Clustering US Counties to Find Patterns Related to the COVID-19 Pandemic (preprint)

When COVID-19 first started spreading and quarantine was implemented, the Society for Industrial and Applied Mathematics (SIAM) Student Chapter at the University of Minnesota-Twin Cities began a collaboration with Ecolab to use our skills as data scientists and mathematicians to extract useful insights from relevant data relating to the pandemic. This collaboration consisted of multiple groups working on different projects. In this write-up we focus on using clustering techniques to help us find groups of similar counties in the US and use that to help us understand the pandemic. Our team for this project consisted of University of Minnesota students Cora Brown, Sarah Milstein, Tianyi Sun, and Cooper Zhao, with help from Ecolab Data Scientist Jimmy Broomfield and University of Minnesota student Skye Ke. In the sections below we describe all of the work done for this project. In Section 2, we list the data we gathered, as well as the feature engineering we performed. In Section 3, we describe the metrics we used for evaluating our models. In Section 4, we explain the methods we used for interpreting the results of our various clustering approaches. In Section 5, we describe the different clustering methods we implemented. In Section 6, we present the results of our clustering techniques and provide relevant interpretation. Finally, in Section 7, we provide some concluding remarks comparing the different clustering methods.

Clinical Characteristics, Racial Inequities, and Outcomes in Patients with Breast Cancer and COVID-19: A COVID-19 and Cancer Consortium (CCC19) Cohort Study (preprint)

Title: Clinical Characteristics, Racial Inequities, and Outcomes in Patients with Breast Cancer and COVID-19: A COVID-19 and Cancer Consortium (CCC19) Cohort Study Background: Limited information is available for patients with breast cancer (BC) and coronavirus disease 2019 (COVID-19), especially among underrepresented racial/ethnic populations. Methods: This is a COVID-19 and Cancer Consortium (CCC19) registry-based retrospective cohort study of females with active or history of BC and laboratory-confirmed severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection diagnosed between March 2020 and June 2021 in the US. Primary outcome was COVID-19 severity measured on a five-level ordinal scale, including none of the following complications, hospitalization, intensive care unit admission, mechanical ventilation, and all-cause mortality. Multivariable ordinal logistic regression model identified characteristics associated with COVID-19 severity. Results: 1,383 female patient records with BC and COVID-19 were included in the analysis, the median age was 61 years, and median follow-up was 90 days. Multivariable analysis revealed higher odds of COVID-19 severity for older age (aOR per decade, 1.48 [95% CI, 1.32 - 1.67]); Black patients (aOR 1.74; 95 CI 1.24-2.45), Asian Americans and Pacific Islander patients (aOR 3.40; 95 CI 1.70 - 6.79) and Other (aOR 2.97; 95 CI 1.71-5.17) racial/ethnic groups; worse ECOG performance status (ECOG PS [≥]2: aOR, 7.78 [95% CI, 4.83 - 12.5]); pre-existing cardiovascular (aOR, 2.26 [95% CI, 1.63 - 3.15])/pulmonary comorbidities (aOR, 1.65 [95% CI, 1.20 - 2.29]); diabetes mellitus (aOR, 2.25 [95% CI, 1.66 - 3.04]); and active and progressing cancer (aOR, 12.5 [95% CI, 6.89 - 22.6]). Hispanic ethnicity, timing and type of anti-cancer therapy modalities were not significantly associated with worse COVID-19 outcomes. The total all-cause mortality and hospitalization rate for the entire cohort was 9% and 37%, respectively however, it varied according to the BC disease status. Conclusions: Using one of the largest registries on cancer and COVID-19, we identified patient and BC related factors associated with worse COVID-19 outcomes. After adjusting for baseline characteristics, underrepresented racial/ethnic patients experienced worse outcomes compared to Non-Hispanic White patients. Funding: This study was partly supported by National Cancer Institute grant number P30 CA068485 to Tianyi Sun, Sanjay Mishra, Benjamin French, Jeremy L. Warner; P30-CA046592 to Christopher R. Friese; P30 CA023100 for Rana R McKay; P30-CA054174 for Pankil K. Shah and Dimpy P. Shah; and the American Cancer Society and Hope Foundation for Cancer Research (MRSG-16-152-01 -CCE) and P30-CA054174 for Dimpy P. Shah. REDCap is developed and supported by Vanderbilt Institute for Clinical and Translational Research grant support (UL1 TR000445 from NCATS/NIH). The funding sources had no role in the writing of the manuscript or the decision to submit it for publication. Clinical trial number: CCC19 registry is registered on ClinicalTrials.gov, NCT04354701.