.

Researchers and public officials tend to agree that until a vaccine is readily available, stopping SARS-CoV-2 transmission is the name of the game. Testing is the key to preventing the spread, especially by asymptomatic individuals. With testing capacity restricted, group testing is an appealing alternative for comprehensive screening and has recently received FDA emergency authorization. This technique tests pools of individual samples, thereby often requiring fewer testing resources while potentially providing multiple folds of speedup. We approach group testing from a data science perspective and offer two contributions. First, we provide an extensive empirical comparison of modern group testing techniques based on simulated data. Second, we propose a simple one-round method based on ${\ell _{1}}$-norm sparse recovery, which outperforms current state-of-the-art approaches at certain disease prevalence rates.

As the major target of many vaccines and neutralizing antibodies against SARS-CoV-2, the spike (S) protein is observed to mutate over time. In this paper, we present statistical approaches to tackle some challenges associated with the analysis of S-protein data. We build a Bayesian hierarchical model to study the temporal and spatial evolution of S-protein sequences, after grouping the sequences into representative clusters. We then apply sampling methods to investigate possible changes to the S-protein’s 3-D structure as a result of commonly observed mutations. While the increasing spread of D614G variants has been noted in other research, our results also show that the co-occurring mutations of D614G together with S477N or A222V may spread even more rapidly, as quantified by our model estimates.