@article{SigelSwartzGoldenetal.2020,
  author    = {Sigel, Keith Magnus and Swartz, Talia H. and Golden, Eddye and Paranjpe, Ishan and Somani, Sulaiman and Richter, Felix and De Freitas, Jessica K. and Miotto, Riccardo and Zhao, Shan and Polak, Paz and Mutetwa, Tinaye and Factor, Stephanie and Mehandru, Saurabh and Mullen, Michael and Cossarini, Francesca and B{\"o}ttinger, Erwin and Fayad, Zahi and Merad, Miriam and Gnjatic, Sacha and Aberg, Judith and Charney, Alexander and Nadkarni, Girish and Glicksberg, Benjamin S.},
  title     = {Coronavirus 2019 and people living with human immunodeficiency virus},
  series = {Clinical infectious diseases : electronic edition},
  volume    = {71},
  journal   = {Clinical infectious diseases : electronic edition},
  number    = {11},
  publisher = {Oxford Univ. Press},
  address   = {Cary, NC},
  issn      = {1058-4838},
  doi       = {10.1093/cid/ciaa880},
  pages     = {2933 -- 2938},
  year      = {2020},
  abstract  = {Background: There are limited data regarding the clinical impact of coronavirus disease 2019 (COVID-19) on people living with human immunodeficiency virus (PLWH). In this study, we compared outcomes for PLWH with COVID-19 to a matched comparison group. Methods: We identified 88 PLWH hospitalized with laboratory-confirmed COVID-19 in our hospital system in New York City between 12 March and 23 April 2020. We collected data on baseline clinical characteristics, laboratory values, HIV status, treatment, and outcomes from this group and matched comparators (1 PLWH to up to 5 patients by age, sex, race/ethnicity, and calendar week of infection). We compared clinical characteristics and outcomes (death, mechanical ventilation, hospital discharge) for these groups, as well as cumulative incidence of death by HIV status. Results: Patients did not differ significantly by HIV status by age, sex, or race/ethnicity due to the matching algorithm. PLWH hospitalized with COVID-19 had high proportions of HIV virologic control on antiretroviral therapy. PLWH had greater proportions of smoking (P < .001) and comorbid illness than uninfected comparators. There was no difference in COVID-19 severity on admission by HIV status (P = .15). Poor outcomes for hospitalized PLWH were frequent but similar to proportions in comparators; 18\% required mechanical ventilation and 21\% died during follow-up (compared with 23\% and 20\%, respectively). There was similar cumulative incidence of death over time by HIV status (P = .94). Conclusions: We found no differences in adverse outcomes associated with HIV infection for hospitalized COVID-19 patients compared with a demographically similar patient group.},
  language  = {en}
}
@article{VaidSomaniRussaketal.2020,
  author    = {Vaid, Akhil and Somani, Sulaiman and Russak, Adam J. and De Freitas, Jessica K. and Chaudhry, Fayzan F. and Paranjpe, Ishan and Johnson, Kipp W. and Lee, Samuel J. and Miotto, Riccardo and Richter, Felix and Zhao, Shan and Beckmann, Noam D. and Naik, Nidhi and Kia, Arash and Timsina, Prem and Lala, Anuradha and Paranjpe, Manish and Golden, Eddye and Danieletto, Matteo and Singh, Manbir and Meyer, Dara and O'Reilly, Paul F. and Huckins, Laura and Kovatch, Patricia and Finkelstein, Joseph and Freeman, Robert M. and Argulian, Edgar and Kasarskis, Andrew and Percha, Bethany and Aberg, Judith A. and Bagiella, Emilia and Horowitz, Carol R. and Murphy, Barbara and Nestler, Eric J. and Schadt, Eric E. and Cho, Judy H. and Cordon-Cardo, Carlos and Fuster, Valentin and Charney, Dennis S. and Reich, David L. and B{\"o}ttinger, Erwin and Levin, Matthew A. and Narula, Jagat and Fayad, Zahi A. and Just, Allan C. and Charney, Alexander W. and Nadkarni, Girish N. and Glicksberg, Benjamin S.},
  title     = {Machine learning to predict mortality and critical events in a cohort of patients with COVID-19 in New York City: model development and validation},
  series = {Journal of medical internet research : international scientific journal for medical research, information and communication on the internet ; JMIR},
  volume    = {22},
  journal   = {Journal of medical internet research : international scientific journal for medical research, information and communication on the internet ; JMIR},
  number    = {11},
  publisher = {Healthcare World},
  address   = {Richmond, Va.},
  issn      = {1439-4456},
  doi       = {10.2196/24018},
  pages     = {19},
  year      = {2020},
  abstract  = {Background: COVID-19 has infected millions of people worldwide and is responsible for several hundred thousand fatalities. The COVID-19 pandemic has necessitated thoughtful resource allocation and early identification of high-risk patients. However, effective methods to meet these needs are lacking. Objective: The aims of this study were to analyze the electronic health records (EHRs) of patients who tested positive for COVID-19 and were admitted to hospitals in the Mount Sinai Health System in New York City; to develop machine learning models for making predictions about the hospital course of the patients over clinically meaningful time horizons based on patient characteristics at admission; and to assess the performance of these models at multiple hospitals and time points. Methods: We used Extreme Gradient Boosting (XGBoost) and baseline comparator models to predict in-hospital mortality and critical events at time windows of 3, 5, 7, and 10 days from admission. Our study population included harmonized EHR data from five hospitals in New York City for 4098 COVID-19-positive patients admitted from March 15 to May 22, 2020. The models were first trained on patients from a single hospital (n=1514) before or on May 1, externally validated on patients from four other hospitals (n=2201) before or on May 1, and prospectively validated on all patients after May 1 (n=383). Finally, we established model interpretability to identify and rank variables that drive model predictions. Results: Upon cross-validation, the XGBoost classifier outperformed baseline models, with an area under the receiver operating characteristic curve (AUC-ROC) for mortality of 0.89 at 3 days, 0.85 at 5 and 7 days, and 0.84 at 10 days. XGBoost also performed well for critical event prediction, with an AUC-ROC of 0.80 at 3 days, 0.79 at 5 days, 0.80 at 7 days, and 0.81 at 10 days. In external validation, XGBoost achieved an AUC-ROC of 0.88 at 3 days, 0.86 at 5 days, 0.86 at 7 days, and 0.84 at 10 days for mortality prediction. Similarly, the unimputed XGBoost model achieved an AUC-ROC of 0.78 at 3 days, 0.79 at 5 days, 0.80 at 7 days, and 0.81 at 10 days. Trends in performance on prospective validation sets were similar. At 7 days, acute kidney injury on admission, elevated LDH, tachypnea, and hyperglycemia were the strongest drivers of critical event prediction, while higher age, anion gap, and C-reactive protein were the strongest drivers of mortality prediction. Conclusions: We externally and prospectively trained and validated machine learning models for mortality and critical events for patients with COVID-19 at different time horizons. These models identified at-risk patients and uncovered underlying relationships that predicted outcomes.},
  language  = {en}
}